FN Clarivate Analytics Web of Science
VR 1.0
PT J
AU GIOVANNONI, SJ
   BRITSCHGI, TB
   MOYER, CL
   FIELD, KG
AF GIOVANNONI, SJ
   BRITSCHGI, TB
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TI GENETIC DIVERSITY IN SARGASSO SEA BACTERIOPLANKTON
SO NATURE
DT Article
RP OREGON STATE UNIV, DEPT MICROBIOL, CORVALLIS, OR 97331 USA.
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NR 30
TC 1223
Z9 1372
PD MAY 3
PY 1990
VL 345
IS 6270
BP 60
EP 63
DI 10.1038/345060a0
UT WOS:A1990DB95700056
DA 2025-07-30
ER

PT J
AU Herlemann, DPR
   Woelk, J
   Labrenz, M
   Jürgens, K
AF Herlemann, Daniel P. R.
   Woelk, Jana
   Labrenz, Matthias
   Juergens, Klaus
TI Diversity and abundance of "Pelagibacterales" (SAR11) in the
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SO SYSTEMATIC AND APPLIED MICROBIOLOGY
DT Article
AB The candidate order "Pelagibacterales" (SARI 1) is one of the most abundant bacterial orders in ocean surface waters and, periodically, in freshwater lakes. The presence of several stable phylogenetic lineages comprising "Pelagibacterales" correlates with the physico-chemical parameters in aquatic environments. A previous amplicon sequencing study covering the bacterial community in the salinity gradient of the Baltic Sea suggested that pelagibacteral subclade SAR11-I was replaced by SARI 1-IIIa in the mesohaline region of the Baltic Sea. In this current study, we investigated the cellular abundances of "Pelagibacterales" subclades along the Baltic Sea salinity gradient using catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). The results obtained with a newly designed probe, which exclusively detected SAR11-IIIa, were compared to CARD-FISH abundances of the marine SAR11-I/II subclade and the freshwater lineage SAR11-IIIb (LD12). The results showed that SAR11-IIIa was abundant in oligohaline-mesohaline conditions (salinities 2.7-13.3), with maximal abundances at a salinity of 7 (up to 35% of total Bacteria, quantified with a universal bacterial probe EUB). As expected, SAR11-I/II was abundant (27% of EUB) in the marine parts of the Baltic Sea, whereas counts of the freshwater lineage SAR11-IIIb were below the detection limit at all stations. The shift from SAR11-IIIa to SAR11-I/II was confirmed in the vertical salinity gradient in the deeper basins of the Baltic Sea. These findings were consistent with an overlapping but defined distribution of SARI 1-I/II and SAR11-IIIa in the salinity gradient of the Baltic Sea and suggested the adaptation of SARI 1-IIIa for growth and survival in mesohaline conditions. (C) 2014 Elsevier GmbH.
C1 [Herlemann, Daniel P. R.; Woelk, Jana; Labrenz, Matthias; Juergens, Klaus] Leibniz Inst Baltic Sea Res, Dept Biol Oceanog, D-18119 Rostock, Germany.
RP Herlemann, DPR (corresponding author), Leibniz Inst Baltic Sea Res, Dept Biol Oceanog, Seestr 15, D-18119 Rostock, Germany.
EM daniel.herlemann@io-warnemuende.de
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NR 37
TC 52
Z9 57
PD DEC
PY 2014
VL 37
IS 8
BP 601
EP 604
DI 10.1016/j.syapm.2014.09.002
UT WOS:000346758600007
DA 2025-07-30
ER

PT J
AU Chen, LX
   Zhao, YL
   McMahon, KD
   Mori, JF
   Jessen, GL
   Nelson, TC
   Warren, LA
   Banfield, JF
AF Chen, Lin-Xing
   Zhao, Yanlin
   McMahon, Katherine D.
   Mori, Jiro F.
   Jessen, Gerdhard L.
   Nelson, Tara Colenbrander
   Warren, Lesley A.
   Banfield, Jillian F.
TI Wide Distribution of Phage That Infect Freshwater SAR11 Bacteria
SO MSYSTEMS
DT Article
AB Fonsibacter (LD12 subclade) is among the most abundant bacterioplankton in freshwater ecosystems. These bacteria belong to the order Pelagibacterales (SAR11) and are related to Pelagibacter (marine SAR11), which dominates many marine habitats. Although a few Pelagibacter phage (Pelagiphage) have been described, no phage that infect Fonsibacter have been reported. In this study, we describe two groups of Podoviridae phage that infect Fonsibacter. A complete Fonsibacter genome containing a prophage was reconstructed from metagenomic data. A circularized and complete genome related to the prophage, referred to as uv-Fonsiphage-EPL (lysogenic strategy), shows high similarity to marine Pelagiphage HTVC025P. Additionally, we reconstructed three complete genomes and one draft genome of phage related to marine Pelagiphage HTVC010P and predicted a lytic strategy. The similarity in codon usage and cooccurrence patterns of HTVC010P-related phage and Fonsibacter suggested that these phage infect Fonsibacter. Similar phage were detected in Lake Mendota, Wisconsin, where Fonsibacter is also present. A search of related phage revealed the worldwide distribution of some genotypes in freshwater ecosystems, suggesting their substantial role in shaping indigenous microbial assemblages and influence on biogeochemical cycling. However, the uv-Fonsiphage-EPL and one group of HTVC010P-related phage have a more limited distribution in freshwater ecosystems. Overall, the findings provide insights into the genomic features of phage that infect Fonsibacter and expand understanding of the ecology and evolution of these important bacteria.
   IMPORTANCE Fonsibacter represents a significant microbial group of freshwater ecosystems. Although the genomic and metabolic features of these bacteria have been well studied, no phage infecting them has been reported. In this study, we reconstructed complete genomes of Fonsibacter and infecting phage and revealed their close relatedness to the phage infecting marine SAR11 members. Also, we illustrated that phage that infect Fonsibacter are widely distributed in freshwater habitats. In summary, the results contribute new insights into the ecology and evolution of Fonsibacter and phage.
C1 [Chen, Lin-Xing; Banfield, Jillian F.] Univ Calif Berkeley, Dept Earth & Planetary Sci, Berkeley, CA 94720 USA.
   [Zhao, Yanlin] Fujian Agr & Forestry Univ, Fujian Prov Key Lab Agroecol Proc & Safety Monito, Coll Life Sci, Fuzhou, Fujian, Peoples R China.
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   [Banfield, Jillian F.] Chan Zuckerberg Biohub, San Francisco, CA 94158 USA.
   [Banfield, Jillian F.] Univ Calif Berkeley, Innovat Genom Inst, Berkeley, CA 94720 USA.
   [Banfield, Jillian F.] Univ Melbourne, Melbourne, Vic, Australia.
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   [Mori, Jiro F.] Yokohama City Univ, Grad Sch Nanobiosci, Yokohama, Kanagawa, Japan.
   [Jessen, Gerdhard L.] Univ Austral Chile, Fac Ciencias, Inst Ciencias Marinas & Limnol, Valdivia, Chile.
RP Banfield, JF (corresponding author), Univ Calif Berkeley, Dept Earth & Planetary Sci, Berkeley, CA 94720 USA.; Banfield, JF (corresponding author), Lawrence Berkeley Natl Lab, Earth Sci Div, Berkeley, CA 94720 USA.; Banfield, JF (corresponding author), Univ Calif Berkeley, Dept Environm Sci Policy & Management, Berkeley, CA 94720 USA.; Banfield, JF (corresponding author), Chan Zuckerberg Biohub, San Francisco, CA 94158 USA.; Banfield, JF (corresponding author), Univ Calif Berkeley, Innovat Genom Inst, Berkeley, CA 94720 USA.; Banfield, JF (corresponding author), Univ Melbourne, Melbourne, Vic, Australia.
EM jbanfield@berkeley.edu
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TC 14
Z9 15
PD SEP-OCT
PY 2019
VL 4
IS 5
AR e00410-19
DI 10.1128/mSystems.00410-19
UT WOS:000500493300003
DA 2025-07-30
ER

PT J
AU Gilbert, JA
   Mühling, M
   Joint, I
AF Gilbert, Jack A.
   Muehling, Martin
   Joint, Ian
TI A rare SAR11 fosmid clone confirming genetic variability in the
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SO ISME JOURNAL
DT Article
AB A sequence analysis is described of a fosmid clone from a coastal marine metagenomic library that contains a 16S rRNA gene with high sequence similarity to that of the SAR11 bacterium 'Candidatus Pelagibacter ubique' HTCC1062. The sequence of the fosmid clone was 32 086 bp in length and contained 23 187 bp of the 48-kb hyper-variable region 2 (HVR2) present in the genome of 'Cand. P. ubique'. However, half of the sequences within the HVR2 region of the fosmid clone show little sequence similarity to or have no representative homologues in the genome sequence of 'Cand. P. ubique' HTCC1062. Given their putative functions, the acquisition of these genes suggests that SAR11 could harbour more diverse phenotypes than represented by the 16S rRNA taxonomy. Variation in SAR11 genomes from different locations might explain why SAR11 is abundant in so many diverse marine provinces.
C1 [Gilbert, Jack A.; Muehling, Martin; Joint, Ian] Plymouth Marine Lab, Plymouth PL1 3DH, Devon, England.
RP Gilbert, JA (corresponding author), Plymouth Marine Lab, Prospect Pl, Plymouth PL1 3DH, Devon, England.
EM jagi@pml.ac.uk
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TC 21
Z9 22
PD JUL
PY 2008
VL 2
IS 7
BP 790
EP 793
DI 10.1038/ismej.2008.49
UT WOS:000257829700010
DA 2025-07-30
ER

PT J
AU Tripp, HJ
AF Tripp, H. James
TI The Unique Metabolism of SAR11 Aquatic Bacteria
SO JOURNAL OF MICROBIOLOGY
DT Review
AB The deeply branching clade of abundant, globally distributed aquatic alpha-Proteobacteria known as "SAR11", are adapted to nutrient-poor environments such as the surface waters of the open ocean. Unknown prior to 1990, uncultured until 2002, members of the SAR11 clade can now be cultured in artificial, defined media to densities three orders of magnitude higher than in unamended natural media. Cultivation in natural and defined media has confirmed genomic and metagenomic predictions such as an inability to reduce sulfate to sulfide, a requirement for pyruvate, an ability to oxidize a wide variety of methylated and one-carbon compounds for energy, and an unusual form of conditional glycine auxotrophy. Here we describe the metabolism of the SAR11 type strain Candidatus "Pelagibacter ubique" sir. HTCC1062, as revealed by genome-assisted studies of laboratory cultures. We also describe the discovery of SAR11 and field studies that have been done on natural populations.
C1 Joint Genome Inst, Walnut Creek, CA 94598 USA.
RP Tripp, HJ (corresponding author), Joint Genome Inst, 2800 Mitchell Dr, Walnut Creek, CA 94598 USA.
EM hjtripp@lbl.gov
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TC 38
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PD APR
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VL 51
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BP 147
EP 153
DI 10.1007/s12275-013-2671-2
UT WOS:000318198800001
DA 2025-07-30
ER

PT J
AU Jimenez-Infante, F
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   Vinu, M
   Blom, J
   Alam, I
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   Stingl, U
AF Jimenez-Infante, Francy
   Ngugi, David Kamanda
   Vinu, Manikandan
   Blom, Jochen
   Alam, Intikhab
   Bajic, Vladimir B.
   Stingl, Ulrich
TI Genomic characterization of two novel SAR11 isolates from the Red Sea,
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SO FEMS MICROBIOLOGY ECOLOGY
DT Article
AB The SAR11 clade (Pelagibacterales) is a diverse group that forms a monophyletic clade within the Alphaproteobacteria, and constitutes up to one third of all prokaryotic cells in the photic zone of most oceans. Pelagibacterales are very abundant in the warm and highly saline surface waters of the Red Sea, raising the question of adaptive traits of SAR11 populations in this water body and warmer oceans through the world. In this study, two pure cultures were successfully obtained from surface waters on the Red Sea: one isolate of subgroup Ia and one of the previously uncultured SAR11 Ib lineage. The novel genomes were very similar to each other and to genomes of isolates of SAR11 subgroup Ia (Ia pan-genome), both in terms of gene content and synteny. Among the genes that were not present in the Ia pan-genome, 108 (RS39, Ia) and 151 genes (RS40, Ib) were strain specific. Detailed analyses showed that only 51 (RS39, Ia) and 55 (RS40, Ib) of these strain-specific genes had not reported before on genome fragments of Pelagibacterales. Further analyses revealed the potential production of phosphonates by some SAR11 members and possible adaptations for oligotrophic life, including pentose sugar utilization and adhesion to marine particulate matter.
C1 [Jimenez-Infante, Francy; Ngugi, David Kamanda; Vinu, Manikandan; Stingl, Ulrich] King Abdullah Univ Sci & Technol, Red Sea Res Ctr, Thuwal 239556900, Saudi Arabia.
   [Blom, Jochen] Justus Liebig Univ, Bioinformat & Syst Biol, D-35392 Giessen, Germany.
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RP Stingl, U (corresponding author), Univ Florida, Ft Lauderdale Res & Educ Ctr, Dept Microbiol & Cell Sci, UF IFAS, Davie, FL 33314 USA.
EM ustingl@ufl.edu
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AR fix083
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ER

PT J
AU Viklund, J
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AF Viklund, Johan
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TI Independent Genome Reduction and Phylogenetic Reclassification of the
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DT Article
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C1 [Viklund, Johan; Ettema, Thijs J. G.; Andersson, Siv G. E.] Uppsala Univ, Sci Life Lab, Dept Mol Evolut, Evolutionary Biol Ctr, Uppsala, Sweden.
RP Andersson, SGE (corresponding author), Uppsala Univ, Sci Life Lab, Dept Mol Evolut, Evolutionary Biol Ctr, Uppsala, Sweden.
EM siv.andersson@ebc.uu.se
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DT Article
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   [Eich, Andreas] PSL Res Univ, EPHE, CNRS, UAR 3278 CRIOBE,UPVD, Moorea, France.
RP Bruewer, JD; Fuchs, BM (corresponding author), Max Planck Inst Marine Microbiol, D-28359 Bremen, Germany.
EM jbruewer@mpi-bremen.de; bfuchs@mpi-bremen.de
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NR 54
TC 3
Z9 3
PD MAY 2
PY 2024
VL 15
IS 1
AR 3715
DI 10.1038/s41467-024-48172-w
UT WOS:001262129900002
DA 2025-07-30
ER

PT J
AU Monaghan, EA
   Freel, KC
   Rappé, MS
AF Monaghan, Elizabeth A.
   Freel, Kelle C.
   Rappe, Michael S.
TI Isolation of SAR11 Marine Bacteria from Cryopreserved Seawater
SO MSYSTEMS
DT Article
AB While marine microorganisms are frequently studied in their natural environment, isolated strains are invaluable resources that can be used in controlled experiments to expand upon direct observations from natural systems. Here, we sought a means to enhance culture collections of SAR11 marine bacteria by testing the use of seawater cryopreserved with glycerol as an inoculum. Using a raw seawater sample collected from the tropical Pacific Ocean, a subsample was diluted in seawater growth medium to create 5762-ml dilution cultures containing 5 cells each and incubated for a high-throughput culturing (HTC) experiment, while another portion was cryopreserved in 10% glycerol. After 10 months, a cryopreserved aliquot was thawed and used to create a second cultivation experiment of 480 2-ml cultures containing 5 cells each and 470 cultures containing 105 cells each. The raw seawater cultivation experiment resulted in the successful isolation of 54 monocultures and 29 mixed cultures, while cryopreserved seawater resulted in 59 monocultures and 29 mixed cultures. Combined, the cultures included 51 SAR11 isolates spanning 11 unique 16S rRNA gene amplicon sequence variants (ASVs) from the raw seawater inoculum and 74 SAR11 isolates spanning 13 unique ASVs from cryopreserved seawater. A vast majority (92%) of SAR11 isolates from the two HTC experiments were members of SAR11 subclade la, though subclades lila and Va were also recovered from cryopreserved seawater and subclade lb was recovered from both. The four most abundant SAR11 subclade la ASVs found in the initial seawater environmental sample were isolated by both approaches.
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RP Rappé, MS (corresponding author), Univ Hawaii Manoa, Hawaii Inst Marine Biol, Sch Ocean & Earth Sci & Technol, Kaneohe, HI 96744 USA.
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NR 66
TC 6
Z9 7
PD NOV-DEC
PY 2020
VL 5
IS 6
AR e00954-20
DI 10.1128/mSystems.00954-20
UT WOS:000630974900025
DA 2025-07-30
ER

PT J
AU Eggleston, EM
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AF Eggleston, Erin M.
   Hewson, Ian
TI Abundance of Two Pelagibacter ubique Bacteriophage
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SO FRONTIERS IN MICROBIOLOGY
DT Article
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C1 [Eggleston, Erin M.; Hewson, Ian] Cornell Univ, Dept Microbiol, Ithaca, NY 14850 USA.
   [Eggleston, Erin M.] St Lawrence Univ, Biol Dept, Canton, NY 13617 USA.
RP Eggleston, EM (corresponding author), Cornell Univ, Dept Microbiol, Ithaca, NY 14850 USA.; Eggleston, EM (corresponding author), St Lawrence Univ, Biol Dept, Canton, NY 13617 USA.
EM eegaleston@stlawu.edu
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TC 12
Z9 12
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PY 2016
VL 7
AR 1534
DI 10.3389/fmicb.2016.01534
UT WOS:000384202100001
DA 2025-07-30
ER

PT J
AU Zhao, XW
   Schwartz, CL
   Pierson, J
   Giovannoni, SJ
   McIntosh, JR
   Nicastroa, D
AF Zhao, Xiaowei
   Schwartz, Cindi L.
   Pierson, Jason
   Giovannoni, Stephen J.
   McIntosh, J. Richard
   Nicastroa, Daniela
TI Three-Dimensional Structure of the Ultraoligotrophic Marine Bacterium
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB SAR11 bacteria are small, heterotrophic, marine alphaproteobacteria found throughout the oceans. They thrive at the low nutrient concentrations typical of open ocean conditions, although the adaptations required for life under those conditions are not well understood. To illuminate this issue, we used cryo-electron tomography to study "Candidatus Pelagibacter ubique" strain HTCC1062, a member of the SAR11 clade. Our results revealed its cellular dimensions and details of its intracellular organization. Frozen-hydrated cells, which were preserved in a life-like state, had an average cell volume (enclosed by the outer membrane) of 0.037 +/- 0.011 mu m(3). Strikingly, the periplasmic space occupied similar to 20% to 50% of the total cell volume in log-phase cells and similar to 50% to 70% in stationary-phase cells. The nucleoid occupied the convex side of the crescent-shaped cells and the ribosomes predominantly occupied the concave side, at a relatively high concentration of 10,000 to 12,000 ribosomes/similar to m(3). Outer membrane pore complexes, likely composed of PilQ, were frequently observed in both log-phase and stationary-phase cells. Long filaments, most likely type IV pili, were found on dividing cells. The physical dimensions, intracellular organization, and morphological changes throughout the life cycle of "Ca. Pelagibacter ubique" provide structural insights into the functional adaptions of these oligotrophic ultramicrobacteria to their habitat.
   IMPORTANCE Bacterioplankton of the SAR11 clade (Pelagibacterales) are of interest because of their global biogeochemical significance and because they appear to have been molded by unusual evolutionary circumstances that favor simplicity and efficiency. They have adapted to an ecosystem in which nutrient concentrations are near the extreme limits at which transport systems can function adequately, and they have evolved streamlined genomes to execute only functions essential for life. However, little is known about the actual size limitations and cellular features of living oligotrophic ultramicrobacteria. In this study, we have used cryo-electron tomography to obtain accurate physical information about the cellular architecture of "Candidatus Pelagibacter ubique," the first cultivated member of the SAR11 clade. These results provide foundational information for answering questions about the cell architecture and functions of these ultrasmall oligotrophic bacteria.
C1 [Zhao, Xiaowei; Nicastroa, Daniela] Univ Texas Southwestern Med Ctr Dallas, Dept Cell Biol & Biophys, Dallas, TX 75390 USA.
   [Schwartz, Cindi L.; Pierson, Jason; McIntosh, J. Richard; Nicastroa, Daniela] Univ Colorado, Dept Mol Cellular & Dev Biol, Boulder, CO 80309 USA.
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   [Schwartz, Cindi L.] NIAID, NIH, Rocky Mt Labs, Hamilton, MT USA.
   [Pierson, Jason] FEI Co, Hillsboro, OR USA.
RP Nicastroa, D (corresponding author), Univ Texas Southwestern Med Ctr Dallas, Dept Cell Biol & Biophys, Dallas, TX 75390 USA.; Nicastroa, D (corresponding author), Univ Colorado, Dept Mol Cellular & Dev Biol, Boulder, CO 80309 USA.
EM daniela.nicastro@utsouthwestern.edu
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NR 85
TC 39
Z9 43
PD FEB
PY 2017
VL 83
IS 3
AR e02807-16
DI 10.1128/AEM.02807-16
UT WOS:000393480900022
DA 2025-07-30
ER

PT J
AU Buchholz, HH
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   Temperton, B
AF Buchholz, Holger H.
   Bolanos, Luis M.
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   Temperton, Ben
TI Novel pelagiphage isolate Polarivirus skadi is a polar specialist
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SO ISME JOURNAL
DT Article
AB The SAR11 clade are the most abundant members of surface marine bacterioplankton and a critical component of global biogeochemical cycles. Similarly, pelagiphages that infect SAR11 are ubiquitous and highly abundant in the oceans. Pelagiphages are predicted to shape SAR11 community structures and increase carbon turnover throughout the oceans. Yet, ecological drivers of host and niche specificity of pelagiphage populations are poorly understood. Here we report the global distribution of a novel pelagiphage called "Polarivirus skadi", which is the sole representative of a novel genus. P. skadi was isolated from the Western English Channel using a cold-water ecotype of SAR11 as bait. P. skadi is closely related to the globally dominant pelagiphage HTVC010P. Along with other HTVC010P-type viruses, P. skadi belongs to a distinct viral family within the order Caudovirales, for which we propose the name Ubiqueviridae. Metagenomic read recruitment identified P. skadi as one of the most abundant pelagiphages on Earth. P. skadi is a polar specialist, replacing HTVC010P at high latitudes. Experimental evaluation of P. skadi host range against cold- and warm-water SAR11 ecotypes supported cold-water specialism. Relative abundance of P. skadi in marine metagenomes correlated negatively with temperature, and positively with nutrients, available oxygen, and chlorophyll concentrations. In contrast, relative abundance of HTVC010P correlated negatively with oxygen and positively with salinity, with no significant correlation to temperature. The majority of other pelagiphages were scarce in most marine provinces, with a few representatives constrained to discrete ecological niches. Our results suggest that pelagiphage populations persist within a global viral seed bank, with environmental parameters and host availability selecting for a few ecotypes that dominate ocean viromes.
C1 [Buchholz, Holger H.; Bolanos, Luis M.; Bell, Ashley G.; Michelsen, Michelle L.; Allen, Michael J.; Temperton, Ben] Univ Exeter, Sch Biosci, Exeter, England.
RP Temperton, B (corresponding author), Univ Exeter, Sch Biosci, Exeter, England.
EM b.temperton@exeter.ac.uk
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NR 86
TC 8
Z9 8
PD OCT
PY 2023
VL 17
IS 10
BP 1660
EP 1670
DI 10.1038/s41396-023-01466-1
EA JUL 2023
UT WOS:001028399800001
DA 2025-07-30
ER

PT J
AU Moore, ER
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AF Moore, Eric R.
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TI Metabolism of key atmospheric volatile organic compounds by the marine
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
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C1 [Moore, Eric R.; Weaver, Alec J.; Davis, Edward W.; Giovannoni, Stephen J.; Halsey, Kimberly H.] Oregon State Univ, Dept Microbiol, 226 Nash Hall, Corvallis, OR 97331 USA.
   [Halsey, Kimberly H.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM 87545 USA.
RP Halsey, KH (corresponding author), Oregon State Univ, Dept Microbiol, 226 Nash Hall, Corvallis, OR 97331 USA.; Halsey, KH (corresponding author), Los Alamos Natl Lab, Biosci Div, Los Alamos, NM 87545 USA.
EM halseyk@science.oregonstate.edu
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NR 66
TC 11
Z9 11
PD JAN
PY 2022
VL 24
IS 1
BP 212
EP 222
DI 10.1111/1462-2920.15837
EA NOV 2021
UT WOS:000723454300001
DA 2025-07-30
ER

PT J
AU Tucker, SJ
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   Rappé, MS
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   Monaghan, Elizabeth A.
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TI Spatial and temporal dynamics of SAR11 marine bacteria across a
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SO PEERJ
DT Article
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NR 91
TC 6
Z9 7
PD NOV 4
PY 2021
VL 9
AR e12274
DI 10.7717/peerj.12274
UT WOS:000718109500005
DA 2025-07-30
ER

PT J
AU Bennett, BD
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AF Bennett, Brittany D.
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TI Polyhydroxybutyrate production by freshwater SAR11 (LD12)
SO ISME JOURNAL
DT Article
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C1 [Bennett, Brittany D.; Lanclos, V. Celeste; Asrari, Hasti; Thrash, J. Cameron] Univ Southern Calif, Dept Biol Sci, 3616 Trousdale Pkwy, AHF 107, Los Angeles, CA 90089 USA.
   [Meier, David A. O.; Coates, John D.] Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA 94720 USA.
RP Thrash, JC (corresponding author), Univ Southern Calif, Dept Biol Sci, 3616 Trousdale Pkwy, AHF 107, Los Angeles, CA 90089 USA.
EM thrash@usc.edu
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NR 70
TC 0
Z9 0
PD JAN
PY 2025
VL 19
IS 1
AR wraf087
DI 10.1093/ismejo/wraf087
UT WOS:001497011600001
DA 2025-07-30
ER

PT J
AU Vergin, KL
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AF Vergin, Kevin L.
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   Denver, Dee R.
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   Giovannoni, Stephen J.
TI High intraspecific recombination rate in a native population of
   Candidatus Pelagibacter ubique (SAR11)
SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Recombination is an important process in microbial evolution. Rates of recombination with extracellular DNA matter because models of microbial population structure are profoundly influenced by the degree to which recombination is occurring within the population. Low rates of recombination may be sufficient to ensure the lateral propagation of genes that have a high selective advantage without disrupting the clonal pattern of inheritance for other genes. High rates of recombination potentially can obscure clonal patterns, leading to linkage equilibrium, and give microbial populations a population genetic structure more akin to sexually interbreeding eukaryotic populations. We examined eight loci from nine strains of candidatus Pelagibacter ubique (SAR11), isolated from a single 2L niskin sample of natural seawater, for evidence of genetic recombination between strains. The Shimodaira-Hasegawa test revealed significant phylogenetic incongruence in seven of the genes, indicating that frequent recombination obscures phylogenetic signals from the linear inheritance of genes in this population. Statistical evidence for intragenic recombination was found for six loci. An informative sites matrix showed extensive evidence for a widespread breakdown of linkage disequilibrium. Although the mechanisms of genetic transfer in native SAR11 populations are unknown, we measured recombination rates, rho, that are much higher than point mutation rates, theta, as a source of genetic diversity in this clade. The eukaryotic model of species sharing a common pool of alleles is more apt for this SAR11 population than a strictly clonal model of inheritance in which allelic diversity is controlled by periodic selection.
C1 Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
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   Univ Hawaii Manoa, SOEST, Hawaii Inst Marine Biol, Kaneohe, HI 96744 USA.
RP Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
EM Steve.Giovannoni@oregonstate.edu
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NR 42
TC 55
Z9 65
PD OCT
PY 2007
VL 9
IS 10
BP 2430
EP 2440
DI 10.1111/j.1462-2920.2007.01361.x
UT WOS:000249222600006
DA 2025-07-30
ER

PT J
AU Smith, DP
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   Smith, RD
   Giovannoni, SJ
AF Smith, Daniel P.
   Nicora, Carrie D.
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TI Proteome Remodeling in Response to Sulfur Limitation in
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SO MSYSTEMS
DT Article
AB The alphaproteobacterium "Candidatus Pelagibacter ubique" strain HTCC1062 and most other members of the SAR11 clade lack genes for assimilatory sulfate reduction, making them dependent on organosulfur compounds that occur naturally in seawater. To investigate how these cells adapt to sulfur limitation, batch cultures were grown in defined medium containing either limiting or nonlimiting amounts of dimethylsulfoniopropionate (DMSP) as the sole sulfur source. Protein and mRNA expression were measured before, during, and after the transition from exponential growth to stationary phase. Two distinct responses were observed, one as DMSP became exhausted and another as the cells acclimated to a sulfur-limited environment. The first response was characterized by increased transcription and translation of all "Ca. Pelagibacter ubique" genes downstream from the previously confirmed S-adenosyl methionine (SAM) riboswitches bhmT, mmuM, and metY. The proteins encoded by these genes were up to 33 times more abundant as DMSP became limiting. Their predicted function is to shunt all available sulfur to methionine. The secondary response, observed during sulfur-limited stationary phase, was a 6- to 10-fold increase in the transcription of the heme c shuttle-encoding gene ccmC and two small genes of unknown function (SAR11_1163 and SAR11_1164). This bacterium's strategy for coping with sulfur stress appears to be intracellular redistribution to support methionine biosynthesis rather than increasing organosulfur import. Many of the genes and SAM riboswitches involved in this response are located in a hypervariable genome region (HVR). One of these HVR genes, ordL, is located downstream from a conserved motif that evidence suggests is a novel riboswitch.
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C1 [Smith, Daniel P.; Carini, Paul; Giovannoni, Stephen J.] Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
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   [Smith, Daniel P.] Baylor Coll Med, Dept Mol Virol & Microbiol, Houston, TX 77030 USA.
   [Carini, Paul] Univ Colorado, Cooperat Inst Res Environm Sci, Boulder, CO 80309 USA.
RP Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
EM steve.giovannoni@oregonstate.edu
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TC 17
Z9 18
PD JUL-AUG
PY 2016
VL 1
IS 4
AR e00068-16
DI 10.1128/mSystems.00068-16
UT WOS:000408191700008
DA 2025-07-30
ER

PT J
AU Getz, EW
   Lanclos, VC
   Kojima, CY
   Cheng, C
   Henson, MW
   Schön, ME
   Ettema, TJG
   Faircloth, BC
   Thrash, JC
AF Getz, Eric W.
   Lanclos, V. Celeste
   Kojima, Conner Y.
   Cheng, Chuankai
   Henson, Michael W.
   Schon, Max Emil
   Ettema, Thijs J. G.
   Faircloth, Brant C.
   Thrash, J. Cameron
TI The AEGEAN-169 clade of bacterioplankton is synonymous with SAR11
   subclade V (HIMB59) and metabolically distinct
SO MSYSTEMS
DT Article
AB Bacterioplankton of the SAR11 clade are the most abundant marine microorganisms and consist of numerous subclades spanning order-level divergence (Pelagibacterales). The assignment of the earliest diverging subclade V (a.k.a. HIMB59) to the Pelagibacterales is highly controversial, with multiple recent phylogenetic studies placing them completely separate from SAR11. Other than through phylogenomics, subclade V has not received detailed examination due to limited genomes from this group. Here, we assessed the ecogenomic characteristics of subclade V to better understand the role of this group in comparison to the Pelagibacterales. We used a new isolate genome, recently released single-amplified genomes and metagenome-assembled genomes, and previously established SAR11 genomes to perform a comprehensive comparative genomics analysis. We paired this analysis with the recruitment of metagenomes spanning the open ocean, coastal, and brackish systems. Phylogenomics, average amino acid identity, and 16S rRNA gene phylogeny indicate that SAR11 subclade V is synonymous with the ubiquitous AEGEAN-169 clade and support the contention that this group represents a taxonomic family. AEGEAN-169 shared many bulk genome qualities with SAR11, such as streamlining and low GC content, but genomes were generally larger. AEGEAN-169 had overlapping distributions with SAR11 but was metabolically distinct from SAR11 in its potential to transport and utilize a broader range of sugars as well as in the transport of trace metals and thiamin. Thus, regardless of the ultimate phylogenetic placement of AEGEAN-169, these organisms have distinct metabolic capacities that likely allow them to differentiate their niche from canonical SAR11 taxa.
   IMPORTANCE One goal of marine microbiologists is to uncover the roles various microorganisms are playing in biogeochemical cycles. Success in this endeavor relies on differentiating groups of microbes and circumscribing their relationships. An early-diverging group (subclade V) of the most abundant bacterioplankton, SAR11, has recently been proposed as a separate lineage that does not share a most recent common ancestor. But beyond phylogenetics, little has been done to evaluate how these organisms compare with SAR11. Our work leverages dozens of new genomes to demonstrate the similarities and differences between subclade V and SAR11. In our analysis, we also establish that subclade V is synonymous with a group of bacteria established from 16S rRNA gene sequences, AEGEAN-169. Subclade V/AEGEAN-169 has clear metabolic distinctions from SAR11 and their shared traits point to remarkable convergent evolution if they do not share a most recent common ancestor.
C1 [Getz, Eric W.; Lanclos, V. Celeste; Kojima, Conner Y.; Cheng, Chuankai; Thrash, J. Cameron] Univ Southern Calif, Dept Biol Sci, Los Angeles, CA 90007 USA.
   [Henson, Michael W.] Univ Chicago, Dept Geophys Sci, Chicago, IL USA.
   [Schon, Max Emil] Uppsala Univ, Sci Life Lab, Dept Cell & Mol Biol, Uppsala, Sweden.
   [Ettema, Thijs J. G.] Wageningen Univ & Res, Lab Microbiol, Wageningen, Netherlands.
   [Faircloth, Brant C.] Louisiana State Univ, Dept Biol Sci, Baton Rouge, LA USA.
   [Faircloth, Brant C.] Louisiana State Univ, Museum Nat Sci, Baton Rouge, LA USA.
RP Thrash, JC (corresponding author), Univ Southern Calif, Dept Biol Sci, Los Angeles, CA 90007 USA.
EM thrash@usc.edu
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NR 98
TC 7
Z9 7
PD JUN 29
PY 2023
VL 8
IS 3
DI 10.1128/msystems.00179-23
EA MAY 2023
UT WOS:001026276900001
DA 2025-07-30
ER

PT J
AU Noell, SE
   Barrell, GE
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   Morré, J
   Gable, KP
   Graff, JR
   VerWey, BJ
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   Giovannoni, SJ
AF Noell, Stephen E.
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   Morre, Jeff
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   VerWey, Brian J.
   Hellweger, Ferdi L.
   Giovannoni, Stephen J.
TI SAR11 Cells Rely on Enzyme Multifunctionality To Metabolize a Range of
   Polyamine Compounds
SO MBIO
DT Article
AB In the ocean surface layer and cell culture, the polyamine transport protein PotD of SAR11 bacteria is often one of the most abundant proteins detected. Polyamines are organic cations at seawater pH produced by all living organisms and are thought to be an important component of dissolved organic matter (DOM) produced in planktonic ecosystems. We hypothesized that SAR11 cells uptake and metabolize multiple poly amines and use them as sources of carbon and nitrogen. Metabolic footprinting and fin-gerprinting were used to measure the uptake of five polyamine compounds (putrescine, cadaverine, agmatine, norspermidine, and spermidine) in two SAR11 strains that represent the majority of SAR11 cells in the surface ocean environment, "Candidatus Pelagibacter" strain HTCC7211 and "Candidatus Pelagibacter ubique" strain HTCC1062. Both strains took up all five polyamines and concentrated them to micromolar or milli molar intracellular concentrations. Both strains could use most of the polyamines to meet their nitrogen requirements, but polyamines did not fully substitute for their requirements of glycine (or related compounds) or pyruvate (or related compounds). Our data suggest that potABCD transports all five polyamines and that spermidine synthase, speE, is reversible, catalyzing the breakdown of spermidine and norspermidine, in addition to its usual biosynthetic role. These findings provide support for the hypothesis that enzyme multifunctionality enables streamlined cells in planktonic ecosystems to increase the range of DOM compounds they metabolize.
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C1 [Noell, Stephen E.; Barrell, Gregory E.; Suffridge, Christopher; Giovannoni, Stephen J.] Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
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RP Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
EM steve.giovannoni@oregonstate.edu
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NR 85
TC 14
Z9 14
PD JUL-AUG
PY 2021
VL 12
IS 4
AR e01091-21
DI 10.1128/mBio.01091-21
UT WOS:000693469500001
DA 2025-07-30
ER

PT J
AU Martinez-Hernandez, F
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AF Martinez-Hernandez, Francisco
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   Martinez-Garcia, Manuel
TI Droplet Digital PCR for Estimating Absolute Abundances of Widespread
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SO FRONTIERS IN MICROBIOLOGY
DT Article
AB Absolute abundances of prokaryotes are typically determined by FISH. Due to the lack of a universal conserved gene among all viruses, metagenomic fragment recruitment is commonly used to estimate the relative viral abundance. However, the paucity of absolute virus abundance data hinders our ability to fully understand how viruses drive global microbial populations. The cosmopolitan marine Pelagibacter ubique is host for the highly widespread HTVC010P pelagiphage isolate and the extremely abundant uncultured virus vSAG 37-F6 recently discovered by single-virus genomics. Here we applied droplet digital PCR (ddPCR) to calculate the absolute abundance of these pelagiphage genotypes in the Mediterranean Sea and the Gulf of Maine. Abundances were between 360 and 8,510 virus mL-1 and 1,270-14,400 virus mL-1 for vSAG 37-F6 and HTVC010P, respectively. Illumina PCR-amplicon sequencing corroborated the absence of ddPCR non-specific amplifications for vSAG 37-F6, but showed an overestimation of 6% for HTVC010P from off-targets, genetically unrelated viruses. Absolute abundances of both pelagiphages, two of the most abundance marine viruses, suggest a large viral pelagiphage diversity in marine environments, and show the efficiency and power of ddPCR to disentangle the structure of marine viral communities. Results also highlight the need for a standardized workflow to obtain accurate quantification that allows cross data comparison.
C1 [Martinez-Hernandez, Francisco; Garcia-Heredia, Inmaculada; Liuesma Gomez, Monica; Maestre-Carballa, Lucia; Martinez-Garcia, Manuel] Univ Alicante, Dept Physiol Genet & Microbiol, Alicante, Spain.
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RP Martinez-Garcia, M (corresponding author), Univ Alicante, Dept Physiol Genet & Microbiol, Alicante, Spain.
EM m.martinez@ua.es
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NR 62
TC 27
Z9 29
PD JUN 12
PY 2019
VL 10
AR 1226
DI 10.3389/fmicb.2019.01226
UT WOS:000471155200002
DA 2025-07-30
ER

PT J
AU Brown, MV
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AF Brown, Mark V.
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TI Global biogeography of SAR11 marine bacteria
SO MOLECULAR SYSTEMS BIOLOGY
DT Article
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C1 [Brown, Mark V.; Lauro, Federico M.; DeMaere, Matthew Z.; Wilkins, David; Thomas, Torsten; Cavicchioli, Ricardo] Univ New S Wales, Sch Biotechnol & Biomol Sci, Sydney, NSW 2052, Australia.
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RP Cavicchioli, R (corresponding author), Univ New S Wales, Sch Biotechnol & Biomol Sci, Sydney, NSW 2052, Australia.
EM r.cavicchioli@unsw.edu.au
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NR 53
TC 182
Z9 208
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PY 2012
VL 8
AR 595
DI 10.1038/msb.2012.28
UT WOS:000307174800005
DA 2025-07-30
ER

PT J
AU Haro-Moreno, JM
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AF Haro-Moreno, Jose M.
   Lopez-Perez, Mario
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   Rodriguez-Valera, Francisco
TI Large diversity in the O-chain biosynthetic cluster within populations
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SO MBIO
DT Article
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C1 [Haro-Moreno, Jose M.; Lopez-Perez, Mario; Molina-Pardines, Carmen; Rodriguez-Valera, Francisco] Univ Miguel Hernandez, Div Microbiol, Evolutionary Genom Grp, Alicante, Spain.
RP Rodriguez-Valera, F (corresponding author), Univ Miguel Hernandez, Div Microbiol, Evolutionary Genom Grp, Alicante, Spain.
EM frvalera@umh.es
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NR 105
TC 1
Z9 1
PD MAR 12
PY 2025
VL 16
IS 3
DI 10.1128/mbio.03455-24
EA FEB 2025
UT WOS:001425486300001
DA 2025-07-30
ER

PT J
AU Zhao, YL
   Temperton, B
   Thrash, JC
   Schwalbach, MS
   Vergin, KL
   Landry, ZC
   Ellisman, M
   Deerinck, T
   Sullivan, MB
   Giovannoni, SJ
AF Zhao, Yanlin
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   Deerinck, Tom
   Sullivan, Matthew B.
   Giovannoni, Stephen J.
TI Abundant SAR11 viruses in the ocean
SO NATURE
DT Article
AB Several reports proposed that the extraordinary dominance of the SAR11 bacterial clade in ocean ecosystems could be a consequence of unusual mechanisms of resistance to bacteriophage infection, including 'cryptic escape' through reduced cell size(1) and/or K-strategist defence specialism(2). Alternatively, the evolution of high surface-to-volume ratios coupled with minimal genomes containing high-affinity transporters enables unusually efficient metabolism for oxidizing dissolved organic matter in the world's oceans that could support vast population sizes despite phage susceptibility. These ideas are important for understanding plankton ecology because they emphasize the potentially important role of top-down mechanisms in predation, thus determining the size of SAR11 populations and their concomitant role in biogeochemical cycling. Here we report the isolation of diverse SAR11 viruses belonging to two virus families in culture, for which we propose the name 'pelagiphage', after their host. Notably; the pelagiphage genomes were highly represented in marine viral metagenomes, demonstrating their importance in nature. One of the new phages, HTVC010P, represents a new podovirus subfamily more abundant than any seen previously, in all data sets tested, and may represent one of the most abundant virus subfamilies in the biosphere. This discovery disproves the theory that SAR11 cells are immune to viral predation and is consistent with the interpretation that the success of this highly abundant microbial clade is the result of successfully evolved adaptation to resource competition.
C1 [Zhao, Yanlin; Temperton, Ben; Thrash, J. Cameron; Vergin, Kevin L.; Landry, Zachary C.; Giovannoni, Stephen J.] Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
   [Schwalbach, Michael S.] Univ Wisconsin, Great Lakes Bioenergy Res Ctr, Madison, WI 53706 USA.
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   [Sullivan, Matthew B.] Univ Arizona, Dept Ecol & Evolutionary Biol, Tucson, AZ 85721 USA.
RP Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
EM steve.giovannoni@oregonstate.edu
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TC 266
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VL 494
IS 7437
BP 357
EP 360
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UT WOS:000315312900039
DA 2025-07-30
ER

PT J
AU Sun, J
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   Thrash, JC
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   Temperton, B
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   Giovannoni, SJ
AF Sun, Jing
   Todd, Jonathan D.
   Thrash, J. Cameron
   Qian, Yanping
   Qian, Michael C.
   Temperton, Ben
   Guo, Jiazhen
   Fowler, Emily K.
   Aldrich, Joshua T.
   Nicora, Carrie D.
   Lipton, Mary S.
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   De Leenheer, Patrick
   Payne, Samuel H.
   Johnston, Andrew W. B.
   Davie-Martin, Cleo L.
   Halsey, Kimberly H.
   Giovannoni, Stephen J.
TI The abundant marine bacterium Pelagibacter simultaneously
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SO NATURE MICROBIOLOGY
DT Article
AB Marine phytoplankton produce similar to 10(9) tonnes of dimethylsulfoniopropionate (DMSP) per year(1,2), an estimated 10% of which is catabolized by bacteria through the DMSP cleavage pathway to the climatically active gas dimethyl sulfide3,4. SAR11 Alphaproteobacteria (order Pelagibacterales), the most abundant chemo-organotrophic bacteria in the oceans, have been shown to assimilate DMSP into biomass, thereby supplying this cell's unusual requirement for reduced sulfur(5,6). Here, we report that Pelagibacter HTCC1062 produces the gas methanethiol, and that a second DMSP catabolic pathway, mediated by a cupin-like DMSP lyase, DddK, simultaneously shunts as much as 59% of DMSP uptake to dimethyl sulfide production. We propose a model in which the allocation of DMSP between these pathways is kinetically controlled to release increasing amounts of dimethyl sulfide as the supply of DMSP exceeds cellular sulfur demands for biosynthesis.
C1 [Sun, Jing; Davie-Martin, Cleo L.; Halsey, Kimberly H.; Giovannoni, Stephen J.] Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
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   [Qian, Yanping; Qian, Michael C.] Oregon State Univ, Dept Food Sci, Corvallis, OR 97331 USA.
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   [De Leenheer, Patrick] Oregon State Univ, Dept Math, Corvallis, OR 97331 USA.
RP Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
EM steve.giovannoni@oregonstate.edu
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NR 35
TC 78
Z9 93
PD AUG
PY 2016
VL 1
IS 8
AR 16065
DI 10.1038/NMICROBIOL.2016.65
UT WOS:000383605900014
DA 2025-07-30
ER

PT J
AU Gao, C
   Zhang, N
   He, XY
   Wang, N
   Zhang, XY
   Wang, P
   Chen, XL
   Zhang, YZ
   Ding, JM
   Li, CY
AF Gao, Chao
   Zhang, Nan
   He, Xiao-Yan
   Wang, Ning
   Zhang, Xi-Ying
   Wang, Peng
   Chen, Xiu-Lan
   Zhang, Yu-Zhong
   Ding, Jun-Mei
   Li, Chun-Yang
TI Characterization of the Trimethylamine N-Oxide Transporter From
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SO FRONTIERS IN MICROBIOLOGY
DT Article
AB Trimethylamine N-oxide (TMAO), which was detected at nanomolar concentrations in surface seawaters, is an important carbon, nitrogen and/or energy source for marine bacteria. It can be metabolized by marine bacteria into volatile methylated amines, the second largest source of nitrogen after N-2 gas in the oceans. The SAR11 bacteria are the most abundant oligotrophic plankton in the oceans, which represents approximately 30% of the bacterial cells in marine surface waters. Genomic analysis suggested that most SAR11 bacteria possess an ATP-binding cassette transporter TmoXWV that may be responsible for importing TMAO. However, it was still unclear whether SAR11 bacteria can utilize TMAO as the sole nitrogen source and how they import TMAO. Here, our results showed that Pelagibacter strain HTCC1062, a SAR11 bacterium, can grow with TMAO as the sole nitrogen source. TmoXWV from strain HTCC1062 (TmoXWV(1062)) was verified to be a functional TMAO importer. Furthermore, TmoX(1062), the periplasmic substrate binding protein of TmoXWV(1062), was shown to have high binding affinities toward TMAO at 4 degrees C (K-d = 920 nM), 10 degrees C (K-d = 500 nM) and 25 degrees C (K-d = 520 nM). The high TMAO binding affinity and strong temperature adaptability of TmoX(1062) reveal a possible oligotrophic niche adaptation strategy of strain HTCC1062, which may help it gain a competitive advantage over other bacteria. Structure comparison and mutational analysis indicated that the TMAO binding mechanism of TmoX(1062) may have differences from the previously reported mechanism of TmoX of Ruegeria pomeroyi DSS-3. This study provides new insight into TMAO utilization by the widespread SAR11 bacteria.
C1 [Gao, Chao; He, Xiao-Yan; Wang, Ning; Zhang, Xi-Ying; Wang, Peng; Chen, Xiu-Lan; Zhang, Yu-Zhong] Shandong Univ, Marine Biotechnol Res Ctr, State Key Lab Microbial Technol, Qingdao, Peoples R China.
   [Gao, Chao; Wang, Peng; Zhang, Yu-Zhong; Li, Chun-Yang] Ocean Univ China, Coll Marine Life Sci, Frontiers Sci Ctr Deep Ocean Multispheres & Earth, Qingdao, Peoples R China.
   [Gao, Chao; Chen, Xiu-Lan; Zhang, Yu-Zhong; Li, Chun-Yang] Pilot Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao, Peoples R China.
   [Zhang, Nan] Qilu Univ Technol, Sch Bioengn, Jinan, Peoples R China.
   [Ding, Jun-Mei] Yunnan Normal Univ, Engn Res Ctr Sustainable Dev & Utilizat Biomass E, Minist Educ, Kunming, Peoples R China.
RP Li, CY (corresponding author), Ocean Univ China, Coll Marine Life Sci, Frontiers Sci Ctr Deep Ocean Multispheres & Earth, Qingdao, Peoples R China.; Li, CY (corresponding author), Pilot Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao, Peoples R China.; Ding, JM (corresponding author), Yunnan Normal Univ, Engn Res Ctr Sustainable Dev & Utilizat Biomass E, Minist Educ, Kunming, Peoples R China.
EM djm3417@163.com; Lcy@ouc.edu.cn
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NR 38
TC 3
Z9 6
PD FEB 28
PY 2022
VL 13
AR 838608
DI 10.3389/fmicb.2022.838608
UT WOS:000772688900001
DA 2025-07-30
ER

PT J
AU López-Pérez, M
   Haro-Moreno, JM
   Coutinho, FH
   Martinez-Garcia, M
   Rodriguez-Valera, F
AF Lopez-Perez, Mario
   Haro-Moreno, Jose M.
   Hernandes Coutinho, Felipe
   Martinez-Garcia, Manuel
   Rodriguez-Valera, Francisco
TI The Evolutionary Success of the Marine Bacterium SAR11 Analyzed through
   a Metagenomic Perspective
SO MSYSTEMS
DT Article
AB The SAR11 clade of Alphaproteobacteria is the most abundant group of planktonic cells in the near-surface epipelagic waters of the ocean, but the mechanisms underlying its exceptional success have not been fully elucidated. Here, we applied a metagenomic approach to explore microdiversity patterns by measuring the accumulation of synonymous and nonsynonymous mutations as well as homologous recombination in populations of SAR11 from different aquatic habitats (marine epipelagic, bathypelagic, and surface freshwater). The patterns of mutation accumulation and recombination were compared to those of other groups of representative marine microbes with multiple ecological strategies that share the same marine habitat, namely, Cyanobacteria (Prochlorococcus and Synechococcus), Archaea ("Candidatus Nitrosopelagicus" and Marine Group II Thalassoarchaea), and some heterotrophic marine bacteria (Alteromonas and Erythrobacter). SAR11 populations showed widespread recombination among distantly related members, preventing divergence leading to a genetically stable population. Moreover, their high intrapopulation sequence diversity with an enrichment in synonymous replacements supports the idea of a very ancient divergence and the coexistence of multiple different clones. However, other microbes analyzed seem to follow different evolutionary dynamics where processes of diversification driven by geographic and ecological instability produce a higher number of nonsynonymous replacements and lower intrapopulation sequence diversity. Together, these data shed light on some of the evolutionary and ecological processes that lead to the large genomic diversity in SAR11. Furthermore, this approach can be applied to other similar microbes that are difficult to culture in the laboratory, but abundant in nature, to investigate the underlying dynamics of their genomic evolution.
   IMPORTANCE As the most abundant bacteria in oceans, the Pelagibacterales order (here SAR11) plays an important role in the global carbon cycle, but the study of the evolutionary forces driving its evolution has lagged considerably due to the inherent difficulty of obtaining pure cultures. Multiple evolutionary models have been proposed to explain the diversification of distinct lineages within a population; however, the identification of many of these patterns in natural populations remains mostly enigmatic. We have used a metagenomic approach to explore microdiversity patterns in their natural habitats. Comparison with a collection of bacterial and archaeal groups from the same environments shows that SAR11 populations have a different evolutionary regime, where multiple genotypes coexist within the same population and remain stable over time. Widespread homologous recombination could be one of the main driving factors of this homogenization.
C1 [Lopez-Perez, Mario; Haro-Moreno, Jose M.; Hernandes Coutinho, Felipe; Rodriguez-Valera, Francisco] Univ Miguel Hernandez, Div Microbiol, Evolutionary Genom Grp, Alicante, Spain.
   [Martinez-Garcia, Manuel] Univ Alicante, Dept Physiol Genet & Microbiol, Alicante, Spain.
   [Rodriguez-Valera, Francisco] Moscow Inst Phys & Technol, Res Ctr Mol Mech Aging & Age Related Dis, Dolgoprudnyi, Russia.
RP López-Pérez, M (corresponding author), Univ Miguel Hernandez, Div Microbiol, Evolutionary Genom Grp, Alicante, Spain.
EM mario.lopezp@umh.es
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NR 84
TC 25
Z9 25
PD SEP-OCT
PY 2020
VL 5
IS 5
AR e00605-20
DI 10.1128/mSystems.00605-20
UT WOS:000579368300037
DA 2025-07-30
ER

PT J
AU Wei, T
   Zhao, CM
   Quareshy, M
   Wu, N
   Huang, S
   Zhao, YZ
   Yang, PF
   Mao, DB
   Chen, Y
AF Wei, Tao
   Zhao, Caimeng
   Quareshy, Mussa
   Wu, Nan
   Huang, Shen
   Zhao, Yuezhe
   Yang, Pengfei
   Mao, Duobin
   Chen, Yin
TI A Glycolipid Glycosyltransferase with Broad Substrate Specificity from
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   HTCC7211
SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB In the marine environment, phosphorus availability significantly affects the lipid composition in many cosmopolitan marine heterotrophic bacteria, including members of the SAR11 Glade and the Roseobacter Glade. Under phosphorus stress conditions, nonphosphorus sugar-containing glycoglycerolipids are substitutes for phospholipids in these bacteria. Although these glycoglycerolipids play an important role as surrogates for phospholipids under phosphate deprivation, glycoglycerolipid synthases in marine microbes are poorly studied. In the present study, we biochemically characterized a glycolipid glycosyltransferase (GT(cp)) from the marine bacterium "Candidatus Pelagibacter sp." strain HTCC7211, a member of the SAR11 Glade. Our results showed that GT(cp) is able to act as a multifunctional enzyme by synthesizing different glycoglycerolipids with UDP-glucose, UDP-galactose, or UDP-glucuronic acid as sugar donors and diacylglycerol (DAG) as the acceptor. Analyses of enzyme kinetic parameters demonstrated that Mg2+ notably changes the enzyme's affinity for UDP-glucose, which improves its catalytic efficiency. Homology modeling and mutational analyses revealed binding sites for the sugar donor and the diacylglycerol lipid acceptor, which provided insights into the retaining mechanism of GT(cp) with its GT-B fold. A phylogenetic analysis showed that GT(cp) and its homologs form a group in the GT4 glycosyltransferase family. These results not only provide new insights into the glycoglycerolipid synthesis mechanism in lipid remodeling but also describe an efficient enzymatic tool for the future synthesis of bioactive molecules.
   IMPORTANCE The bilayer formed by membrane lipids serves as the containment unit for living microbial cells. In the marine environment, it has been firmly established that phytoplankton and heterotrophic bacteria can replace phospholipids with nonphosphorus sugar-containing glycoglycerolipids in response to phosphorus limitation. However, little is known about how these glycoglycerolipids are synthesized. Here, we determined the biochemical characteristics of a glycolipid glycosyltransferase (GT(cp)) from the marine bacterium "Candidatus Pelagibacter sp." strain HTCC7211. GT(cp) and its homologs form a group in the GT4 glycosyltransferase family and can synthesize neutral glycolipids (monoglucosyl-1,2-diacyl-sn-glycerol [MGlc-DAG] and monogalactosyl [MGaI]-DAG) and monoglucuronic acid diacylglycerol (MGlcA-DAG). We also uncovered the key residues for DAG binding through molecular docking, site-direct mutagenesis, and subsequent enzyme activity assays. Our data provide new insights into the glycoglycerolipid synthesis mechanism in lipid remodeling.
C1 [Wei, Tao; Zhao, Caimeng; Wu, Nan; Huang, Shen; Zhao, Yuezhe; Yang, Pengfei; Mao, Duobin] Zhengzhou Univ Light Ind, Sch Food & Biol Engn, Zhengzhou, Peoples R China.
   [Quareshy, Mussa; Chen, Yin] Univ Warwick, Sch Life Sci, Coventry, W Midlands, England.
RP Wei, T (corresponding author), Zhengzhou Univ Light Ind, Sch Food & Biol Engn, Zhengzhou, Peoples R China.; Chen, Y (corresponding author), Univ Warwick, Sch Life Sci, Coventry, W Midlands, England.
EM weit8008@zzuli.edu.cn; Y.chen.25@warwick.ac.uk
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NR 51
TC 7
Z9 8
PD JUL
PY 2021
VL 87
IS 14
AR e00326-21
DI 10.1128/AEM.00326-21
UT WOS:000693249500008
DA 2025-07-30
ER

PT J
AU Smith, DP
   Thrash, JC
   Nicora, CD
   Lipton, MS
   Burnum-Johnson, KE
   Carini, P
   Smith, RD
   Giovannoni, SJ
AF Smith, Daniel P.
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   Carini, Paul
   Smith, Richard D.
   Giovannoni, Stephen J.
TI Proteomic and Transcriptomic Analyses of "Candidatus Pelagibacter
   ubique" Describe the First PII-Independent Response to
   Nitrogen Limitation in a Free-Living Alphaproteobacterium
SO MBIO
DT Article
AB Nitrogen is one of the major nutrients limiting microbial productivity in the ocean, and as a result, most marine microorganisms have evolved systems for responding to nitrogen stress. The highly abundant alphaproteobacterium "Candidatus Pelagibacter ubique," a cultured member of the order Pelagibacterales (SAR11), lacks the canonical GlnB, GlnD, GlnK, and NtrB/NtrC genes for regulating nitrogen assimilation, raising questions about how these organisms respond to nitrogen limitation. A survey of 266 Alphaproteobacteria genomes found these five regulatory genes nearly universally conserved, absent only in intracellular parasites and members of the order Pelagibacterales, including "Ca. Pelagibacter ubique." Global differences in mRNA and protein expression between nitrogen-limited and nitrogen-replete cultures were measured to identify nitrogen stress responses in "Ca. Pelagibacter ubique" strain HTCC1062. Transporters for ammonium (AmtB), taurine (TauA), amino acids (YhdW), and opines (OccT) were all elevated in nitrogen-limited cells, indicating that they devote increased resources to the assimilation of nitrogenous organic compounds. Enzymes for assimilating amine into glutamine (GlnA), glutamate (GltBD), and glycine (AspC) were similarly upregulated. Differential regulation of the transcriptional regulator NtrX in the two-component signaling system NtrY/NtrX was also observed, implicating it in control of the nitrogen starvation response. Comparisons of the transcriptome and proteome supported previous observations of uncoupling between transcription and translation in nutrient-deprived "Ca. Pelagibacter ubique" cells. Overall, these data reveal a streamlined, P-II-independent response to nitrogen stress in "Ca. Pelagibacter ubique," and likely other Pelagibacterales, and show that they respond to nitrogen stress by allocating more resources to the assimilation of nitrogen-rich organic compounds.
   IMPORTANCE Pelagibacterales are extraordinarily abundant and play a pivotal role in marine geochemical cycles, as one of the major recyclers of labile dissolved organic matter. They are also models for understanding how streamlining selection can reshape chemoheterotroph metabolism. Streamlining and its broad importance to environmental microbiology are emerging slowly from studies that reveal the complete genomes of uncultured organisms. Here, we report another remarkable example of streamlined metabolism in Pelagibacterales, this time in systems that control nitrogen assimilation. Pelagibacterales are major contributors to metatranscriptomes and metaproteomes from ocean systems, where patterns of gene expression are used to gain insight into ocean conditions and geochemical cycles. The data presented here supply background that is essential to interpreting data from field studies.
C1 [Smith, Daniel P.; Thrash, J. Cameron; Carini, Paul; Giovannoni, Stephen J.] Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
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RP Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
EM steve.giovannoni@oregonstate.edu
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NR 107
TC 74
Z9 76
PD NOV-DEC
PY 2013
VL 4
IS 6
AR e00133-12
DI 10.1128/mBio.00133-12
UT WOS:000329174500001
DA 2025-07-30
ER

PT J
AU Jones, LR
   Manrique, JM
AF Jones, Leandro R.
   Manrique, Julieta M.
TI High-throughput metabarcoding of SAR11 assemblages from the southwest
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   abundance distributions
SO QUANTITATIVE BIOLOGY
DT Article
AB Background: Massively parallel sequencing of environmental DNA allows microbiological studies to be performed in greater detail than was possible with first-generation sequencing. For example, it facilitates the use of approaches hitherto largely applied to flora and fauna, such as rank abundance distribution (RAD) analyses. Methods: Here, we set out to advance the knowledge on Ca. Pelagibacterales (SAR11) communities from southern South America using environmental sequences from the open ocean in the Argentine sea, the uncharted Engano Bay, as well as a river and an oligohaline shallow lake from the Patagonian Steppe ecoregion. The structures of the SAR11 assemblages present in these ecosystems were dissected by direct and rarefaction-based estimates of species richness, and evaluations of the corresponding abundance distributions (ADs), which was addressed by RAD analyses.Results: Microbial community composition analyses revealed that the studied SAR11 assemblages coexist with 27 bacterial phyla. SAR11 richness was in general very high, but ADs turned out to be highly uneven. The results were compatible with prior knowledge, and similar to that derived from point estimates of diversity. However, our comprehensive dissection allowed for more detailed quantitative comparisons to be made between the environments surveyed, and revealed differences regarding both richness and the underlying ADs.Conclusions: Despite SAR11 assemblages being extremely rich, their ADs are very uneven. Richness and ADs can vary, not only between fresh and salt water, but also between oceanic and coastal marine environments. The obtained results provide insights on general topics such as adaptation and the contrast between marine and freshwater radiations.
C1 [Jones, Leandro R.; Manrique, Julieta M.] Univ Nacl Patagonia San Juan Bosco, Lab Virol & Genet Mol, RA-9100 Trelew, Argentina.
RP Jones, LR (corresponding author), Univ Nacl Patagonia San Juan Bosco, Lab Virol & Genet Mol, RA-9100 Trelew, Argentina.
EM lrj000@gmail.com
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NR 47
TC 0
Z9 0
PD SEP
PY 2023
VL 11
IS 3
BP 332
EP 342
DI 10.15302/J-QB-023-0329
UT WOS:001119788400011
DA 2025-07-30
ER

PT J
AU Sánchez, O
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AF Sanchez, Olga
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TI Influence of primer mismatch and microdiversity on DGGE results: a case
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SO AQUATIC MICROBIAL ECOLOGY
DT Article
AB Although SAR11 is usually the dominant bacterial group in most marine ecosystems when analyzed with clone libraries and fluorescence in situ hybridization, it is often not retrieved in studies where denaturing gradient gel electrophoresis (DGGE) has been used. We analyzed the microdiversity of SAR11 in Blanes Bay (NW Mediterranean) and we suggest that the high evenness of multiple microdiverse phylotypes, none of which being particularly dominant, is the probable reason for this methodological discrepancy. We used seeding experiments in which different amounts of 2 SAR11-affiliated clones were mixed with DNA from an environmental sample obtained from the Blanes Bay Microbial Observatory. Two primer sets differing at 2 base positions produced DGGE images that varied in their SAR11 detection threshold concentration. Our results show that primer mismatches and/or the presence of faint bands due to microdiversity could explain why SAR11 is frequently not retrieved from DGGE gels.
C1 [Sanchez, Olga; Mast, Jordi] Univ Autonoma Barcelona, Dept Genet & Microbiol, Bellaterra 08193, Spain.
   [Gasol, Josep M.; Balague, Vanessa; Massana, Ramon; Pedros-Alio, Carlos] CSIC, Inst Ciencias Mar, CMIMA, Dept Biol Marina & Oceanog, E-08003 Barcelona, Spain.
RP Sánchez, O (corresponding author), Univ Autonoma Barcelona, Dept Genet & Microbiol, Bellaterra 08193, Spain.
EM olga.sanchez@uab.es
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NR 34
TC 8
Z9 9
PY 2009
VL 54
IS 2
BP 211
EP 216
DI 10.3354/ame01267
UT WOS:000265158200009
DA 2025-07-30
ER

PT J
AU Salcher, MM
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AF Salcher, Michaela M.
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SO ISME JOURNAL
DT Article
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RP Salcher, MM (corresponding author), Univ Zurich, Dept Limnol, Inst Plant Biol, Seestr 187, CH-8802 Kilchberg, Switzerland.
EM msalcher@limnol.uzh.ch
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NR 60
TC 149
Z9 164
PD AUG
PY 2011
VL 5
IS 8
BP 1242
EP 1252
DI 10.1038/ismej.2011.8
UT WOS:000295782200002
DA 2025-07-30
ER

PT J
AU Carini, P
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TI SAR11 lipid renovation in response to phosphate starvation
SO PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
   AMERICA
DT Article
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RP Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
EM steve.giovannoni@oregonstate.edu
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NR 46
TC 81
Z9 86
PD JUN 23
PY 2015
VL 112
IS 25
BP 7767
EP 7772
DI 10.1073/pnas.1505034112
UT WOS:000356731300071
DA 2025-07-30
ER

PT J
AU Lami, R
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AF Lami, Raphael
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SO AQUATIC MICROBIAL ECOLOGY
DT Article
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RP Lami, R (corresponding author), Univ Delaware, Sch Marine Sci & Policy, Lewes, DE 19958 USA.
EM raphael.lami@obs-banyuls.fr
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NR 44
TC 9
Z9 10
PY 2014
VL 73
IS 3
BP 185
EP 194
DI 10.3354/ame01716
UT WOS:000347763200001
DA 2025-07-30
ER

PT J
AU Haro-Moreno, JM
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   Rosselli, R
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AF Haro-Moreno, Jose M.
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   Lopez-Perez, Mario
TI Ecogenomics of the SAR11 clade
SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Members of the SAR11 clade, despite their high abundance, are often poorly represented by metagenome-assembled genomes. This fact has hampered our knowledge about their ecology and genetic diversity. Here we examined 175 SAR11 genomes, including 47 new single-amplified genomes. The presence of the first genomes associated with subclade IV suggests that, in the same way as subclade V, they might be outside the proposed Pelagibacterales order. An expanded phylogenomic classification together with patterns of metagenomic recruitment at a global scale have allowed us to define new ecogenomic units of classification (genomospecies), appearing at different, and sometimes restricted, metagenomic data sets. We detected greater microdiversity across the water column at a single location than in samples collected from similar depth across the global ocean, suggesting little influence of biogeography. In addition, pangenome analysis revealed that the flexible genome was essential to shape genomospecies distribution. In one genomospecies preferentially found within the Mediterranean, a set of genes involved in phosphonate utilization was detected. While another, with a more cosmopolitan distribution, was unique in having an aerobic purine degradation pathway. Together, these results provide a glimpse of the enormous genomic diversity within this clade at a finer resolution than the currently defined clades.
C1 [Haro-Moreno, Jose M.; Rodriguez-Valera, Francisco; Rosselli, Riccardo; Roda-Garcia, Juan J.; Lopez-Perez, Mario] Univ Miguel Hernandez, Evolutionary Genom Grp, Div Microbiol, Apartado 18, Alicante 03550, Spain.
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   [Rosselli, Riccardo] Royal Netherlands Inst Sea Res NIOZ, Dept Marine Microbiol & Biogeochem, Texel, Netherlands.
   [Martinez-Hernandez, Francisco; Gomez, Monica Lluesma; Martinez-Garcia, Manuel] Univ Alicante, Dept Physiol Genet & Microbiol, Alicante, Spain.
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RP López-Pérez, M (corresponding author), Univ Miguel Hernandez, Evolutionary Genom Grp, Div Microbiol, Apartado 18, Alicante 03550, Spain.
EM mario.lopezp@umh.es
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NR 85
TC 58
Z9 64
PD MAY
PY 2020
VL 22
IS 5
BP 1748
EP 1763
DI 10.1111/1462-2920.14896
EA DEC 2019
UT WOS:000504289300001
DA 2025-07-30
ER

PT J
AU White, AE
   Giovannoni, SI
   Zhao, YL
   Vergin, K
   Carlson, CA
AF White, Angelicque E.
   Giovannoni, Stephen, I
   Zhao, Yanlin
   Vergin, Kevin
   Carlson, Craig A.
TI Elemental content and stoichiometry of SAR11 chemoheterotrophic marine
   bacteria
SO LIMNOLOGY AND OCEANOGRAPHY LETTERS
DT Article
AB We measured the carbon, nitrogen, and phosphorus content and production of cultured SAR11 cells in the genus Pelagibacter, from members of the 1a.1 and 1a.3 lineages, which are adapted to productive coastal waters and oligotrophic tropical/subtropical environments, respectively. The average growing SAR11 cell contained -6.5 fgC, from which we calculated a global standing stock of 1.4x10(13)gC. Calculations that consider uncertainties in cell turnover rates and growth efficiencies indicate this stock could oxidize 6% to 37% of gross ocean primary production. We also found that SAR11 do not incorporate H-3-thymidine but do incorporate H-3-leucine. We estimate conversion factors of 0.74-1.51kgCmol(-1) leu, which are comparable to the low end of published leucine conversion factors for marine chemoheterotrophic bacterioplankton production. The molar ratio of elements C : N : P in growing cells was on average 25 : 6 : 1, significantly less than the mean (-50 : 10 : 1) for heterotrophic bacteria, indicating these strains are C and N poor relative to P.
C1 [White, Angelicque E.] Univ Hawaii, Dept Oceanog, Honolulu, HI 96822 USA.
   [White, Angelicque E.] Daniel K Inouye Ctr Microbial Oceanog Res & Educ, Honolulu, HI USA.
   [Giovannoni, Stephen, I; Zhao, Yanlin; Vergin, Kevin] Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
   [Carlson, Craig A.] Univ Calif Santa Barbara, Marine Sci Inst, Santa Barbara, CA 93106 USA.
   [Zhao, Yanlin] Fujian Agr & Forestry Univ, Coll Life Sci, Fuzhou, Fujian, Peoples R China.
RP Giovannoni, SI (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
EM steve.giovannoni@oregonstate.edu
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NR 34
TC 30
Z9 33
PD APR
PY 2019
VL 4
IS 2
BP 44
EP 51
DI 10.1002/lol2.10103
UT WOS:000460720800002
DA 2025-07-30
ER

PT J
AU Sun, J
   Steindler, L
   Thrash, JC
   Halsey, KH
   Smith, DP
   Carter, AE
   Landry, ZC
   Giovannoni, SJ
AF Sun, Jing
   Steindler, Laura
   Thrash, J. Cameron
   Halsey, Kimberly H.
   Smith, Daniel P.
   Carter, Amy E.
   Landry, Zachary C.
   Giovannoni, Stephen J.
TI One Carbon Metabolism in SAR11 Pelagic Marine Bacteria
SO PLOS ONE
DT Article
AB The SAR11 Alphaproteobacteria are the most abundant heterotrophs in the oceans and are believed to play a major role in mineralizing marine dissolved organic carbon. Their genomes are among the smallest known for free-living heterotrophic cells, raising questions about how they successfully utilize complex organic matter with a limited metabolic repertoire. Here we show that conserved genes in SAR11 subgroup Ia (Candidatus Pelagibacter ubique) genomes encode pathways for the oxidation of a variety of one-carbon compounds and methyl functional groups from methylated compounds. These pathways were predicted to produce energy by tetrahydrofolate (THF)-mediated oxidation, but not to support the net assimilation of biomass from C1 compounds. Measurements of cellular ATP content and the oxidation of C-14-labeled compounds to (CO2)-C-14 indicated that methanol, formaldehyde, methylamine, and methyl groups from glycine betaine (GBT), trimethylamine (TMA), trimethylamine N-oxide (TMAO), and dimethylsulfoniopropionate (DMSP) were oxidized by axenic cultures of the SAR11 strain Ca. P. ubique HTCC1062. Analyses of metagenomic data showed that genes for C1 metabolism occur at a high frequency in natural SAR11 populations. In short term incubations, natural communities of Sargasso Sea microbial plankton expressed a potential for the oxidation of C-14-labeled formate, formaldehyde, methanol and TMAO that was similar to cultured SAR11 cells and, like cultured SAR11 cells, incorporated a much larger percentage of pyruvate and glucose (27-35%) than of C1 compounds (2-6%) into biomass. Collectively, these genomic, cellular and environmental data show a surprising capacity for demethylation and C1 oxidation in SAR11 cultures and in natural microbial communities dominated by SAR11, and support the conclusion that C1 oxidation might be a significant conduit by which dissolved organic carbon is recycled to CO2 in the upper ocean.
C1 [Sun, Jing; Steindler, Laura; Thrash, J. Cameron; Smith, Daniel P.; Carter, Amy E.; Landry, Zachary C.; Giovannoni, Stephen J.] Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
   [Halsey, Kimberly H.] Oregon State Univ, Dept Bot & Plant Pathol, Corvallis, OR 97331 USA.
RP Sun, J (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
EM steve.giovannoni@oregonstate.edu
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NR 82
TC 141
Z9 155
PD AUG 23
PY 2011
VL 6
IS 8
AR e23973
DI 10.1371/journal.pone.0023973
UT WOS:000294253500041
DA 2025-07-30
ER

PT J
AU Carini, P
   White, AE
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   Giovannoni, SJ
AF Carini, Paul
   White, Angelicque E.
   Campbell, Emily O.
   Giovannoni, Stephen J.
TI Methane production by phosphate-starved SAR11 chemoheterotrophic marine
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SO NATURE COMMUNICATIONS
DT Article
AB The oxygenated surface waters of the world's oceans are supersaturated with methane relative to the atmosphere, a phenomenon termed the 'marine methane paradox'. The production of methylphosphonic acid (MPn) by marine archaea related to Nitrosopumilus maritimus and subsequent decomposition of MPn by phosphate-starved bacterioplankton may partially explain the excess methane in surface waters. Here we show that Pelagibacterales sp. strain HTCC7211, an isolate of the SAR11 clade of marine alpha-proteobacteria, produces methane from MPn, stoichiometric to phosphorus consumption, when starved for phosphate. Gene transcripts encoding phosphonate transport and hydrolysis proteins are upregulated under phosphate limitation, suggesting a genetic basis for the methanogenic phenotype. Strain HTCC7211 can also use 2-aminoethylphosphonate and assorted phosphate esters for phosphorus nutrition. Despite strain-specific differences in phosphorus utilization, these findings identify Pelagibacterales bacteria as a source of biogenic methane and further implicate phosphate starvation of chemoheterotrophic bacteria in the long-observed methane supersaturation in oxygenated waters.
C1 [Carini, Paul; Campbell, Emily O.; Giovannoni, Stephen J.] Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
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RP Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
EM steve.giovannoni@oregonstate.edu
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TC 119
Z9 144
PD JUL
PY 2014
VL 5
AR 4346
DI 10.1038/ncomms5346
UT WOS:000340615500037
DA 2025-07-30
ER

PT J
AU Giovannoni, SJ
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DT Article
AB Proteorhodopsins are light-dependent proton pumps that are predicted to have an important role in the ecology of the oceans by supplying energy for microbial metabolism(1,2). Proteorhodopsin genes were first discovered through the cloning and sequencing of large genomic DNA fragments from seawater(1). They were later shown to be widely distributed, phylogenetically diverse, and active in the oceans(3-7). Proteorhodopsin genes have not been found in cultured bacteria, and on the basis of environmental sequence data, it has not yet been possible to reconstruct the genomes of uncultured bacterial strains that have proteorhodopsin genes. Although the metabolic effect of proteorhodopsins is uncertain, they are thought to function in cells for which the primary mode of metabolism is the heterotrophic assimilation of dissolved organic carbon. Here we report that SAR11 strain HTCC1062 ('Pelagibacter ubique')(8), the first cultivated member of the extraordinarily abundant SAR11 clade, expresses a proteorhodopsin gene when cultured in autoclaved seawater and in its natural environment, the ocean. The Pelagibacter proteorhodopsin functions as a light-dependent proton pump. The gene is expressed by cells grown in either diurnal light or in darkness, and there is no difference between the growth rates or cell yields of cultures grown in light or darkness.
C1 Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
   Oregon State Univ, Dept Chem, Corvallis, OR 97331 USA.
   Oregon State Univ, Coll Ocean & Atmospher Sci, Corvallis, OR 97331 USA.
   Diversa Corp, San Diego, CA 92121 USA.
RP Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
EM steve.giovannoni@oregonstate.edu
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TC 251
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VL 438
IS 7064
BP 82
EP 85
DI 10.1038/nature04032
UT WOS:000232979000045
DA 2025-07-30
ER

PT J
AU Carlson, CA
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AF Carlson, Craig A.
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DT Article
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C1 [Carlson, Craig A.; Morris, Robert] Univ Calif Santa Barbara, Dept Ecol Evolut & Marine Biol, Santa Barbara, CA 93106 USA.
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RP Carlson, CA (corresponding author), Univ Calif Santa Barbara, Dept Ecol Evolut & Marine Biol, Santa Barbara, CA 93106 USA.
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PD MAR
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IS 3
BP 283
EP 295
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UT WOS:000263914100002
DA 2025-07-30
ER

PT J
AU Vila-Nistal, M
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AF Vila-Nistal, Marina
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   Gasol, Josep M.
   Martinez-Garcia, Manuel
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DT Article
AB Viruses play a pivotal role in ecosystems by influencing biochemical cycles and impacting the structure and evolution of their host cells. The widespread pelagiphages infect Pelagibacter spp., the most abundant marine microbe on Earth, and thus play a significant role in carbon transformation through the viral shunt. Among these viruses, the uncultured lytic pelagiphage vSAG 37-F6, uncovered by single-virus genomics, is likely the most numerous virus in the ocean. While previous research has delved into the diversity and spatial distribution of vSAG 37-F6, there is still a gap in understanding its temporal dynamics, hindering our insight into its ecological impact. We explored the temporal dynamics of vSAG 37-F6, assessing periodic fluctuations in abundance and evolutionary patterns using long- and short-term data series. In the long-term series (7 years), metagenomics showed negative selection acting on all viral genes, with a highly conserved overall diversity over time composed of a pool of yearly emergent, highly similar novel strains that exhibited a seasonal abundance pattern with two peaks during winter and fall and a decrease in months with higher UV radiation. Most non-synonymous polymorphisms occurred in structural viral proteins located in regions with low conformational restrictions, suggesting that many of the viral genes of this population are highly purified over its evolution. At the fine-scale resolution (24 h time series), combining digital PCR and metagenomics, we identified two peaks of cellular infection for the targeted vSAG 37-F6 viral strain (up to approximately 103 copies/ng of prokaryotic DNA), one before sunrise and the second shortly after midday. Considering the high number of co-occurring strains of this microdiverse virus, the abundance values at the species or genus level could be orders of magnitudes higher. These findings represent a significant advancement in understanding the dynamics of the potentially most abundant oceanic virus, providing valuable insights into ecologically relevant marine viruses.
C1 [Vila-Nistal, Marina; Martinez-Garcia, Manuel] Univ Alicante, Dept Physiol Genet & Microbiol, Carretera San Vicente Raspeig, Alicante 03690, Spain.
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   [Logares, Ramiro; Gasol, Josep M.] CSIC, Inst Ciencies Mar ICM, Barcelona 08003, Spain.
RP Martinez-Garcia, M (corresponding author), Univ Alicante, Dept Physiol Genet & Microbiol, Carretera San Vicente Raspeig, Alicante 03690, Spain.; Martinez-Garcia, M (corresponding author), Univ Alicante, Multidisciplinary Inst Environm Studies IMEM, Carretera San Vicente Raspeig, Alicante 03690, Spain.
EM marina.vila@ua.es; ramiro.logares@icm.csic.es; pepgasol@icm.csic.es;
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NR 44
TC 0
Z9 0
PD NOV
PY 2024
VL 16
IS 11
AR 1669
DI 10.3390/v16111669
UT WOS:001366371000001
DA 2025-07-30
ER

PT J
AU Thrash, JC
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AF Thrash, J. Cameron
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TI Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype
SO ISME JOURNAL
DT Article
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RP Thrash, JC (corresponding author), Louisiana State Univ, Dept Biol Sci, Baton Rouge, LA 70803 USA.
EM thrashc@lsu.edu
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TC 77
Z9 83
PD JUL
PY 2014
VL 8
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BP 1440
EP 1451
DI 10.1038/ismej.2013.243
UT WOS:000338213900009
DA 2025-07-30
ER

PT J
AU Logares, R
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AF Logares, Ramiro
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DT Article
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RP Logares, R (corresponding author), Uppsala Univ, Limnol Dept Ecol & Evolut, Uppsala, Sweden.
EM ramiro.logares@gmail.com
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TC 57
Z9 60
PD FEB
PY 2010
VL 27
IS 2
BP 347
EP 357
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DA 2025-07-30
ER

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TI Energy Starved Candidatus Pelagibacter Ubique Substitutes
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DT Article
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RP Steindler, L (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
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NR 43
TC 155
Z9 175
PD MAY 9
PY 2011
VL 6
IS 5
AR e19725
DI 10.1371/journal.pone.0019725
UT WOS:000290386800033
DA 2025-07-30
ER

PT J
AU Zhao, X
   Wan, XG
   He, RL
   Yau, SST
AF Zhao, Xin
   Wan, Xiaogeng
   He, Rong L.
   Yau, Stephen S. -T.
TI A new method for studying the evolutionary origin of the SAR11 Glade
   marine bacteria
SO MOLECULAR PHYLOGENETICS AND EVOLUTION
DT Article
AB The free-living SARI I Glade is a globally abundant group of oceanic Alphaproteobacteria, with small genome sizes and rich genomic A+T content. However, the taxonomy of SAR11 has become controversial recently. Some researchers argue that the position of SAR11 is a sister group to Rickettsiales. Other researchers advocate that SAR11 is located within free-living lineages of Alphaproteobacteria. Here, we use the natural vector representation method to identify the evolutionary origin of the SAR11 Glade. This alignment-free method does not depend on any model assumptions. With this approach, the correspondence between proteome sequences and their natural vectors is one-to-one. After fixing a set of proteins, each bacterium is represented by a set of vectors. The Hausdorff distance is then used to compute the dissimilarity distance between two bacteria. The phylogenetic tree can be reconstructed based on these distances. Using our method, we systematically analyze four data sets of alphaproteobacterial proteomes in order to reconstruct the phylogeny of Alphaproteobacteria. From this we can see that the phylogenetic position of the SAR11 group is within a group of other free-living lineages of Alphaproteobacteria. (C) 2016 Elsevier Inc. All rights reserved.
C1 [Zhao, Xin; Wan, Xiaogeng; Yau, Stephen S. -T.] Tsinghua Univ, Dept Math Sci, Beijing 100084, Peoples R China.
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RP Yau, SST (corresponding author), Tsinghua Univ, Dept Math Sci, Beijing 100084, Peoples R China.
EM yau@uic.edu
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TC 12
Z9 13
PD MAY
PY 2016
VL 98
BP 271
EP 279
DI 10.1016/j.ympev.2016.02.015
UT WOS:000374206900025
DA 2025-07-30
ER

PT J
AU Manrique, JM
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AF Manrique, Julieta M.
   Jones, Leandro R.
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SO MOLECULAR PHYLOGENETICS AND EVOLUTION
DT Article
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C1 Consejo Nacl Invest Cient & Tecn, Av Rivadavia 1917,C1083ACA, Buenos Aires, DF, Argentina.
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RP Jones, LR (corresponding author), Univ Nacl Patagonia San Juan Bosco, Fac Ciencias Nat Sede Trelew, Lab Virol & Genet Mol, 9 Julio & Belgrano S-N, RA-9100 Trelew, Chubut, Argentina.
EM ljones@conicet.gov.ar
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NR 40
TC 9
Z9 10
PD FEB
PY 2017
VL 107
BP 324
EP 337
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UT WOS:000394200500031
DA 2025-07-30
ER

PT J
AU Henson, MW
   Lanclos, VC
   Faircloth, BC
   Thrash, JC
AF Henson, Michael W.
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   Thrash, J. Cameron
TI Cultivation and genomics of the first freshwater SAR11 (LD12) isolate
SO ISME JOURNAL
DT Article
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RP Thrash, JC (corresponding author), Louisiana State Univ, Dept Biol Sci, Baton Rouge, LA 70803 USA.
EM thrashc@lsu.edu
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IS 7
BP 1846
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UT WOS:000436623600019
DA 2025-07-30
ER

PT J
AU Zhao, YL
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AF Zhao, Yanlin
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB The Pelagibacterales order (SAR11) in Alphaproteobacteria dominates marine surface bacterioplankton communities, where it plays a key role in carbon and nutrient cycling. SAR11 phages, known as pelagiphages, are among the most abundant phages in the ocean. Four pelagiphages that infect Pelagibacter HTCC1062 have been reported. Here, we report 11 new pelagiphages in the Podoviridae family. Comparative genomics classified these pelagiphages into the HTVC019Pvirus genus, which includes the previously reported pelagiphages HTVC011P and HTVC019P. Phylogenomic analysis clustered HTVC019Pvirus pelagiphages into three subgroups. Integrases were identified in all but one HTVC019Pvirus genome. Site-specific integration of HTVC019Pvirus pelagiphages into host tRNA genes was verified experimentally, demonstrating the capacity of these pelagiphages to propagate by both lytic and lysogenic infection. Evidence of pelagiphage integration was also retrieved from the Global Ocean Survey database, showing that prophages are found in natural SAR11 populations. HTVC019Pvirus pelagiphages could impact SAR11 populations by a variety of mechanisms, including mortality, genetic transduction and prophage-induced viral immunity. HTVC019Pvirus pelagiphages are a rare example of cultured lysogenic phage that can be implicated in ecological processes on broad scales. These pelagiphages have the potential to become a useful model for investigating strategies of host infection and phage-dependent horizontal gene transfer.
C1 [Zhao, Yanlin; Qin, Fang; Zhang, Zefeng; Du, Sen] Fujian Agr & Forestry Univ, Fujian Prov Key Lab Agroecol Proc & Safety Monito, Coll Life Sci, Fuzhou, Fujian, Peoples R China.
   [Zhang, Rui] Xiamen Univ, State Key Lab Marine Environm Sci, Coll Ocean & Earth Sci, Inst Marine Microbes & Ecospheres, Xiamen, Fujian, Peoples R China.
   [Giovannoni, Stephen J.; Sun, Jing] Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
   [Rensing, Christopher] Fujian Agr & Forestry Univ, Fujian Prov Key Lab Soil Environm Hlth & Regulat, Coll Resources & Environm, Fuzhou, Fujian, Peoples R China.
   [Zhao, Yanlin] Chinese Acad Fishery Sci, Yellow Sea Fisheries Res Inst, Qingdao, Shandong, Peoples R China.
RP Zhao, Y (corresponding author), Fujian Agr & Forestry Univ, Fujian Prov Key Lab Agroecol Proc & Safety Monito, Coll Life Sci, Fuzhou, Fujian, Peoples R China.; Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.; Zhao, Y (corresponding author), Chinese Acad Fishery Sci, Yellow Sea Fisheries Res Inst, Qingdao, Shandong, Peoples R China.
EM yanlinzhao@fafu.edu.cn; steve.giovannoni@oregonstate.edu
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NR 74
TC 47
Z9 49
PD JUN
PY 2019
VL 21
IS 6
BP 1989
EP 2001
DI 10.1111/1462-2920.14487
UT WOS:000469995900009
DA 2025-07-30
ER

PT J
AU Noell, SE
   Giovannoni, SJ
AF Noell, Stephen E.
   Giovannoni, Stephen J.
TI SAR11 bacteria have a high affinity and multifunctional glycine betaine
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
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RP Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
EM steve.giovannoni@oregonstate.edu
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NR 95
TC 41
Z9 44
PD JUL
PY 2019
VL 21
IS 7
BP 2559
EP 2575
DI 10.1111/1462-2920.14649
UT WOS:000474294900026
DA 2025-07-30
ER

PT J
AU Song, J
   Oh, HM
   Cho, JC
AF Song, Jaeho
   Oh, Hyun-Myung
   Cho, Jang-Cheon
TI Improved culturability of SAR11 strains in dilution-to-extinction
   culturing from the East Sea, West Pacific Ocean
SO FEMS MICROBIOLOGY LETTERS
DT Article
AB Although the SAR11 clade of the Alphaproteobacteria represents the most abundant and ubiquitous bacterioplankton in the ocean, very few laboratories have successfully cultured SAR11 cells. All of the SAR11 strains isolated thus far have been retrieved from the Oregon coast and the Sargasso Sea. In this study, a modified dilution-to-extinction culturing with prolonged incubation at low temperature was applied in an effort to cultivate major bacterioplankton lineages in the East Sea, Western Pacific Ocean. Five to 10 cells were inoculated into each well of 48-well plates, followed by the incubation of the plates at 10 degrees C for 4, 8, 20, and 24 weeks. Among a total of 35 isolated strains, 18 strains assigned to the SAR11 clade were isolated after 8, 20, and 24 weeks of incubation, whereas no SAR11 cells were detected in the samples after 4 weeks of incubation. The SAR11 isolates, noticeably, comprised 64-82% of the total isolates from the plates incubated for 20 and 24 weeks. Extinction cultures belonging to the Roseobacter, OM43, and SAR92 clades were also cultivated. The results of this study suggest that long-term incubation at low temperatures might prove an alternative for the efficient cultivation of new variants of the members of the SAR11 clade.
C1 [Song, Jaeho; Oh, Hyun-Myung; Cho, Jang-Cheon] Inha Univ, Div Biol & Ocean Sci, Inchon 402751, South Korea.
RP Cho, JC (corresponding author), Inha Univ, Div Biol & Ocean Sci, Inchon 402751, South Korea.
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BP 141
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DA 2025-07-30
ER

PT J
AU Bahr, M
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AF Bahr, M
   Hobbie, JE
   Sogin, ML
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SO AQUATIC MICROBIAL ECOLOGY
DT Article
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RP MARINE BIOL LAB, CTR ECOSYST, WOODS HOLE, MA 02543 USA.
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DA 2025-07-30
ER

PT J
AU Tripp, HJ
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   Giovannoni, SJ
AF Tripp, H. James
   Kitner, Joshua B.
   Schwalbach, Michael S.
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   Giovannoni, Stephen J.
TI SAR11 marine bacteria require exogenous reduced sulphur for growth
SO NATURE
DT Article
AB Sulphur is a universally required cell nutrient found in two amino acids and other small organic molecules. All aerobic marine bacteria are known to use assimilatory sulphate reduction to supply sulphur for biosynthesis, although many can assimilate sulphur from organic compounds that contain reduced sulphur atoms(1-3). An analysis of three complete 'Candidatus Pelagibacter ubique' genomes, and public ocean metagenomic data sets, suggested that members of the ubiquitous and abundant SAR11 alphaproteobacterial clade are deficient in assimilatory sulphate reduction genes. Here we show that SAR11 requires exogenous sources of reduced sulphur, such as methionine or 3-dimethylsulphoniopropionate (DMSP) for growth. Titrations of the algal osmolyte DMSP in seawater medium containing all other macronutrients in excess showed that 1.5 x 10(8) SAR11 cells are produced per nanomole of DMSP. Although it has been shown that other marine alphaproteobacteria use sulphur from DMSP in preference to sulphate(1,2), our results indicate that 'Cand. P. ubique' relies exclusively on reduced sulphur compounds that originate from other plankton.
C1 [Tripp, H. James; Kitner, Joshua B.; Schwalbach, Michael S.; Wilhelm, Larry J.; Giovannoni, Stephen J.] Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
   [Dacey, John W. H.] Woods Hole Oceanog Inst, Woods Hole, MA 02543 USA.
RP Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, 220 Nash Hall, Corvallis, OR 97331 USA.
EM steve.giovannoni@oregonstate.edu
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BP 741
EP 744
DI 10.1038/nature06776
UT WOS:000254792500043
DA 2025-07-30
ER

PT J
AU Apprill, A
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   Parsons, R
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AF Apprill, Amy
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   Weber, Laura
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SO AQUATIC MICROBIAL ECOLOGY
DT Article
AB High-throughput sequencing of small subunit ribosomal RNA (SSU rRNA) genes from marine environments is a widely applied method used to uncover the composition of microbial communities. We conducted an analysis of surface ocean waters with the commonly employed hypervariable 4 region SSU rRNA gene primers 515F and 806R, and found that bacteria belonging to the SAR11 clade of Alphaproteobacteria, a group typically making up 20 to 40% of the bacterioplankton in this environment, were greatly underrepresented and comprised <4% of the total community. Using the SILVA reference database, we found a single nucleotide mismatch to nearly all SAR11 subclades, and revised the 806R primer so that it increased the detection of SAR11 clade sequences in the database from 2.6 to 96.7%. We then compared the performance of the original and revised 806R primers in surface seawater samples, and found that SAR11 comprised 0.3 to 3.9% of sequences with the original primers and 17.5 to 30.5% of the sequences with the revised 806R primer. Furthermore, an investigation of seawater obtained from aquaria re vealed that SAR11 sequences acquired with the revised 806R primer were more similar to natural cellular abundances of SAR11 detected using fluorescence in situ hybridization counts. Collectively, these results demonstrate that a minor adjustment to the 806R primer will greatly increase detection of the globally abundant SAR11 clade in marine and lake environments, and enable inclusion of this important bacterial lineage in experimental and environmental-based studies.
C1 [Apprill, Amy; McNally, Sean; Weber, Laura] Woods Hole Oceanog Inst, Woods Hole, MA 02543 USA.
   [McNally, Sean; Parsons, Rachel] Bermuda Inst Ocean Sci, Ferry Reach, St Georges, Bermuda.
RP Apprill, A (corresponding author), Woods Hole Oceanog Inst, Woods Hole, MA 02543 USA.
EM apprill@whoi.edu
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TC 1682
Z9 1914
PY 2015
VL 75
IS 2
BP 129
EP 137
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UT WOS:000357106200004
HC Y
HP N
DA 2025-07-30
ER

PT J
AU Tsementzi, D
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   Ruiz-Perez, CA
   Meziti, A
   Hatt, JK
   Konstantinidis, KT
AF Tsementzi, Despina
   Rodriguez-R, Luis M.
   Ruiz-Perez, Carlos A.
   Meziti, Alexandra
   Hatt, Janet K.
   Konstantinidis, Konstantinos T.
TI Ecogenomic characterization of widespread, closely-related SAR11 clades
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DT Article
AB The ubiquitous alpha-proteobacteria of the order "Candidatus Pelagibacterales" (SAR11) are highly abundant in aquatic environments, and among them, members of the monophyletic lineage LD12 (also known as SAR11 Glade IIIb) are specifically found in lacustrine ecosystems. Clade IIIb bacteria are some of the most prominent members of freshwater environments, but little is known about their biology due to the lack of genome representatives. Only recently, the first non-marine isolate was cultured and described as "Candidatus Fonsibacter ubiquis". Here, we expand the collection of freshwater IIIb representatives and describe a new IIIb species of the genus "Ca. Fonsibacter". Specifically, we assembled a collection of 67 freshwater metagenomic datasets from the interconnected lakes of the Chattahoochee River basin (GA, USA) and obtained nearly complete metagenome-assembled genomes (MAGs) representing 5 distinct IIIb subclades, roughly equivalent to species based on genomic standards, including the previously described "Ca. F. ubiquis". Genomic comparisons between members of the IIIb species revealed high similarity in gene content. However, when comparing their abundance profiles in the Chattahoochee basin and various aquatic environments, differences in temporal and spatial distributions among the distinct species were observed implying niche differentiation might be underlying the coexistence of the highly functionally similar representatives. The name Ca. Fonsibacter lacus sp. nov. is proposed for the most abundant and widespread species in the Chattahoochee River basin and various freshwater ecosystems. (C) 2019 Elsevier GmbH. All rights reserved.
C1 [Tsementzi, Despina; Rodriguez-R, Luis M.; Meziti, Alexandra; Hatt, Janet K.; Konstantinidis, Konstantinos T.] Georgia Inst Technol, Sch Civil & Environm Engn, Ford Environm Sci & Technol Bldg,311 Ferst Dr, Atlanta, GA 30332 USA.
   [Ruiz-Perez, Carlos A.; Konstantinidis, Konstantinos T.] Georgia Inst Technol, Sch Biol Sci, Ford Environm Sci & Technol Bldg,311 Ferst Dr, Atlanta, GA 30332 USA.
RP Konstantinidis, KT (corresponding author), Georgia Inst Technol, Sch Civil & Environm Engn, 311 Ferst Dr, Atlanta, GA 30332 USA.; Konstantinidis, KT (corresponding author), Georgia Inst Technol, Sch Biol, 311 Ferst Dr, Atlanta, GA 30332 USA.
EM kostas@ce.gatech.edu
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NR 64
TC 24
Z9 25
PD JUL
PY 2019
VL 42
IS 4
BP 495
EP 505
DI 10.1016/j.syapm.2019.03.007
UT WOS:000474343600008
DA 2025-07-30
ER

PT J
AU Lanclos, VC
   Rasmussen, AN
   Kojima, CY
   Cheng, CK
   Henson, MW
   Faircloth, BC
   Francis, CA
   Thrash, JC
AF Lanclos, V. Celeste
   Rasmussen, Anna N. N.
   Kojima, Conner Y. Y.
   Cheng, Chuankai
   Henson, Michael W. W.
   Faircloth, Brant C. C.
   Francis, Christopher A. A.
   Thrash, J. Cameron
TI Ecophysiology and genomics of the brackish water adapted SAR11 subclade
   IIIa
SO ISME JOURNAL
DT Article
AB The Order Pelagibacterales (SAR11) is the most abundant group of heterotrophic bacterioplankton in global oceans and comprises multiple subclades with unique spatiotemporal distributions. Subclade IIIa is the primary SAR11 group in brackish waters and shares a common ancestor with the dominant freshwater IIIb (LD12) subclade. Despite its dominance in brackish environments, subclade IIIa lacks systematic genomic or ecological studies. Here, we combine closed genomes from new IIIa isolates, new IIIa MAGS from San Francisco Bay (SFB), and 460 highly complete publicly available SAR11 genomes for the most comprehensive pangenomic study of subclade IIIa to date. Subclade IIIa represents a taxonomic family containing three genera (denoted as subgroups IIIa.1, IIIa.2, and IIIa.3) that had distinct ecological distributions related to salinity. The expansion of taxon selection within subclade IIIa also established previously noted metabolic differentiation in subclade IIIa compared to other SAR11 subclades such as glycine/serine prototrophy, mosaic glyoxylate shunt presence, and polyhydroxyalkanoate synthesis potential. Our analysis further shows metabolic flexibility among subgroups within IIIa. Additionally, we find that subclade IIIa.3 bridges the marine and freshwater clades based on its potential for compatible solute transport, iron utilization, and bicarbonate management potential. Pure culture experimentation validated differential salinity ranges in IIIa.1 and IIIa.3 and provided detailed IIIa cell size and volume data. This study is an important step forward for understanding the genomic, ecological, and physiological differentiation of subclade IIIa and the overall evolutionary history of SAR11.
C1 [Lanclos, V. Celeste; Kojima, Conner Y. Y.; Cheng, Chuankai; Thrash, J. Cameron] Univ Southern Calif, Dept Biol Sci, Los Angeles, CA 90089 USA.
   [Rasmussen, Anna N. N.; Francis, Christopher A. A.] Stanford Univ, Dept Earth Syst Sci, Stanford, CA 94305 USA.
   [Henson, Michael W. W.] Univ Chicago, Dept Geophys Sci, Chicago, IL 60637 USA.
   [Faircloth, Brant C. C.] Louisiana State Univ, Dept Biol Sci, Baton Rouge, LA 70803 USA.
   [Faircloth, Brant C. C.] Louisiana State Univ, Museum Nat Sci, Baton Rouge, LA 70803 USA.
RP Thrash, JC (corresponding author), Univ Southern Calif, Dept Biol Sci, Los Angeles, CA 90089 USA.
EM thrash@usc.edu
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NR 97
TC 16
Z9 16
PD APR
PY 2023
VL 17
IS 4
BP 620
EP 629
DI 10.1038/s41396-023-01376-2
EA FEB 2023
UT WOS:000925942900001
DA 2025-07-30
ER

PT J
AU Dadon-Pilosof, A
   Conley, KR
   Jacobi, Y
   Haber, M
   Lombard, F
   Sutherland, KR
   Steindler, L
   Tikochinski, Y
   Richter, M
   Glöckner, FO
   Suzuki, MT
   West, NJ
   Genin, A
   Yahel, G
AF Dadon-Pilosof, Ayelet
   Conley, Keats R.
   Jacobi, Yuval
   Haber, Markus
   Lombard, Fabien
   Sutherland, Kelly R.
   Steindler, Laura
   Tikochinski, Yaron
   Richter, Michael
   Gloeckner, Frank Oliver
   Suzuki, Marcelino T.
   West, Nyree J.
   Genin, Amatzia
   Yahel, Gitai
TI Surface properties of SAR11 bacteria facilitate grazing avoidance
SO NATURE MICROBIOLOGY
DT Article
AB Oceanic ecosystems are dominated by minute microorganisms that play a major role in food webs and biogeochemical cycles(1). Many microorganisms thrive in the dilute environment due to their capacity to locate, attach to, and use patches of nutrients and organic matter(2,3). We propose that some free-living planktonic bacteria have traded their ability to stick to nutrient-rich organic particles for a non-stick cell surface that helps them evade predation by mucous filter feeders. We used a combination of in situ sampling techniques and next-generation sequencing to study the biological filtration of microorganisms at the phylotype level. Our data indicate that some marine bacteria, most notably the highly abundant Pelagibacter ubique and most other members of the SAR 11 clade of the Alphaproteobacteria, can evade filtration by slipping through the mucous nets of both pelagic and benthic tunicates. While 0.3 mu m polystyrene beads and other similarly-sized bacteria were efficiently filtered, SAR11 members were not captured. Reversed-phase chromatography revealed that most SAR11 bacteria have a much less hydrophobic cell surface than that of other planktonic bacteria. Our data call for a reconsideration of the role of surface properties in biological filtration and predator-prey interactions in aquatic systems.
C1 [Dadon-Pilosof, Ayelet; Jacobi, Yuval; Tikochinski, Yaron; Yahel, Gitai] Ruppin Acad Ctr, Sch Marine Sci, IL-4029700 Michmoret, Israel.
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   [Suzuki, Marcelino T.] Sorbonne Univ, UPMC Univ Paris 06, CNRS, LBBM,Observ Oceanol, F-66650 Banyuls Sur Mer, France.
   [West, Nyree J.] Sorbonne Univ, UPMC Univ Paris 06, CNRS, OOB, F-66650 Banyuls Sur Mer, France.
   [Genin, Amatzia] Interuniv Inst Marine Sci Eilat, IL-8810302 Elat, Israel.
RP Dadon-Pilosof, A (corresponding author), Ruppin Acad Ctr, Sch Marine Sci, IL-4029700 Michmoret, Israel.; Dadon-Pilosof, A (corresponding author), Hebrew Univ Jerusalem, Dept Ecol Evolut & Behav, IL-9190401 Jerusalem, Israel.
EM ayelet@ruppin.ac.il
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NR 57
TC 54
Z9 57
PD DEC
PY 2017
VL 2
IS 12
BP 1608
EP 1615
DI 10.1038/s41564-017-0030-5
UT WOS:000417976600012
DA 2025-07-30
ER

PT J
AU Luo, HW
   Thompson, LR
   Stingl, U
   Hughes, AL
AF Luo, Haiwei
   Thompson, Luke R.
   Stingl, Ulrich
   Hughes, Austin L.
TI Selection Maintains Low Genomic GC Content in Marine SAR11 Lineages
SO MOLECULAR BIOLOGY AND EVOLUTION
DT Article
AB The genomic G+C content of ocean bacteria varies from below 30% to over 60%. This broad range of base composition is likely shaped by distinct mutational processes, recombination, effective population size, and selection driven by environmental factors. A number of studies have hypothesized that depletion of G/C in genomes of marine bacterioplankton cells is an adaptation to the nitrogen-poor pelagic oceans, but they failed to disentangle environmental factors from mutational biases and population history. Here, we reconstructed the evolutionary changes of bases at synonymous sites in genomes of two marine SAR11 populations and a freshwater counterpart with its evolutionary origin rooted in the marine lineage. Although they all have similar genome sizes, DNA repair gene repertoire, and base compositions, there is a stronger bias toward A/T changes, a reduced frequency of nitrogenous amino acids, and an exclusive occurrence of polyamine, opine, and taurine transport systems in the ocean populations, consistent with a greater nitrogen stress in surface oceans compared with freshwater lakes. Furthermore, the ratio of nonsynoymous to synonymous nucleotide diversity is not statistically distinguishable among these populations, suggesting that population history has a limited effect. Taken together, the ecological transition of SAR11 from ocean to freshwater habitats makes nitrogen more available to these organisms, and thus relaxation of purifying selection drove a genome-wide reduction in the frequency of G/C to A/T changes in the freshwater population.
C1 [Luo, Haiwei] Chinese Univ Hong Kong, Simon FS Li Marine Sci Lab, Sch Life Sci, Shatin, Hong Kong, Peoples R China.
   [Thompson, Luke R.; Stingl, Ulrich] King Abdullah Univ Sci & Technol, Red Sea Res Ctr, Thuwal, Saudi Arabia.
   [Hughes, Austin L.] Univ S Carolina, Dept Biol Sci, Columbia, SC 29208 USA.
RP Luo, HW (corresponding author), Chinese Univ Hong Kong, Simon FS Li Marine Sci Lab, Sch Life Sci, Shatin, Hong Kong, Peoples R China.
EM hluo2006@gmail.com
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NR 80
TC 39
Z9 45
PD OCT
PY 2015
VL 32
IS 10
BP 2738
EP 2748
DI 10.1093/molbev/msv149
UT WOS:000361987100021
DA 2025-07-30
ER

PT J
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DT Article
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RP Simon, M (corresponding author), Carl von Ossietzky Univ Oldenburg, Inst Chem & Biol Marine Environm ICBM, D-26111 Oldenburg, Germany.
EM m.simon@icbm.de
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NR 58
TC 107
Z9 114
PD JAN
PY 2011
VL 5
IS 1
BP 8
EP 19
DI 10.1038/ismej.2010.87
UT WOS:000285845200002
DA 2025-07-30
ER

PT J
AU Vergin, KL
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   Monier, A
   Thrash, JC
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AF Vergin, Kevin L.
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TI High-resolution SAR11 ecotype dynamics at the Bermuda Atlantic
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SO ISME JOURNAL
DT Article
AB Advances in next-generation sequencing technologies are providing longer nucleotide sequence reads that contain more information about phylogenetic relationships. We sought to use this information to understand the evolution and ecology of bacterioplankton at our long-term study site in the Western Sargasso Sea. A bioinformatics pipeline called PhyloAssigner was developed to align pyrosequencing reads to a reference multiple sequence alignment of 16S ribosomal RNA (rRNA) genes and assign them phylogenetic positions in a reference tree using a maximum likelihood algorithm. Here, we used this pipeline to investigate the ecologically important SAR11 clade of Alphaproteobacteria. A combined set of 2.7 million pyrosequencing reads from the 16S rRNA V1-V2 regions, representing 9 years at the Bermuda Atlantic Time-series Study (BATS) site, was quality checked and parsed into a comprehensive bacterial tree, yielding 929 036 Alphaproteobacteria reads. Phylogenetic structure within the SAR11 clade was linked to seasonally recurring spatiotemporal patterns. This analysis resolved four new SAR11 ecotypes in addition to five others that had been described previously at BATS. The data support a conclusion reached previously that the SAR11 clade diversified by subdivision of niche space in the ocean water column, but the new data reveal a more complex pattern in which deep branches of the clade diversified repeatedly across depth strata and seasonal regimes. The new data also revealed the presence of an unrecognized clade of Alphaproteobacteria, here named SMA-1 (Sargasso Mesopelagic Alphaproteobacteria, group 1), in the upper mesopelagic zone. The high-resolution phylogenetic analyses performed herein highlight significant, previously unknown, patterns of evolutionary diversification, within perhaps the most widely distributed heterotrophic marine bacterial clade, and strongly links to ecosystem regimes.
C1 [Vergin, Kevin L.; Beszteri, Bank; Thrash, J. Cameron; Temperton, Ben; Treusch, Alexander H.; Giovannoni, Stephen J.] Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
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   [Treusch, Alexander H.] Univ Southern Denmark, Nord Ctr Earth Evolut NordCEE, Odense, Denmark.
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RP Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, 220 Nash Hall, Corvallis, OR 97331 USA.
EM steve.giovannoni@oregonstate.edu
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NR 58
TC 144
Z9 166
PD JUL
PY 2013
VL 7
IS 7
BP 1322
EP 1332
DI 10.1038/ismej.2013.32
UT WOS:000320852100008
DA 2025-07-30
ER

PT J
AU Delmont, TO
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AF Delmont, Tom O.
   Kiefl, Evan
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   Rappe, Michael S.
   Giovannoni, Steven
   Eren, A. Murat
TI Single-amino acid variants reveal evolutionary processes that shape the
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SO ELIFE
DT Article
AB Members of the SAR11 order Pelagibacterales dominate the surface oceans. Their extensive diversity challenges emerging operational boundaries defined for microbial 'species ' and complicates efforts of population genetics to study their evolution. Here, we employed single-amino acid variants (SAAVs) to investigate ecological and evolutionary forces that maintain the genomic heterogeneity within ubiquitous SAR11 populations we accessed through metagenomic read recruitment using a single isolate genome. Integrating amino acid and protein biochemistry with metagenomics revealed that systematic purifying selection against deleterious variants governs non-synonymous variation among very closely related populations of SAR11. SAAVs partitioned metagenomes into two main groups matching large-scale oceanic current temperatures, and six finer proteotypes that connect distant oceanic regions. These findings suggest that environmentally-mediated selection plays a critical role in the journey of cosmopolitan surface ocean microbial populations, and the idea 'everything is everywhere but the environment selects' has credence even at the finest resolutions.
C1 [Delmont, Tom O.; Kiefl, Evan; Esen, Ozcan C.; Eren, A. Murat] Univ Chicago, Dept Med, Chicago, IL 60637 USA.
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RP Eren, AM (corresponding author), Univ Chicago, Dept Med, Chicago, IL 60637 USA.; Eren, AM (corresponding author), Marine Biol Lab, Woods Hole, MA 02543 USA.
EM meren@uchicago.edu
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NR 93
TC 74
Z9 83
PD SEP 3
PY 2019
VL 8
AR e46497
DI 10.7554/eLife.46497
UT WOS:000484182200001
DA 2025-07-30
ER

PT J
AU Rodríguez-Ezpeleta, N
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AF Rodriguez-Ezpeleta, Naiara
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TI The SAR11 Group of Alpha-Proteobacteria Is Not Related to the Origin of
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DT Article
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C1 [Rodriguez-Ezpeleta, Naiara; Embley, T. Martin] Newcastle Univ, Inst Cell & Mol Biosci, Newcastle Upon Tyne NE1 7RU, Tyne & Wear, England.
RP Rodríguez-Ezpeleta, N (corresponding author), Txatxarramendi Ugartea ZG, AZTI Tecnalia, Marine Res Unit, Sukarrieta, Bizkaia, Spain.
EM nrodriguez@azti.es
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NR 42
TC 63
Z9 68
PD JAN 23
PY 2012
VL 7
IS 1
AR e30520
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UT WOS:000301570600053
DA 2025-07-30
ER

PT J
AU Sowell, SM
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DT Article
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C1 [Sowell, Sarah M.] Oregon State Univ, Mol & Cellular Biol Program, Corvallis, OR 97331 USA.
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RP Giovanonni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, 220 Nash Hall, Corvallis, OR 97331 USA.
EM steve.giovannoni@oregonstate.edu
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NR 68
TC 249
Z9 270
PD JAN
PY 2009
VL 3
IS 1
BP 93
EP 105
DI 10.1038/ismej.2008.83
UT WOS:000262297400008
DA 2025-07-30
ER

PT J
AU Grant, SR
   Church, MJ
   Ferrón, S
   Laws, EA
   Rappé, MS
AF Grant, Scott R.
   Church, Matthew J.
   Ferron, Sara
   Laws, Edward A.
   Rappe, Michael S.
TI Elemental Composition, Phosphorous Uptake, and Characteristics of Growth
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SO MSYSTEMS
DT Article
AB In this study, a strain of SAR11 subgroup Illa (termed HIMB114) was grown in seawater-based batch and continuous culture in order to quantify cellular features and metabolism relevant to SAR11 ecology. We report some of the first direct measurements of cellular elemental quotas for nitrogen (N) and phosphorus (P) for SAR11, grown in batch culture: 1.4 +/- 0.9 fg N and 0.44 +/- 0.01 fg P, respectively, that were consistent with the small size of HIMB114 cells (average volume of 0.09 mu m(3)). However, the mean carbon (C) cellular quota of 50 +/- 47 fg C was anomalously high, but variable. The rates of phosphate (PO43-) uptake measured from both batch and continuous cultures were exceptionally slow: in chemostats growing at 0.3 day(-1), HIMB114 took up 1.1 +/- 0.3 amol P cell day(-1), suggesting that <30% of the cellular P requirement of HIMB114 was met by PO43- assimilation. The mean rate of leucine incorporation, a measure of bacterial production, during late-log-phase growth of batch HIMB114 cultures was 0.042 +/- 0.02 amol Leu cell(-1) h(-1). While only weakly correlated with changes in specific growth rates, the onset of stationary phase resulted in decreases in cell-specific leucine incorporation that were proportional to changes in growth rate. The rates of cellular production, respiratory oxygen consumption, and changes in total organic C concentrations constrained cellular growth efficiencies to 13% +/- 4%. Hence, despite a small genome and diminutively sized cells, SAR11 strain HIMB114 appears to grow at efficiencies similar to those of naturally occurring bacterioplankton communities.
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C1 [Grant, Scott R.; Ferron, Sara] Univ Hawaii Manoa, Sch Ocean & Earth Sci & Technol, Dept Oceanog, Honolulu, HI 96822 USA.
   [Church, Matthew J.] Univ Montana, Flathead Lake Biol Stn, Polson, MT 59860 USA.
   [Ferron, Sara] Univ Hawaii Manoa, Daniel K Inouye Ctr Microbial Oceanog Res & Educ, Sch Ocean & Earth Sci & Technol, Honolulu, HI 96822 USA.
   [Laws, Edward A.] Louisiana State Univ, Coll Coast & Environm, Dept Environm Sci, Baton Rouge, LA 70803 USA.
   [Rappe, Michael S.] Univ Hawaii Manoa, Sch Ocean & Earth Sci & Technol, Hawaii Inst Marine Biol, Kaneohe, HI 96822 USA.
RP Rappé, MS (corresponding author), Univ Hawaii Manoa, Sch Ocean & Earth Sci & Technol, Hawaii Inst Marine Biol, Kaneohe, HI 96822 USA.
EM rappe@hawaii.edu
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NR 49
TC 8
Z9 10
PD JUL-AUG
PY 2019
VL 4
IS 4
AR e00218-18
DI 10.1128/mSystems.00218-18
UT WOS:000482629400016
DA 2025-07-30
ER

PT J
AU Morris, RM
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   Hvorecny, KL
   Kollman, JM
AF Morris, Robert M.
   Cain, Kelsy R.
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   Kollman, Justin M.
TI Lysogenic host-virus interactions in SAR11 marine bacteria
SO NATURE MICROBIOLOGY
DT Article
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C1 [Morris, Robert M.; Cain, Kelsy R.] Univ Washington, Sch Oceanog, Seattle, WA 98195 USA.
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RP Morris, RM (corresponding author), Univ Washington, Sch Oceanog, Seattle, WA 98195 USA.
EM morrisrm@u.washington.edu
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NR 46
TC 26
Z9 32
PD AUG
PY 2020
VL 5
IS 8
BP 1011
EP +
DI 10.1038/s41564-020-0725-x
EA MAY 2020
UT WOS:000534311100003
DA 2025-07-30
ER

PT J
AU Heinrich, F
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AF Heinrich, Friederike
   Eiler, Alexander
   Bertilsson, Stefan
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SO AQUATIC MICROBIAL ECOLOGY
DT Article
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C1 [Bertilsson, Stefan] Uppsala Univ, Dept Ecol & Genet, S-75236 Uppsala, Sweden.
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RP Bertilsson, S (corresponding author), Uppsala Univ, Dept Ecol & Genet, S-75236 Uppsala, Sweden.
EM stebe@ebc.uu.se
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NR 63
TC 33
Z9 36
PY 2013
VL 70
IS 1
BP 33
EP 44
DI 10.3354/ame01637
UT WOS:000322999500003
DA 2025-07-30
ER

PT J
AU Becker, JW
   Hogle, SL
   Rosendo, K
   Chisholm, SW
AF Becker, Jamie W.
   Hogle, Shane L.
   Rosendo, Kali
   Chisholm, Sallie W.
TI Co-culture and biogeography of Prochlorococcus and SAR11
SO ISME JOURNAL
DT Article
AB Prochlorococcus and SAR11 are among the smallest and most abundant organisms on Earth. With a combined global population of about 2.7 x 10(28) cells, they numerically dominate bacterioplankton communities in oligotrophic ocean gyres and yet they have never been grown together in vitro. Here we describe co-cultures of Prochlorococcus and SAR11 isolates representing both high- and low-light adapted clades. We examined: (1) the influence of Prochlorococcus on the growth of SAR11 and vice-versa, (2) whether Prochlorococcus can meet specific nutrient requirements of SAR11, and (3) how co-culture dynamics vary when Prochlorococcus is grown with SAR11 compared with sympatric copiotrophic bacteria. SAR11 grew 15-70% faster in co-culture with Prochlorococcus, while the growth of the latter was unaffected. When Prochlorococcus populations entered stationary phase, this commensal relationship rapidly became amensal, as SAR11 abundances decreased dramatically. In parallel experiments with copiotrophic bacteria; however, the heterotrophic partner increased in abundance as Prochlorococcus densities leveled off. The presence of Prochlorococcus was able to meet SAR11's central requirement for organic carbon, but not reduced sulfur. Prochlorococcus strain MIT9313, but not MED4, could meet the unique glycine requirement of SAR11, which could be due to the production and release of glycine betaine by MIT9313, as supported by comparative genomic evidence. Our findings also suggest, but do not confirm, that Prochlorococcus MIT9313 may compete with SAR11 for the uptake of 3-dimethylsulfoniopropionate (DMSP). To give our results an ecological context, we assessed the relative contribution of Prochlorococcus and SAR11 genome equivalents to those of identifiable bacteria and archaea in over 800 marine metagenomes. At many locations, more than half of the identifiable genome equivalents in the euphotic zone belonged to Prochlorococcus and SAR11 - highlighting the biogeochemical potential of these two groups.
C1 [Becker, Jamie W.; Hogle, Shane L.; Rosendo, Kali; Chisholm, Sallie W.] MIT, Dept Civil & Environm Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA.
   [Chisholm, Sallie W.] MIT, Dept Biol, Cambridge, MA 02139 USA.
   [Becker, Jamie W.] Haverford Coll, Dept Biol, Haverford, PA 19041 USA.
RP Becker, JW; Chisholm, SW (corresponding author), MIT, Dept Civil & Environm Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA.; Chisholm, SW (corresponding author), MIT, Dept Biol, Cambridge, MA 02139 USA.; Becker, JW (corresponding author), Haverford Coll, Dept Biol, Haverford, PA 19041 USA.
EM jbecker1@haverford.edu; chisholm@mit.edu
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NR 78
TC 62
Z9 73
PD JUN
PY 2019
VL 13
IS 6
BP 1506
EP 1519
DI 10.1038/s41396-019-0365-4
UT WOS:000468529400010
DA 2025-07-30
ER

PT J
AU Green, RT
   Todd, JD
   Johnston, AWB
AF Green, Robert T.
   Todd, Jonathan D.
   Johnston, Andrew W. B.
TI Manganese uptake in marine bacteria; the novel MntX transporter is
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SO ISME JOURNAL
DT Article
AB We showed that two very different manganese transporters occur in various important genera of marine bacteria. The ABC transporter encoded by sitABCD of the model Roseobacter-clade bacterium Ruegeria pomeroyi DSS-3 is required for Mn2+ import and was repressed by the Mur (Manganese uptake regulator) transcriptional regulator in Mn-replete media. Most genome-sequenced Roseobacter strains contain SitABCD, which are in at least two sub-groups, judged by their amino-acid sequences. However, a few Roseobacters, for example, Roseovarius nubinhibens, lack sitABCD, but these contain another gene, mntX, which encodes a predicted inner membrane polypeptide and is preceded by cis-acting Mur-responsive MRS sequences. It was confirmed directly that mntX of Roseovarius nubinhibens encodes a manganese transporter that was required for growth in Mn-depleted media and that its expression was repressed by Mur in Mn-replete conditions. MntX homologues occur in the deduced proteomes of several bacterial species. Strikingly, all of these live in marine habitats, but are in distantly related taxonomic groups, in the gamma-and alpha-proteobacteria. Notably, MntX was prevalent in nearly all strains of Vibrionales, including the important pathogen, Vibrio cholerae. It also occurs in a strain of the hugely abundant Candidatus Pelagibacter (SAR11), and in another populous marine bacterium, Candidatus Puniceispirillum marinum (SAR116). Consistent with this, MntX was abundant in marine bacterial metagenomes, with one sub-type occurring in an as-yet unknown bacterial clade. The ISME Journal (2013) 7, 581-591; doi:10.1038/ismej.2012.140; published online 29 November 2012
C1 [Green, Robert T.; Todd, Jonathan D.; Johnston, Andrew W. B.] Univ E Anglia, Sch Biol Sci, Norwich NR4 7TJ, Norfolk, England.
   [Green, Robert T.] Inst Food Res, Norwich, Norfolk, England.
RP Johnston, AWB (corresponding author), Univ E Anglia, Sch Biol Sci, Norwich Res Pk, Norwich NR4 7TJ, Norfolk, England.
EM a.johnston@uea.ac.uk
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NR 54
TC 26
Z9 31
PD MAR
PY 2013
VL 7
IS 3
BP 581
EP 591
DI 10.1038/ismej.2012.140
UT WOS:000316726400014
DA 2025-07-30
ER

PT J
AU Thompson, LR
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AF Thompson, Luke R.
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   Stingl, Ulrich
TI Red Sea SAR11 and Prochlorococcus Single-Cell Genomes Reflect
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Evidence suggests many marine bacteria are cosmopolitan, with widespread but sparse strains poised to seed abundant populations under conducive growth conditions. However, studies supporting this "microbial seed bank" hypothesis have analyzed taxonomic marker genes rather than whole genomes/metagenomes, leaving open the possibility that disparate ocean regions harbor endemic gene content. The Red Sea is isolated geographically from the rest of the ocean and has a combination of high irradiance, high temperature, and high salinity that is unique among the oceans; we therefore asked whether it harbors endemic gene content. We sequenced and assembled single-cell genomes of 21 SAR11 (subclades Ia, Ib, Id, and II) and 5 Prochlorococcus (ecotype HLII) samples from the Red Sea and combined them with globally sourced reference genomes to cluster genes into ortholog groups (OGs). Ordination of OG composition could distinguish clades, including phylogenetically cryptic Prochlorococcus ecotypes LLII and LLIII. Compared with reference genomes, 1% of Prochlorococcus and 17% of SAR11 OGs were unique to the Red Sea genomes (RS-OGs). Most (83%) RS-OGs had no annotated function, but 65% of RS-OGs were expressed in diel Red Sea metatranscriptomes, suggesting they are functional. Searching Tara Oceans metagenomes, RS-OGs were as likely to be found as non-RS-OGs; nevertheless, Red Sea and other warm samples could be distinguished from cooler samples using the relative abundances of OGs. The results suggest that the prevalence of OGs in these surface ocean bacteria is largely cosmopolitan, with differences in population metagenomes manifested by differences in relative abundance rather than complete presence/absence of OGs.
   IMPORTANCE Studies have shown that as we sequence seawater from a selected environment deeper and deeper, we approach finding every bacterial taxon known for the ocean as a whole. However, such studies have focused on taxonomic marker genes rather than on whole genomes, raising the possibility that the lack of endemism results from the method of investigation. We took a geographically isolated water body, the Red Sea, and sequenced single cells from it. We compared those single-cell genomes to available genomes from around the ocean and to ocean-spanning metagenomes. We showed that gene ortholog groups found in Red Sea genomes but not in other genomes are nevertheless common across global ocean metagenomes. These results suggest that Baas Beckings hypothesis "everything is everywhere, but the environment selects" also applies to gene ortholog groups. This widely dispersed functional diversity may give oceanic microbial communities the functional capacity to respond rapidly to changing conditions.
C1 [Thompson, Luke R.; Haroon, Mohamed F.; Shibl, Ahmed A.; Cahill, Matt J.; Ngugi, David K.; Stingl, Ulrich] King Abdullah Univ Sci & Technol, Red Sea Res Ctr, Thuwal, Saudi Arabia.
   [Thompson, Luke R.] Univ Southern Mississippi, Dept Biol Sci, Hattiesburg, MS 39406 USA.
   [Thompson, Luke R.] Univ Southern Mississippi, Northern Gulf Inst, Hattiesburg, MS 39406 USA.
   [Thompson, Luke R.; Goodwin, Kelly D.] NOAA, Ocean Chem & Ecosyst Div, Atlantic Oceanog & Meteorol Lab, Southwest Fisheries Sci Ctr, La Jolla, CA 92037 USA.
   [Williams, Gareth J.] Bangor Univ, Sch Ocean Sci, Anglesey, Wales.
   [Morton, James T.; Knight, Rob] Univ Calif San Diego, Dept Pediat, La Jolla, CA 92093 USA.
   [Morton, James T.; Knight, Rob] Univ Calif San Diego, Dept Comp Sci & Engn, La Jolla, CA 92093 USA.
   [Knight, Rob] Univ Calif San Diego, Ctr Microbiome Innovat, La Jolla, CA 92093 USA.
   [Stingl, Ulrich] Univ Florida, Dept Microbiol & Cell Sci, Ft Lauderdale Res & Educ Ctr, UF Inst Food & Agr Sci, Davie, FL USA.
   [Shibl, Ahmed A.] NYU, Marine Microbial Ecol Lab, Biol Program, Abu Dhabi, U Arab Emirates.
RP Thompson, LR; Stingl, U (corresponding author), King Abdullah Univ Sci & Technol, Red Sea Res Ctr, Thuwal, Saudi Arabia.; Thompson, LR (corresponding author), Univ Southern Mississippi, Dept Biol Sci, Hattiesburg, MS 39406 USA.; Thompson, LR (corresponding author), Univ Southern Mississippi, Northern Gulf Inst, Hattiesburg, MS 39406 USA.
EM lukethompson@gmail.com; ulistingl@gmail.com
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NR 59
TC 10
Z9 12
PD JUL
PY 2019
VL 85
IS 13
AR e00369-19
DI 10.1128/AEM.00369-19
UT WOS:000473717900011
DA 2025-07-30
ER

PT J
AU Martinez-Hernandez, F
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   Haro-Moreno, JM
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AF Martinez-Hernandez, Francisco
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   Maestre-Carballa, Lucia
   Lopez-Perez, Mario
   Haro-Moreno, Jose M.
   Rodriguez-Valera, Francisco
   Martinez-Garcia, Manuel
TI Single-cell genomics uncover Pelagibacter as the putative host of the
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SO ISME JOURNAL
DT Article
AB The identification of relevant virus host pairs that globally account for a large pool of carbon and nutrients in the ocean is paramount to build accurate ecological models. A previous work using single-virus genomics led to the discovery of the uncultured single-virus vSAG 37-F6, originally sorted from the Mediterranean Sea (Blanes Bay Microbial Observatory), that represents one of the most abundant dsDNA viral population in the marine surface virosphere. Here, from same sampling site, we report that a Pelagibacter single-cell contained a viral member of vSAG 37-F6 population, by means of PCR screening of sorted, genome-amplified single cells with vSAG 37-F6-specific primers and whole-genome sequencing. Furthermore, viruses from this population were also found in three other Pelagibacter single cells from the South Pacific and Atlantic oceans. These new uncultured pelagiphages were genetically different from the previously characterized pelagiphage isolates. Data showed that the uncultured vSAG 37-F6 population represents the Pelagibacter phages that inhabit the sunlit ocean better, and contains a vast unrecognized microdiversity.
C1 [Martinez-Hernandez, Francisco; Lluesma Gomez, Monica; Garcia-Heredia, Inmaculada; Maestre-Carballa, Lucia; Martinez-Garcia, Manuel] Univ Alicante, Dept Physiol Genet & Microbiol, Alicante, Spain.
   [Fornas, Oscar] Pompeu Fabra Univ, Flow Cytometry Unit, Barcelona, Spain.
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   [Lopez-Perez, Mario; Haro-Moreno, Jose M.; Rodriguez-Valera, Francisco] Univ Miguel Hernandez, Evolutionary Genom Grp, Div Microbiol, Apartado 18, Alicante 03550, Spain.
RP Martinez-Garcia, M (corresponding author), Univ Alicante, Dept Physiol Genet & Microbiol, Alicante, Spain.
EM m.martinez@ua.es
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NR 26
TC 31
Z9 36
PD JAN
PY 2019
VL 13
IS 1
BP 232
EP 236
DI 10.1038/s41396-018-0278-7
UT WOS:000453576600019
DA 2025-07-30
ER

PT J
AU Viklund, J
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AF Viklund, Johan
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TI Comparative and Phylogenomic Evidence That the Alphaproteobacterium
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SO PLOS ONE
DT Article
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RP Andersson, SGE (corresponding author), Biomed Ctr, Dept Mol Evolut, Sci Life Lab, Uppsala, Sweden.
EM Siv.Andersson@icm.uu.se
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NR 27
TC 31
Z9 33
PD NOV 1
PY 2013
VL 8
IS 11
AR e78858
DI 10.1371/journal.pone.0078858
UT WOS:000326499300036
DA 2025-07-30
ER

PT J
AU Stingl, U
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AF Stingl, Ulrich
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C1 Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
RP Stingl, U (corresponding author), Oregon State Univ, Dept Microbiol, 220 Nash Hall, Corvallis, OR 97331 USA.
EM stinglu@science.oregonstate.edu
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NR 46
TC 136
Z9 157
PD AUG
PY 2007
VL 1
IS 4
BP 361
EP 371
DI 10.1038/ismej.2007.49
UT WOS:000249216300011
DA 2025-07-30
ER

PT J
AU Ruiz-Perez, CA
   Bertagnolli, AD
   Tsementzi, D
   Woyke, T
   Stewart, FJ
   Konstantinidis, KT
AF Ruiz-Perez, Carlos A.
   Bertagnolli, Anthony D.
   Tsementzi, Despina
   Woyke, Tanja
   Stewart, Frank J.
   Konstantinidis, Konstantinos T.
TI Description of Candidatus Mesopelagibacter carboxydoxydans and
   Candidatus Anoxipelagibacter denitrificans: Nitrate-reducing SAR11
   genera that dominate mesopelagic and anoxic marine zones
SO SYSTEMATIC AND APPLIED MICROBIOLOGY
DT Article
AB The diverse and ubiquitous members of the SAR11 lineage (Alphaproteobacteria) represent up to 30-40% of the surface and mesopelagic oceanic microbial communities. However, the molecular and ecological mechanisms that differentiate closely related, yet distinct, SAR11 members that often co-occur under similar environmental conditions remain speculative. Recently, two mesopelagic and oxygen minimum zone (OMZ)-associated subclades of SAR11 (Ic and IIa.A) were described using single-cell amplified genomes (SAGs) linked to nitrate reduction in OMZs. In this current study, the collection of genomes belonging to these two subclades was expanded with thirteen new metagenome-assembled genomes (MAGs), thus providing a more detailed phylogenetic and functional characterization of these subclades. Gene content based predictions of metabolic functions revealed similarities in central carbon metabolism between subclades Ic and IIa.A and surface SAR11 clades, with small variations in central pathways. These variations included more versatile sulfur assimilation pathways, as well as a previously predicted capacity for nitrate reduction that conferred unique versatility on mesopelagic-adapted clades compared to their surface counterparts. Finally, consistent with previously reported abundances of carbon monoxide (CO) in surface and mesopelagic waters, subclades Ia (surface) and Ic (mesopelagic) have the genetic potential to oxidize carbon monoxide (CO), presumably taking advantage of this abundant compound as an electron donor. Based on genomic analyses, environmental distribution and metabolic reconstruction, we propose two new SAR11 genera, Ca. Mesopelagibacter carboxydoxydans (subclade Ic) and Ca. Anoxipelagibacter denitrificans (subclade IIa.A), which represent members of the mesopelagic and OMZ-adapted SAR11 clades. (c) 2021 Elsevier GmbH. All rights reserved.
C1 [Ruiz-Perez, Carlos A.; Bertagnolli, Anthony D.; Stewart, Frank J.; Konstantinidis, Konstantinos T.] Georgia Inst Technol, Sch Biol Sci, Atlanta, GA 30332 USA.
   [Tsementzi, Despina; Konstantinidis, Konstantinos T.] Georgia Inst Technol, Sch Civil & Environm Engn, Atlanta, GA 30332 USA.
   [Woyke, Tanja] DOE Joint Genome Inst, One Cyclotron Rd,Mail Stop 91R0183, Berkeley, CA 94720 USA.
   [Stewart, Frank J.] Georgia Inst Technol, Ctr Microbial Dynam & Infect, Atlanta, GA 30332 USA.
   [Stewart, Frank J.] Montana State Univ, Dept Microbiol & Immunol, Bozeman, MT 59717 USA.
   [Konstantinidis, Konstantinos T.] Georgia Inst Technol, Ctr Bioinformat & Computat Genom, Atlanta, GA 30332 USA.
RP Konstantinidis, KT (corresponding author), Georgia Inst Technol, Sch Civil & Environm Engn, Atlanta, GA 30332 USA.
EM kostas@ce.gatech.edu
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NR 124
TC 12
Z9 13
PD APR
PY 2021
VL 44
IS 2
AR 126185
DI 10.1016/j.syapm.2021.126185
EA MAR 2021
UT WOS:000740924400003
DA 2025-07-30
ER

PT J
AU Giovannoni, SJ
   Halsey, KH
   Saw, J
   Muslin, O
   Suffridge, CP
   Sun, J
   Lee, CP
   Moore, ER
   Temperton, B
   Noell, SE
AF Giovannoni, Stephen J.
   Halsey, Kimberly H.
   Saw, Jimmy
   Muslin, Omran
   Suffridge, Christopher P.
   Sun, Jing
   Lee, Chih-Ping
   Moore, Eric R.
   Temperton, Ben
   Noell, Stephen E.
TI A Parasitic Arsenic Cycle That Shuttles Energy from Phytoplankton to
   Heterotrophic Bacterioplankton
SO MBIO
DT Article
AB In many regions of the world oceans, phytoplankton face the problem of discriminating between phosphate, an essential nutrient, and arsenate, a toxic analogue. Many phytoplankton, including the most abundant phytoplankton group known, Prochlorococcus, detoxify arsenate (AsV) by reduction to arsenite (AsIII), followed by methylation and excretion of the methylated arsenic products. We synthesized [C-14]dimethyl arsenate (DMA) and used it to show that cultured Pelagibacter strain HTCC7211 (SAR11) cells oxidize the methyl group carbons of DMA, producing (CO2)-C-14 and ATP. We measured [C-14] DMA oxidation rates in the P-depleted surface waters of the Sargasso Sea, a subtropical ocean gyre. [C-14]DMA was oxidized to (CO2)-C-14 by Sargasso Sea plankton communities at a rate that would cause turnover of the estimated DMA standing stock every 8.1 days. SAR11 strain HTCC7211, which was isolated from the Sargasso Sea, has a pair of arsenate resistance genes and was resistant to arsenate, showing no growth inhibition at As/P ratios of >65:1. Across the global oceans, there was a strong inverse relationship between the frequency of the arsenate reductase (LMWPc_ArsC) in Pelagibacter genomes and phosphate concentrations. We propose that the demethylation of methylated arsenic compounds by Pelagibacter and possibly other bacterioplankton, coupled with arsenate resistance, results in the transfer of energy from phytoplankton to bacteria. We dub this a parasitic cycle because the release of arsenate by Pelagibacter in principle creates a positive-feedback loop that forces phytoplankton to continually regenerate arsenate detoxification products, producing a flow of energy to P-limited ocean regions.
   IMPORTANCE In vast, warm regions of the oceans, phytoplankton face the problem of arsenic poisoning. Arsenate is toxic because it is chemically similar to phosphate, a scarce nutrient that phytoplankton cells need for growth. Many phytoplankton, including the commonest phytoplankton type in warm oceans, Prochlorococcus, detoxify arsenate by adding methyl groups. Here we show that the most abundant non-photosynthetic plankton in the oceans, SAR11 bacteria, remove the methyl groups, releasing poisonous forms of arsenic back into the water. We postulate that the methylation and demethylation of arsenic compounds creates a cycle in which the phytoplankton can never get ahead and must continually transfer energy to the SAR11 bacteria. We dub this a parasitic process and suggest that it might help explain why SAR11 bacteria are so successful, surpassing all other plankton in their numbers. Field experiments were done in the Sargasso Sea, a subtropical ocean gyre that is sometimes called an ocean desert because, throughout much of the year, there is not enough phosphorous in the water to support large blooms of phytoplankton. Ocean deserts are expanding as the oceans absorb heat and grow warmer.
C1 [Giovannoni, Stephen J.; Halsey, Kimberly H.; Saw, Jimmy; Muslin, Omran; Suffridge, Christopher P.; Sun, Jing; Lee, Chih-Ping; Moore, Eric R.; Temperton, Ben; Noell, Stephen E.] Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
   [Saw, Jimmy] George Washington Univ, Washington, DC USA.
   [Sun, Jing] Chinese Acad Fishery Sci, Yellow Sea Fisheries Res Inst, Qingdao, Shandong, Peoples R China.
   [Temperton, Ben] Univ Exeter, Biosci, Exeter, Devon, England.
RP Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
EM steve.giovannoni@oregonstate.edu
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NR 47
TC 23
Z9 25
PD MAR-APR
PY 2019
VL 10
IS 2
AR e00246-19
DI 10.1128/mBio.00246-19
UT WOS:000465077600037
DA 2025-07-30
ER

PT J
AU West, NJ
   Lepère, C
   Manes, CLD
   Catala, P
   Scanlan, DJ
   Lebaron, P
AF West, Nyree J.
   Lepere, Cecile
   Manes, Carmem-Lara de O.
   Catala, Philippe
   Scanlan, David J.
   Lebaron, Philippe
TI Distinct Spatial Patterns of SAR11, SAR86, and Actinobacteria Diversity
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SO FRONTIERS IN MICROBIOLOGY
DT Article
AB Distinct distribution patterns of members of the major bacterial clades SARI 1, SAR86, and Actinobacteria were observed across a transect from the Marquesas islands through the ultra-oligotrophic South Pacific Gyre into the Chilean upwelling using 16S rRNA gene sequencing and RNA-DNA fingerprinting. Three different Actinobacteria sequence clusters belonging to "Candidatus Actinomarinidae" were localized in the western half of the transect, one was limited to the gyre deep chlorophyll maximum (DCM) and sequences affiliated to the OCS155 Glade were unique to the upwelling. The structure of the surface bacterial community was highly correlated with water mass and remained similar across the whole central gyre (1300 nautical miles). The surface hyperoligotrophic gyre was dominated (>70% of all sequences) by highly diverse SAR11 and SAR86 operational taxonomic units and these communities were significantly different from those in the DCM. Analysis of 16S rRNA fingerprints generated from RNA allowed insights into the potential activity of assigned bacterial groups. SAR11 and Prochlorococcus showed the highest potential activity in all water masses except for the upwelling, accounting together for 65% of the total bacterial 16S rRNA in the gyre surface waters in equal proportions whereas the contribution of SAR11 decreased significantly at the DCM.
C1 [West, Nyree J.] Univ Paris 06, Sorbonne Univ, CNRS, Observ Oceanol Banyuls, Banyuls Sur Mer, France.
   [Lepere, Cecile] Univ Blaise Pascal, Univ Clermont Auvergne, CNRS, Lab Microorganismes Genome & Environm, Aubiere, France.
   [Manes, Carmem-Lara de O.; Lebaron, Philippe] Univ Paris 06, Sorbonne Univ, CNRS, Lab Biodivers & Blotechnol Microbiennes,Observ Oc, Banyuls Sur Mer, France.
   [Catala, Philippe] Univ Paris 06, Sorbonne Univ, CNRS, Lab Oceanog Microbienne,Observ Oceanol, Banyuls Sur Mer, France.
   [Scanlan, David J.] Univ Warwick, Sch Life Sci, Coventry CV4 7AL, W Midlands, England.
   [Manes, Carmem-Lara de O.] Observ Oceanog, Microbia Environm, Banyuls Sur Mer, France.
RP West, NJ (corresponding author), Univ Paris 06, Sorbonne Univ, CNRS, Observ Oceanol Banyuls, Banyuls Sur Mer, France.
EM nyree.west@obs-banyuls.fr
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NR 68
TC 41
Z9 47
PD MAR 8
PY 2016
VL 7
AR 234
DI 10.3389/fmicb.2016.00234
UT WOS:000371538500001
DA 2025-07-30
ER

PT J
AU Sperling, M
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AF Sperling, Martin
   Giebel, Helge-Ansgar
   Rink, Beate
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   Simon, Meinhard
TI Differential effects of hydrographic and biogeo chemical properties on
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SO AQUATIC MICROBIAL ECOLOGY
DT Article
AB The SAR11 clade and the Roseobacter clade affiliated (RCA) cluster belong to the most prominent bacterioplankton groups in temperate to polar seas. Despite some insights into biological controls of both lineages, little is known about environmental, hydrographic and biogeochemical controls. Therefore, we assessed the abundance of both lineages using quantitative PCR in the southern North Sea, subjected them to a multiple linear regression analysis and related their occurrence to current patterns by backtracking the water masses found at individual stations for the preceding 24 to 27 d. SAR11 constituted <1 to 47% of total bacterial 16S rRNA genes. The abundance of this clade was inversely correlated to the salinity change of the water masses at the stations, indicating a preference for stable and presumably nutrient depleted waters. The RCA cluster constituted <1 to 5% of total bacterial 16S rRNA genes but did not exhibit any correlation to hydrographic properties. However, a multiple linear regression analysis showed that the RCA cluster was significantly correlated to a suite of biogeochemical parameters, bacterial abundance, concentrations of chlorophyll a, particulate organic carbon and suspended particulate matter and salinity changes, explaining 94.3% of the variability of the RCA data. These results show that backtracking water masses and relating them to bacterioplankton populations aids in the understanding of the growth dynamics of specific bacterioplankton populations and sheds new light on why high abundances of the SAR11 clade are usually found in stratified water masses.
C1 [Sperling, Martin; Giebel, Helge-Ansgar; Rink, Beate; Grayek, Sebastian; Stanev, Emil; Simon, Meinhard] Carl von Ossietzky Univ Oldenburg, Inst Chem & Biol Marine Environm, D-26111 Oldenburg, Germany.
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RP Simon, M (corresponding author), Carl von Ossietzky Univ Oldenburg, Inst Chem & Biol Marine Environm, D-26111 Oldenburg, Germany.
EM m.simon@icbm.de
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NR 41
TC 13
Z9 13
PY 2012
VL 67
IS 1
BP 25
EP 34
DI 10.3354/ame01580
UT WOS:000308651800003
DA 2025-07-30
ER

PT J
AU Wittmers, F
   Needham, DM
   Hehenberger, E
   Giovannoni, SJ
   Worden, AZ
AF Wittmers, Fabian
   Needham, David M.
   Hehenberger, Elisabeth
   Giovannoni, Stephen J.
   Worden, Alexandra Z.
TI Genomes from Uncultivated Pelagiphages Reveal Multiple Phylogenetic
   Clades Exhibiting Extensive Auxiliary Metabolic Genes and Cross-Family
   Multigene Transfers
SO MSYSTEMS
DT Article
AB For the abundant marine Alphaproteobacterium Pelagibacter (SARI 1), and other bacteria, phages are powerful forces of mortality. However, little is known about the most abundant Pelagiphages in nature, such as the widespread HTVC023P-type, which is currently represented by two cultured phages. Using viral metagenomic data sets and fluorescence-activated cell sorting, we recovered 80 complete, undescribed Podoviridae genomes that form 10 phylogenomically distinct clades (herein, named Clades I to X) related to the HTVC023P-type. These expanded the HTVC023P-type pangenome by 15-fold and revealed 41 previously unknown auxiliary metabolic genes (AMGs) in this viral lineage. Numerous instances of partner-AMGs (colocated and involved in related functions) were observed, including partners in nucleotide metabolism, DNA hypermodification, and Curli biogenesis. The Type VIII secretion system (T8SS) responsible for Curli biogenesis was identified in nine genomes and expanded the repertoire of T8SS proteins reported thus far in viruses. Additionally, the identified T8SS gene cluster contained an iron-dependent regulator (FecR), as well as a histidine kinase and adenylate cyclase that can be implicated in T8SS function but are not within T8SS operons in bacteria. While T8SS are lacking in known Pelagibacter, they contribute to aggregation and biofilm formation in other bacteria. Phylogenetic reconstructions of partner-AMGs indicate derivation from cellular lineages with a more recent transfer between viral families. For example, homologs of all T8SS genes are present in syntenic regions of distant Myoviridae Pelagiphages, and they appear to have alphaproteobacterial origins with a later transfer between viral families. The results point to an unprecedented multipartner-AMG transfer between marine Myoviridae and Podoviridae. Together with the expansion of known metabolic functions, our studies provide new prospects for understanding the ecology and evolution of marine phages and their hosts.
   IMPORTANCE One of the most abundant and diverse marine bacterial groups is Pelagibacter. Phages have roles in shaping Pelagibacter ecology; however, several Pelagiphage lineages are represented by only a few genomes. This paucity of data from even the most widespread lineages has imposed limits on the understanding of the diversity of Pelagiphages and their impacts on hosts. Here, we report 80 complete genomes, assembled directly from environmental data, which are from undescribed Pelagiphages and render new insights into the manipulation of host metabolism during infection. Notably, the viruses have functionally related partner genes that appear to be transferred between distant viruses, including a suite that encode a secretion system which both brings a new functional capability to the host and is abundant in phages across the ocean. Together, these functions have important implications for phage evolution and for how Pelagiphage infection influences host biology in manners extending beyond canonical viral lysis and mortality.
C1 [Wittmers, Fabian; Needham, David M.; Hehenberger, Elisabeth; Worden, Alexandra Z.] GEOMAR Helmholtz Ctr Ocean Res Kiel, Ocean EcoSyst Biol Unit, RD3, Kiel, Germany.
   [Wittmers, Fabian; Worden, Alexandra Z.] Univ Kiel, Kiel, Germany.
   [Giovannoni, Stephen J.] Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
   [Worden, Alexandra Z.] Marine Biol Lab, Woods Hole, MA 02543 USA.
   [Worden, Alexandra Z.] Max Planck Inst Evolutionary Biol, Plon, Germany.
RP Needham, DM; Worden, AZ (corresponding author), GEOMAR Helmholtz Ctr Ocean Res Kiel, Ocean EcoSyst Biol Unit, RD3, Kiel, Germany.; Worden, AZ (corresponding author), Univ Kiel, Kiel, Germany.; Worden, AZ (corresponding author), Marine Biol Lab, Woods Hole, MA 02543 USA.; Worden, AZ (corresponding author), Max Planck Inst Evolutionary Biol, Plon, Germany.
EM dneedham@geomar.de; azworder@geomar.de
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NR 73
TC 11
Z9 12
PD OCT 26
PY 2022
VL 7
IS 5
DI 10.1128/msystems.01522-21
EA AUG 2022
UT WOS:000841790800002
DA 2025-07-30
ER

PT J
AU Morris, RM
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   Connon, SA
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   Giovannoni, SJ
AF Morris, RM
   Rappé, MS
   Connon, SA
   Vergin, KL
   Siebold, WA
   Carlson, CA
   Giovannoni, SJ
TI SAR11 clade dominates ocean surface bacterioplankton communities
SO NATURE
DT Article
AB The most abundant class of bacterial ribosomal RNA genes detected in seawater DNA by gene cloning belongs to SAR11-an alpha-proteobacterial clade(1). Other than indications of their prevalence in seawater, little is known about these organisms. Here we report quantitative measurements of the cellular abundance of the SAR11 clade in northwestern Sargasso Sea waters to 3,000 m and in Oregon coastal surface waters. On average, the SAR11 clade accounts for a third of the cells present in surface waters and nearly a fifth of the cells present in the mesopelagic zone. In some regions, members of the SAR11 clade represent as much as 50% of the total surface microbial community and 25% of the subeuphotic microbial community. By extrapolation, we estimate that globally there are 2.4 x 10(28) SAR11 cells in the oceans, half of which are located in the euphotic zone. Although the biogeochemical role of the SAR11 clade remains uncertain, these data support the conclusion that this microbial group is among the most successful organisms on Earth.
C1 Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
   Univ Calif Santa Barbara, Dept Ecol Evolut & Marine Biol, Santa Barbara, CA 93106 USA.
RP Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
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NR 27
TC 872
Z9 993
PD DEC 26
PY 2002
VL 420
IS 6917
BP 806
EP 810
DI 10.1038/nature01240
UT WOS:000179897300054
DA 2025-07-30
ER

PT J
AU Molina-Pardines, C
   Haro-Moreno, JM
   Rodriguez-Valera, F
   López-Pérez, M
AF Molina-Pardines, Carmen
   Haro-Moreno, Jose M.
   Rodriguez-Valera, Francisco
   Lopez-Perez, Mario
TI Extensive paralogism in the environmental pangenome: a key factor in the
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SO MICROBIOME
DT Article
AB Background The oceanic microbiome is dominated by members of the SAR11 clade. Despite their abundance, challenges in recovering the full genetic diversity of natural populations have hindered our understanding of the eco-evolutionary mechanisms driving intra-species variation. In this study, we employed a combination of single-amplified genomes and long-read metagenomics to recover the genomic diversity of natural populations within the SAR11 genomospecies Ia.3/VII, the dominant group in the Mediterranean Sea.
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C1 [Molina-Pardines, Carmen; Haro-Moreno, Jose M.; Rodriguez-Valera, Francisco; Lopez-Perez, Mario] Univ Miguel Hernandez, Div Microbiol, Evolutionary Genom Grp, Apartado 18,San Juan, Alicante 03550, Spain.
RP López-Pérez, M (corresponding author), Univ Miguel Hernandez, Div Microbiol, Evolutionary Genom Grp, Apartado 18,San Juan, Alicante 03550, Spain.
EM mario.lopezp@umh.es
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NR 87
TC 1
Z9 1
PD FEB 4
PY 2025
VL 13
IS 1
AR 41
DI 10.1186/s40168-025-02037-6
UT WOS:001414687600004
DA 2025-07-30
ER

PT J
AU Vidanage, PW
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AF Vidanage, Poorna Weerarathna
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DT Article
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C1 [Vidanage, Poorna Weerarathna; Oh, Seungdae] Nanyang Technol Univ, Sch Civil & Environm Engn, Singapore 639798, Singapore.
   [Ko, Seok-Oh; Oh, Seungdae] Kyung Hee Univ, Dept Civil Engn, Yongin 1732, Gyeonggi Do, South Korea.
RP Oh, S (corresponding author), Nanyang Technol Univ, Sch Civil & Environm Engn, Singapore 639798, Singapore.; Ko, SO; Oh, S (corresponding author), Kyung Hee Univ, Dept Civil Engn, Yongin 1732, Gyeonggi Do, South Korea.
EM poorna001@e.ntu.edu.sg; soko@khu.ac.kr; soh@khu.ac.kr
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NR 43
TC 7
Z9 7
PD FEB
PY 2020
VL 12
IS 2
AR 501
DI 10.3390/w12020501
UT WOS:000519846500192
DA 2025-07-30
ER

PT J
AU Tripp, HJ
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   Meyer, MM
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   Breaker, RR
   Giovannoni, SJ
AF Tripp, H. James
   Schwalbach, Michael S.
   Meyer, Michelle M.
   Kitner, Joshua B.
   Breaker, Ronald R.
   Giovannoni, Stephen J.
TI Unique glycine-activated riboswitch linked to glycine-serine auxotrophy
   in SAR11
SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB The genome sequence of the marine bacterium 'Candidatus Pelagibacter ubique' and subsequent analyses have shown that while it has a genome as small as many obligate parasites, it nonetheless possesses a metabolic repertoire that allows it to grow as one of the most successful free-living cells in the ocean. An early report based on metabolic reconstruction indicated that SAR11 cells are prototrophs for all amino acids. However, here we report experimental evidence that 'Cand. P. ubique' is effectively auxotrophic for glycine and serine. With glucose and acetate added to seawater to supply organic carbon, the addition of 125 nM to 1.5 mu M glycine to growth medium containing all other nutrients in excess resulted in a linear increase in maximum cell density from 1.14 x 10(6) cells ml(-1) to 8.16 x 10(6) cells ml(-1) (R-2 = 0.992). Serine was capable of substituting for glycine at 1.5 mu M. 'Cand. P. ubique' contains a glycine-activated riboswitch preceding malate synthase, an unusual genomic context that is conserved in the SAR11 group. Malate synthase plays a critical role in central metabolism by enabling TCA intermediates to be regenerated through the glyoxylate cycle. In vitro analysis of this riboswitch indicated that it responds solely to glycine but not close structural analogues, such as glycine betaine, malate, glyoxylate, glycolate, alanine, serine or threonine. We conclude that 'Cand. P. ubique' is therefore a glycine-serine auxotroph that appears to use intracellular glycine level to regulate its use of carbon for biosynthesis and energy. Comparative genomics and metagenomics indicate that these conclusions may hold throughout much of the SAR11 clade.
C1 [Tripp, H. James; Schwalbach, Michael S.; Kitner, Joshua B.; Giovannoni, Stephen J.] Oregon State Univ, Dept Microbiol, Corvallis, OR 97333 USA.
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RP Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97333 USA.
EM steve.giovannoni@oregonstate.edu
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NR 37
TC 80
Z9 89
PD JAN
PY 2009
VL 11
IS 1
BP 230
EP 238
DI 10.1111/j.1462-2920.2008.01758.x
UT WOS:000262150300020
DA 2025-07-30
ER

PT J
AU Saini, P
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AF Saini, Priya
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   Kumar, Ranjai
   Chhabra, Ravneet
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   Sareen, Dipti
TI Trigger factor assisted folding of the recombinant epoxide hydrolases
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SO PROTEIN EXPRESSION AND PURIFICATION
DT Article
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C1 [Saini, Priya; Wani, Shadil Ibrahim; Kumar, Ranjai; Chhabra, Ravneet; Sareen, Dipti] Panjab Univ, Dept Biochem, Chandigarh 160014, India.
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RP Sareen, D (corresponding author), Panjab Univ, Dept Biochem, Sect 14, Chandigarh 160014, India.
EM 27priyasaini@gmail.com; shandil.wani@gmail.com; ranjai.pu@gmail.com;
   chhabra.ravneet9@gmail.com; sschimni@yahoo.com; diptsare@pu.ac.in
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NR 60
TC 19
Z9 20
PD DEC
PY 2014
VL 104
BP 71
EP 84
DI 10.1016/j.pep.2014.09.004
UT WOS:000345255200011
DA 2025-07-30
ER

PT J
AU Gómez-Pereira, PR
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AF Gomez-Pereira, Paola R.
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TI Comparable light stimulation of organic nutrient uptake by SAR11 and
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DT Article
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RP Zubkov, MV (corresponding author), Natl Oceanog Ctr, Ocean Biogeochem & Ecosyst Res Grp, European Way, Southampton SO14 3ZH, Hants, England.
EM mvz@noc.ac.uk
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NR 57
TC 55
Z9 58
PD MAR
PY 2013
VL 7
IS 3
BP 603
EP 614
DI 10.1038/ismej.2012.126
UT WOS:000316726400016
DA 2025-07-30
ER

PT J
AU García-Martínez, J
   Rodríguez-Valera, F
AF García-Martínez, J
   Rodríguez-Valera, F
TI Microdiversity of uncultured marine prokaryotes:: the SAR11 cluster and
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SO MOLECULAR ECOLOGY
DT Article
AB The SAR11 cluster and the Group I of marine Archaea represent probably the best two examples of uncultured marine prokaryotes of widespread occurrence. To study their microdiversity and distribution, a total of 81 and 48 clones, respectively, were sequenced from Mediterranean and Antarctic waters at different locations and depths. The DNA regions chosen for the analysis were the last third, approximately, of the 16S rRNA gene and the 16S-23S intergenic spacer (also known as internal transcribed spacer [ITS]). There was a high concordance in both, even with the extremely variable ITS, where potential probes have been proposed for the identification and isolation of these micro-organisms. In terms of community structure, our results show that although depth-related factors seem to be predominant in the final associations of the clones, geography also plays a significant role. A major group of surface-associated sequences was found in both SAR11 and marine Archaea. In both cases this group was relatively homogeneous containing little diversity in terms of sequence, while sequences retrieved from deep samples and some surface clones contained much more heterogeneity. As a whole, both groups of prokaryotes seem to fall within the limits of well-defined taxonomic units.
C1 Univ Miguel Hernandez, Div Microbiol, Alicante 03550, Spain.
RP Rodríguez-Valera, F (corresponding author), Univ Miguel Hernandez, Div Microbiol, Campus San Juan,Carretera Valencia Km 87,Apartado, Alicante 03550, Spain.
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NR 62
TC 125
Z9 136
PD JUL
PY 2000
VL 9
IS 7
BP 935
EP 948
DI 10.1046/j.1365-294x.2000.00953.x
UT WOS:000088579300010
DA 2025-07-30
ER

PT J
AU Brindefalk, B
   Ettema, TJG
   Viklund, J
   Thollesson, M
   Andersson, SGE
AF Brindefalk, Bjorn
   Ettema, Thijs J. G.
   Viklund, Johan
   Thollesson, Mikael
   Andersson, Siv G. E.
TI A Phylometagenomic Exploration of Oceanic Alphaproteobacteria Reveals
   Mitochondrial Relatives Unrelated to the SAR11 Clade
SO PLOS ONE
DT Article
AB Background: According to the endosymbiont hypothesis, the mitochondrial system for aerobic respiration was derived from an ancestral Alphaproteobacterium. Phylogenetic studies indicate that the mitochondrial ancestor is most closely related to the Rickettsiales. Recently, it was suggested that Candidatus Pelagibacter ubique, a member of the SAR11 clade that is highly abundant in the oceans, is a sister taxon to the mitochondrial-Rickettsiales clade. The availability of ocean metagenome data substantially increases the sampling of Alphaproteobacteria inhabiting the oxygen-containing waters of the oceans that likely resemble the originating environment of mitochondria.
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C1 [Brindefalk, Bjorn; Ettema, Thijs J. G.; Viklund, Johan; Thollesson, Mikael; Andersson, Siv G. E.] Evolutionary Biol Ctr, Dept Mol Evolut, Sci Life Lab, Uppsala, Sweden.
RP Brindefalk, B (corresponding author), Evolutionary Biol Ctr, Dept Mol Evolut, Sci Life Lab, Uppsala, Sweden.
EM Siv.Andersson@ebc.uu.se
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NR 47
TC 44
Z9 50
PD SEP 14
PY 2011
VL 6
IS 9
AR e24457
DI 10.1371/journal.pone.0024457
UT WOS:000295039700022
DA 2025-07-30
ER

PT J
AU Larkin, AA
   Hagstrom, G
   Brock, ML
   Garcia, NS
   Martiny, AC
AF Larkin, Alyse A.
   Hagstrom, George, I
   Brock, Melissa L.
   Garcia, Nathan S.
   Martiny, Adam C.
TI Basin-scale biogeography of Prochlorococcus and SAR11 ecotype
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SO ISME JOURNAL
DT Article
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C1 [Larkin, Alyse A.; Garcia, Nathan S.; Martiny, Adam C.] Univ Calif Irvine, Dept Earth Syst Sci, Irvine, CA 92717 USA.
   [Hagstrom, George, I] Princeton Univ, Dept Ecol & Evolut Biol, Princeton, NJ 08544 USA.
   [Brock, Melissa L.; Martiny, Adam C.] Univ Calif Irvine, Dept Ecol & Evolutionary Biol, Irvine, CA 92717 USA.
RP Martiny, AC (corresponding author), Univ Calif Irvine, Dept Earth Syst Sci, Irvine, CA 92717 USA.; Martiny, AC (corresponding author), Univ Calif Irvine, Dept Ecol & Evolutionary Biol, Irvine, CA 92717 USA.
EM amartiny@uci.edu
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NR 70
TC 8
Z9 8
PD FEB
PY 2023
VL 17
IS 2
BP 185
EP 194
DI 10.1038/s41396-022-01332-6
EA OCT 2022
UT WOS:000871174100001
DA 2025-07-30
ER

PT J
AU Baker, BJ
   Hyde, EMY
   Leao, P
AF Baker, Brett J.
   Hyde, Emily
   Leao, Pedro
TI Nature should be the model for microbial sciences
SO JOURNAL OF BACTERIOLOGY
DT Review
AB Until recently, microbiologists have relied on cultures to understand the microbial world. As a result, model organisms have been the focus of research into understanding Bacteria and Archaea at a molecular level. Diversity surveys and metagenomic sequencing have revealed that these model species are often present in low abundance in the environment; instead, there are microbial taxa that are cosmopolitan in nature. Due to the numerical dominance of these microorganisms and the size of their habitats, these lineages comprise mind-boggling population sizes upward of 10(28) cells on the planet. Many of these dominant groups have cultured representatives and have been shown to be involved in mediating key processes in nature. Given their importance and the increasing need to understand changes due to climate change, we propose that members of Nitrosophaerota (Nitrosopumilus maritimus), SAR11 (Pelagibacter ubique), Hadesarchaeia, Bathyarchaeia, and others become models in the future. Abundance should not be the only measure of a good model system; there are other organisms that are well suited to advance our understanding of ecology and evolution. For example, the most well-studied symbiotic bacteria, like Buchnera, Aliivibrio, and Rhizobium, should be models for understanding host-associations. Also, there are organisms that hold new insights into major transitions in the evolution of life on the planet like the Asgard Archaea (Heimdallarchaeia). Innovations in a variety of in situ techniques have enabled us to circumvent culturing when studying everything from genetics to physiology. Our deepest understanding of microbiology and its impact on the planet will come from studying these microbes in nature. Laboratory-based studies must be grounded in nature, not the other way around.
C1 [Baker, Brett J.; Leao, Pedro] Univ Texas Austin, Marine Sci Inst, Dept Marine Sci, Port Aransas, TX 78712 USA.
   [Baker, Brett J.; Hyde, Emily] Univ Texas Austin, Dept Integrat Biol, Austin, TX 78712 USA.
   [Leao, Pedro] Radboud Univ Nijmegen, Dept Microbiol RIBES, Nijmegen, Netherlands.
RP Baker, BJ (corresponding author), Univ Texas Austin, Marine Sci Inst, Dept Marine Sci, Port Aransas, TX 78712 USA.; Baker, BJ (corresponding author), Univ Texas Austin, Dept Integrat Biol, Austin, TX 78712 USA.
EM acidophile@gmail.com
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NR 78
TC 1
Z9 1
PD SEP 19
PY 2024
VL 206
IS 9
DI 10.1128/jb.00228-24
EA AUG 2024
UT WOS:001293662200001
DA 2025-07-30
ER

PT J
AU Reisch, CR
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AF Reisch, Chris R.
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TI Bacterial catabolism of dimethylsulfoniopropionate (DMSP)
SO FRONTIERS IN MICROBIOLOGY
DT Review
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C1 [Reisch, Chris R.; Whitman, William B.] Univ Georgia, Dept Microbiol, Athens, GA 30602 USA.
   [Moran, Mary Ann] Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
RP Whitman, WB (corresponding author), Univ Georgia, Dept Microbiol, Athens, GA 30602 USA.
EM whitman@uga.edu
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NR 106
TC 162
Z9 193
PY 2011
VL 2
AR 172
DI 10.3389/fmicb.2011.00172
UT WOS:000208863500181
DA 2025-07-30
ER

PT J
AU Du, S
   Qin, F
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AF Du, Sen
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   Zhao, Yanlin
TI Genomic diversity, life strategies and ecology of marine HTVC010P-type
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SO MICROBIAL GENOMICS
DT Article
AB SAR11 bacteria dominate ocean surface bacterioplankton communities, and play an important role in marine carbon and nutrient cycling. The biology and ecology of SAR11 are impacted by SAR11 phages (pelagiphages) that are highly diverse and abundant in the ocean. Among the currently known pelagiphages, HTVC010P represents an extremely abundant but under- studied phage group in the ocean. In this study, we have isolated seven new HTVC010P- type pelagiphages, and recovered 77 nearly full- length HTVC010P- type metagenomic viral genomes from marine metagenomes. Comparative genomic and phylogenomic analyses showed that HTVC010P- type pelagiphages display genome synteny and can be clustered into two major subgroups, with subgroup I consisting of strictly lytic phages and subgroup II mostly consisting of phages with potential lysogenic life cycles. All but one member of the subgroup II contain an integrase gene. Site- specific integration of subgroup II HTVC010P- type pelagiphage was either verified experimentally or identified by in silico genomic sequence analyses, which revealed that various SAR11 tRNA genes can serve as the integration sites of HTVC010P- type pelagiphages. Moreover, HTVC010P- type pelagiphage integration was confirmed by the detection of several Global Ocean Survey (GOS) fragments that contain hybrid phage-host integration sites. Metagenomic recruitment analysis revealed that these HTVC010P- type phages were globally distributed and most lytic subgroup I members exhibited higher relative abundance. Altogether, this study significantly expands our knowledge about the genetic diversity, life strategies and ecology of HTVC010P- type pelagiphages.
C1 [Du, Sen; Qin, Fang; Zhang, Zefeng; Tian, Zhen; Yang, Mingyu; Liu, Xinxin; Zhao, Guiyuan; Xia, Qian; Zhao, Yanlin] Fujian Agr & Forestry Univ, Fujian Prov Key & Aboratory Agroecol Proc & Safet, Coll Life Sci, Fuzhou, Peoples R China.
RP Zhao, YL (corresponding author), Fujian Agr & Forestry Univ, Fujian Prov Key & Aboratory Agroecol Proc & Safet, Coll Life Sci, Fuzhou, Peoples R China.
EM yanlinzhao@fafu.edu.cn
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NR 66
TC 11
Z9 11
PD JUL
PY 2021
VL 7
IS 7
AR 000596
DI 10.1099/mgen.0.000596
UT WOS:000681473100009
DA 2025-07-30
ER

PT J
AU Thompson, LR
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   Ngugi, DK
   Siam, R
   El Dorry, H
   Stingl, U
AF Thompson, Luke R.
   Field, Chris
   Romanuk, Tamara
   Ngugi, David Kamanda
   Siam, Rania
   El Dorry, Hamza
   Stingl, Ulrich
TI Patterns of ecological specialization among microbial populations in the
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SO ECOLOGY AND EVOLUTION
DT Article
AB Large swaths of the nutrient-poor surface ocean are dominated numerically by cyanobacteria (Prochlorococcus), cyanobacterial viruses (cyanophage), and alphaproteobacteria (SAR11). How these groups thrive in the diverse physicochemical environments of different oceanic regions remains poorly understood. Comparative metagenomics can reveal adaptive responses linked to ecosystem-specific selective pressures. The Red Sea is well-suited for studying adaptation of pelagic-microbes, with salinities, temperatures, and light levels at the extreme end for the surface ocean, and low nutrient concentrations, yet no metagenomic studies have been done there. The Red Sea (high salinity, high light, low N and P) compares favorably with the Mediterranean Sea (high salinity, low P), Sargasso Sea (low P), and North Pacific Subtropical Gyre (high light, low N). We quantified the relative abundance of genetic functions among Prochlorococcus, cyanophage, and SAR11 from these four regions. Gene frequencies indicate selection for phosphorus acquisition (Mediterranean/Sargasso), DNA repair and high-light responses (Red Sea/Pacific Prochlorococcus), and osmolyte C1 oxidation (Red Sea/Mediterranean SAR11). The unexpected connection between salinity-dependent osmolyte production and SAR11 C1 metabolism represents a potentially major coevolutionary adaptation and biogeochemical flux. Among Prochlorococcus and cyanophage, genes enriched in specific environments had ecotype distributions similar to nonenriched genes, suggesting that inter-ecotype gene transfer is not a major source of environment-specific adaptation. Clustering of metagenomes using gene frequencies shows similarities in populations (Red Sea with Pacific, Mediterranean with Sargasso) that belie their geographic distances. Taken together, the genetic functions enriched in specific environments indicate competitive strategies for maintaining carrying capacity in the face of physical stressors and low nutrient availability.
C1 [Thompson, Luke R.; Ngugi, David Kamanda; Stingl, Ulrich] King Abdullah Univ Sci & Technol KAUST, Red Sea Res Ctr, Thuwal 239556900, Saudi Arabia.
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RP Thompson, LR (corresponding author), 4700 King Abdullah Univ Sci & Technol, Red Sea Res Ctr, Off 3216 WS14, Bldg 2, Thuwal 239556900, Saudi Arabia.
EM luke.thompson@kaust.edu.sa
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NR 63
TC 38
Z9 39
PD JUN
PY 2013
VL 3
IS 6
BP 1780
EP 1797
DI 10.1002/ece3.593
UT WOS:000320274400030
DA 2025-07-30
ER

PT J
AU Tsementzi, D
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AF Tsementzi, Despina
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TI SAR11 bacteria linked to ocean anoxia and nitrogen loss
SO NATURE
DT Article
AB Bacteria of the SAR11 clade constitute up to one half of all microbial cells in the oxygen-rich surface ocean. SAR11 bacteria are also abundant in oxygen minimum zones (OMZs), where oxygen falls below detection and anaerobic microbes have vital roles in converting bioavailable nitrogen to N-2 gas. Anaerobic metabolism has not yet been observed in SAR11, and it remains unknown how these bacteria contribute to OMZ biogeochemical cycling. Here, genomic analysis of single cells from the world's largest OMZ revealed previously uncharacterized SAR11 lineages with adaptations for life without oxygen, including genes for respiratory nitrate reductases (Nar). SAR11 nar genes were experimentally verified to encode proteins catalysing the nitrite-producing first step of denitrification and constituted similar to 40% of OMZ nar transcripts, with transcription peaking in the anoxic zone of maximum nitrate reduction activity. These results link SAR11 to pathways of ocean nitrogen loss, redefining the ecological niche of Earth's most abundant organismal group.
C1 [Tsementzi, Despina; Konstantinidis, Konstantinos T.] Georgia Inst Technol, Sch Civil & Environm Engn, Ford Environm Sci & Technol Bldg,311 Ferst Dr, Atlanta, GA 30332 USA.
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RP Stewart, FJ (corresponding author), Georgia Inst Technol, Sch Biol Sci, Ford Environm Sci & Technol Bldg,311 Ferst Dr, Atlanta, GA 30332 USA.
EM frank.stewart@biology.gatech.edu
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NR 76
TC 127
Z9 144
PD AUG 11
PY 2016
VL 536
IS 7615
BP 179
EP +
DI 10.1038/nature19068
UT WOS:000381472100029
DA 2025-07-30
ER

PT J
AU Kraemer, S
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   Lovejoy, C
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AF Kraemer, Susanne
   Ramachandran, Arthi
   Colatriano, David
   Lovejoy, Connie
   Walsh, David A.
TI Diversity and biogeography of SAR11 bacteria from the Arctic Ocean
SO ISME JOURNAL
DT Article
AB The Arctic Ocean is relatively isolated from other oceans and consists of strongly stratified water masses with distinct histories, nutrient, temperature, and salinity characteristics, therefore providing an optimal environment to investigate local adaptation. The globally distributed SAR11 bacterial group consists of multiple ecotypes that are associated with particular marine environments, yet relatively little is known about Arctic SAR11 diversity. Here, we examined SAR11 diversity using ITS analysis and metagenome-assembled genomes (MAGs). Arctic SAR11 assemblages were comprised of the S1a, S1b, S2, and S3 clades, and structured by water mass and depth. The fresher surface layer was dominated by an ecotype (S3-derived P3.2) previously associated with Arctic and brackish water. In contrast, deeper waters of Pacific origin were dominated by the P2.3 ecotype of the S2 clade, within which we identified a novel subdivision (P2.3s1) that was rare outside the Arctic Ocean. Arctic S2-derived SAR11 MAGs were restricted to high latitudes and included MAGs related to the recently defined S2b subclade, a finding consistent with bi-polar ecotypes and Arctic endemism. These results place the stratified Arctic Ocean into the SAR11 global biogeography and have identified SAR11 lineages for future investigation of adaptive evolution in the Arctic Ocean.
C1 [Kraemer, Susanne; Ramachandran, Arthi; Colatriano, David; Walsh, David A.] Concordia Univ, Dept Biol, 7141 Sherbrooke St West, Sherbrooke, PQ H4B 1R6, Canada.
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RP Walsh, DA (corresponding author), Concordia Univ, Dept Biol, 7141 Sherbrooke St West, Sherbrooke, PQ H4B 1R6, Canada.
EM david.walsh@concordia.ca
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PY 2020
VL 14
IS 1
BP 79
EP 90
DI 10.1038/s41396-019-0499-4
UT WOS:000502553200008
DA 2025-07-30
ER

PT S
AU Giovannoni, SJ
AF Giovannoni, Stephen J.
GP Annual Reviews
TI SAR11 Bacteria: The Most Abundant Plankton in the Oceans
SO ANNUAL REVIEW OF MARINE SCIENCE, VOL 9
SE Annual Review of Marine Science
DT Review; Book Chapter
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RP Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
EM steve.giovannoni@oregonstate.edu
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NR 117
TC 356
Z9 391
PY 2017
VL 9
BP 231
EP 255
DI 10.1146/annurev-marine-010814-015934
UT WOS:000400926700011
HC Y
HP N
DA 2025-07-30
ER

PT J
AU Carini, P
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   Thrash, JC
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AF Carini, Paul
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   Temperton, Ben
   Begley, Tadhg
   Giovannoni, Stephen J.
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SO ISME JOURNAL
DT Article
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   [Morre, Jeff] Oregon State Univ, Dept Chem, Corvallis, OR 97331 USA.
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RP Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, Nash Hall, Corvallis, OR 97331 USA.
EM steve.giovannoni@oregonstate.edu
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NR 70
TC 99
Z9 113
PD AUG
PY 2014
VL 8
IS 8
BP 1727
EP 1738
DI 10.1038/ismej.2014.61
UT WOS:000340029800016
DA 2025-07-30
ER

PT J
AU Sowell, SM
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   Nicora, CD
   Callister, SJ
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AF Sowell, Sarah M.
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TI Proteomic analysis of stationary phase in the marine bacterium
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB "Candidatus Pelagibacter ubique," an abundant marine alphaproteobacterium, subsists in nature at low ambient nutrient concentrations and may often be exposed to nutrient limitation, but its genome reveals no evidence of global regulatory mechanisms for adaptation to stationary phase. High-resolution capillary liquid chromatography coupled online to an LTQ mass spectrometer was used to build an accurate mass and time (AMT) tag library that enabled quantitative examination of proteomic differences between exponential- and stationary-phase "Ca. Pelagibacter ubique" cells cultivated in a seawater medium. The AMT tag library represented 65% of the predicted protein-encoding genes. "Ca. Pelagibacter ubique" appears to respond adaptively to stationary phase by increasing the abundance of a suite of proteins that contribute to homeostasis rather than undergoing a major remodeling of its proteome. Stationary-phase abundances increased significantly for OsmC and thioredoxin reductase, which may mitigate oxidative damage in "Ca. Pelagibacter," as well as for molecular chaperones, enzymes involved in methionine and cysteine biosynthesis, proteins involved in p-dependent transcription termination, and the signal transduction enzyme CheY-FisH. We speculate that this limited response may enable "Ca. Pelagibacter ubique" to cope with ambient conditions that deprive it of nutrients for short periods and, furthermore, that the ability to resume growth overrides the need for a more comprehensive global stationary-phase response to create a capacity for long-term survival.
C1 [Giovannoni, Stephen J.] Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
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RP Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, 220 Nash Hall, Corvallis, OR 97331 USA.
EM steve.giovannoni@oregonstate.edu
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NR 53
TC 61
Z9 69
PD JUL
PY 2008
VL 74
IS 13
BP 4091
EP 4100
DI 10.1128/AEM.00599-08
UT WOS:000257446900020
DA 2025-07-30
ER

PT J
AU Mary, I
   Heywood, JL
   Fuchs, BM
   Amann, R
   Tarran, GA
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AF Mary, I.
   Heywood, J. L.
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TI SAR11 dominance among metabolically active low nucleic acid
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SO AQUATIC MICROBIAL ECOLOGY
DT Article
AB Low nucleic acid (LNA) bacterioplankton (sorted by flow cytometry) were characterised in surface water samples along a mericlional transect from 48 degrees N to 40 degrees S across the Atlantic Ocean. The LNA bacterioplankton abundance and metabolic activity, assessed by their S-35-methionine uptake rate, were similar along the transect, representing 36 +/- 6 and 36 +/- 11 % of total bacterioplankton, respectively. Fluorescence in situ hybridisation analysis of the flow-sorted cells revealed that the LNA bacterioplankton population was dominated (59 4 %) by and contained virtually all the identifiable SAR11 clade cells throughout the Atlantic Ocean. Therefore, the present study provides ecological characterisation of this flow-sorted group and suggests both phylogenetic and functional constancy of the LNA bacterioplankton at the basin-scale.
C1 Univ Southampton, Natl Oceanog Ctr, Southampton SO14 3ZH, Hants, England.
   Max Planck Inst Marine Microbiol, D-28359 Bremen, Germany.
   Plymouth Marine Lab, Plymouth PL1 3DH, Devon, England.
RP Zubkov, MV (corresponding author), Univ Southampton, Natl Oceanog Ctr, Waterfront Campus,European Way, Southampton SO14 3ZH, Hants, England.
EM mvz@noc.soton.ac.uk
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NR 31
TC 88
Z9 94
PD NOV 24
PY 2006
VL 45
IS 2
BP 107
EP 113
DI 10.3354/ame045107
UT WOS:000243038700002
DA 2025-07-30
ER

PT J
AU Carini, P
   Steindler, L
   Beszteri, S
   Giovannoni, SJ
AF Carini, Paul
   Steindler, Laura
   Beszteri, Sara
   Giovannoni, Stephen J.
TI Nutrient requirements for growth of the extreme oligotroph
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SO ISME JOURNAL
DT Article
AB Chemoheterotrophic marine bacteria of the SAR11 clade are Earth's most abundant organisms. Following the first cultivation of a SAR11 bacterium, 'Candidatus Pelagibacter ubique' strain HTCC1062 (Ca. P. ubique) in 2002, unusual nutritional requirements were identified for reduced sulfur compounds and glycine or serine. These requirements were linked to genome streamlining resulting from selection for efficient resource utilization in nutrient-limited ocean habitats. Here we report the first successful cultivation of Ca. P. ubique on a defined artificial seawater medium (AMS1), and an additional requirement for pyruvate or pyruvate precursors. Optimal growth was observed with the collective addition of inorganic macro-and micronutrients, vitamins, methionine, glycine and pyruvate. Methionine served as the sole sulfur source but methionine and glycine were not sufficient to support growth. Optimal cell yields were obtained when the stoichiometry between glycine and pyruvate was 1: 4, and incomplete cell division was observed in cultures starved for pyruvate. Glucose and oxaloacetate could fully replace pyruvate, but not acetate, taurine or a variety of tricarboxylic acid cycle intermediates. Moreover, both glycine betaine and serine could substitute for glycine. Interestingly, glycolate partially restored growth in the absence of glycine. We propose that this is the result of the use of glycolate, a product of phytoplankton metabolism, as both a carbon source for respiration and as a precursor to glycine. These findings are important because they provide support for the hypothesis that some micro-organisms are challenging to cultivate because of unusual nutrient requirements caused by streamlining selection and gene loss. Our findings also illustrate unusual metabolic rearrangements that adapt these cells to extreme oligotrophy, and underscore the challenge of reconstructing metabolism from genome sequences in organisms that have non-canonical metabolic pathways. The ISME Journal (2013) 7, 592-602; doi:10.1038/ismej.2012.122; published online 25 October 2012
C1 [Carini, Paul; Steindler, Laura; Beszteri, Sara; Giovannoni, Stephen J.] Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
RP Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, 220 Nash Hall, Corvallis, OR 97331 USA.
EM steve.giovannoni@oregonstate.edu
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TC 174
Z9 193
PD MAR
PY 2013
VL 7
IS 3
BP 592
EP 602
DI 10.1038/ismej.2012.122
UT WOS:000316726400015
DA 2025-07-30
ER

PT J
AU Rappé, MS
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   Giovannoni, SJ
AF Rappé, MS
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TI Cultivation of the ubiquitous SAR11 marine bacterioplankton clade
SO NATURE
DT Article
AB The alpha-proteobacterial lineage that contains SAR11 and related ribosomal RNA gene clones was among the first groups of organisms to be identified when cultivation-independent approaches based on rRNA gene cloning and sequencing were applied to survey microbial diversity in natural ecosystems(1). This group accounts for 26% of all ribosomal RNA genes that have been identified in sea water and has been found in nearly every pelagic marine bacterioplankton community studied by these methods(2). The SAR11 clade represents a pervasive problem in microbiology: despite its ubiquity, it has defied cultivation efforts. Genetic evidence suggests that diverse uncultivated microbial taxa dominate most natural ecosystems(3-5), which has prompted widespread efforts to elucidate the geochemical activities of these organisms without the benefit of cultures for study(6,7). Here we report the isolation of representatives of the SAR11 clade. Eighteen cultures were initially obtained by means of high-throughput procedures for isolating cell cultures through the dilution of natural microbial communities into very low nutrient media. Eleven of these cultures have been successfully passaged and cryopreserved for future study. The volume of these cells, about 0.01 mum(3), places them among the smallest free-living cells in culture.
C1 Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
RP Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
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TC 717
Z9 835
PD AUG 8
PY 2002
VL 418
IS 6898
BP 630
EP 633
DI 10.1038/nature00917
UT WOS:000177305600040
DA 2025-07-30
ER

PT J
AU Martinez-Hernandez, F
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AF Martinez-Hernandez, Francisco
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SO ENVIRONMENTAL MICROBIOLOGY REPORTS
DT Article
AB The spatiotemporal dynamics for marine viral populations has only recently been explored. However, nothing is known about temporal activities of the uncultured Pelagibacter virus vSAG 37-F6, which was discovered by single-virus genomics as potentially the most abundant marine virus. Here, we investigate the diel cycling of 37-F6 virus and the putative SAR11 host using coastal and oceanic transcriptomic and viromic time-series data from Osaka Bay and North Pacific Subtropical Gyre. Virus 37-F6 and relatives displayed diel cycling of transcriptional activities synchronized with its putative host. In both virus and host, the lowest transcription rates were observed at 14:00-15:00, coinciding roughly with maximum solar irradiance, while higher transcriptional rates were detected during the night/early morning and afternoon. Diel abundance of free viruses of 37-F6 in seawater roughly mirrored the transcriptional activities of both virus and host. In Osaka Bay, among viral relatives (genus level), virus 37-F6 specifically showed the highest ratio of transcriptional activity to virome abundance, a proxy for viral transcriptional activity relative to free viral particle abundance. This high ratio suggests high infection rate efficiencies in vSAG 37-F6 virus compared to viral relatives. Thus, time-series data revealed temporal transcript activities in one of the most abundant viruses in Earth.
C1 [Martinez-Hernandez, Francisco; Martinez-Garcia, Manuel] Univ Alicante, Dept Physiol Genet & Microbiol, Alicante, Spain.
   [Luo, Elaine; DeLong, Edward F.] Univ Hawaii Manoa, Daniel K Inouye Ctr Microbial Oceanog Res & Educ, Honolulu, HI 96822 USA.
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RP Martinez-Garcia, M (corresponding author), Univ Alicante, Dept Physiol Genet & Microbiol, Alicante, Spain.
EM m.martinez@ua.es
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TC 7
Z9 7
PD APR
PY 2020
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IS 2
BP 214
EP 219
DI 10.1111/1758-2229.12825
EA FEB 2020
UT WOS:000511405400001
DA 2025-07-30
ER

PT J
AU Brennan, E
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AF Brennan, Elizabeth
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SO ENVIRONMENTAL MICROBIOLOGY REPORTS
DT Article
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C1 [Brennan, Elizabeth; Giovannoni, Stephen J.; Suffridge, Christopher P.] Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
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RP Giovannoni, SJ; Suffridge, CP (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
EM steve.giovannoni@oregonstate.edu; suffridc@oregonstate.edu
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NR 65
TC 2
Z9 2
PD OCT
PY 2024
VL 16
IS 5
AR e70023
DI 10.1111/1758-2229.70023
UT WOS:001328848300001
DA 2025-07-30
ER

PT J
AU Moore, ER
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AF Moore, Eric R.
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TI Pelagibacter metabolism of diatom-derived volatile organic
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
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C1 [Moore, Eric R.; Davie-Martin, Cleo L.; Giovannoni, Stephen J.; Halsey, Kimberly H.] Oregon State Univ Corvallis, Dept Microbiol, 354 Nash Hall, Corvallis, OR 97331 USA.
   [Davie-Martin, Cleo L.] Univ Copenhagen, Terr Ecol Sect, Dept Biol, DK-2100 Copenhagen O, Denmark.
RP Halsey, KH (corresponding author), Oregon State Univ Corvallis, Dept Microbiol, 354 Nash Hall, Corvallis, OR 97331 USA.
EM halseyk@science.oregonstate.edu
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NR 60
TC 26
Z9 29
PD MAY
PY 2020
VL 22
IS 5
BP 1720
EP 1733
DI 10.1111/1462-2920.14861
EA DEC 2019
UT WOS:000502062000001
DA 2025-07-30
ER

PT J
AU Salter, I
   Galand, PE
   Fagervold, SK
   Lebaron, P
   Obernosterer, I
   Oliver, MJ
   Suzuki, MT
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AF Salter, Ian
   Galand, Pierre E.
   Fagervold, Sonja K.
   Lebaron, Philippe
   Obernosterer, Ingrid
   Oliver, Matthew J.
   Suzuki, Marcelino T.
   Tricoire, Cyrielle
TI Seasonal dynamics of active SAR11 ecotypes in the oligotrophic Northwest
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SO ISME JOURNAL
DT Article
AB A seven-year oceanographic time series in NW Mediterranean surface waters was combined with pyrosequencing of ribosomal RNA (16S rRNA) and ribosomal RNA gene copies (16S rDNA) to examine the environmental controls on SAR11 ecotype dynamics and potential activity. SAR11 diversity exhibited pronounced seasonal cycles remarkably similar to total bacterial diversity. The timing of diversity maxima was similar across narrow and broad phylogenetic clades and strongly associated with deep winter mixing. Diversity minima were associated with periods of stratification that were low in nutrients and phytoplankton biomass and characterised by intense phosphate limitation (turnover timeo5 h). We propose a conceptual framework in which physical mixing of the water column periodically resets SAR11 communities to a high diversity state and the seasonal evolution of phosphate limitation competitively excludes deeper-dwelling ecotypes to promote low diversity states dominated (>80%) by SAR11 Ia. A partial least squares (PLS) regression model was developed that could reliably predict sequence abundances of SAR11 ecotypes (Q(2) = 0.70) from measured environmental variables, of which mixed layer depth was quantitatively the most important. Comparison of clade-level SAR11 rRNA: rDNA signals with leucine incorporation enabled us to partially validate the use of these ratios as an in-situ activity measure. However, temporal trends in the activity of SAR11 ecotypes and their relationship to environmental variables were unclear. The strong and predictable temporal patterns observed in SAR11 sequence abundance was not linked to metabolic activity of different ecotypes at the phylogenetic and temporal resolution of our study.
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RP Salter, I (corresponding author), Alfred Wegener Inst, Helmholtz Ctr Polar & Marine Res, Handelshafen 12, D-27570 Bremerhaven, Germany.
EM ian.salter@awi.de
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TC 79
Z9 87
PD FEB
PY 2015
VL 9
IS 2
BP 347
EP 360
DI 10.1038/ismej.2014.129
UT WOS:000348213600007
DA 2025-07-30
ER

PT J
AU Schwalbach, MS
   Tripp, HJ
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   Giovannoni, SJ
AF Schwalbach, M. S.
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
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C1 [Schwalbach, M. S.; Tripp, H. J.; Steindler, L.; Smith, D. P.; Giovannoni, S. J.] Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
RP Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, 220 Nash Hall, Corvallis, OR 97331 USA.
EM steve.giovannoni@oregonstate.edu
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NR 61
TC 93
Z9 106
PD FEB
PY 2010
VL 12
IS 2
BP 490
EP 500
DI 10.1111/j.1462-2920.2009.02092.x
UT WOS:000274234600017
DA 2025-07-30
ER

PT J
AU Thrash, JC
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AF Thrash, J. Cameron
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TI Phylogenomic evidence for a common ancestor of mitochondria and the
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SO SCIENTIFIC REPORTS
DT Article
AB Mitochondria share a common ancestor with the Alphaproteobacteria, but determining their precise origins is challenging due to inherent difficulties in phylogenetically reconstructing ancient evolutionary events. Nonetheless, phylogenetic accuracy improves with more refined tools and expanded taxon sampling. We investigated mitochondrial origins with the benefit of new, deeply branching genome sequences from the ancient and prolific SAR11 clade of Alphaproteobacteria and publicly available alphaproteobacterial and mitochondrial genome sequences. Using the automated phylogenomic pipeline Hal, we systematically studied the effect of taxon sampling and missing data to accommodate small mitochondrial genomes. The evidence supports a common origin of mitochondria and SAR11 as a sister group to the Rickettsiales. The simplest explanation of these data is that mitochondria evolved from a planktonic marine alphaproteobacterial lineage that participated in multiple inter-specific cell colonization events, in some cases yielding parasitic relationships, but in at least one case producing a symbiosis that characterizes modern eukaryotic life.
C1 [Thrash, J. Cameron; Carini, Paul; Giovannoni, Stephen J.] Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
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RP Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
EM steve.giovannoni@oregonstate.edu
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TC 120
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PD JUN 14
PY 2011
VL 1
AR 13
DI 10.1038/srep00013
UT WOS:000296046200013
DA 2025-07-30
ER

PT J
AU Malmstrom, RR
   Kiene, RP
   Cottrell, MT
   Kirchman, DL
AF Malmstrom, RR
   Kiene, RP
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   Kirchman, DL
TI Contribution of SAR11 bacteria to dissolved dimethylsulfoniopropionate
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB SAR11 bacteria are abundant in marine environments, often accounting for 35% of total prokaryotes in the surface ocean, but little is known about their involvement in marine biogeochemical cycles. Previous studies reported that SAR11 bacteria are very small and potentially have few ribosomes, indicating that SAR11 bacteria could have low metabolic activities and could play a smaller role in the flux of dissolved organic matter than suggested by their abundance. To determine the ecological activity of SAR11 bacteria, we used a combination of microautoradiography and fluorescence in situ hybridization (Micro-FISH) to measure assimilation of (3)H-amino acids and [(35)S]dimethylsulfoniopropionate (DMSP) by SAR11 bacteria in the coastal North Atlantic Ocean and the Sargasso Sea. We found that SAR11 bacteria were often abundant in surface waters, accounting for 25% of all prokaryotes on average. SAR11 bacteria were typically as large as, if not larger than, other prokaryotes. Additionally, more than half of SAR11 bacteria assimilated dissolved amino acids and DMSP, whereas about 40% of other prokaryotes assimilated these compounds. Due to their high abundance and activity, SAR11 bacteria were responsible for about 50% of amino acid assimilation and 30% of DMSP assimilation in surface waters. The contribution of SAR11 bacteria to amino acid assimilation was greater than would be expected based on their overall abundance, implying that SAR11 bacteria outcompete other prokaryotes for these labile compounds. These data suggest that SAR11 bacteria are highly active and play a significant role in C, N, and S cycling in the ocean.
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RP Kirchman, DL (corresponding author), Univ Delaware, Coll Marine Studies, 700 Pilottown Rd, Lewes, DE 19958 USA.
EM kirchman@cms.udel.edu
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Z9 204
PD JUL
PY 2004
VL 70
IS 7
BP 4129
EP 4135
DI 10.1128/AEM.70.7.4129-4135.2004
UT WOS:000222758600045
DA 2025-07-30
ER

PT J
AU Hartmann, M
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   Leakey, RJG
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AF Hartmann, Manuela
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   Achterberg, Eric P.
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TI Resilience of SAR11 bacteria to rapid acidification in the high-latitude
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SO FEMS MICROBIOLOGY ECOLOGY
DT Article
AB Ubiquitous SAR11 Alphaproteobacteria numerically dominate marine planktonic communities. Because they are excruciatingly difficult to cultivate, there is comparatively little known about their physiology and metabolic responses to long-and short-term environmental changes. As surface oceans take up anthropogenic, atmospheric CO2, the consequential process of ocean acidification could affect the global biogeochemical significance of SAR11. Shipping accidents or inadvertent release of chemicals from industrial plants can have strong short-term local effects on oceanic SAR11. This study investigated the effect of 2.5-fold acidification of seawater on the metabolism of SAR11 and other heterotrophic bacterioplankton along a natural temperature gradient crossing the North Atlantic Ocean, Norwegian and Greenland Seas. Uptake rates of the amino acid leucine by SAR11 cells as well as other bacterioplankton remained similar to controls despite an instant similar to 50% increase in leucine bioavailability upon acidification. This high physiological resilience to acidification even without acclimation, suggests that open ocean dominant bacterioplankton are able to cope even with sudden and therefore more likely with long-term acidification effects.
C1 [Hartmann, Manuela; Hill, Polly G.; Zubkov, Mikhail V.] Natl Oceanog Ctr, European Way, Southampton SO14 3ZH, Hants, England.
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   [Leakey, Raymond J. G.] Scottish Marine Inst, Scottish Assoc Marine Sci, Oban PA37 1QA, Argyll, Scotland.
RP Zubkov, MV (corresponding author), Natl Oceanog Ctr, Ocean Biogeochem & Ecosyst Res Grp, European Way, Southampton SO14 3ZH, Hants, England.
EM mvz@noc.ac.uk
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NR 53
TC 9
Z9 9
PD FEB
PY 2016
VL 92
IS 2
AR fiv161
DI 10.1093/femsec/fiv161
UT WOS:000371249600007
DA 2025-07-30
ER

PT J
AU Amrine, KCH
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   Ardell, DH
AF Amrine, Katherine C. H.
   Swingley, Wesley D.
   Ardell, David H.
TI tRNA Signatures Reveal a Polyphyletic Origin of SAR11 Strains among
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SO PLOS COMPUTATIONAL BIOLOGY
DT Article
AB Molecular phylogenetics and phylogenomics are subject to noise from horizontal gene transfer (HGT) and bias from convergence in macromolecular compositions. Extensive variation in size, structure and base composition of alphaproteobacterial genomes has complicated their phylogenomics, sparking controversy over the origins and closest relatives of the SAR11 strains. SAR11 are highly abundant, cosmopolitan aquatic Alphaproteobacteria with streamlined, A+T-biased genomes. A dominant view holds that SAR11 are monophyletic and related to both Rickettsiales and the ancestor of mitochondria. Other studies dispute this, finding evidence of a polyphyletic origin of SAR11 with most strains distantly related to Rickettsiales. Although careful evolutionary modeling can reduce bias and noise in phylogenomic inference, entirely different approaches may be useful to extract robust phylogenetic signals from genomes. Here we develop simple phyloclassifiers from bioinformatically derived tRNA Class-Informative Features (CIFs), features predicted to target tRNAs for specific interactions within the tRNA interaction network. Our tRNA CIF-based model robustly and accurately classifies alphaproteobacterial genomes into one of seven undisputed monophyletic orders or families, despite great variability in tRNA gene complement sizes and base compositions. Our model robustly rejects monophyly of SAR11, classifying all but one strain as Rhizobiales with strong statistical support. Yet remarkably, conventional phylogenetic analysis of tRNAs classifies all SAR11 strains identically as Rickettsiales. We attribute this discrepancy to convergence of SAR11 and Rickettsiales tRNA base compositions. Thus, tRNA CIFs appear more robust to compositional convergence than tRNA sequences generally. Our results suggest that tRNA-CIF-based phyloclassification is robust to HGT of components of the tRNA interaction network, such as aminoacyl-tRNA synthetases. We explain why tRNAs are especially advantageous for prediction of traits governing macromolecular interactions from genomic data, and why such traits may be advantageous in the search for robust signals to address difficult problems in classification and phylogeny.
   Author Summary
   If gene products work well in the networks of foreign cells, their genes may transfer horizontally between unrelated genomes. What factors dictate the ability to integrate into foreign networks? Different RNAs and proteins must interact specifically in order to function well as a system. For example, tRNA functions are determined by the interactions they have with other macromolecules. We have developed ways to predict, from genomic data alone, how tRNAs distinguish themselves to their specific interaction partners. Here, as proof of concept, we built a robust computational model from these bioinformatic predictions in seven lineages of Alphaproteobacteria. We validated our model by classifying hundreds of diverse alphaproteobacterial taxa and tested it on eight strains of SAR11, a phylogenetically controversial group that is highly abundant in the world's oceans. We found that different strains of SAR11 are more distantly related, both to each other and to mitochondria, than widely believed. We explain conflicting results about SAR11 as an artifact of bias created by the variability in base contents of alphaproteobacterial genomes. While this bias affects tRNAs too, our classifier appears unexpectedly robust to it.
   More broadly, our results suggest that traits governing macromolecular interactions may be more faithfully vertically inherited than the macromolecules themselves.
C1 [Amrine, Katherine C. H.; Swingley, Wesley D.; Ardell, David H.] Univ Calif Merced, Program Quantitat & Syst Biol, Merced, CA 95344 USA.
RP Amrine, KCH (corresponding author), Univ Calif Merced, Program Quantitat & Syst Biol, Merced, CA 95344 USA.
EM dardell@ucmerced.edu
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NR 94
TC 6
Z9 7
PD FEB
PY 2014
VL 10
IS 2
DI 10.1371/journal.pcbi.1003454
UT WOS:000332016700010
DA 2025-07-30
ER

PT J
AU Wei, T
   Quareshy, M
   Zhang, YZ
   Scanlan, DJ
   Chen, Y
AF Wei, Tao
   Quareshy, Mussa
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   Scanlan, David J.
   Chen, Yin
TI Manganese Is Essential for PlcP Metallophosphoesterase Activity Involved
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB In vast areas of the ocean, microbes must adapt to the availability of scarce nutrients, and a key strategy for reducing the cellular phosphorus (P) quota is to remodel membranes by replacing phospholipids with non-P surrogate lipids. A metallo-phosphoesterase, PlcP, is essential for lipid remodeling in cosmopolitan marine bacteria of the Roseobacter (e.g., Phaeobacter sp. strain MED193) and SAR11 (e.g., Pelagibacter sp. strain HTCC7211) clades, and transcription of plcP is known to be induced by P limitation. In order to better understand PlcP-mediated lipid remodeling, we sought to characterize PlcP for its metal ion requirement and to determine its selectivity for native bacterial phospholipids. Here, we report the occurrence of a highly conserved binuclear ion center in PlcPs from MED193 and HTCC7211 and show that manganese is the preferred metal for metallophosphoesterase activity. PlcP displayed high activity towards the major bacterial phospholipids, e.g., phosphatidylglycerol but also phosphatidic acid, a key intermediate in phospholipid biosynthesis. In contrast, phosphatidylserine and phosphatidylinositol, both of which are rare lipids in bacteria, are not preferred substrates. These data suggest that PlcP undertakes a generic lipid remodeling role during the cellular response of marine bacteria to P deficiency and that manganese availability may play a key role in regulating the lipid remodeling process.
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C1 [Wei, Tao] Zhengzhou Univ Light Ind, Sch Food & Biol Engn, Zhengzhou, Henan, Peoples R China.
   [Wei, Tao; Quareshy, Mussa; Scanlan, David J.; Chen, Yin] Univ Warwick, Sch Life Sci, Coventry, W Midlands, England.
   [Zhang, Yu-Zhong] Shandong Univ, Marine Biotechnol Res Ctr, State Key Lab Microbial Technol, Jinan, Shandong, Peoples R China.
   [Zhang, Yu-Zhong] Ocean Univ China, Coll Marine Life Sci, Qingdao, Peoples R China.
RP Wei, T (corresponding author), Zhengzhou Univ Light Ind, Sch Food & Biol Engn, Zhengzhou, Henan, Peoples R China.; Wei, T; Chen, Y (corresponding author), Univ Warwick, Sch Life Sci, Coventry, W Midlands, England.
EM weit8008@zzuli.edu.cn; Y.chen.25@warwick.ac.uk
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NR 32
TC 14
Z9 15
PD AUG
PY 2018
VL 84
IS 15
AR e01109
DI 10.1128/AEM.01109-18
UT WOS:000438891500020
DA 2025-07-30
ER

PT J
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SO MICROBIAL ECOLOGY
DT Article
AB We investigated the abundance and activity of SAR11 on a monthly time scale between January 2008 and October 2008 in the oligotrophic NW Mediterranean Sea. Applying MICRO-CARD-FISH, we observed that SAR11 had a large contribution to bulk abundance (37 +/- 6% of DAPI-stained cells) and to bulk bacterial heterotrophic production (BHP), as estimated from leucine incorporation (55 +/- 15% of DAPI-cells assimilating leucine) in surface waters (5 m) throughout the study period. SAR11 contributed also substantially to the assimilation of glucose, ATP, and a combination of amino acids (44 +/- 17%, 37 +/- 14%, and 43 +/- 12% of DAPI cells assimilating these compounds, respectively), organic compounds that provide either single or combined sources of C, P, and N. Temporal changes in the abundance of SAR11 cells that assimilated leucine, glucose, amino acids, and ATP revealed a pattern consistent with that of substrate-active DAPI cells, suggesting that the activity of SAR11 can explain to a large extent the variability in total cells contributing to the utilization of these compounds. Short-term nutrient enrichment experiments performed on each sampling date revealed a strong co-limitation of at least two of the three elements analyzed (C, N, P), in particular, during summer and early autumn. The in situ abundance of SAR11 cells assimilating leucine appeared to increase with P limitation as determined in the nutrient enrichment experiments (r = 0.81, p = 0.015). Our results demonstrate that SAR11 is an important component of the active bacterial community in the NW Mediterranean Sea. Our observations further indicate that the activity of the bulk bacterial community is linked to the activity of SAR11, possibly due to its adaptation to nutrient limitation.
C1 [Laghdass, Melissa; Catala, Philippe; Caparros, Jocelyne; Oriol, Louise; Lebaron, Philippe; Obernosterer, Ingrid] CNRS, UMR 7621, LOM, Observ Oceanol, F-66650 Banyuls Sur Mer, France.
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RP Obernosterer, I (corresponding author), CNRS, UMR 7621, LOM, Observ Oceanol, F-66650 Banyuls Sur Mer, France.
EM ingrid.obernosterer@obs-banyuls.fr
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NR 63
TC 21
Z9 22
PD FEB
PY 2012
VL 63
IS 2
BP 324
EP 333
DI 10.1007/s00248-011-9915-7
UT WOS:000300316500008
DA 2025-07-30
ER

PT J
AU Tada, Y
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   Taniguchi, A
   Hamasaki, K
AF Tada, Yuya
   Makabe, Ryosuke
   Kasamatsu-Takazawa, Nobue
   Taniguchi, Akito
   Hamasaki, Koji
TI Growth and distribution patterns of
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SO POLAR BIOLOGY
DT Article
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C1 [Tada, Yuya; Hamasaki, Koji] Univ Tokyo, Atmosphere & Ocean Res Inst, Kashiwa, Chiba 2778564, Japan.
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RP Tada, Y (corresponding author), Univ Tokyo, Atmosphere & Ocean Res Inst, 5-1-5 Kashiwanoha, Kashiwa, Chiba 2778564, Japan.
EM yatada@aori.u-tokyo.ac.jp
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NR 72
TC 16
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PD MAY
PY 2013
VL 36
IS 5
BP 691
EP 704
DI 10.1007/s00300-013-1294-8
UT WOS:000317858500006
DA 2025-07-30
ER

PT J
AU Dinasquet, J
   Landa, M
   Obernosterer, II
AF Dinasquet, Julie
   Landa, Marine
   Obernosterer, I. Ingrid
TI SAR11 clade microdiversity and activity during the early spring blooms
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SO ENVIRONMENTAL MICROBIOLOGY REPORTS
DT Article
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C1 [Dinasquet, Julie; Landa, Marine; Obernosterer, I. Ingrid] Sorbonne Univ, Lab Oceanog Microbienne, LOMIC, CNRS, Banyuls Sur Mer, France.
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RP Dinasquet, J (corresponding author), Scripps Inst Oceanog, Biol Grade, Hubbs Hall, La Jolla, CA 92037 USA.
EM jdinasquet@ucsd.edu
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NR 72
TC 7
Z9 7
PD DEC
PY 2022
VL 14
IS 6
BP 907
EP 916
DI 10.1111/1758-2229.13117
EA AUG 2022
UT WOS:000846495500001
DA 2025-07-30
ER

PT J
AU Malmstrom, RR
   Cottrell, MT
   Elifantz, H
   Kirchman, DL
AF Malmstrom, RR
   Cottrell, MT
   Elifantz, H
   Kirchman, DL
TI Biomass production and assimilation of dissolved organic matter by SAR11
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Members of the SAR11 clade often dominate the composition of marine microbial communities, yet their contribution to biomass production and the flux of dissolved organic matter (DOM) is unclear. In addition, little is known about the specific components of the DOM pool utilized by SAR11 bacteria. To better understand the role of SAR11 bacteria in the flux of DOM, we examined the assimilation of leucine (a measure of biomass production), as well as free amino acids, protein, and glucose, by SAR11 bacteria in the Northwest Atlantic Ocean. We found that when SAR11 bacteria were > 25 % of total prokaryotes, they accounted for about 30 to 50 % of leucine incorporation, suggesting that SARII bacteria were major contributors to bacterial biomass production and the DOM flux. Specific growth rates of SAR11 bacteria either equaled or exceeded growth rates for the total prokaryotic community. In addition, SAR11 bacteria were typically responsible for a greater portion of amino acid assimilation (34 to 61 %) and glucose assimilation (45 to 57 %) than of protein assimilation (<= 34 %). These data suggest that SAR11 bacteria do not utilize various components of the DOM pool equally and may be more important to the flux of low-molecular-weight monomers than to that of high-molecular-weight polymers.
C1 Univ Delaware, Coll Marine Studies, Lewes, DE 19958 USA.
RP Univ Delaware, Coll Marine Studies, Lewes, DE 19958 USA.
EM kirchman@cms.udel.edu
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NR 35
TC 141
Z9 155
PD JUN
PY 2005
VL 71
IS 6
BP 2979
EP 2986
DI 10.1128/AEM.71.6.2979-2986.2005
UT WOS:000229790900023
DA 2025-07-30
ER

PT J
AU Zaremba-Niedzwiedzka, K
   Viklund, J
   Zhao, WZ
   Ast, J
   Sczyrba, A
   Woyke, T
   McMahon, K
   Bertilsson, S
   Stepanauskas, R
   Andersson, SGE
AF Zaremba-Niedzwiedzka, Katarzyna
   Viklund, Johan
   Zhao, Weizhou
   Ast, Jennifer
   Sczyrba, Alexander
   Woyke, Tanja
   McMahon, Katherina
   Bertilsson, Stefan
   Stepanauskas, Ramunas
   Andersson, Siv G. E.
TI Single-cell genomics reveal low recombination frequencies in freshwater
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SO GENOME BIOLOGY
DT Article
AB Background: The SAR11 group of Alphaproteobacteria is highly abundant in the oceans. It contains a recently diverged freshwater clade, which offers the opportunity to compare adaptations to salt-and freshwaters in a monophyletic bacterial group. However, there are no cultivated members of the freshwater SAR11 group and no genomes have been sequenced yet.
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C1 [Zaremba-Niedzwiedzka, Katarzyna; Viklund, Johan; Zhao, Weizhou; Ast, Jennifer; Andersson, Siv G. E.] Uppsala Univ, Dept Mol Evolut, S-75124 Uppsala, Sweden.
   [Zaremba-Niedzwiedzka, Katarzyna; Viklund, Johan; Zhao, Weizhou; Ast, Jennifer; Andersson, Siv G. E.] Uppsala Univ, Sci Life Lab, S-75124 Uppsala, Sweden.
   [Sczyrba, Alexander] Univ Bielefeld, Ctr Biotechnol, D-33501 Bielefeld, Germany.
   [Woyke, Tanja] US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA.
   [McMahon, Katherina] Univ Wisconsin, Dept Civil & Environm Engn, Madison, WI 53706 USA.
   [McMahon, Katherina] Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA.
   [Bertilsson, Stefan] Uppsala Univ, Dept Ecol & Genet, Limnol & Sci Life Lab, S-75236 Uppsala, Sweden.
   [Stepanauskas, Ramunas] Bigelow Lab Ocean Sci, East Boothbay, ME 04544 USA.
RP Andersson, SGE (corresponding author), Uppsala Univ, Dept Mol Evolut, S-75124 Uppsala, Sweden.
EM Siv.Andersson@icm.uu.se
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NR 47
TC 59
Z9 65
PY 2013
VL 14
IS 11
AR R130
DI 10.1186/gb-2013-14-11-r130
UT WOS:000330616200009
DA 2025-07-30
ER

PT J
AU Field, KG
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AF Field, KG
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DT Article
AB Small-subunit (SSU) ribosomal DNA (rDNA) gene clusters are phylogenetically related sets of SSU rRNA genes, commonly encountered in genes amplified from natural populations. Genetic variability in gene clusters could result from artifacts (polymerase error or PCR chimera formation), microevolution (variation among rrn copies within strains), or macroevolution (genetic divergence correlated with long-term evolutionary divergence). To better understand gene clusters, this study assessed genetic diversity and distribution of a single environmental SSU rDNA gene cluster, the SAR11 cluster. SAR11 cluster genes, from an uncultured group of the a subclass of the class Proteobacteria, have been recovered from coastal and midoceanic waters of the North Atlantic and Pacific. We cloned and bidirectionally sequenced 23 new SAR11 cluster 16S rRNA genes, from 80 and 250 m in the Sargasso Sea and from surface coastal waters of the Atlantic and Pacific, and analyzed them with previously published sequences. Two SAR11 genes were obviously PCR chimeras, but the biological (nonchimeric) origins of most subgroups, within the cluster were confirmed by independent recovery from separate gene libraries. Using group-specific oligonucleotide probes, we analyzed depth profiles of nucleic acids, targeting both amplified rDNAs and bulk RNAs. Two subgroups within the SAR11 cluster showed different highly depth-specific distributions. We conclude that some of the genetic diversity, within the SAR11 gene cluster represents macroevolutionary divergence correlated with niche specialization. Furthermore, we demonstrate the utility for marine microbial ecology of oligonucleotide probes based on gene sequences amplified from natural populations and show that a detailed knowledge of sequence variability may be needed to effectively design these probes.
RP Field, KG (corresponding author), OREGON STATE UNIV,DEPT MICROBIOL,CORVALLIS,OR 97331, USA.
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BP 63
EP 70
DI 10.1128/AEM.63.1.63-70.1997
UT WOS:A1997WA16800011
DA 2025-07-30
ER

PT J
AU Oh, S
   Zhang, R
   Wu, QL
   Liu, WT
AF Oh, Seungdae
   Zhang, Rui
   Wu, Qinglong L.
   Liu, Wen-Tso
TI Evolution and adaptation of SAR11 and Cyanobium in a saline
   Tibetan lake
SO ENVIRONMENTAL MICROBIOLOGY REPORTS
DT Article
AB Lake Qinghai is a unique lacustrine ecosystem located on the Tibetan Plateau and exhibits oligotrophic, alkaline, and saline conditions. Previous studies have focused on the community phylogenetic diversity of bacterioplankton in the ecosystem. This study aimed to address the ecotype diversity of bacterioplankton populations in the unique microbial habitat, using metagenomic sequencing and analysis. Phylogenetic analysis revealed two major bacterial populations: SAR11 IIIa (14% of the total) and Cyanobium (14%). Although the two populations shared high 16S rRNA gene sequence identity (> 98% identity) with their closest marine counterparts, they displayed substantial genomic divergence (<= 80% average amino acid sequence identity). Comparative genomic analysis identified conservation of carbon and energy storage metabolism (biosynthesis of polyphosphate and polyhydroxyalkanoate) gene operons in the SAR11 IIIa and a cyanate (potential nitrogen source in alkaline conditions) transporter gene operon in the Cyanobium. We further identified genetic signature of positive selection acting on an exodeoxyribonuclease gene of the SAR11 IIIa popula-tion, which is potentially associated with DNA repair responsive to strong UV radiation on the high altitude mountain. Taken together, our results revealed the ecosystem-specific gene content of the bacterioplankton populations and provided new insights into their adaptations unique to the Tibetan lake.
C1 [Oh, Seungdae] Nanyang Technol Univ, Sch Civil & Environm Engn, Singapore, Singapore.
   [Oh, Seungdae; Liu, Wen-Tso] Univ Illinois, Dept Civil & Environm Engn, Urbana, IL USA.
   [Zhang, Rui] Xiamen Univ, State Key Lab Marine Environm Sci, Xiamen, Fuijan, Peoples R China.
   [Zhang, Rui] Xiamen Univ, Inst Marine Microbes & Ecospheres, Xiamen, Fuijan, Peoples R China.
   [Wu, Qinglong L.] Chinese Acad Sci, Nanjing Inst Geog & Limnol, State Key Lab Lake Sci & Environm, Nanjing, Jiangsu, Peoples R China.
RP Liu, WT (corresponding author), Univ Illinois, Dept Civil & Environm Engn, Urbana, IL USA.
EM wtliu@illinois.edu
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NR 45
TC 8
Z9 8
PD OCT
PY 2016
VL 8
IS 5
SI SI
BP 595
EP 604
DI 10.1111/1758-2229.12408
UT WOS:000395002300012
DA 2025-07-30
ER

PT J
AU Grote, J
   Thrash, JC
   Huggett, MJ
   Landry, ZC
   Carini, P
   Giovannoni, SJ
   Rappé, MS
AF Grote, Jana
   Thrash, J. Cameron
   Huggett, Megan J.
   Landry, Zachary C.
   Carini, Paul
   Giovannoni, Stephen J.
   Rappe, Michael S.
TI Streamlining and Core Genome Conservation among Highly Divergent Members
   of the SAR11 Clade
SO MBIO
DT Article
AB SAR11 is an ancient and diverse clade of heterotrophic bacteria that are abundant throughout the world's oceans, where they play a major role in the ocean carbon cycle. Correlations between the phylogenetic branching order and spatiotemporal patterns in cell distributions from planktonic ocean environments indicate that SAR11 has evolved into perhaps a dozen or more specialized ecotypes that span evolutionary distances equivalent to a bacterial order. We isolated and sequenced genomes from diverse SAR11 cultures that represent three major lineages and encompass the full breadth of the clade. The new data expand observations about genome evolution and gene content that previously had been restricted to the SAR11 Ia subclade, providing a much broader perspective on the clade's origins, evolution, and ecology. We found small genomes throughout the clade and a very high proportion of core genome genes (48 to 56%), indicating that small genome size is probably an ancestral characteristic. In their level of core genome conservation, the members of SAR11 are outliers, the most conserved free-living bacteria known. Shared features of the clade include low GC content, high gene synteny, a large hypervariable region bounded by rRNA genes, and low numbers of paralogs. Variation among the genomes included genes for phosphorus metabolism, glycolysis, and C1 metabolism, suggesting that adaptive specialization in nutrient resource utilization is important to niche partitioning and ecotype divergence within the clade. These data provide support for the conclusion that streamlining selection for efficient cell replication in the planktonic habitat has occurred throughout the evolution and diversification of this clade.
   IMPORTANCE The SAR11 clade is the most abundant group of marine microorganisms worldwide, making them key players in the global carbon cycle. Growing knowledge about their biochemistry and metabolism is leading to a more mechanistic understanding of organic carbon oxidation and sequestration in the oceans. The discovery of small genomes in SAR11 provided crucial support for the theory that streamlining selection can drive genome reduction in low-nutrient environments. Study of isolates in culture revealed atypical organic nutrient requirements that can be attributed to genome reduction, such as conditional auxotrophy for glycine and its precursors, a requirement for reduced sulfur compounds, and evidence for widespread cycling of C1 compounds in marine environments. However, understanding the genetic variation and distribution of such pathways and characteristics like streamlining throughout the group has required the isolation and genome sequencing of diverse SAR11 representatives, an analysis of which we provide here.
C1 [Grote, Jana; Huggett, Megan J.; Rappe, Michael S.] Univ Hawaii Manoa, Ctr Microbial Oceanog Res & Educ, SOEST, Honolulu, HI 96822 USA.
   [Grote, Jana; Huggett, Megan J.; Rappe, Michael S.] Univ Hawaii Manoa, Hawaii Inst Marine Biol, SOEST, Kaneohe, HI USA.
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RP Rappé, MS (corresponding author), Univ Hawaii Manoa, Ctr Microbial Oceanog Res & Educ, SOEST, Honolulu, HI 96822 USA.
EM steve.giovannoni@oregonstate.edu; rappe@hawaii.edu
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NR 90
TC 225
Z9 249
PD SEP-OCT
PY 2012
VL 3
IS 5
AR e00252-12
DI 10.1128/mBio.00252-12
UT WOS:000310585000011
DA 2025-07-30
ER

PT J
AU Temperton, B
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AF Temperton, Ben
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   Gilbert, Jack A.
TI Bias in assessments of marine microbial biodiversity in fosmid libraries
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SO ISME JOURNAL
DT Article
AB On the basis of 16S rRNA gene sequencing, the SAR11 clade of marine bacteria has an almost universal distribution, being detected as abundant sequences in all marine provinces. Yet, SAR11 sequences are rarely detected in fosmid libraries, suggesting that the widespread abundance may be an artefact of PCR cloning and that SAR11 has a relatively low abundance. Here the relative abundance of SAR11 is explored in both a fosmid library and a metagenomic sequence data set from the same biological community taken from fjord surface water from Bergen, Norway. Pyrosequenced data and 16S clone data confirmed an 11-15% relative abundance of SAR11 within the community. In contrast, not a single SAR11 fosmid was identified in a pooled shotgun sequence data set of 100 fosmid clones. This underrepresentation was evidenced by comparative abundances of SAR11 sequences assessed by taxonomic annotation and fragment recruitment. Analysis revealed a similar underrepresentation of low-GC Flavobacteriaceae. We speculate that a contributing factor towards the fosmid bias may be DNA fragmentation during preparation because of the low GC content of SAR11 sequences and other underrepresented taxa. This study suggests that, although fosmid libraries can be extremely useful, caution must be taken when directly inferring community composition from metagenomic fosmid libraries. The ISME Journal (2009) 3, 792-796; doi: 10.1038/ismej.2009.32; published online 2 April 2009
C1 [Temperton, Ben; Muehling, Martin; Joint, Ian; Gilbert, Jack A.] Plymouth Marine Lab, Plymouth PL1 3DH, Devon, England.
   [Field, Dawn; Oliver, Anna; Tiwari, Bela] CEH Oxford, NERC Ctr Ecol & Hydrol, Oxford, England.
RP Gilbert, JA (corresponding author), Plymouth Marine Lab, Prospect Pl, Plymouth PL1 3DH, Devon, England.
EM jagi@pml.ac.uk
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NR 19
TC 34
Z9 39
PD JUL
PY 2009
VL 3
IS 7
BP 792
EP 796
DI 10.1038/ismej.2009.32
UT WOS:000267818100004
DA 2025-07-30
ER

PT J
AU Peng, M
   Chen, XL
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AF Peng, Ming
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TI Structure-Function Analysis Indicates that an Active-Site Water Molecule
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB The osmolyte dimethylsulfoniopropionate (DMSP) is produced in petagram quantities in marine environments and has important roles in global sulfur and carbon cycling. Many marine microorganisms catabolize DMSP via DMSP lyases, generating the climate-active gas dimethyl sulfide (DMS). DMS oxidation products participate in forming cloud condensation nuclei and, thus, may influence weather and climate. SAR11 bacteria are the most abundant marine heterotrophic bacteria; many of them contain the DMSP lyase DddK, and their dddK transcripts are relatively abundant in seawater. In a recently described catalytic mechanism for DddK, Tyr64 is predicted to act as the catalytic base initiating the beta-elimination reaction of DMSP. Tyr64 was proposed to be deprotonated by coordination to the metal cofactor or its neighboring His96. To further probe this mechanism, we purified and characterized the DddK protein from Pelagibacter ubique strain HICC1062 and determined the crystal structures of wild-type DddK and its Y64A and Y122A mutants (bearing a change of Y to A at position 64 or 122, respectively), where the Y122A mutant is complexed with DMSP. The structural and mutational analyses largely support the catalytic role of Tyr64, but not the method of its deprotonation. Our data indicate that an active water molecule in the active site of DddK plays an important role in the deprotonation of Tyr64 and that this is far more likely than coordination to the metal or His96. Sequence alignment and phylogenetic analysis suggest that the proposed catalytic mechanism of DddK has universal significance. Our results provide new mechanistic insights into DddK and enrich our understanding of DMS generation by SAR11 bacteria.
   IMPORTANCE The climate-active gas dimethyl sulfide (DMS) plays an important role in global sulfur cycling and atmospheric chemistry. DMS is mainly produced through the bacterial cleavage of marine dimethylsulfoniopropionate (DMSP). When released into the atmosphere from the oceans, DMS can be photochemically oxidized into DMSO or sulfate aerosols, which form cloud condensation nuclei that influence the reflectivity of clouds and, thereby, global temperature. SAR11 bacteria are the most abundant marine heterotrophic bacteria, and many of them contain DMSP lyase DddK to cleave DMSP, generating DMS. In this study, based on structural analyses and mutational assays, we revealed the catalytic mechanism of DddK, which has universal significance in SAR11 bacteria. This study provides new insights into the catalytic mechanism of DddK, leading to a better understanding of how SAR11 bacteria generate DMS.
C1 [Peng, Ming; Chen, Xiu-Lan; Zhang, Dian; Wang, Xiu-Juan; Wang, Ning; Wang, Peng; Zhang, Yu-Zhong; Li, Chun-Yang] Shandong Univ, Marine Biotechnol Res Ctr, State Key Lab Microbial Technol, Qingdao, Shandong, Peoples R China.
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   [Chen, Xiu-Lan; Zhang, Yu-Zhong] Qingdao Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao, Shandong, Peoples R China.
   [Todd, Jonathan D.] Univ East Anglia, Sch Biol Sci, Norwich, Norfolk, England.
   [Li, Chun-Yang] Shandong Univ, Suzhou Inst, Suzhou, Peoples R China.
RP Li, CY (corresponding author), Shandong Univ, Marine Biotechnol Res Ctr, State Key Lab Microbial Technol, Qingdao, Shandong, Peoples R China.; Li, CY (corresponding author), Ocean Univ China, Coll Marine Life Sci, Qingdao, Shandong, Peoples R China.; Li, CY (corresponding author), Shandong Univ, Suzhou Inst, Suzhou, Peoples R China.
EM lingdongzhihui@126.com
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NR 37
TC 12
Z9 15
PD APR
PY 2019
VL 85
IS 8
AR e03127-18
DI 10.1128/AEM.03127-18
UT WOS:000463407200016
DA 2025-07-30
ER

PT J
AU Bolanos, LM
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AF Bolanos, Luis M.
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   Temperton, Ben
TI Influence of short and long term processes on SAR11 communities in open
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SO ISME COMMUNICATIONS
DT Article
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RP Bolanos, LM; Temperton, B (corresponding author), Univ Exeter, Sch Biosci, Exeter, England.
EM l.bolanos-avellaneda@exeter.ac.uk; b.temperton@exeter.ac.uk
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NR 75
TC 15
Z9 15
PD NOV 19
PY 2022
VL 2
IS 1
AR 116
DI 10.1038/s43705-022-00198-1
UT WOS:001105642100001
DA 2025-07-30
ER

PT J
AU Wang, XJ
   Zhang, N
   Teng, ZJ
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   Chen, XL
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AF Wang, Xiu-Juan
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   Fu, Hui-Hui
   Li, Chun-Yang
TI Structural and Mechanistic Insights Into Dimethylsulfoxide Formation
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SO FRONTIERS IN MICROBIOLOGY
DT Article
AB Dimethylsulfide (DMS) and dimethylsulfoxide (DMSO) are widespread in marine environment, and are important participants in the global sulfur cycle. Microbiol oxidation of DMS to DMSO represents a major sink of DMS in marine surface waters. The SAR11 clade and the marine Roseobacter clade (MRC) are the most abundant heterotrophic bacteria in the ocean surface seawater. It has been reported that trimethylamine monooxygenase (Tmm, EC 1.14.13.148) from both MRC and SAR11 bacteria likely oxidizes DMS to generate DMSO. However, the structural basis of DMS oxidation has not been explained. Here, we characterized a Tmm homolog from the SAR11 bacterium Pelagibacter sp. HTCC7211 (Tmm(7211)). Tmm(7211) exhibits DMS oxidation activity in vitro. We further solved the crystal structures of Tmm(7211) and Tmm(7211) soaked with DMS, and proposed the catalytic mechanism of Tmm(7211), which comprises a reductive half-reaction and an oxidative half-reaction. FAD and NADPH molecules are essential for the catalysis of Tmm(7211). In the reductive half-reaction, FAD is reduced by NADPH. In the oxidative half-reaction, the reduced FAD reacts with O-2 to form the C4a-(hydro)peroxyflavin. The binding of DMS may repel the nicotinamide ring of NADP(+), and make NADP(+) generate a conformational change, shutting off the substrate entrance and exposing the active C4a-(hydro)peroxyflavin to DMS to complete the oxidation of DMS. The proposed catalytic mechanism of Tmm(7211) may be widely adopted by MRC and SAR11 bacteria. This study provides important insight into the conversion of DMS into DMSO in marine bacteria, leading to a better understanding of the global sulfur cycle.
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RP Fu, HH; Li, CY (corresponding author), Ocean Univ China, Coll Marine Life Sci, Frontiers Sci Ctr Deep Ocean Multispheres & Earth, Qingdao, Peoples R China.; Li, CY (corresponding author), Pilot Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao, Peoples R China.
EM fuhuihui@ouc.edu.cn; icy@ouc.edu.cn
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NR 52
TC 5
Z9 6
PD SEP 24
PY 2021
VL 12
AR 735793
DI 10.3389/fmicb.2021.735793
UT WOS:000705908400001
DA 2025-07-30
ER

PT J
AU Alonso, C
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AF Alonso, Cecilia
   Pernthaler, Jakob
TI Roseobacter and SAR11 dominate microbial glucose uptake in
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Bacterial assemblages in coastal pelagic environments are exposed to pronounced temporal and spatial fluctuations in the availability of monomeric substrates. Little is known about the response of particular bacterial groups to such variability. We studied glucose incorporation at various concentrations (0.1-100 nM) by bacteria related to Roseobacter, SAR11, Gammaproteobacteria and Cytophaga-Flavobacteria in coastal North Sea waters in late winter and during a spring phytoplankton bloom dominated by Phaeocystis sp. (March and May 2004 respectively). Both the fraction of glucose-assimilating bacterial cells and the rate of substrate incorporation per active cell were higher in May. The respective contributions of the studied groups to all glucose-assimilating Bacteria were related to substrate concentration. The majority of glucose-incorporating bacterial cells at the lower concentrations were members of the Roseobacter and SAR11 clades. At both time-points the two groups formed approximately equal fractions of all glucose-incorporating bacteria. This was due to a small population of highly active Roseobacter cells and high abundances of SAR11 bacteria with low proportions of glucose-incorporating cells. By contrast, the proportion of active cells from the Cytophaga-Flavobacteria lineage substantially increased at higher levels of available substrate. The determination of concentration-dependent substrate incorporation patterns may help to better understand the different ecophysiological niches of bacterioplankton populations.
C1 Univ Zurich, Limnol Stn Kilchberg, Zurich, Switzerland.
RP Pernthaler, J (corresponding author), Univ Zurich, Limnol Stn Kilchberg, Zurich, Switzerland.
EM pernthaler@limnol.unizh.ch
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NR 55
TC 131
Z9 139
PD NOV
PY 2006
VL 8
IS 11
BP 2022
EP 2030
DI 10.1111/j.1462-2920.2006.01082.x
UT WOS:000240919300014
DA 2025-07-30
ER

PT J
AU Giebel, HA
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   Simon, M
AF Giebel, Helge-Ansgar
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   Simon, Meinhard
TI Distribution of Roseobacter RCA and SAR11 lineages and distinct
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
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C1 [Giebel, Helge-Ansgar; Brinkhoff, Thorsten; Zwisler, Walter; Selje, Natascha; Simon, Meinhard] Carl von Ossietzky Univ Oldenburg, Inst Chem & Biol Marine Environm, D-26111 Oldenburg, Germany.
RP Simon, M (corresponding author), Carl von Ossietzky Univ Oldenburg, Inst Chem & Biol Marine Environm, D-26111 Oldenburg, Germany.
EM m.simon@icbm.de
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TC 74
Z9 81
PD AUG
PY 2009
VL 11
IS 8
BP 2164
EP 2178
DI 10.1111/j.1462-2920.2009.01942.x
UT WOS:000268655000020
DA 2025-07-30
ER

PT J
AU Eiler, A
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AF Eiler, Alexander
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TI Dynamics of the SAR11 bacterioplankton lineage in relation to
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
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C1 [Eiler, Alexander; Hayakawa, Darin H.; Rappe, Michael S.] Univ Hawaii, Hawaii Inst Marine Biol, SOEST, Kaneohe, HI 96744 USA.
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RP Rappé, MS (corresponding author), Univ Hawaii, Hawaii Inst Marine Biol, SOEST, Kaneohe, HI 96744 USA.
EM rappe@hawaii.edu
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TC 76
Z9 82
PD SEP
PY 2009
VL 11
IS 9
BP 2291
EP 2300
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UT WOS:000269539700011
DA 2025-07-30
ER

PT J
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AF Lami, Raphael
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB P>Proteorhodopsin (PR)-containing bacteria are hypothesized to use both light and organic compounds as energy sources. Recent studies have found that PR is common in marine microorganisms, but the impact of light on the growth of PR-containing organisms and PR transcription in the environment remains unclear. We examined the diversity of PR genes and transcripts by PCR amplification and sequencing in Delaware coastal waters. Clone libraries of PR DNA and cDNA (from mRNA) revealed large differences between bacterial groups in expression of PR genes. We then evaluated by quantitative PCR the impact of light on growth and PR expression in PR-containing SAR11 bacteria (SAR11-PR) and a population of Flavobacteria (Flavobacteria-PR). This experiment was conducted in 30 l microcosms exposed to continuous light, continuous dark, and 12 h-12 h dark-light cycles for 5 days. We found a strong upregulation of PR expression by light in Flavobacteria-PR and SAR11-PR. The abundance of PR transcripts per PR cell was enhanced up to 120-fold under continuous light and up to 20-fold under dark-light cycles while continuous darkness led to very low levels of PR mRNA. This upregulation of PR expression was correlated with the abundance of PR genes, indicating net growth of SAR11-PR cells and Flavobacteria-PR under dark-light cycles. SAR11-PR and Flavobacteria-PR abundance decreased under continuous light despite upregulation of PR expression, and continuous darkness led to low abundances of both populations. Collectively, these data suggest that light affects growth of PR-containing bacteria and regulation of PR mRNA synthesis in natural communities.
C1 [Lami, Raphael; Cottrell, Matthew T.; Campbell, Barbara J.; Kirchman, David L.] Univ Delaware, Sch Marine Sci & Policy, Lewes, DE 19958 USA.
RP Kirchman, DL (corresponding author), Univ Delaware, Sch Marine Sci & Policy, 700 Pilottown Rd, Lewes, DE 19958 USA.
EM kirchman@udel.edu
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NR 32
TC 55
Z9 57
PD DEC
PY 2009
VL 11
IS 12
BP 3201
EP 3209
DI 10.1111/j.1462-2920.2009.02028.x
UT WOS:000273182500023
DA 2025-07-30
ER

PT J
AU Cermak, N
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   Manalis, SR
   Polz, MF
AF Cermak, Nathan
   Becker, Jamie W.
   Knudsen, Scott M.
   Chisholm, Sallie W.
   Manalis, Scott R.
   Polz, Martin F.
TI Direct single-cell biomass estimates for marine bacteria via Archimedes'
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SO ISME JOURNAL
DT Article
AB Microbes are an essential component of marine food webs and biogeochemical cycles, and therefore precise estimates of their biomass are of significant value. Here, we measured single-cell biomass distributions of isolates from several numerically abundant marine bacterial groups, including Pelagibacter (SAR11), Prochlorococcus and Vibrio using a microfluidic mass sensor known as a suspended microchannel resonator (SMR). We show that the SMR can provide biomass (dry mass) measurements for cells spanning more than two orders of magnitude and that these estimates are consistent with other independent measures. We find that Pelagibacterales strain HTCC1062 has a median biomass of 11.9 +/- 0.7 fg per cell, which is five- to twelve-fold smaller than the median Prochlorococcus cell's biomass (depending upon strain) and nearly 100-fold lower than that of rapidly growing V. splendidus strain 13B01. Knowing the biomass contributions from various taxonomic groups will provide more precise estimates of total marine biomass, aiding models of nutrient flux in the ocean.
C1 [Cermak, Nathan] MIT, Program Computat & Syst Biol, 77 Massachusetts Ave, Cambridge, MA 02139 USA.
   [Becker, Jamie W.; Chisholm, Sallie W.; Polz, Martin F.] MIT, Dept Civil & Environm Engn, 77 Massachusetts Ave,48-417, Cambridge, MA 02140 USA.
   [Knudsen, Scott M.; Manalis, Scott R.] MIT, Dept Biol Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA.
   [Chisholm, Sallie W.] MIT, Dept Biol, Cambridge, MA USA.
   [Manalis, Scott R.] MIT, Dept Mech Engn, Cambridge, MA 02139 USA.
RP Polz, MF (corresponding author), MIT, Dept Civil & Environm Engn, 77 Massachusetts Ave,48-417, Cambridge, MA 02140 USA.
EM mpolz@mit.edu
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TC 48
Z9 54
PD MAR
PY 2017
VL 11
IS 3
BP 825
EP 828
DI 10.1038/ismej.2016.161
UT WOS:000394542000022
DA 2025-07-30
ER

PT J
AU Mendoza-Cano, F
   Encinas-García, T
   Muhlia-Almazán, A
   Porchas-Cornejo, M
   de la Re-Vega, E
   Sánchez-Paza, A
AF Mendoza-Cano, F.
   Encinas-Garcia, T.
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TI Development and validation of a real-time PCR assay protocol for the
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SO MARINE ENVIRONMENTAL RESEARCH
DT Article
AB Earth is inhabited by numerous adaptations of cellular forms shaped by the persistent scrutiny of natural selection. Thus, as natural selection has fixed beneficial adaptations of functional traits, cellular life has conquered almost all environmental niches on our planet. However, cellular life succumbs in number and genetic diversity to viruses. Among all viruses, phages are highly prevalent in diverse environments, and due to their vast genetic diversity and abundance, their relevant role as significant players in several ecological processes is now fully recognized. Pelagiphages, bacteriophages infecting bacteria of the SAR11 clade, are the most abundant viruses in the oceans. However, the ecological contribution of pelagiphages on populations of Pelagibacterales remains largely underestimated. An essential aspect of estimating the impact of bacteriophages is their absolute and precise quantification, which provides relevant information about the host-virus interactions and the structure of viral assemblages. Consequently, due to its abundance and claimed influence in the biogeochemical cycling of elements, the accurate quantification of pelagiphages results in an essential task. This study describes the development and validation of a sensitive, specific, accurate and reproducible qPCR platform targeting pelagiphages. Moreover, this method allowed the detection and quantification of pelagiphages in the Gulf of California for the first time.
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   [Porchas-Cornejo, M.] Ctr Invest Biol Noroeste, SC Km 2 35 Carretera Tinajas S-N, Guaymas 85460, Sonora, Mexico.
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RP Sánchez-Paza, A (corresponding author), Ctr Invest Biol Noroeste SC, Lab Virol, Hermosa 101, Hermosillo 83106, Sonora, Mexico.
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NR 78
TC 2
Z9 2
PD OCT
PY 2023
VL 191
AR 106168
DI 10.1016/j.marenvres.2023.106168
EA SEP 2023
UT WOS:001079724200001
DA 2025-07-30
ER

PT J
AU Reisch, CR
   Moran, MA
   Whitman, WB
AF Reisch, Chris R.
   Moran, Mary Ann
   Whitman, William B.
TI Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from
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SO JOURNAL OF BACTERIOLOGY
DT Article
AB The ubiquitous algal metabolite dimethylsulfoniopropionate ( DMSP) is a major source of carbon and reduced sulfur for marine bacteria. Recently, the enzyme responsible for the demethylation of DMSP, designated DmdA, was identified, and homologs were found to be common in marine bacterioplankton cells. The recombinant DmdA proteins from the cultured marine bacteria Pelagibacter ubique HTCC1062 and Silicibacter pomeroyi DSS-3 were purified with a three-step procedure using anion-exchange, hydrophobic interaction, and hydroxyapatite chromatographies. The P. ubique enzyme possessed an M-r on sodium dodecyl sulfate-polyacrylamide gel electrophoresis of 38,500. Under nondenaturing conditions, the M-r was 68,000, suggesting that the enzyme was likely to be a dimer. The purified enzyme exhibited strict substrate specificity for DMSP, as DmdA from both S. pomeroyi and P. ubique possessed no detectable demethylase activity with glycine betaine, dimethyl glycine, methylmercaptopropionate, methionine, or dimethylsulfonioacetate. Less than 1% activity was found with dimethylsulfoniobutanoate and dimethylsulfoniopentanoate. The apparent K(m)s for DMSP were 13.2 +/- 2.0 and 5.4 +/- 2.3 mM for the P. ubique and S. pomeroyi enzymes, respectively. In cell extracts of S. pomeroyi DSS-3, the apparent K-m for DMSP was 8.6 +/- 1.2 mM, similar to that of purified recombinant DmdA. The intracellular concentration of DMSP in chemostat-grown S. pomeroyi DSS-3 was 70 mM. These results suggest that marine bacterioplankton may actively accumulate DMSP to osmotically significant concentrations that favor near-maximal rates of DMSP demethylation activity.
C1 [Reisch, Chris R.; Whitman, William B.] Univ Georgia, Dept Microbiol, Athens, GA 30602 USA.
   [Moran, Mary Ann] Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
RP Whitman, WB (corresponding author), Univ Georgia, Dept Microbiol, Athens, GA 30602 USA.
EM whitman@uga.edu
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NR 46
TC 98
Z9 111
PD DEC
PY 2008
VL 190
IS 24
BP 8018
EP 8024
DI 10.1128/JB.00770-08
UT WOS:000261217900020
DA 2025-07-30
ER

PT J
AU Georgiades, K
   Madoui, MA
   Le, P
   Robert, C
   Raoult, D
AF Georgiades, Kalliopi
   Madoui, Mohammed-Amine
   Le, Phuong
   Robert, Catherine
   Raoult, Didier
TI Phylogenomic Analysis of Odyssella thessalonicensis Fortifies the
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SO PLOS ONE
DT Article
AB Background: The evolution of the Alphaproteobacteria and origin of the mitochondria are topics of considerable debate. Most studies have placed the mitochondria ancestor within the Rickettsiales order. Ten years ago, the bacterium Odyssella thessalonicensis was isolated from Acanthamoeba spp., and the 16S rDNA phylogeny placed it within the Rickettsiales. Recently, the whole genome of O. thessalonicensis has been sequenced, and 16S rDNA phylogeny and more robust and accurate phylogenomic analyses have been performed with 65 highly conserved proteins.
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C1 [Georgiades, Kalliopi; Madoui, Mohammed-Amine; Le, Phuong; Robert, Catherine; Raoult, Didier] Univ Mediterranee, Fac Med, URMITE, CNRS IRD UMR 6236, Marseille, France.
   [Le, Phuong] Univ Aix Marseille 1, LATP UMR CNRS 6632, FR 3098, IFR48, Marseille, France.
RP Georgiades, K (corresponding author), Univ Mediterranee, Fac Med, URMITE, CNRS IRD UMR 6236, Marseille, France.
EM didier.raoult@gmail.com
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NR 35
TC 45
Z9 48
PD SEP 21
PY 2011
VL 6
IS 9
AR e24857
DI 10.1371/journal.pone.0024857
UT WOS:000295262100022
DA 2025-07-30
ER

PT J
AU Jing, XY
   Gong, YH
   Xu, T
   Davison, PA
   MacGregor-Chatwin, C
   Hunter, CN
   Xu, L
   Meng, Y
   Ji, YT
   Ma, B
   Xu, J
   Huang, WE
AF Jing, Xiaoyan
   Gong, Yanhai
   Xu, Teng
   Davison, Paul A.
   MacGregor-Chatwin, Craig
   Hunter, C. Neil
   Xu, La
   Meng, Yu
   Ji, Yuetong
   Ma, Bo
   Xu, Jian
   Huang, Wei E.
TI Revealing CO2-Fixing 2-Fixing SAR11 Bacteria in the Ocean by Raman-
   Based Single-Cell Metabolic Profiling and Genomics
SO BIODESIGN RESEARCH
DT Article
AB The majority of marine microbes remain uncultured, which hinders the identification fi cation and mining of CO2-fixing 2- fi xing genes, pathways, and chassis from the oceans. Here, we investigated CO2-fixing 2- fi xing microbes in seawater from the euphotic zone of the Yellow Sea of China by detecting and tracking their 13 C-bicarbonate (13C-HCO3 13 C-HCO 3- ) intake via single-cell Raman spectra (SCRS) analysis. The target cells were then isolated by Raman-activated Gravity-driven Encapsulation (RAGE), and their genomes were amplified fi ed and sequenced at one-cell resolution. The single-cell metabolism, phenotype and genome are consistent. We identified fi ed a not- yet-cultured Pelagibacter spp., which actively assimilates 13 C-HCO 3- , and also possesses most of the genes encoding enzymes of the Calvin-Benson cycle for CO2 2 fi xation, a complete gene set for a rhodopsin-based light-harvesting system, and the full genes necessary for carotenoid synthesis. The four proteorhodopsin (PR) genes identified fi ed in the Pelagibacter spp. were confirmed fi rmed by heterologous expression in E. coli. . These results suggest that hitherto uncultured Pelagibacter spp. uses light-powered metabolism to contribute to global carbon cycling.
C1 [Jing, Xiaoyan; Gong, Yanhai; Xu, Teng; Meng, Yu; Ma, Bo; Xu, Jian] Chinese Acad Sci, Single Cell Ctr, CAS Key Lab Biofuels, Shandong Key Lab Energy Genet,Qingdao Inst Bioener, Qingdao, Shandong, Peoples R China.
   [Jing, Xiaoyan; Gong, Yanhai; Xu, Teng; Meng, Yu; Ji, Yuetong; Ma, Bo; Xu, Jian] Chinese Acad Sci, Qingdao Inst Bioenergy & Bioproc Technol, Shandong Inst Energy Res, Qingdao, Shandong, Peoples R China.
   [Jing, Xiaoyan; Xu, Jian] Qingdao Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao, Shandong, Peoples R China.
   [Jing, Xiaoyan; Gong, Yanhai; Xu, Teng; Meng, Yu; Ma, Bo; Xu, Jian] Univ Chinese Acad Sci, Beijing, Peoples R China.
   [Davison, Paul A.; MacGregor-Chatwin, Craig; Hunter, C. Neil] Univ Sheffield, Plants Photosynth & Soil Sch Biosci, Sheffield S10 2TN, England.
   [Xu, La] Marine Biol Inst Shandong Prov, Dis & Fishery Drugs Res Ctr, Qingdao, Shandong, Peoples R China.
   [Ji, Yuetong] Single Cell Biotechnol Ltd, Qingdao, Shandong, Peoples R China.
   [Huang, Wei E.] Univ Oxford, Dept Engn Sci, Parks Rd, Oxford OX1 3PJ, England.
RP Xu, J (corresponding author), Chinese Acad Sci, Single Cell Ctr, CAS Key Lab Biofuels, Shandong Key Lab Energy Genet,Qingdao Inst Bioener, Qingdao, Shandong, Peoples R China.; Xu, J (corresponding author), Qingdao Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao, Shandong, Peoples R China.; Xu, J (corresponding author), Univ Chinese Acad Sci, Beijing, Peoples R China.; Huang, WE (corresponding author), Univ Oxford, Dept Engn Sci, Parks Rd, Oxford OX1 3PJ, England.
EM xujian@qibebt.ac.cn; wei.huang@eng.ox.ac.uk
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NR 83
TC 13
Z9 16
PD OCT 21
PY 2022
VL 2022
AR 9782712
DI 10.34133/2022/9782712
UT WOS:001281920700001
DA 2025-07-30
ER

PT J
AU Meyer, MM
   Ames, TD
   Smith, DP
   Weinberg, Z
   Schwalbach, MS
   Giovannoni, SJ
   Breaker, RR
AF Meyer, Michelle M.
   Ames, Tyler D.
   Smith, Daniel P.
   Weinberg, Zasha
   Schwalbach, Michael S.
   Giovannoni, Stephen J.
   Breaker, Ronald R.
TI Identification of candidate structured RNAs in the marine organism
   'Candidatus Pelagibacter ubique'
SO BMC GENOMICS
DT Article
AB Background: Metagenomic sequence data are proving to be a vast resource for the discovery of biological components. Yet analysis of this data to identify functional RNAs lags behind efforts to characterize protein diversity. The genome of 'Candidatus Pelagibacter ubique' HTCC 1062 is the closest match for approximately 20% of marine metagenomic sequence reads. It is also small, contains little non-coding DNA, and has strikingly low GC content.
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C1 [Meyer, Michelle M.; Ames, Tyler D.; Breaker, Ronald R.] Yale Univ, Dept Mol Cellular & Dev Biol, New Haven, CT 06520 USA.
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   [Weinberg, Zasha; Breaker, Ronald R.] Yale Univ, Howard Hughes Med Inst, New Haven, CT 06520 USA.
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RP Breaker, RR (corresponding author), Yale Univ, Dept Mol Cellular & Dev Biol, Box 208103, New Haven, CT 06520 USA.
EM michelle.meyer@yale.edu; tyler.ames@yale.edu; dansmith@orst.edu;
   zasha.weinberg@yale.edu; schwalbm@onid.orst.edu;
   steve.giovannoni@oregonstate.edu; ronald.breaker@yale.edu
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NR 98
TC 56
Z9 74
PD JUN 16
PY 2009
VL 10
AR 268
DI 10.1186/1471-2164-10-268
UT WOS:000267738200001
DA 2025-07-30
ER

PT J
AU Martocello, DE
   Morel, FMM
   McRose, DL
AF Martocello, Donald E., III
   Morel, Francois M. M.
   McRose, Darcy L.
TI H-Aquil: a chemically defined cell culture medium for trace metal
   studies in Vibrios and other marine heterotrophic bacteria
SO BIOMETALS
DT Article
AB A variety of trace metals, including prominently iron (Fe) are necessary for marine microorganisms. Chemically defined medium recipes have been used for several decades to study phytoplankton, but similar methods have not been adopted as widely in studies of marine heterotrophic bacteria. Medium recipes for these organisms frequently include tryptone, casamino acids, as well as yeast and animal extracts. These components introduce unknown concentrations of trace elements and organic compounds, complicating metal speciation. Minimal medium recipes utilizing known carbon and nitrogen sources do exist but often have high background trace metal concentrations. Here we present H-Aquil, a version of the phytoplankton medium Aquil adapted for marine heterotrophic bacteria. This medium consists of artificial seawater supplemented with a carbon source, phosphate, amino acids, and vitamins. As in Aquil, trace metals are controlled using the synthetic chelator EDTA. We also address concerns of EDTA toxicity, showing that concentrations up to 100 mu M EDTA do not lead to growth defects in the copiotrophic bacterium Vibrio harveyi or the oligotrophic bacterium Candidatus Pelagibacter ubique HTCC1062, a member of the SAR11 clade. H-Aquil is used successfully to culture species of Vibrio, Phaeobacter, and Silicibacter, as well as several environmental isolates. We report a substantial decrease in growth rate between cultures grown with or without added Fe, making the medium suitable for conducting Fe-limitation studies in a variety of marine heterotrophic bacteria.
C1 [Martocello, Donald E., III; Morel, Francois M. M.; McRose, Darcy L.] Princeton Univ, Dept Geosci, Princeton, NJ 08544 USA.
   [Martocello, Donald E., III] Woods Hole Oceanog Inst, Dept Marine Chem & Geochem, Woods Hole, MA 02543 USA.
   [Martocello, Donald E., III] MIT, Dept Earth Atmospher & Planetary Sci, Cambridge, MA 02139 USA.
   [McRose, Darcy L.] CALTECH, Div Geol & Planetary Sci, 1200 E Calif Blvd, Pasadena, CA 91125 USA.
   [McRose, Darcy L.] CALTECH, Div Biol & Biol Engn, 1200 E Calif Blvd, Pasadena, CA 91125 USA.
RP McRose, DL (corresponding author), CALTECH, Div Geol & Planetary Sci, 1200 E Calif Blvd, Pasadena, CA 91125 USA.; McRose, DL (corresponding author), CALTECH, Div Biol & Biol Engn, 1200 E Calif Blvd, Pasadena, CA 91125 USA.
EM dmcrose@caltech.edu
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NR 41
TC 1
Z9 2
PD DEC
PY 2019
VL 32
IS 6
BP 819
EP 828
DI 10.1007/s10534-019-00215-2
UT WOS:000504206300001
DA 2025-07-30
ER

PT J
AU Beman, JM
   Steele, JA
   Fuhrman, JA
AF Beman, J. Michael
   Steele, Joshua A.
   Fuhrman, Jed A.
TI Co-occurrence patterns for abundant marine archaeal and bacterial
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SO ISME JOURNAL
DT Article
AB Microorganisms remineralize and respire half of marine primary production, yet the niches occupied by specific microbial groups, and how these different groups may interact, are poorly understood. In this study, we identify co-occurrence patterns for marine Archaea and specific bacterial groups in the chlorophyll maximum of the Southern California Bight. Quantitative PCR time series of marine group 1 (MG1) Crenarchaeota 16S rRNA genes varied substantially over time but were well-correlated (r(2)=0.94, P<0.001) with ammonia monooxygenase subunit A (amoA) genes, and were more weakly related to 16S rRNA genes for all Archaea (r(2)=0.39), indicating that other archaeal groups (for example, Euryarchaeota) were numerically important. These data sets were compared with variability in bacterial community composition based on automated ribosomal intergenic spacer analysis (ARISA). We found that archaeal amoA gene copies and a SAR11 (or Pelagibacter) group Ib operational taxonomic unit (OTU) displayed strong co-variation through time (r(2)=0.55, P<0.05), and archaeal amoA and MG1 16S rRNA genes also co-occurred with two SAR86 and two Bacteroidetes OTUs. The relative abundance of these groups increased and decreased in synchrony over the course of the time series, and peaked during periods of seasonal transition. By using a combination of quantitative and relative abundance estimates, our findings show that abundant microbial OTUs-including the marine Crenarchaeota, SAR11, SAR86 and the Bacteroidetes-co-occur non-randomly; they consequently have important implications for our understanding of microbial community ecology in the sea. The ISME Journal (2011) 5, 1077-1085; doi:10.1038/ismej.2010.204; published online 13 January 2011 Subject Category: microbial population and community ecology
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   Univ So Calif, Wrigley Inst Environm Studies, Los Angeles, CA USA.
RP Beman, JM (corresponding author), Univ Calif, Sch Nat Sci, Dept Biol Sci, 5200 N Lake Rd, Merced, CA 95343 USA.
EM jmbeman@gmail.com
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PD JUL
PY 2011
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BP 1077
EP 1085
DI 10.1038/ismej.2010.204
UT WOS:000295688500001
DA 2025-07-30
ER

PT J
AU Schnicker, NJ
   De Silva, SM
   Todd, JD
   Dey, M
AF Schnicker, Nicholas J.
   De Silva, Saumya M.
   Todd, Jonathan D.
   Dey, Mishtu
TI Structural and Biochemical Insights into Dimethylsulfoniopropionate
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SO BIOCHEMISTRY
DT Article
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C1 [Schnicker, Nicholas J.; De Silva, Saumya M.; Dey, Mishtu] Univ Iowa, Dept Chem, Iowa City, IA 52242 USA.
   [Todd, Jonathan D.] Univ East Anglia, Sch Biol Sci, Norwich Res Pk, Norwich NR4 7TJ, Norfolk, England.
RP Dey, M (corresponding author), Univ Iowa, Dept Chem, Iowa City, IA 52242 USA.
EM mishtu-dey@uiowa.edu
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TC 23
Z9 30
PD JUN 13
PY 2017
VL 56
IS 23
BP 2873
EP 2885
DI 10.1021/acs.biochem.7b00099
UT WOS:000403529900003
DA 2025-07-30
ER

PT J
AU Cabello-Yeves, PJ
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   Rosselli, R
   Coutinho, FH
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   Blinov, VV
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AF Cabello-Yeves, Pedro J.
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   Rosselli, Riccardo
   Coutinho, Felipe H.
   Zakharenko, Alexandra S.
   Blinov, Vadim V.
   Rodriguez-Valera, Francisco
TI Genomes of Novel Microbial Lineages Assembled from the Sub-Ice Waters of
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB We present a metagenomic study of Lake Baikal (East Siberia). Two samples obtained from the water column under the ice cover (5 and 20 m deep) in March 2016 have been deep sequenced and the reads assembled to generate metagenome-assembled genomes (MAGs) that are representative of the microbes living in this special environment. Compared with freshwater bodies studied around the world, Lake Baikal had an unusually high fraction of Verrucomicrobia. Other groups, such as Actinobacteria and Proteobacteria, were in proportions similar to those found in other lakes. The genomes (and probably cells) tended to be small, presumably reflecting the extremely oligotrophic and cold prevalent conditions. Baikal microbes are novel lineages recruiting very little from other water bodies and are distantly related to other freshwater microbes. Despite their novelty, they showed the closest relationship to genomes discovered by similar approaches from other freshwater lakes and reservoirs. Some of them were particularly similar to MAGs from the Baltic Sea, which, although it is brackish, connected to the ocean, and much more eutrophic, has similar climatological conditions. Many of the microbes contained rhodopsin genes, indicating that, in spite of the decreased light penetration allowed by the thick ice/snow cover, photoheterotrophy could be widespread in the water column, either because enough light penetrates or because the microbes are already adapted to the summer ice-less conditions. We have found a freshwater SAR11 subtype I/II representative showing striking synteny with Pelagibacter ubique strains, as well as a phage infecting the widespread freshwater bacterium Polynucleobacter.
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C1 [Cabello-Yeves, Pedro J.; Rosselli, Riccardo; Coutinho, Felipe H.; Rodriguez-Valera, Francisco] Univ Miguel Hernandez, Evolutionary Genom Grp, Dept Prod Vegetal & Microbiol, Alicante, Spain.
   [Zakharenko, Alexandra S.; Blinov, Vadim V.] Russian Acad Sci, Limnol Inst, Siberian Branch, Irkutsk, Russia.
RP Rodriguez-Valera, F (corresponding author), Univ Miguel Hernandez, Evolutionary Genom Grp, Dept Prod Vegetal & Microbiol, Alicante, Spain.
EM frvalera@umh.es
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NR 100
TC 76
Z9 85
PD JAN
PY 2018
VL 84
IS 1
AR e02132-17
DI 10.1128/AEM.02132-17
UT WOS:000418039700030
DA 2025-07-30
ER

PT J
AU Hill, PG
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AF Hill, Polly G.
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   Purdie, Duncan A.
TI Differential responses of Prochlorococcus and SAR11-dominated
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SO FEMS MICROBIOLOGY LETTERS
DT Article
AB The metabolic responses of indigenous dominant bacterioplankton populations to additions of dust were examined in the tropical northeast Atlantic. Subsurface seawater samples were treated with dust, added directly or indirectly as a 'leachate' after its rapid dissolution in deionized water. Samples were incubated at ambient temperature and light for up to 24 h and microbial metabolic responses were assessed by 35S-methionine (35S-Met) uptake. Prochlorococcus and low nucleic acid (LNA) cells were sorted by flow cytometry to determine their group-specific responses. Sorted cells were also phylogenetically affiliated using FISH. The high-light-adapted ecotype II dominated the Prochlorococcus group and 73 +/- 14% of LNA prokaryotes belonged to the SAR11 clade of Alphaproteobacteria. Both Prochlorococcus and LNA cells were metabolically impaired by the addition of dust (40 +/- 28% and 37 +/- 22% decrease in 35S-Met uptake compared with controls, respectively). However, LNA bacterioplankton showed minor positive responses to dust leachate additions (7 +/- 4% increase in 35S-Met uptake), while the metabolic activity of Prochlorococcus cells decreased in the presence of dust leachate by 16 +/- 11%. Thus, dust dissolution in situ appears to be more deleterious to Prochlorococcus than SAR11-dominated LNA bacterioplankton and hence could initiate a compositional shift in the indigenous bacterioplankton.
C1 [Hill, Polly G.; Zubkov, Mikhail V.; Purdie, Duncan A.] Univ Southampton, Natl Oceanog Ctr, Southampton SO14 3ZH, Hants, England.
RP Hill, PG (corresponding author), Univ Southampton, Natl Oceanog Ctr, European Way, Southampton SO14 3ZH, Hants, England.
EM polly.hill@noc.soton.ac.uk
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NR 46
TC 34
Z9 37
PD MAY
PY 2010
VL 306
IS 1
BP 82
EP 89
DI 10.1111/j.1574-6968.2010.01940.x
UT WOS:000276246200012
DA 2025-07-30
ER

PT J
AU Sharma, AK
   Becker, JW
   Ottesen, EA
   Bryant, JA
   Duhamel, S
   Karl, DM
   Cordero, OX
   Repeta, DJ
   DeLong, EF
AF Sharma, Adrian K.
   Becker, Jamie W.
   Ottesen, Elizabeth A.
   Bryant, Jessica A.
   Duhamel, Solange
   Karl, David M.
   Cordero, Otto X.
   Repeta, Daniel J.
   DeLong, Edward F.
TI Distinct dissolved organic matter sources induce rapid transcriptional
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB A considerable fraction of the Earth's organic carbon exists in dissolved form in seawater. To investigate the roles of planktonic marine microbes in the biogeochemical cycling of this dissolved organic matter (DOM), we performed controlled seawater incubation experiments and followed the responses of an oligotrophic surface water microbial assemblage to perturbations with DOM derived from an axenic culture of Prochlorococcus, or high-molecular weight DOM concentrated from nearby surface waters. The rapid transcriptional responses of both Prochlorococcus and Pelagibacter populations suggested the utilization of organic nitrogen compounds common to both DOM treatments. Along with these responses, both populations demonstrated decreases in gene transcripts associated with nitrogen stress, including those involved in ammonium acquisition. In contrast, responses from low abundance organisms of the NOR5/OM60 gammaproteobacteria were observed later in the experiment, and included elevated levels of gene transcripts associated with polysaccharide uptake and oxidation. In total, these results suggest that numerically dominant oligotrophic microbes rapidly acquire nitrogen from commonly available organic sources, and also point to an important role for carbohydrates found within the DOM pool for sustaining the less abundant microorganisms in these oligotrophic systems.
C1 [Sharma, Adrian K.; Ottesen, Elizabeth A.; Bryant, Jessica A.; Cordero, Otto X.; DeLong, Edward F.] MIT, Dept Civil & Environm Engn, Cambridge, MA 02139 USA.
   [Sharma, Adrian K.; Ottesen, Elizabeth A.; Bryant, Jessica A.; Cordero, Otto X.; DeLong, Edward F.] MIT, Dept Biol Engn, Cambridge, MA 02139 USA.
   [Becker, Jamie W.; Duhamel, Solange; Repeta, Daniel J.] Woods Hole Oceanog Inst, Dept Marine Chem & Geochem, Woods Hole, MA 02543 USA.
   [Ottesen, Elizabeth A.] Univ Georgia, Dept Microbiol, Athens, GA 30602 USA.
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   [Karl, David M.] Univ Hawaii, SOEST, Dept Oceanog, Honolulu, HI 96822 USA.
   [Sharma, Adrian K.; Becker, Jamie W.; Ottesen, Elizabeth A.; Bryant, Jessica A.; Duhamel, Solange; Karl, David M.; Repeta, Daniel J.; DeLong, Edward F.] C MORE, Honolulu, HI 96822 USA.
RP DeLong, EF (corresponding author), MIT, Dept Civil & Environm Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA.
EM delong@mit.edu
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NR 62
TC 41
Z9 45
PD SEP
PY 2014
VL 16
IS 9
SI SI
BP 2815
EP 2830
DI 10.1111/1462-2920.12254
UT WOS:000341579700016
DA 2025-07-30
ER

PT J
AU Beier, S
   Gálvez, MJ
   Molina, V
   Sarthou, G
   Quéroué, F
   Blain, S
   Obernosterer, I
AF Beier, Sara
   Galvez, Maria J.
   Molina, Veronica
   Sarthou, Geraldine
   Queroue, Fabien
   Blain, Stephane
   Obernosterer, Ingrid
TI The transcriptional regulation of the glyoxylate cycle in SAR11 in
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SO ENVIRONMENTAL MICROBIOLOGY REPORTS
DT Article
AB The tricarboxylic acid (TCA) cycle is a central metabolic pathway that is present in all aerobic organisms and initiates the respiration of organic material. The glyoxylate cycle is a variation of the TCA cycle, where organic material is recycled for subsequent assimilation into cell material instead of being released as carbon dioxide. Despite the importance for the fate of organic matter, the environmental factors that induce the glyoxylate cycle in microbial communities remain poorly understood. In this study, we assessed the expression of isocitrate lyase, the enzyme that induces the switch to the glyoxylate cycle, of the ubiquitous SAR11 clade in response to natural iron fertilization in the Southern Ocean. The cell-specific transcriptional regulation of the glyoxylate cycle, as determined by the ratio between copy numbers of isocitrate lyase gene transcripts and isocitrate genes, was consistently lower in iron fertilized than in high-nutrient, low chlorophyll waters (by 2.4- to 16.5-fold). SAR11 cell-specific isocitrate lyase gene transcription was negatively correlated to chlorophyll a, and bulk bacterial heterotrophic metabolism. We conclude that the glyoxylate cycle is a metabolic strategy for SAR11 that is highly sensitive to the degree of iron and carbon limitation in the marine environment.
C1 [Beier, Sara; Galvez, Maria J.; Blain, Stephane; Obernosterer, Ingrid] Univ Paris 06, Sorbonne Univ, CNRS, Lab Oceanog Microbienne LOMIC,Observ Oceanol, F-66650 Banyuls Sur Mer, France.
   [Galvez, Maria J.] Univ Concepcion, Dept Oceanog, Grad Program Oceanog, Concepcion, Chile.
   [Molina, Veronica] Univ Playa Ancha, Fac Ciencias Nat & Exactas, Dept Biol, Valparaiso, Chile.
   [Sarthou, Geraldine; Queroue, Fabien] LEMAR UMR CNRS UBO IRD 6539, F-29280 Plouzane, France.
   [Queroue, Fabien] Univ Tasmania, Inst Marine & Antarctic Studies, Hobart, Tas 7001, Australia.
   [Queroue, Fabien] Univ Tasmania, Antarctic Climate & Ecosyst Cooperat Res Ctr, Hobart, Tas 7001, Australia.
RP Beier, S (corresponding author), Leibniz Inst Balt Sea Res, Seestr 15, D-18119 Rostock, Germany.
EM sara.beier@io-warnemuende.de
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NR 39
TC 17
Z9 18
PD JUN
PY 2015
VL 7
IS 3
BP 427
EP 434
DI 10.1111/1758-2229.12267
UT WOS:000354375100007
DA 2025-07-30
ER

PT J
AU Oh, HM
   Kang, I
   Lee, K
   Jang, Y
   Lim, SI
   Cho, JC
AF Oh, Hyun-Myung
   Kang, Ilnam
   Lee, Kiyoung
   Jang, Yoonra
   Lim, Seung-Il
   Cho, Jang-Cheon
TI Complete Genome Sequence of Strain IMCC9063, Belonging to SAR11 Subgroup
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SO JOURNAL OF BACTERIOLOGY
DT Article
AB Strain IMCC9063 is a novel isolate of the SAR11 clade and is distantly related to other cultured representatives in this clade. The strain was isolated off the coast of Svalbard, Norway, by applying high-throughput culturing methods based on dilution to extinction. Here we present the finished genome sequence of strain IMCC9063.
C1 [Oh, Hyun-Myung; Kang, Ilnam; Lee, Kiyoung; Jang, Yoonra; Lim, Seung-Il; Cho, Jang-Cheon] Inha Univ, Div Biol & Ocean Sci, Inchon 402751, South Korea.
RP Cho, JC (corresponding author), Inha Univ, Div Biol & Ocean Sci, Inchon 402751, South Korea.
EM chojc@inha.ac.kr
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NR 11
TC 25
Z9 28
PD JUL
PY 2011
VL 193
IS 13
BP 3379
EP 3380
DI 10.1128/JB.05033-11
UT WOS:000291592600023
DA 2025-07-30
ER

PT J
AU Morris, RM
   Frazar, CD
   Carlson, CA
AF Morris, Robert M.
   Frazar, Christian D.
   Carlson, Craig A.
TI Basin-scale patterns in the abundance of SAR11 subclades, marine
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   South Atlantic
SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Bacterioplankton are major biogeochemical agents responsible for mediating the flux of dissolved organic matter (DOM) and subsequent cycling of nutrients in the oceans. Most information about the composition of bacterioplankton communities has come from studies along well-defined biogeochemical gradients in the northern hemisphere. This study extends observations of spatial and temporal dynamics for SAR11, Actinobacteria and OCS116 in the North Atlantic by demonstrating distinct spatial variability in the abundance and distribution of these and other lineages across the South Atlantic gyre and in the Benguela upwelling system. We identified shifts in SAR11, Actinobacteria, OCS116, SAR86, SAR116 and members of the Roseobacter clade along basin-scale gradients in nutrients, chlorophyll and dissolved organic carbon (DOC). Distinct SAR11 subclades dominated the western and eastern regions of the gyre, and Actinobacteria, OCS116 and members of the Roseobacter lineages were most abundant at the deep chlorophyll maxima. SAR86 and SAR116 accounted for a significant fraction of coastal and open ocean communities, respectively, and members of the gamma sulfur oxidizer (GSO) clade persisted in the Benguela upwelling system. These data suggest that distinct communities are partitioned along basin-scale biogeochemical gradients, that SAR11 community structure varies across the gyre and that Actinobacteria, OCS116, and members of the Roseobacter clade are closely associated with phytoplankton in the gyre.
C1 [Morris, Robert M.; Frazar, Christian D.] Univ Washington, Sch Oceanog, Seattle, WA 98195 USA.
   [Carlson, Craig A.] Univ Calif Santa Barbara, Dept Ecol Evolut & Marine Biol, Santa Barbara, CA 93106 USA.
RP Morris, RM (corresponding author), Univ Washington, Sch Oceanog, Seattle, WA 98195 USA.
EM morrisrm@uw.edu
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NR 43
TC 70
Z9 78
PD MAY
PY 2012
VL 14
IS 5
BP 1133
EP 1144
DI 10.1111/j.1462-2920.2011.02694.x
UT WOS:000302934000003
DA 2025-07-30
ER

PT J
AU Thiele, S
   Basse, A
   Becker, JW
   Lipski, A
   Iversen, MH
   Mollenhauer, G
AF Thiele, Stefan
   Basse, Andreas
   Becker, Jamie W.
   Lipski, Andre
   Iversen, Morten H.
   Mollenhauer, Gesine
TI Microbial communities in the nepheloid layers and hypoxic zones of the
   Canary Current upwelling system
SO MICROBIOLOGYOPEN
DT Article
AB Eastern boundary upwelling systems (EBUSs) are among the most productive marine environments in the world. The Canary Current upwelling system off the coast of Mauritania and Morocco is the second most productive of the four EBUS, where nutrient-rich waters fuel perennial phytoplankton blooms, evident by high chlorophyll a concentrations off Cape Blanc, Mauritania. High primary production leads to eutrophic waters in the surface layers, whereas sinking phytoplankton debris and horizontally dispersed particles form nepheloid layers (NLs) and hypoxic waters at depth. We used Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH) in combination with fatty acid (measured as methyl ester; FAME) profiles to investigate the bacterial and archaeal community composition along transects from neritic to pelagic waters within the "giant Cape Blanc filament" in two consecutive years (2010 and 2011), and to evaluate the usage of FAME data for microbial community studies. We also report the first fatty acid profile of Pelagibacterales strain HTCC7211 which was used as a reference profile for the SAR11 clade. Unexpectedly, the reference profile contained low concentrations of long chain fatty acids 18:1 cis11, 18:1 cis11 11methyl, and 19:0 cyclo11-12 fatty acids, the main compounds in other Alphaproteobacteria. Members of the free-living SAR11 clade were found at increased relative abundance in the hypoxic waters in both years. In contrast, the depth profiles of Gammaproteobacteria (including Alteromonas and Pseudoalteromonas), Bacteroidetes, Roseobacter, and Synechococcus showed high abundances of these groups in layers where particle abundance was high, suggesting that particle attachment or association is an important mechanisms of dispersal for these groups. Collectively, our results highlight the influence of NLs, horizontal particle transport, and low oxygen on the structure and dispersal of microbial communities in upwelling systems.
C1 [Thiele, Stefan] Max Planck Inst Marine Microbiol, Bremen, Germany.
   [Basse, Andreas; Iversen, Morten H.; Mollenhauer, Gesine] Alfred Wegener Inst Polar & Marine Res, Handelshafen 12, D-27570 Bremerhaven, Germany.
   [Becker, Jamie W.] Haverford Coll, Dept Biol, Haverford, PA 19041 USA.
   [Lipski, Andre] Rheinische Friedrich Wilhelms Univ Bonn, Dept Food Microbiol & Hyg, Bonn, Germany.
   [Basse, Andreas; Iversen, Morten H.; Mollenhauer, Gesine] MARUM, Bremen, Germany.
   [Basse, Andreas; Iversen, Morten H.; Mollenhauer, Gesine] Univ Bremen, Bremen, Germany.
   [Thiele, Stefan] Friedrich Schiller Univ, Jena, Germany.
RP Mollenhauer, G (corresponding author), Alfred Wegener Inst Polar & Marine Res, Handelshafen 12, D-27570 Bremerhaven, Germany.
EM Gesine.Mollenhauer@awi.de
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NR 79
TC 9
Z9 9
PD MAY
PY 2019
VL 8
IS 5
AR e705
DI 10.1002/mbo3.705
UT WOS:000468628800001
DA 2025-07-30
ER

PT J
AU Ameryk, A
   Kownacka, J
   Zalewski, M
   Piwosz, K
AF Ameryk, Anetta
   Kownacka, Janina
   Zalewski, Mariusz
   Piwosz, Kasia
TI Typical freshwater and marine bacterial lineages dynamics at salinity
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SO ESTUARINE COASTAL AND SHELF SCIENCE
DT Article
AB The Vistula Lagoon is an almost closed basin at the southern coast of the Baltic Sea. Its mild salinity gradient provides a unique environment for the coexistence of freshwater and marine bacteria. This study employs catalysed reporter deposition-fluorescence in situ hybridisation (CARD-FISH) to investigate seasonal dynamics of marine (SAR11 clade I/II) and freshwater (SAR11 clade IIIb (LD12), Limnohabitans clades B, C, D, Burkholderiales (former Betaproteobacteria)) bacterial groups. Samples were collected from below the ice in February, and then monthly from April to October 2011 from three stations with different salinity. The abundance of SAR11 clade I/II strongly positively correlated with salinity, with the highest abundance in autumn at time of inflows of saline waters from the Baltic Sea. Two groups (spring-summer and autumn-winter) were distinguished within this clade, based on a scatter chart between SAR11-I/II abundance and salinity. Salinity explained 69% of the variability of the spring-summer group and 77% of the autumn-winter group. This suggests that the presence of marine SAR11-I/II in the Vistula Lagoon was caused by passive inflow with waters from the open Baltic Sea, and this environment is not suitable for its regular existence. The abundance of the freshwater SAR11 clade IIIb was similar to that of SAR11-I/II. However, it depended on temperature, organic and inorganic phosphorous, and not on salinity, suggesting that SAR11-IIIb found a regular niche in the eutrophic Vistula Lagoon. Burkholderiales positively correlated with temperature, chlorophyll-a, organic and inorganic phosphorous, and heterotrophic nanoflagellates, suggesting that their role in the Vistula Lagoon may be similar to that in lakes. Interestingly, Burkholderiales had the highest relative abundance under ice in February. Finally, the abundance of Limnohabitans clades B, C, D positively depended on temperature, chlorophyll-a and negatively on salinity. This together with positive correlation with Cryptophytes and with heterotrophic nanoflagellates emphasis its importance in this ecosystem. These results show that the conditions in the Vistula Lagoon are rather inappropriate for typical marine bacteria, while freshwater bacteria may find their niches despite slightly elevated salinity.
C1 [Ameryk, Anetta; Kownacka, Janina; Zalewski, Mariusz; Piwosz, Kasia] Natl Marine Fisheries Res Inst, Kollataja 1, PL-81332 Gdynia, Poland.
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RP Ameryk, A (corresponding author), Natl Marine Fisheries Res Inst, Kollataja 1, PL-81332 Gdynia, Poland.
EM aameryk@mir.gdynia.pl; jkownacka@mir.gdynia.pl; mzalewski@mir.gdynia.pl;
   kpiwosz@mir.gdynia.pl
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NR 67
TC 6
Z9 6
PD MAR 5
PY 2021
VL 250
AR 107100
DI 10.1016/j.ecss.2020.107100
UT WOS:000620821100004
DA 2025-07-30
ER

PT J
AU Bruewer, JD
   Orellana, LH
   Sidhu, C
   Klip, HCL
   Meunier, CL
   Boersma, M
   Wiltshire, KH
   Amann, R
   Fuchs, BM
AF Bruewer, Jan D.
   Orellana, Luis H.
   Sidhu, Chandni
   Klip, Helena C. L.
   Meunier, Cedric L.
   Boersma, Maarten
   Wiltshire, Karen H.
   Amann, Rudolf
   Fuchs, Bernhard M.
TI In situ cell division and mortality rates of SAR11, SAR86,
   Bacteroidetes, and Aurantivirga during phytoplankton
   blooms reveal differences in population controls
SO MSYSTEMS
DT Article
AB Net growth of microbial populations, that is, changes in abundances over time, can be studied using 16S rRNA fluorescence in situ hybridization (FISH). However, this approach does not differentiate between mortality and cell division rates. We used FISH-based image cytometry in combination with dilution culture experiments to study net growth, cell division, and mortality rates of four bacterial taxa over two distinct phytoplankton blooms: the oligotrophs SAR11 and SAR86, and the copiotrophic phylum Bacteroidetes, and its genus Aurantivirga. Cell volumes, ribosome content, and frequency of dividing cells (FDC) co-varied over time. Among the three, FDC was the most suitable predictor to calculate cell division rates for the selected taxa. The FDC-derived cell division rates for SAR86 of up to 0.8/day and Aurantivirga of up to 1.9/day differed, as expected for oligotrophs and copiotrophs. Surprisingly, SAR11 also reached high cell division rates of up to 1.9/day, even before the onset of phytoplankton blooms. For all four taxonomic groups, the abundance-derived net growth (-0.6 to 0.5/day) was about an order of magnitude lower than the cell division rates. Consequently, mortality rates were comparably high to cell division rates, indicating that about 90% of bacterial production is recycled without apparent time lag within 1 day. Our study shows that determining taxon-specific cell division rates complements omics-based tools and provides unprecedented clues on individual bacterial growth strategies including bottom-up and top-down controls.
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C1 [Bruewer, Jan D.; Orellana, Luis H.; Sidhu, Chandni; Amann, Rudolf; Fuchs, Bernhard M.] Max Planck Inst Marine Microbiol, Bremen, Germany.
   [Klip, Helena C. L.; Meunier, Cedric L.; Boersma, Maarten; Wiltshire, Karen H.] Alfred Wegener Inst, Biol Anstalt Helgoland, Helmholtz Zentrum Polar & Meeresforsch, Helgoland, Germany.
   [Boersma, Maarten] Univ Bremen, Bremen, Germany.
   [Wiltshire, Karen H.] Alfred Wegener Inst, Helmholtz Zentrum Polar & Meeresforsch, Wattenmeerstn, Bremerhaven, Germany.
RP Fuchs, BM (corresponding author), Max Planck Inst Marine Microbiol, Bremen, Germany.
EM bfuchs@mpi-bremen.de
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NR 93
TC 8
Z9 8
PD JUN 29
PY 2023
VL 8
IS 3
DI 10.1128/msystems.01287-22
EA MAY 2023
UT WOS:001026306200001
DA 2025-07-30
ER

PT J
AU Long, ZD
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AF Long, Zhangde
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TI A novel thermophilic β-carotene 15,15′-monooxygenase with broad
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   Pelagibacter sp. HTCC7211
SO BIOTECHNOLOGY LETTERS
DT Article
AB To characterize a novel thermophilic beta-carotene 15,15 '-monooxygenase BCMO7211 isolated from the marine bacterium Candidatus Pelagibacter sp. HTCC7211. BCMO7211 was functionally overexpressed in Escherichia coli and purified to homogeneity by Ni-NTA affinity chromatography and Superdex-200 gel filtration chromatography. Labeling experiments with (H2O)-O-18 demonstrated that the oxygen atom in the terminal aldehyde group of the produced retinal molecules was provided from both molecular oxygen and water, indicating that BCMO7211 is the first characterized bacterial beta-carotene 15,15 '-monooxygenase. BCMO7211 exhibited broad carotenoid substrate specificity toward alpha-carotene, beta-cryptoxanthin, beta-carotene, zeaxanthin, and lutein. The optimum temperature, pH, and concentrations of the substrate and enzyme for retinal production were 60 degrees C, 9.0, 500 mg beta-carotene/L, and 2.5 U/ml, respectively. Under optimum conditions, 888.3 mg/L retinal was produced in 60 min with a conversion rate of 89.0% (w/w). BCMO7211 is a potential candidate for the enzymatic synthesis of retinal in biotechnological applications.
C1 [Long, Zhangde; Xue, Yun; Li, Jigang; Su, Zan; Sun, Jiansheng; Liu, Qibin; Liu, Hong] China Tobacco Guangxi Ind Co Ltd, Nanning 530001, Peoples R China.
   [Long, Zhangde; Zhao, Yuzhe; Xue, Yun; Wang, Min; Mao, Duobin; Wei, Tao] Zhengzhou Univ Light Ind, Sch Food & Biol Engn, 5 Dongfeng Rd, Zhengzhou 450002, Peoples R China.
RP Wei, T (corresponding author), Zhengzhou Univ Light Ind, Sch Food & Biol Engn, 5 Dongfeng Rd, Zhengzhou 450002, Peoples R China.
EM weit8008@zzuli.edu.cn
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NR 24
TC 1
Z9 1
PD DEC
PY 2021
VL 43
IS 12
BP 2233
EP 2241
DI 10.1007/s10529-021-03188-w
EA OCT 2021
UT WOS:000705777800001
DA 2025-07-30
ER

PT J
AU Zaragoza-Solas, A
   Rodriguez-Valera, F
   López-Pérez, M
AF Zaragoza-Solas, Asier
   Rodriguez-Valera, Francisco
   Lopez-Perez, Mario
TI Metagenome Mining Reveals Hidden Genomic Diversity of Pelagimyophages in
   Aquatic Environments
SO MSYSTEMS
DT Article
AB The SAR11 Glade is one of the most abundant bacterioplankton groups in surface waters of most of the oceans and lakes. However, only 15 SAR11 phages have been isolated thus far, and only one of them belongs to the Myoviridae family (pelagimyophages). Here, we have analyzed 26 sequences of myophages that putatively infect the SAR11 Glade. They have been retrieved by mining ca. 45 Gbp aquatic assembled cellular metagenomes and viromes. Most of the myophages were obtained from the cellular fraction (0.2 mu m), indicating a bias against this type of virus in viromes. We have found the first myophages that putatively infect Candidatus Fonsibacter (freshwater SAR11) and another group putatively infecting bathypelagic SAR11 phylogroup Ic. The genomes have similar sizes and maintain overall synteny in spite of low average nucleotide identity values, revealing high similarity to marine cyanomyophages. Pelagimyophages recruited metagenomic reads widely from several locations but always much more from cellular metagenomes than from viromes, opposite to what happens with pelagipodophages. Comparing the genomes resulted in the identification of a hypervariable island that is related to host recognition. Interestingly, some genes in these islands could be related to host cell wall synthesis and coinfection avoidance. A cluster of curli-related proteins was widespread among the genomes, although its function is unclear.
   IMPORTANCE SAR11 Glade members are among the most abundant bacteria on Earth. Their study is complicated by their great diversity and difficulties in being grown and manipulated in the laboratory. On the other hand, and due to their extraordinary abundance, metagenomic data sets provide enormous richness of information about these microbes. Given the major role played by phages in the lifestyle and evolution of prokaryotic cells, the contribution of several new bacteriophage genomes preying on this Glade opens windows into the infection strategies and life cycle of its viruses. Such strategies could provide models of attack of large-genome phages preying on streamlined aquatic microbes.
C1 [Zaragoza-Solas, Asier; Rodriguez-Valera, Francisco; Lopez-Perez, Mario] Univ Miguel Hernandez, Div Microbiol, Evolutionaiy Genom Grp, Alicante, Spain.
   [Rodriguez-Valera, Francisco] Moscow Inst Phys & Technol, Lab Theoret & Comp Res Biol Macromol & Genomes, Dolgoprudnyi, Russia.
RP Rodriguez-Valera, F; López-Pérez, M (corresponding author), Univ Miguel Hernandez, Div Microbiol, Evolutionaiy Genom Grp, Alicante, Spain.; Rodriguez-Valera, F (corresponding author), Moscow Inst Phys & Technol, Lab Theoret & Comp Res Biol Macromol & Genomes, Dolgoprudnyi, Russia.
EM frvalera@umh.es; mario.lopezp@umh.es
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NR 119
TC 23
Z9 23
PD JAN-FEB
PY 2020
VL 5
IS 1
AR e00905-19
DI 10.1128/mSystems.00905-19
UT WOS:000518855000050
DA 2025-07-30
ER

PT J
AU Smith, DP
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TI Transcriptional and Translational Regulatory Responses to Iron
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SO PLOS ONE
DT Article
AB Iron is recognized as an important micronutrient that limits microbial plankton productivity over vast regions of the oceans. We investigated the gene expression responses of Candidatus Pelagibacter ubique cultures to iron limitation in natural seawater media supplemented with a siderophore to chelate iron. Microarray data indicated transcription of the periplasmic iron binding protein sfuC increased by 16-fold, and iron transporter subunits, iron-sulfur center assembly genes, and the putative ferroxidase rubrerythrin transcripts increased to a lesser extent. Quantitative peptide mass spectrometry revealed that sfuC protein abundance increased 27-fold, despite an average decrease of 59% across the global proteome. Thus, we propose sfuC as a marker gene for indicating iron limitation in marine metatranscriptomic and metaproteomic ecological surveys. The marked proteome reduction was not directly correlated to changes in the transcriptome, implicating post-transcriptional regulatory mechanisms as modulators of protein expression. Two RNA-binding proteins, CspE and CspL, correlated well with iron availability, suggesting that they may contribute to the observed differences between the transcriptome and proteome. We propose a model in which the RNA-binding activity of CspE and CspL selectively enables protein synthesis of the iron acquisition protein SfuC during transient growth-limiting episodes of iron scarcity.
C1 [Smith, Daniel P.] Oregon State Univ, Mol & Cellular Biol Program, Corvallis, OR 97331 USA.
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RP Smith, DP (corresponding author), Oregon State Univ, Mol & Cellular Biol Program, Corvallis, OR 97331 USA.
EM steve.giovannoni@oregonstate.edu
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AF Joint, Ian
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RP Joint, I (corresponding author), Plymouth Marine Lab, Prospect Pl, Plymouth, Devon, England.
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SO PLOS ONE
DT Article
AB Bacteria belonging to the SAR11 clade are among the most abundant prokaryotes in the pelagic zone of the ocean. 16S rRNA gene-based analyses indicate that they constitute up to 60% of the bacterioplankton community in the surface waters of the Red Sea. This extremely oligotrophic water body is further characterized by an epipelagic zone, which has a temperature above 24 degrees C throughout the year, and a remarkable uniform temperature (similar to 22 degrees C) and salinity (similar to 41 psu) from the mixed layer (similar to 200 m) to the bottom at over 2000 m depth. Despite these conditions that set it apart from other marine environments, the microbiology of this ecosystem is still vastly understudied. Prompted by the limited phylogenetic resolution of the 16S rRNA gene, we extended our previous study by sequencing the internal transcribed spacer (ITS) region of SAR11 in different depths of the Red Sea's water column together with the respective 16S fragment. The overall diversity captured by the ITS loci was ten times higher than that of the corresponding 16S rRNA genes. Moreover, species estimates based on the ITS showed a highly diverse population of SAR11 in the mixed layer that became diminished in deep isothermal waters, which was in contrast to results of the related 16S rRNA genes. While the 16S rRNA gene-based sequences clustered into three phylogenetic subgroups, the related ITS fragments fell into several phylotypes that showed clear depth-dependent shifts in relative abundances. Blast-based analyses not only documented the observed vertical partitioning and universal co-occurrence of specific phylotypes in five other distinct oceanic provinces, but also highlighted the influence of ecosystem-specific traits (e. g., temperature, nutrient availability, and concentration of dissolved oxygen) on the population dynamics of this ubiquitous marine bacterium.
C1 [Ngugi, David Kamanda; Stingl, Ulrich] King Abdullah Univ Sci & Technol, Red Sea Res Ctr, Thuwal, Saudi Arabia.
RP Ngugi, DK (corresponding author), King Abdullah Univ Sci & Technol, Red Sea Res Ctr, Thuwal, Saudi Arabia.
EM david.ngugi@kaust.edu.sa
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NR 92
TC 30
Z9 33
PD NOV 20
PY 2012
VL 7
IS 11
AR e50274
DI 10.1371/journal.pone.0050274
UT WOS:000311535700081
DA 2025-07-30
ER

PT J
AU Haro-Moreno, JM
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TI Flotillin-associated rhodopsin (FArhodopsin), a widespread paralog of
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SO MSYSTEMS
DT Article
AB Microbial rhodopsins are found more than once in a single genome (paralogs) often have different functions. We screened a large dataset of open ocean single-amplified genomes (SAGs) for co-occurrences of multiple rhodopsin genes. Many such cases were found among Pelagibacterales (SAR11), HIMB59, and the Gammaproteo-bacteria Pseudothioglobus SAGs. These genomes always had a bona fide proteorhodopsin and a separate cluster of genes containing a second rhodopsin associated with a predicted flotillin coding gene and have thus been named flotillin-associated rhodopsins (FArhodopsins). Although they are members of the proteorhodopsin protein family, they form a separate clade within that family and are quite divergent from known proton-pumping proteorhodopsins. They contain either DTT, DTL, or DNI motifs in their key functional amino acids. FArhodopsins are mainly associated with the lower layers of the epipelagic zone. All marine FArhodopsins had the retinal binding lysine, but we found relatives in freshwater metagenomes lacking this key amino acid. AlphaFold predictions of marine FArhodopsins indicate that their retinal pocket might be very reduced or absent, hinting that they are retinal-less. Freshwater FArhodopsins were more diverse than marine ones, but we could not determine if there were other rhodopsins in the genome due to the lack of SAGs or isolates. Although the function of FArhodopsins could not be established, their conserved genomic context indicated involvement in the formation of membrane microdomains. The conservation of FArhodopsins in diverse and globally abundant microorganisms suggests that they may be important in the adaptation to the twilight zone of aquatic environments.
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C1 [Haro-Moreno, Jose M.; Lopez-Perez, Mario; Rodriguez-Valera, Francisco] Univ Miguel Hernandez, Dept Prod Vegetal & Microbiol, Evolutionary Genom Grp, Alicante, Spain.
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   [Alekseev, Alexey] Univ Med Ctr Gottingen, Inst Auditory Neurosci & InnerEarLab, Gottingen, Germany.
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   [Gordeliy, Valentin] Forschungszentrum Julich, Inst Biol Informat Proc, Struct Biochem, Julich, Germany.
   [Stepanauskas, Ramunas] Bigelow Lab Ocean Sci, East Boothbay, ME USA.
RP Rodriguez-Valera, F (corresponding author), Univ Miguel Hernandez, Dept Prod Vegetal & Microbiol, Evolutionary Genom Grp, Alicante, Spain.
EM frvalera@umh.es
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NR 84
TC 0
Z9 0
PD JUN 29
PY 2023
VL 8
IS 3
DI 10.1128/msystems.00008-23
EA MAY 2023
UT WOS:001026298700001
DA 2025-07-30
ER

PT J
AU Yang, SJ
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AF Yang, Seung-Jo
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SO MICROBIAL ECOLOGY
DT Article
AB High-throughput cultivation (HTC) based on a dilution-to-extinction method has been applied broadly to the cultivation of marine bacterial groups, which has often led to the repeated isolation of abundant lineages such as SAR11 and oligotrophic marine gammaproteobacteria (OMG). In this study, to expand the phylogenetic diversity of HTC isolates, we performed a large-scale HTC with a single surface seawater sample collected from the East Sea, the Western Pacific Ocean. Phylogenetic analyses of the 16S rRNA genes from 847 putative pure cultures demonstrated that some isolates were affiliated with not-yet-cultured clades, including the OPB35 and Puniceicoccaceae marine group of Verrucomicrobia and PS1 of Alphaproteobacteria. In addition, numerous strains were obtained from abundant clades, such as SAR11, marine Roseobacter clade, OMG (e.g., SAR92 and OM60), OM43, and SAR116, thereby increasing the size of available culture resources for representative marine bacterial groups. Comparison between the composition of HTC isolates and the bacterial community structure of the seawater sample used for HTC showed that diverse marine bacterial groups exhibited various growth capabilities under our HTC conditions. The growth response of many bacterial groups, however, was clearly different from that observed with conventional plating methods, as exemplified by numerous isolates of the SAR11 clade and Verrucomicrobia. This study showed that a large number of novel bacterial strains could be obtained by an extensive HTC from even a small number of samples.
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RP Cho, JC (corresponding author), Inha Univ, Dept Biol Sci, Inchon 402751, South Korea.
EM chojc@inha.ac.kr
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NR 87
TC 38
Z9 44
PD JAN
PY 2016
VL 71
IS 1
BP 29
EP 43
DI 10.1007/s00248-015-0695-3
UT WOS:000367097500005
DA 2025-07-30
ER

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C1 [Silovic, Tina; Orlic, Sandi] Rudjer Boskovic Inst, Ctr Marine Res, Rovinj 52210, Croatia.
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RP Silovic, T (corresponding author), Rudjer Boskovic Inst, Ctr Marine Res, G Paliaga 5, Rovinj 52210, Croatia.
EM tina.silovic@cim.irb.hr
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ER

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DT Letter
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AB The human body has twenty-five thousand genes whereas an oceanic bacterium, Pelagibacter ubique (or SAR11), one of the smallest self-replicating cells known, has only one-thousand three hundred and fifty four genes. This paring down the bacterium's genome appears to be evolution's way of conserving genetic energy for an abundant organism in the face of limited resources.
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DI 10.1038/scientificamerican1205-26
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DA 2025-07-30
ER

PT J
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AF Mohapatra, Madhusmita
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   Rastogi, Gurdeep
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SO SCIENCE OF THE TOTAL ENVIRONMENT
DT Article
AB Coastal ecosystems, one of the most productive ecosystems, are subjected to natural and anthropogenic stresses. Coastal bacterioplankton communities are highly dynamic due to spatiotemporal heterogeneity in the environmental parameters. We investigated the seasonal and spatial variation in bacterioplankton communities, their abundances and environmental drivers during one year period in Chilika, a brackish water coastal lagoon of India. High-throughput sequencing of 16S rRNA genes of bacterioplankton communities showed that they were dominated by heterotrophs namely alpha-Proteobacteria SAR11 and their sub-clades (SAR11_Ib Chesapeake-Delaware_Bay, Candidatus_Pelagibacter, and SAR11_Surface_1), acti-nobacterial lineages (hgcI, CL500-29, and Candidatus_Aquiluna), beta-Proteobacteria MWH-UniP1 , beta-Proteobacteria OM43, and verrucomicrobial Glade Spartobacteria 'LD29'. Synechococcus was the dominant member within autotrophic cyanobacterial community. Response ratio derived from comparisons of taxon-specific absolute abundances and indicator analyses showed that SAR11_Surface_1 sub-Glade occupied high-salinity environment especially during summer and winter and emerged as a strong indicator for mesohaline-polyhaline salinity regime. In contrast, Spartobacteria 'LD29', Actinobacteria hgcI, and CL500-29 preferred low-salinity freshwater environment and were strong indicators for oligohaline-mesohaline regimes. Spatiotemporal patterns were governed by 'distance-decay' and 'similarity-time' relationships. Bacterioplankton communities were mostly determined by salinity, dissolved oxygen, phosphate, and pH which resulted 'species sorting' leading to biogeographical patterns in the bacterioplankton communities. Modeling analysis revealed the characteristic shift in the indicator bacterioplankton taxa along with estuarine salinity gradient. This study has provided baseline information on the bacterioplankton communities and their environmental drivers within an anthropogenically impacted cyclone prone coastal lagoon which would be useful in assessing the impact of multiple stressors on this vulnerable ecosystem. (C) 2019 Elsevier B.V. All rights reserved.
C1 [Mohapatra, Madhusmita; Behera, Pratiksha; Rastogi, Gurdeep] Chilika Dev Author, Wetland Res & Training Ctr, Balugaon 752030, Odisha, India.
   [Mohapatra, Madhusmita] KIIT Univ, Sch Biotechnol, Bhubaneswar 751024, Odisha, India.
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RP Rastogi, G (corresponding author), Chilika Dev Author, Wetland Res & Training Ctr, Balugaon 752030, Odisha, India.
EM rastogigurdeep@gmail.com
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NR 61
TC 38
Z9 42
PD FEB 25
PY 2020
VL 705
AR 134729
DI 10.1016/j.scitotenv.2019.134729
UT WOS:000508129700004
DA 2025-07-30
ER

PT J
AU Haber, M
   Rosenberg, DR
   Lalzar, M
   Burgsdorf, I
   Saurav, K
   Lionheart, R
   Lehahn, Y
   Aharonovich, D
   Gomez-Consarnau, L
   Sher, D
   Krom, MD
   Steindler, L
AF Haber, Markus
   Roth Rosenberg, Dalit
   Lalzar, Maya
   Burgsdorf, Ilia
   Saurav, Kumar
   Lionheart, Regina
   Lehahn, Yoav
   Aharonovich, Dikla
   Gomez-Consarnau, Laura
   Sher, Daniel
   Krom, Michael D.
   Steindler, Laura
TI Spatiotemporal Variation of Microbial Communities in the
   Ultra-Oligotrophic Eastern Mediterranean Sea
SO FRONTIERS IN MICROBIOLOGY
DT Article
AB Marine microbial communities vary seasonally and spatially, but these two factors are rarely addressed together. In this study, the temporal and spatial patterns of the bacterial and archaeal community were studied along a coast-to-offshore transect in the Eastern Mediterranean Sea (EMS) over six cruises, in three seasons of 2 consecutive years. Amplicon sequencing of 16S rRNA genes and transcripts was performed to determine presence and activity, respectively. The ultra-oligotrophic status of the Southeastern Mediterranean Sea was reflected in the microbial community composition dominated by oligotrophic bacterial groups such as SAR11, even at the most coastal station sampled, throughout the year. Seasons significantly affected the microbial communities, explaining more than half of the observed variability. However, the same few taxa dominated the community over the 2-year sampling period, varying only in their degree of dominance. While there was no overall effect of station location on the microbial community, the most coastal site (16 km offshore) differed significantly in community structure and activity from the three further offshore stations in early winter and summer. Our data on the microbial community compositions and their seasonality support previous notions that the EMS behaves like an oceanic gyre.
C1 [Haber, Markus; Roth Rosenberg, Dalit; Burgsdorf, Ilia; Saurav, Kumar; Aharonovich, Dikla; Sher, Daniel; Krom, Michael D.; Steindler, Laura] Univ Haifa, Leon H Charney Sch Marine Sci, Dept Marine Biol, Haifa, Israel.
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RP Steindler, L (corresponding author), Univ Haifa, Leon H Charney Sch Marine Sci, Dept Marine Biol, Haifa, Israel.
EM lsteindler@univ.haifa.ac.il
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NR 72
TC 12
Z9 12
PD APR 7
PY 2022
VL 13
AR 867694
DI 10.3389/fmicb.2022.867694
UT WOS:000791062000001
DA 2025-07-30
ER

PT J
AU Fu, YY
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AF Fu, Yunyun
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SO MICROORGANISMS
DT Article
AB The Arctic Ocean is one of the least well-studied marine microbial ecosystems. Its low-temperature and low-salinity conditions are expected to result in distinct bacterial communities, in comparison to lower latitude oceans. However, this is an ocean currently in flux, with climate change exerting pronounced effects on sea-ice coverage and freshwater inputs. How such changes will affect this ecosystem are poorly constrained. In this study, we characterized the bacterial community compositions at different depths in both coastal, freshwater-influenced, and pelagic, sea-ice-covered locations in the Beaufort Sea in the western Canadian Arctic Ocean. The environmental factors controlling the bacterial community composition and diversity were investigated. Alphaproteobacteria dominated the bacterial communities in samples from all depths and stations. The Pelagibacterales and Rhodobacterales groups were the predominant taxonomic representatives within the Alphaproteobacteria. Bacterial communities in coastal and offshore samples differed significantly, and vertical water mass segregation was the controlling factor of community composition among the offshore samples, regardless of the taxonomic level considered. These data provide an important baseline view of the bacterial community in this ocean system that will be of value for future studies investigating possible changes in the Arctic Ocean in response to global change and/or anthropogenic disturbance.
C1 [Fu, Yunyun; Lang, Andrew S.] Mem Univ Newfoundland, Dept Biol, 232 Elizabeth Ave, St John, NF A1B 3X9, Canada.
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RP Lang, AS (corresponding author), Mem Univ Newfoundland, Dept Biol, 232 Elizabeth Ave, St John, NF A1B 3X9, Canada.
EM yunyun.fu@mun.ca; rrivkin@mun.ca; aslang@mun.ca
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NR 102
TC 8
Z9 9
PD OCT
PY 2019
VL 7
IS 10
AR 385
DI 10.3390/microorganisms7100385
UT WOS:000498223100014
DA 2025-07-30
ER

PT J
AU Cottrell, MT
   Kirchman, DL
AF Cottrell, Matthew T.
   Kirchman, David L.
TI Transcriptional Control in Marine Copiotrophic and Oligotrophic Bacteria
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Bacteria often respond to environmental stimuli using transcriptional control, but this may not be the case for marine bacteria such as "Candidatus Pelagibacter ubique," a cultivated representative of the SAR11 clade, the most abundant organism in the ocean. This bacterium has a small, streamlined genome and an unusually low number of transcriptional regulators, suggesting that transcriptional control is low in Pelagibacter and limits its response to environmental conditions. Transcriptome sequencing during batch culture growth revealed that only 0.1% of protein-encoding genes appear to be under transcriptional control in Pelagibacter and in another oligotroph (SAR92) whereas >10% of genes were under transcriptional control in the copiotrophs Polaribacter sp. strain MED152 and Ruegeria pomeroyi. When growth levels changed, transcript levels remained steady in Pelagibacter and SAR92 but shifted in MED152 and R. pomeroyi. Transcript abundances per cell, determined using an internal RNA sequencing standard, were low (<1 transcript per cell) for all but a few of the most highly transcribed genes in all four taxa, and there was no correlation between transcript abundances per cell and shifts in the levels of transcription. These results suggest that low transcriptional control contributes to the success of Pelagibacter and possibly other oligotrophic microbes that dominate microbial communities in the oceans.
C1 [Cottrell, Matthew T.; Kirchman, David L.] Univ Delaware, Sch Marine Sci & Policy, Lewes, DE 19958 USA.
RP Kirchman, DL (corresponding author), Univ Delaware, Sch Marine Sci & Policy, Lewes, DE 19958 USA.
EM kirchman@udel.edu
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NR 52
TC 39
Z9 45
PD OCT
PY 2016
VL 82
IS 19
BP 6010
EP 6018
DI 10.1128/AEM.01299-16
UT WOS:000384048700028
DA 2025-07-30
ER

PT J
AU Alonso-Sáez, L
   Balagué, V
   Sà, EL
   Sánchez, O
   González, JM
   Pinhassi, J
   Massana, R
   Pernthaler, J
   Pedrós-Alió, C
   Gasol, JM
AF Alonso-Saez, Laura
   Balague, Vanessa
   Sa, Elisabet L.
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   Gonzalez, Jose M.
   Pinhassi, Jarone
   Massana, Ramon
   Pernthaler, Jakob
   Pedros-Alio, Carlos
   Gasol, Josep M.
TI Seasonality in bacterial diversity in north-west Mediterranean coastal
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SO FEMS MICROBIOLOGY ECOLOGY
DT Article
AB We combined denaturing gradient gel electrophoresis (DGGE), catalysed reporter deposition-FISH (CARD-FISH) and clone libraries to investigate the seasonality of the bacterial assemblage composition in north-west Mediterranean coastal waters. DGGE analysis indicated that bacterial diversity changed gradually throughout the year, although with a clear distinction of the summer period. Alphaproteobacteria were the dominant group on an annual basis [29% of the DAPI (4',6-diamidino-2-phenylindole) counts by CARD-FISH, and 70% of the bacterial clones]. The SAR11 clade was most abundant during spring and summer (> 20% of DAPI counts), while the Roseobacter clade was abundant primarily in winter and spring (up to 7% of DAPI counts). The phylum Bacteroidetes constituted the second most important group and was quantitatively uniform throughout the year (average 11% of the DAPI counts). Gammaproteobacteria showed a peak during summer (8% of DAPI counts), when most of them belonged to the NOR5 cluster. Clone libraries and CARD-FISH showed reasonable agreement in the quantitative proportions of Bacteroidetes and Gammaproteobacteria, but Alphaproteobacteria were overrepresented in clone libraries. Sequencing of the most predominant DGGE bands failed to detect the SAR11 group despite their high abundance. The combination of the three molecular approaches allowed a comprehensive assessment of seasonal changes in bacterial diversity.
C1 CSIC, CMIMA, Inst Ciencias Mar, Dept Biol Marina Oceanog, E-08003 Barcelona, Spain.
   Univ Autonoma Barcelona, Dept Genet & Microbiol, Bellaterra, Catalunya, Spain.
   Univ La Laguna, Dept Microbiol, San Cristobal la Laguna, Tenerife, Spain.
   Univ Kalmar, Dept Biol & Environm Sci, Kalmar, Sweden.
   Univ Zurich, Inst Plant Biol, Limnol Sect, Zurich, Switzerland.
RP Alonso-Sáez, L (corresponding author), CSIC, CMIMA, Inst Ciencias Mar, Dept Biol Marina Oceanog, E-08003 Barcelona, Spain.
EM lalonso@icm.csic.es
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TC 183
Z9 195
PD APR
PY 2007
VL 60
IS 1
BP 98
EP 112
DI 10.1111/j.1574-6941.2006.00276.x
UT WOS:000244883800010
DA 2025-07-30
ER

PT J
AU Ghai, R
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AF Ghai, Rohit
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   Rodriguez-Valera, Francisco
TI Metagenome of the Mediterranean deep chlorophyll maximum studied by
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SO ISME JOURNAL
DT Article
AB The deep chlorophyll maximum (DCM) is a zone of maximal photosynthetic activity, generally located toward the base of the photic zone in lakes and oceans. In the tropical waters, this is a permanent feature, but in the Mediterranean and other temperate waters, the DCM is a seasonal phenomenon. The metagenome from a single sample of a mature Mediterranean DCM community has been 454 pyrosequenced both directly and after cloning in fosmids. This study is the first to be carried out at this sequencing depth (ca. 600 Mb combining direct and fosmid sequencing) at any DCM. Our results indicate a microbial community massively dominated by the high-light-adapted Prochlorococcus marinus subsp. pastoris, Synechococcus sp., and the heterotroph Candidatus Pelagibacter. The sequences retrieved were remarkably similar to the existing genome of P. marinus subsp. pastoris with a nucleotide identity over 98%. Besides, we found a large number of cyanophages that could prey on this microbe, although sequence conservation was much lower. The high abundance of phage sequences in the cellular size fraction indicated a remarkably high proportion of cells suffering phage lytic attack. In addition, several fosmids clearly belonging to Group II Euryarchaeota were retrieved and recruited many fragments from the total direct DNA sequencing suggesting that this group might be quite abundant in this habitat. The comparison between the direct and fosmids sequencing revealed a bias in the fosmid libraries against low-GC DNA and specifically against the two most dominant members of the community, Candidatus Pelagibacter and P. marinus subsp. pastoris, thus unexpectedly providing a feasible method to obtain large genomic fragments from other less prevalent members of this community. The ISME Journal (2010) 4, 1154-1166; doi: 10.1038/ismej.2010.44; published online 15 April 2010
C1 [Ghai, Rohit; Martin-Cuadrado, Ana-Belen; Gonzaga Molto, Aitor; Garcia Heredia, Inmaculada; Rodriguez-Valera, Francisco] Univ Miguel Hernandez, Dept Prod Vegetal & Microbiol, Evolutionary Genom Grp, Alicante 03350, Spain.
   [Cabrera, Raul; Mira, Alex] Ctr Super Invest Salud Publ, Dept Genom & Hlth, Valencia, Spain.
   [Martin, Javier; Verdu, Miguel] Mediterraneo Serv Marinos SL, Alicante, Spain.
   [Deschamps, Philippe; Moreira, David; Lopez-Garcia, Purificacion] Univ Paris 11, CNRS, UMR8079, Unite Ecol Systemat & Evolut, F-91405 Orsay, France.
RP Rodriguez-Valera, F (corresponding author), Univ Miguel Hernandez, Dept Prod Vegetal & Microbiol, Evolutionary Genom Grp, Apartado 18 San Juan Alicante, Alicante 03350, Spain.
EM frvalera@umh.es
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NR 37
TC 97
Z9 104
PD SEP
PY 2010
VL 4
IS 9
BP 1154
EP 1166
DI 10.1038/ismej.2010.44
UT WOS:000281663700014
DA 2025-07-30
ER

PT J
AU Quéméneur, M
   Hassen, MB
   Armougom, F
   Khammeri, Y
   Lajnef, R
   Bellaaj-Zouari, A
AF Quemeneur, Marianne
   Bel Hassen, Malika
   Armougom, Fabrice
   Khammeri, Yosra
   Lajnef, Rim
   Bellaaj-Zouari, Amel
TI Prokaryotic Diversity and Distribution Along Physical and Nutrient
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SO FRONTIERS IN MICROBIOLOGY
DT Article
AB Prokaryotes play an important role in biogeochemical cycling in marine ecosystems, but little is known about their diversity and composition, and how they may contribute to the ecological functioning of coastal areas in the South Mediterranean Sea. This study investigated bacterial and archaeal community diversity in seawater samples along the Tunisian coast subject to important physicochemical disturbances. The 16S amplicon sequencing survey revealed higher prokaryotic diversity in the northern Tunisian bays than in southeastern waters (Gulf of Gabes). The major taxonomic groups identified in all samples were Alphaproteobacteria (40.9%), Gammaproteobacteria (18.7%), Marine Group II Euryarchaeota (11.3%), and Cyanobacteria (10.9%). Among them, the relative abundance of Alteromonadales, Prochlorococcus, and some clades of Pelagibacterales (SAR11) significantly differed between the northern and the southern bays, whereas no difference was observed across coastal waters in the archaeal Candidatus Poseidoniales (MGII), Synechococcus, and Pelagibacteraceae (SAR11 clade Ia), for which no relationship was observed with the environmental variables. Both Pseudoalteromonas and Alteromonas levels increased with the increasing salinity, density and nutrients (NH4+ and/or PO43-) gradients detected toward the southern waters, while the SAR11 clades Ib and IV and Prochlorococcus, decreased in the shallow, salty and nutrient-rich coastal waters of the Gulf of Gabes. Rhodobacteraceae was positively correlated with Synechococcus and chlorophyll levels, suggesting a relationship with phytoplankton biomass. The present study provides the first insights into planktonic prokaryotic community composition in the South Mediterranean Sea through the analysis of Tunisian seawaters, which may support further investigations on the role of bacterioplankton in the biogeochemistry of these ecosystems.
C1 [Quemeneur, Marianne; Armougom, Fabrice] Univ Toulon & Var, Aix Marseille Univ, CNRS, IRD,MIO UM 110,Mediterranean Inst Oceanog, Marseille, France.
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RP Quéméneur, M (corresponding author), Univ Toulon & Var, Aix Marseille Univ, CNRS, IRD,MIO UM 110,Mediterranean Inst Oceanog, Marseille, France.
EM marianne.quemeneur@ird.fr
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NR 88
TC 13
Z9 14
PD DEC 1
PY 2020
VL 11
AR 593540
DI 10.3389/fmicb.2020.593540
UT WOS:000598460800001
DA 2025-07-30
ER

PT J
AU Thiele, S
   Vader, A
   Ovreås, L
AF Thiele, Stefan
   Vader, Anna
   ovreas, Lise
TI The mystery of the ice cold rose-Microbiome of an Arctic winter frost
   flower
SO MICROBIOLOGYOPEN
DT Editorial Material
AB Under very cold conditions, delicate ice-crystal structures called frost flowers emerge on the surface of newly formed sea ice. These understudied, ephemeral structures include saline brine, organic material, inorganic nutrients, and bacterial and archaeal communities in their brine channels. Hitherto, only a few frost flowers have been studied during spring and these have been reported to be dominated by Rhizobia or members of the SAR11 clade. Here we report on the microbiome of frost flowers sampled during the winter and polar night in the Barents Sea. There was a distinct difference in community profile between the extracted DNA and RNA, but both were dominated by members of the SAR11 clade (78% relative abundance and 41.5% relative activity). The data further suggested the abundance and activity of Cand. Nitrosopumilus, Nitrospinia, and Nitrosomonas. Combined with the inference of marker genes based on the 16S rRNA gene data, this indicates that sulfur and nitrogen cycling are likely the major metabolism in these ephemeral structures.
C1 [Thiele, Stefan; ovreas, Lise] Univ Bergen, Dept Biol Sci, Bergen, Norway.
   [Thiele, Stefan; ovreas, Lise] Bjerknes Ctr Climate Res, Polar Climate Res Grp, Bergen, Norway.
   [Vader, Anna; ovreas, Lise] Univ Ctr Svalbard UNIS, Dept Arctic Biol, Longyearbyen, Norway.
RP Thiele, S (corresponding author), Univ Bergen, Dept Biol Sci, Thormohlensgate 53 A-B, N-5020 Bergen, Norway.
EM stefan.thiele@uib.no
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NR 32
TC 0
Z9 0
PD FEB
PY 2023
VL 12
IS 1
AR e1345
DI 10.1002/mbo3.1345
UT WOS:000929883400001
DA 2025-07-30
ER

PT J
AU Giovannoni, S
   Temperton, B
   Zhao, YL
AF Giovannoni, Stephen
   Temperton, Ben
   Zhao, Yanlin
TI SAR11 viruses and defensive host strains reply
SO NATURE
DT Letter
C1 [Giovannoni, Stephen; Temperton, Ben; Zhao, Yanlin] Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
RP Giovannoni, S (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
EM steve.giovannoni@oregonstate.edu
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TC 22
Z9 22
PD JUL 25
PY 2013
VL 499
IS 7459
BP E4
EP E5
DI 10.1038/nature12388
UT WOS:000322157900002
DA 2025-07-30
ER

PT J
AU Martinez-Garcia, M
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AF Martinez-Garcia, Manuel
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TI Unveiling in situ interactions between marine protists and
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SO ISME JOURNAL
DT Article
AB Heterotrophic protists are a highly diverse and biogeochemically significant component of marine ecosystems, yet little is known about their species-specific prey preferences and symbiotic interactions in situ. Here we demonstrate how these previously unresolved questions can be addressed by sequencing the eukaryote and bacterial SSU rRNA genes from individual, uncultured protist cells collected from their natural marine environment and sorted by flow cytometry. We detected Pelagibacter ubique in association with a MAST-4 protist, an actinobacterium in association with a chrysophyte and three bacteroidetes in association with diverse protist groups. The presence of identical phylotypes among the putative prey and the free bacterioplankton in the same sample provides evidence for predator-prey interactions. Our results also suggest a discovery of novel symbionts, distantly related to Rickettsiales and the candidate divisions ZB3 and TG2, associated with Cercozoa and Chrysophyta cells. This study demonstrates the power of single cell sequencing to untangle ecological interactions between uncultured protists and prokaryotes. The ISME Journal (2012) 6, 703-707; doi: 10.1038/ismej.2011.126; published online 22 September 2011
C1 [Martinez-Garcia, Manuel; Brazel, David; Poulton, Nicole J.; Swan, Brandon K.; Gomez, Monica Lluesma; Masland, Dashiell; Sieracki, Michael E.; Stepanauskas, Ramunas] Bigelow Lab Ocean Sci, Single Cell Genom Ctr, W Boothbay Harbor, ME 04575 USA.
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RP Stepanauskas, R (corresponding author), Bigelow Lab Ocean Sci, Single Cell Genom Ctr, 180 McKown Point Rd, W Boothbay Harbor, ME 04575 USA.
EM rstepanauskas@bigelow.org
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NR 32
TC 97
Z9 102
PD MAR
PY 2012
VL 6
IS 3
BP 703
EP 707
DI 10.1038/ismej.2011.126
UT WOS:000300883200022
DA 2025-07-30
ER

PT J
AU Feingersch, R
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   Shmoish, M
   Sharon, I
   Sabehi, G
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AF Feingersch, Roi
   Suzuki, Marcelino T.
   Shmoish, Michael
   Sharon, Itai
   Sabehi, Gazalah
   Partensky, Frederic
   Beja, Oded
TI Microbial community genomics in eastern Mediterranean Sea surface waters
SO ISME JOURNAL
DT Article
AB Offshore waters of the eastern Mediterranean Sea are one of the most oligotrophic regions on Earth in which the primary productivity is phosphorus limited. To study the unexplored function and physiology of microbes inhabiting this system, we have analyzed a genomic library from the eastern Mediterranean Sea surface waters by sequencing both termini of nearly 5000 clones. Genome recruitment strategies showed that the majority of high-scoring pairs corresponded to genomes from the Alphaproteobacteria (SAR11-like and Rhodobacterales), Cyanobacteria (Synechococcus and high-light adapted Prochlorococcus) and diverse uncultured Gammaproteobacteria. The community structure observed, as evaluated by both protein similarity scores or metabolic potential, was similar to that found in the euphotic zone of the ALOHA station off Hawaii but very different from that of deep aphotic zones in both the Mediterranean Sea and the Pacific Ocean. In addition, a strong enrichment toward phosphate and phosphonate uptake and utilization metabolism was also observed. The ISME Journal (2010) 4, 78-87; doi:10.1038/ismej.2009.92; published online 20 August 2009
C1 [Feingersch, Roi; Sharon, Itai; Sabehi, Gazalah; Beja, Oded] Technion Israel Inst Technol, Fac Biol, IL-32000 Haifa, Israel.
   [Suzuki, Marcelino T.] Univ Maryland, Chesapeake Biol Lab, Ctr Environm Sci, College Pk, MD 20742 USA.
   [Shmoish, Michael] Technion Israel Inst Technol, Bioinformat Knowledge Unit, Lorry I Lokey Interdisciplinary Ctr Life Sci & En, IL-32000 Haifa, Israel.
   [Sharon, Itai] Technion Israel Inst Technol, Dept Comp Sci, IL-32000 Haifa, Israel.
   [Partensky, Frederic] CNRS, Roscoff, France.
   [Partensky, Frederic] Univ Paris 06, UMR 7144, Biol Stn, Roscoff, France.
RP Béjà, O (corresponding author), Technion Israel Inst Technol, Fac Biol, IL-32000 Haifa, Israel.
EM beja@techunix.technion.ac.il
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NR 57
TC 49
Z9 52
PD JAN
PY 2010
VL 4
IS 1
BP 78
EP 87
DI 10.1038/ismej.2009.92
UT WOS:000273350200007
DA 2025-07-30
ER

PT J
AU Henson, MW
   Thrash, JC
AF Henson, Michael W.
   Thrash, J. Cameron
TI Microbial ecology of northern Gulf of Mexico estuarine waters
SO MSYSTEMS
DT Article
AB Estuarine and coastal ecosystems are of high economic and ecological importance, owing to their diverse communities and the disproportionate role they play in carbon cycling, particularly in carbon sequestration. Organisms inhabiting these environments must overcome strong natural fluctuations in salinity, nutrients, and turbidity, as well as numerous climate change-induced disturbances such as land loss, sea level rise, and, in some locations, increasingly severe tropical cyclones that threaten to disrupt future ecosystem health. The northern Gulf of Mexico (nGoM) along the Louisiana coast contains dozens of estuaries, including the Mississippi-Atchafalaya River outflow, which dramatically influence the region due to their vast upstream watershed. Nevertheless, the microbiology of these estuaries and surrounding coastal environments has received little attention. To improve our understanding of microbial ecology in the understudied coastal nGoM, we conducted a 16S rRNA gene amplicon survey at eight sites and multiple time points along the Louisiana coast and one inland swamp spanning freshwater to high brackish salinities, totaling 47 duplicated Sterivex (0.2-2.7 mu m) and prefilter (>2.7 mu m) samples. We cataloged over 13,000 Amplicon Sequence ariants (ASVs) from common freshwater and marine clades such as SAR11 (Alphaproteobacteria), Synechococcus (Cyanobacteria), and acI and Candidatus Actinomarina (Actinobacteria). We observed correlations with freshwater or marine habitats in many organisms and characterized a group of taxa with specialized distributions across brackish water sites, supporting the hypothesis of an endogenous brackish-water community. Additionally, we observed brackish-water associations for several aquatic clades typically considered marine or freshwater taxa, such as SAR11 subclade II, SAR324, and the acI Actinobacteria. The data presented here expand the geographic coverage of microbial ecology in estuarine communities, help delineate the native and transitory members of these environments, and provide critical aquatic microbiological baseline data for coastal and estuarine sites in the nGoM.
C1 [Henson, Michael W.] Northern Univ, Dept Biol Sci, De Kalb, IL 60115 USA.
   [Thrash, J. Cameron] Univ Southern Calif, Dept Biol Sci, Los Angeles, CA 90007 USA.
RP Henson, MW (corresponding author), Northern Univ, Dept Biol Sci, De Kalb, IL 60115 USA.; Thrash, JC (corresponding author), Univ Southern Calif, Dept Biol Sci, Los Angeles, CA 90007 USA.
EM mhenson@niu.edu; thrash@usc.edu
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NR 108
TC 0
Z9 0
PD AUG 20
PY 2024
VL 9
IS 8
DI 10.1128/msystems.01318-23
EA JUL 2024
UT WOS:001268253300003
DA 2025-07-30
ER

PT J
AU Boeuft, D
   Lami, R
   Cunnington, E
   Jeanthon, C
AF Boeuft, Dominique
   Lami, Raphael
   Cunnington, Emelyne
   Jeanthon, Christian
TI Summer Abundance and Distribution of Proteorhodopsin Genes in the
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SO FRONTIERS IN MICROBIOLOGY
DT Article
AB Proteorhodopsins (PR) are phylogenetically diverse and highly expressed proton pumps in marine bacterial communities. The phylogenetic diversity and in situ expression of the main PR groups in polar off-shore, coastal and estuarine waters is poorly known and their abundance has not yet been reported. Here, we show that PR gene sequences of the southern Beaufort Sea including MacKenzie shelf and estuary are mainly affiliated to Gammaproteobacteria, Alphaproteobacteria, and Bacteroidetes. Substantial overlap (78%) between DNA- and cDNA-based librairies indicated in situ PR transcription within a large fraction of PR-containing community. Sets of specific qPCR primers were designed to measure the absolute abundances of the major PR types. Spatial and depth profiles showed that PR-containing bacteria were abundant throughout the photic zone, comprising up to 45% of total bacteria. Although their abundance varied greatly with location and depth, Alphaproteobacteria predominated in the PR community in all water masses, with SAR11 as the major PR type. Low nutrient concentrations rather than light were the environmental drivers that best explained the abundance and distribution of arctic PR types. Together, our data suggests that PR-based phototrophy could be the major phototrophic prokaryotic process during the Arctic Ocean summer.
C1 [Boeuft, Dominique; Cunnington, Emelyne; Jeanthon, Christian] CNRS, UMR Adaptat & Diversite Milieu Marin 7144, Stn Biol, Roscoff, France.
   [Boeuft, Dominique; Cunnington, Emelyne; Jeanthon, Christian] UPMC Univ Paris 06, Sorbonne Univ, Stn Biol, UMR Adaptat & Diversite Milieu Marin 7144, Roscoff, France.
   [Lami, Raphael] CNRS, USR 3579, Lab Biodiversite & Biotechnol Microbiennes, Banyuls Sur Mer, France.
   [Lami, Raphael] UPMC Univ Paris 06, Sorbonne Univ, USR 3579, Observ Oceanol, Banyuls Sur Mer, France.
RP Jeanthon, C (corresponding author), CNRS, UMR Adaptat & Diversite Milieu Marin 7144, Stn Biol, Roscoff, France.; Jeanthon, C (corresponding author), UPMC Univ Paris 06, Sorbonne Univ, Stn Biol, UMR Adaptat & Diversite Milieu Marin 7144, Roscoff, France.
EM jeanthon@sb-roscoff.fr
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NR 67
TC 9
Z9 9
PD OCT 13
PY 2016
VL 7
AR 1584
DI 10.3389/fmicb.2016.01584
UT WOS:000388524600001
DA 2025-07-30
ER

PT J
AU Kirchman, DL
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   DiTullio, GR
AF Kirchman, David L.
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TI Shaping of bacterial community composition and diversity by
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SO AQUATIC MICROBIAL ECOLOGY
DT Article
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C1 [Kirchman, David L.; Cottrel, Matthew T.] Univ Delaware, Sch Marine Sci & Policy, Lewes, DE 19958 USA.
   [DiTullio, Giacomo R.] Hollings Marine Lab, Coll Charleston, Charleston, SC 29412 USA.
RP Kirchman, DL (corresponding author), Univ Delaware, Sch Marine Sci & Policy, Lewes, DE 19958 USA.
EM kirchman@udel.edu
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BP 93
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ER

PT S
AU Kirchman, DL
AF Kirchman, David L.
BE Carlson, CA
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TI Growth Rates of Microbes in the Oceans
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SE Annual Review of Marine Science
DT Review; Book Chapter
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C1 [Kirchman, David L.] Univ Delaware, Sch Marine Sci & Policy, Lewes, DE 19958 USA.
RP Kirchman, DL (corresponding author), Univ Delaware, Sch Marine Sci & Policy, Lewes, DE 19958 USA.
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NR 123
TC 195
Z9 215
PY 2016
VL 8
BP 285
EP +
DI 10.1146/annurev-marine-122414-033938
UT WOS:000368369200013
DA 2025-07-30
ER

PT J
AU Lankiewicz, TS
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   Kirchman, DL
AF Lankiewicz, Thomas S.
   Cottrell, Matthew T.
   Kirchman, David L.
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SO ISME JOURNAL
DT Article
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C1 [Lankiewicz, Thomas S.; Cottrell, Matthew T.; Kirchman, David L.] Univ Delaware, Sch Marine Sci & Policy, Lewes, DE 19958 USA.
RP Kirchman, DL (corresponding author), Univ Delaware, Sch Marine Sci & Policy, Lewes, DE 19958 USA.
EM kirchman@udel.edu
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NR 73
TC 57
Z9 61
PD APR
PY 2016
VL 10
IS 4
BP 823
EP 832
DI 10.1038/ismej.2015.156
UT WOS:000372364000004
DA 2025-07-30
ER

PT J
AU Campbell, BJ
   Waidner, LA
   Cottrell, MT
   Kirchman, DL
AF Campbell, Barbara J.
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   Cottrell, Matthew T.
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TI Abundant proteorhodopsin genes in the north atlantic ocean
SO ENVIRONMENTAL MICROBIOLOGY
DT Article
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C1 [Campbell, Barbara J.; Waidner, Lisa A.; Cottrell, Matthew T.; Kirchman, David L.] Univ Delaware, Coll Marine & Earth Studies, Lewes, DE 19958 USA.
RP Kirchman, DL (corresponding author), Univ Delaware, Coll Marine & Earth Studies, Lewes, DE 19958 USA.
EM kirchman@udel.edu
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NR 39
TC 79
Z9 87
PD JAN
PY 2008
VL 10
IS 1
BP 99
EP 109
DI 10.1111/j.1462-2920.2007.01436.x
UT WOS:000252443000010
DA 2025-07-30
ER

PT J
AU Zhang, Y
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AF Zhang, Yu
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   Wang, Da-Zhi
TI Phosphoproteomics reveals essential regulatory roles of phosphorylation
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SO MARINE LIFE SCIENCE & TECHNOLOGY
DT Article; Early Access
AB Oligotrophic bacteria with reduced genomes have relatively few transcriptional regulators and are thought to rely more than other bacteria on post-transcriptional regulation to respond to environmental stimuli. SAR11 bacteria are the most abundant group of heterotrophic bacteria in marine planktonic systems and are a model for understanding genome reduction in other free-living microorganisms. Here, we report a comprehensive, quantitative protein phosphorylation profile for SAR11 strain HTCC1062 grown under various environmentally relevant conditions, including light/dark cycles, temperature differences, and nutrient limitations, to investigate phosphorylation dynamics in this streamlined organism. Nearly half of proteins encoded by the genome were detected in phosphorylated forms under at least one condition. 1014 Ser/Thr/Tyr phosphorylation sites were observed in 1576 phosphopeptides from 555 phosphoproteins. Protein phosphorylation was concentrated in proteins for functions associated with nutrient acquisition and growth, such as ABC transporters, RNA polymerase, and ribosomal proteins. Prominent patterns in protein phosphorylation were detected across a range of culture conditions. In these cells, which previously have been shown to continuously express nearly their entire proteome, protein phosphorylation was more dynamic than protein abundance, supporting the hypothesis that post-transcriptional regulation by protein phosphorylation might play a large role in modulating protein activity. Our findings support a regulatory model characterized by minimal variation in protein expression but extensive protein phosphorylation. This model diverges from bacterial regulatory paradigms reliant on transcriptional control, and may be relevant to understanding other abundant heterotrophs with reduced genomes.
C1 [Zhang, Yu; Xie, Zhang-Xian; Bai, Zhuo-An; Wang, Ming-Hua; Wang, Da-Zhi] Xiamen Univ, Coll Environm & Ecol, State Key Lab Marine Environm Sci, Xiamen 361005, Peoples R China.
   [He, Yao-Hui] Univ South China, Hengyang Med Sch, MOE Key Lab Rare Pediat Dis, Hengyang 421001, Peoples R China.
   [Xie, Zhang-Xian] Quanzhou Normal Univ, Sch Resources & Environm Sci, Key Lab Rural Environm Remediat & Waste Recycling, Quanzhou 362000, Peoples R China.
   [Hu, Guo-Sheng] Xiamen Univ, Sch Pharmaceut Sci, Fujian Prov Key Lab Innovat Drug Target Res, Xiamen 361102, Peoples R China.
   [Giovannoni, Stephen J.] Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
RP Wang, DZ (corresponding author), Xiamen Univ, Coll Environm & Ecol, State Key Lab Marine Environm Sci, Xiamen 361005, Peoples R China.; Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
EM steve.giovannoni@oregonstate.edu; dzwang@xmu.edu.cn
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Z9 0
PD 2025 JUL 15
PY 2025
DI 10.1007/s42995-025-00305-w
EA JUL 2025
UT WOS:001529142700001
DA 2025-07-30
ER

PT J
AU Thompson, AW
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AF Thompson, Anne W.
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SO PNAS NEXUS
DT Article
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C1 [Thompson, Anne W.] Portland State Univ, Dept Biol, Portland, OR 97201 USA.
   [Nyerges, Gyorgyi] Pacific Univ, Dept Biol, Forest Grove, OR 97116 USA.
   [Lamberson, Kylee M.] Portland State Univ, Dept Chem, Portland, OR 97201 USA.
   [Sutherland, Kelly R.] Univ Oregon, Oregon Inst Marine Biol, Eugene, OR 97403 USA.
RP Thompson, AW (corresponding author), Portland State Univ, Dept Biol, Portland, OR 97201 USA.
EM awt@pdx.edu
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PD FEB 29
PY 2024
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AR pgae091
DI 10.1093/pnasnexus/pgae091
EA MAR 2024
UT WOS:001190766500021
DA 2025-07-30
ER

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C1 Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
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RP Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
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TI An automated approach for the identification of horizontal gene
   transfers from complete genomes reveals the rhizome of Rickettsiales
SO BMC EVOLUTIONARY BIOLOGY
DT Article
AB Background: Horizontal gene transfer (HGT) is considered to be a major force driving the evolutionary history of prokaryotes. HGT is widespread in prokaryotes, contributing to the genomic repertoire of prokaryotic organisms, and is particularly apparent in Rickettsiales genomes. Gene gains from both distantly and closely related organisms play crucial roles in the evolution of bacterial genomes. In this work, we focus on genes transferred from distantly related species into Rickettsiales species.
   Results: We developed an automated approach for the detection of HGT from other organisms (excluding alphaproteobacteria) into Rickettsiales genomes. Our systematic approach consisted of several specialized features including the application of a parsimony method for inferring phyletic patterns followed by blast filter, automated phylogenetic reconstruction and the application of patterns for HGT detection. We identified 42 instances of HGT in 31 complete Rickettsiales genomes, of which 38 were previously unidentified instances of HGT from Anaplasma, Wolbachia, Candidatus Pelagibacter ubique and Rickettsia genomes. Additionally, putative cases with no phylogenetic support were assigned gene ontology terms. Overall, these transfers could be characterized as "rhizome-like".
   Conclusions: Our analysis provides a comprehensive, systematic approach for the automated detection of HGTs from several complete proteome sequences that can be applied to detect instances of HGT within other genomes of interest.
C1 [Phuong Thi Le; Ramulu, Hemalatha Golaconda; Guijarro, Laurent; Paganini, Julien; Gouret, Philippe; Chabrol, Olivier; Pontarotti, Pierre] Aix Marseille Univ, LATP UMR CNRS 7353, F-13331 Marseille, France.
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RP Pontarotti, P (corresponding author), Aix Marseille Univ, LATP UMR CNRS 7353, F-13331 Marseille, France.
EM Pierre.Pontarotti@univ-provence.fr
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NR 95
TC 11
Z9 14
PD DEC 12
PY 2012
VL 12
AR 243
DI 10.1186/1471-2148-12-243
UT WOS:000315049600001
DA 2025-07-30
ER

PT J
AU Miller, D
   Pfreundt, U
   Hou, S
   Lott, SC
   Hess, WR
   Berman-Frank, I
AF Miller, D.
   Pfreundt, U.
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   Lott, S. C.
   Hess, W. R.
   Berman-Frank, I.
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SO AQUATIC MICROBIAL ECOLOGY
DT Article
AB In aquatic systems, changes in temperature and irradiance fundamentally characterize the water column and regulate microbial population structure and function. In systems with stable thermal stratification, the warm surface mixed layer is typically nutrient impoverished, limiting biological production. In periods of destratification, convective mixing of the water column exposes the microorganisms inhabiting these mixed systems to rapid variations in light availability and spectra. We explored the impact of winter deep-mixing (500 m deep mixed layer) on microbial communities from the surface (2.5 m) and the aphotic waters (440 m) in the Gulf of Aqaba by examining changes in both population composition and function via DNA and RNA sequencing. The greatest fraction of 16S sequences was assigned to Euryarchaeota, while metatranscriptomes were dominated by Synechococcus transcripts. Community composition was highly similar at both depths, yet transcription profiles differed. Phototrophic organisms found at the photic surface overexpressed genes related to catabolism and energy metabolism, while genes affiliated with biosynthesis were overexpressed at the aphotic depth. Similar transcriptional trends were ob served in the non-photoautotrophs SAR11, Euryarchaeota, and Thaumarchaeota, with niche partitioning based on differential utilization of nitrogen and phosphorus occurring between the 2 archaeal groups. We did not detect upregulated expression of cyanobacterial genes indicative of mixotrophy or glycogen metabolism in the aphotic zone, suggesting they survive the aphotic period by utilizing photosynthates produced in the photic zone. Indications for a mixotrophic lifestyle were observed for prasinophytes, with genes related to phagocytosis overexpressed at the aphotic depth compared with the surface.
C1 [Miller, D.; Berman-Frank, I.] Bar Ilan Univ, Mina & Everard Goodman Fac Life Sci, Ramat Gan, Israel.
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RP Berman-Frank, I (corresponding author), Bar Ilan Univ, Mina & Everard Goodman Fac Life Sci, Ramat Gan, Israel.
EM ilana.berman-frank@biu.ac.il
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NR 119
TC 4
Z9 5
PY 2018
VL 80
IS 3
BP 223
EP 242
DI 10.3354/ame01854
UT WOS:000418366100002
DA 2025-07-30
ER

PT J
AU Kellom, M
   Pagliara, S
   Richards, TA
   Santoro, AE
AF Kellom, Matthew
   Pagliara, Stefano
   Richards, Thomas A.
   Santoro, Alyson E.
TI Exaggerated trans-membrane charge of ammonium transporters in
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SO OPEN BIOLOGY
DT Article
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RP Kellom, M; Santoro, AE (corresponding author), Univ Calif Santa Barbara, Dept Ecol Evolut & Marine Biol, Santa Barbara, CA 93117 USA.
EM mkellom@lbl.gov; asantoro@ucsb.edu
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TC 3
Z9 4
PD JUL 13
PY 2022
VL 12
IS 7
AR 220041
DI 10.1098/rsob.220041
UT WOS:000848395700001
DA 2025-07-30
ER

PT J
AU Sabehi, G
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AF Sabehi, Gazalah
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DT Article
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   Technion Israel Inst Technol, Dept Biol, IL-32000 Haifa, Israel.
   Bar Ilan Univ, Fac Life Sci, Ramat Gan, Israel.
RP Polz, MF (corresponding author), MIT, Dept Civil & Environm Engn, Cambridge, MA 02139 USA.
EM mpolz@mit.edu; beja@tx.technion.ac.il
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PD MAY
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VL 1
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BP 48
EP 55
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RP Suzuki, MT (corresponding author), Univ Maryland, Chesapeake Biol Lab, Ctr Environm Sci, Solomons, MD 20688 USA.
EM suzuki@cbl.umces.edu
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NR 64
TC 48
Z9 58
PD APR 24
PY 2008
VL 51
IS 1
BP 55
EP 66
DI 10.3354/ame01177
UT WOS:000256190600006
DA 2025-07-30
ER

PT J
AU Parsons, RJ
   Breitbart, M
   Lomas, MW
   Carlson, CA
AF Parsons, Rachel J.
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SO ISME JOURNAL
DT Article
AB There are an estimated 1030 virioplankton in the world oceans, the majority of which are phages (viruses that infect bacteria). Marine phages encompass enormous genetic diversity, affect biogeochemical cycling of elements, and partially control aspects of prokaryotic production and diversity. Despite their importance, there is a paucity of data describing virioplankton distributions over time and depth in oceanic systems. A decade of high-resolution time-series data collected from the upper 300m in the northwestern Sargasso Sea revealed recurring temporal and vertical patterns of virioplankton abundance in unprecedented detail. An annual virioplankton maximum developed between 60 and 100m during periods of summer stratification and eroded during winter convective mixing. The timing and vertical positioning of this seasonal pattern was related to variability in water column stability and the dynamics of specific picophytoplankton and heterotrophic bacterioplankton lineages. Between 60 and 100 m, virioplankton abundance was negatively correlated to the dominant heterotrophic bacterioplankton lineage SAR11, as well as the less abundant picophytoplankton, Synechococcus. In contrast, virioplankton abundance was positively correlated to the dominant picophytoplankton lineage Prochlorococcus, and the less abundant alpha-proteobacteria, Rhodobacteraceae. Seasonally, virioplankton abundances were highly synchronous with Prochl orococcus distributions and the virioplankton to Prochlorococcus ratio remained remarkably constant during periods of water column stratification. The data suggest that a significant fraction of viruses in the mid-euphotic zone of the subtropical gyres may be cyanophages and patterns in their abundance are largely determined by Prochlorococcus dynamics in response to water column stability. This high-resolution, decadal survey of virioplankton abundance provides insight into the possible controls of virioplankton dynamics in the open ocean. The ISME Journal (2012) 6, 273-284; doi: 10.1038/ismej.2011.101; published online 11 August 2011
C1 [Carlson, Craig A.] Univ Calif Santa Barbara, Dept Ecol Evolut & Marine Biol, Santa Barbara, CA 93106 USA.
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RP Carlson, CA (corresponding author), Univ Calif Santa Barbara, Dept Ecol Evolut & Marine Biol, Santa Barbara, CA 93106 USA.
EM carlson@lifesci.ucsb.edu
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TC 117
Z9 142
PD FEB
PY 2012
VL 6
IS 2
BP 273
EP 284
DI 10.1038/ismej.2011.101
UT WOS:000300984200006
DA 2025-07-30
ER

PT J
AU Willis, C
   Desai, D
   LaRoche, J
AF Willis, Ciara
   Desai, Dhwani
   LaRoche, Julie
TI Influence of 16S rRNA variable region on perceived diversity of marine
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SO FEMS MICROBIOLOGY LETTERS
DT Article
AB Marine microbes play essential roles in global energy and nutrient cycles. A primary method of determining their diversity and distribution is through sequencing of 16S ribosomal RNA genes from environmental samples. However, the perceived community composition may vary significantly based on differences in methodology, including choice of 16S variable region(s). This study investigated the influence of 16S variable region selection (V4-V5 or V6-V8) on perceived community composition and diversity for bacteria, Archaea and chloroplasts by tag-Illumina sequencing. We used 24 samples from the photic zone of the Scotian Shelf, northwest Atlantic, collected during a spring phytoplankton bloom. Taxonomic assignment and community composition varied greatly depending on the choice of variable regions while observed patterns of beta diversity were reproducible between variable regions. V4-V5 was considered the preferred variable region for future studies based on its superior recognition of Archaea, which has received little attention in bloom dynamics. The V6-V8 region captured more of the bacterial diversity, including the abundant SAR11 clades and, to a lesser extent, that of chloroplasts. However, the magnitude of difference between variable regions for bacteria and chloroplast was less than for Archaea.
C1 [Willis, Ciara; Desai, Dhwani; LaRoche, Julie] Dalhousie Univ, Dept Biol, Halifax, NS B3H 4R2, Canada.
RP LaRoche, J (corresponding author), Dalhousie Univ, Dept Biol, Halifax, NS B3H 4R2, Canada.
EM Julie.LaRoche@dal.ca
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NR 46
TC 48
Z9 50
PD JUL
PY 2019
VL 366
IS 13
AR fnz152
DI 10.1093/femsle/fnz152
UT WOS:000493065400003
DA 2025-07-30
ER

PT J
AU Kim, HJ
   Kim, KE
   Kim, YJ
   Kang, HG
   Shin, JW
   Kim, S
   Lee, SH
   Jung, SW
   Lee, TK
AF Kim, Hyun-Jung
   Kim, Kang Eun
   Kim, Yu Jin
   Kang, Hangoo
   Shin, Ji Woo
   Kim, Soohyun
   Lee, Sang Heon
   Jung, Seung Won
   Lee, Taek-Kyun
TI Marine Bacterioplankton Community Dynamics and Potentially Pathogenic
   Bacteria in Seawater around Jeju Island, South Korea, via Metabarcoding
SO INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
DT Article
AB Understanding marine bacterioplankton composition and distribution is necessary for improving predictions of ecosystem responses to environmental change. Here, we used 16S rRNA metabarcoding to investigate marine bacterioplankton diversity and identify potential pathogenic bacteria in seawater samples collected in March, May, September, and December 2013 from two sites near Jeju Island, South Korea. We identified 1343 operational taxonomic units (OTUs) and observed that community diversity varied between months. Alpha- and Gamma-proteobacteria were the most abundant classes, and in all months, the predominant genera were Candidatus Pelagibacter, Leisingera, and Citromicrobium. The highest number of OTUs was observed in September, and Vibrio (7.80%), Pseudoalteromonas (6.53%), and Citromicrobium (6.16%) showed higher relative abundances or were detected only in this month. Water temperature and salinity significantly affected bacterial distribution, and these conditions, characteristic of September, were adverse for Aestuariibacter but favored Citromicrobium. Potentially pathogenic bacteria, among which Vibrio (28 OTUs) and Pseudoalteromonas (six OTUs) were the most abundant in September, were detected in 49 OTUs, and their abundances were significantly correlated with water temperature, increasing rapidly in September, the warmest month. These findings suggest that monthly temperature and salinity variations affect marine bacterioplankton diversity and potential pathogen abundance.
C1 [Kim, Hyun-Jung; Kim, Kang Eun; Kim, Yu Jin; Shin, Ji Woo; Kim, Soohyun; Jung, Seung Won] Korea Inst Ocean Sci & Technol, Lib Marine Samples, Geoje 53201, South Korea.
   [Kim, Hyun-Jung; Lee, Sang Heon] Pusan Natl Univ, Dept Oceanog, Busan 46241, South Korea.
   [Kim, Hyun-Jung; Lee, Sang Heon] Pusan Natl Univ, Marine Res Inst, Busan 46241, South Korea.
   [Kim, Kang Eun; Kim, Yu Jin; Jung, Seung Won; Lee, Taek-Kyun] Univ Sci & Technol, Dept Ocean Sci, Daejeon 34113, South Korea.
   [Kang, Hangoo] Korea Inst Ocean Sci & Technol, Vessel Operat & Observat Team, Geoje 53201, South Korea.
   [Lee, Taek-Kyun] Korea Inst Ocean Sci & Technol, Ecol Risk Res Dept, Geoje 53201, South Korea.
RP Jung, SW (corresponding author), Korea Inst Ocean Sci & Technol, Lib Marine Samples, Geoje 53201, South Korea.; Jung, SW; Lee, TK (corresponding author), Univ Sci & Technol, Dept Ocean Sci, Daejeon 34113, South Korea.; Lee, TK (corresponding author), Korea Inst Ocean Sci & Technol, Ecol Risk Res Dept, Geoje 53201, South Korea.
EM diatoms@kiost.ac.kr; tklee@kiost.ac.kr
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NR 104
TC 3
Z9 3
PD SEP
PY 2023
VL 24
IS 17
AR 13561
DI 10.3390/ijms241713561
UT WOS:001144825800001
DA 2025-07-30
ER

PT J
AU Lajnef, R
   Quéméneur, M
   Abdennadher, M
   Walha, LD
   Hamza, A
   Belhassen, M
   Zouari, AB
AF Lajnef, Rim
   Quemeneur, Marianne
   Abdennadher, Moufida
   Walha, Lamia Dammak
   Hamza, Asma
   Belhassen, Malika
   Zouari, Amel Bellaaj
TI Prokaryotic Diversity and Dynamics during Dinoflagellate Bloom Decays in
   Coastal Tunisian Waters
SO DIVERSITY-BASEL
DT Article
AB (1) Background: Harmful algal blooms (HABs) can negatively impact marine ecosystems, but few studies have evaluated the microbial diversity associated with HABs and its potential role in the fates of these proliferations. (2) Methods: Marine prokaryotic diversity was investigated using high-throughput sequencing of the 16S rRNA gene during the bloom declines of two dinoflagellates detected in the summer of 2019 along the northern and southern Tunisian coasts (South Mediterranean Sea). The species Gymnodinium impudicum (Carthage, Tunis Gulf) and Alexandrium minutum (Sfax, Gabes Gulf) were identified using microscopy and molecular methods and were related to physicochemical factors and prokaryotic compositions. (3) Results: The abundance of G. impudicum decreased over time with decreasing phosphate concentrations. During the G. impudicum bloom decay, prokaryotes were predominated by the archaeal MGII group (Thalassarchaeaceae), Pelagibacterales (SAR11), Rhodobacterales, and Flavobacteriales. At Sfax, the abundance of A. minutum declined with decreasing phosphate concentrations and increasing pH. At the A. minutum peak, prokaryotic communities were largely dominated by anoxygenic phototrophic sulfur-oxidizing Chromatiaceae (Gammaproteobacteria) before decreasing at the end of the survey. Both the ubiquitous archaeal MGII group and Pelagibacterales were found in low proportions during the A. minutum decay. Contrary to the photosynthetic Cyanobacteria, the photo-autotrophic and -heterotrophic Rhodobacterales and Flavobacteriales contents remained stable during the dinoflagellate bloom decays. (4) Conclusions: These results indicated changes in prokaryotic community diversity during dinoflagellate bloom decays, suggesting different bacterial adaptations to environmental conditions, with stable core populations that were potentially able to degrade HABs.
C1 [Lajnef, Rim; Abdennadher, Moufida; Walha, Lamia Dammak; Hamza, Asma; Belhassen, Malika; Zouari, Amel Bellaaj] Inst Natl Sci & Technol Mer, 28 Rue 2 Mars 1934, Salammbo 2025, Tunisia.
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RP Zouari, AB (corresponding author), Inst Natl Sci & Technol Mer, 28 Rue 2 Mars 1934, Salammbo 2025, Tunisia.; Quéméneur, M (corresponding author), Univ Toulon & Var, Aix Marseille Univ, CNRS, IRD,MIO UM 110, Marseille, France.
EM amel.zouari@instm.rnrt.tn
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NR 101
TC 1
Z9 1
PD FEB
PY 2023
VL 15
IS 2
AR 273
DI 10.3390/d15020273
UT WOS:000939041200001
DA 2025-07-30
ER

PT J
AU Ngugi, DK
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AF Ngugi, David Kamanda
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TI Biogeography of pelagic bacterioplankton across an antagonistic
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SO MOLECULAR ECOLOGY
DT Article
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C1 [Ngugi, David Kamanda; Antunes, Andre; Stingl, Ulrich] King Abdullah Univ Sci & Technol, Red Sea Res Ctr, Thuwal 239556900, Saudi Arabia.
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RP Ngugi, DK (corresponding author), King Abdullah Univ Sci & Technol, Red Sea Res Ctr, 4700 KAUST, Thuwal 239556900, Saudi Arabia.
EM david.ngugi@kaust.edu.sa
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NR 105
TC 96
Z9 100
PD JAN
PY 2012
VL 21
IS 2
BP 388
EP 405
DI 10.1111/j.1365-294X.2011.05378.x
UT WOS:000298845600013
DA 2025-07-30
ER

PT J
AU Feingersch, R
   Béjà, O
AF Feingersch, Roi
   Beja, Oded
TI Bias in assessments of marine SAR11 biodiversity in environmental fosmid
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SO ISME JOURNAL
DT Editorial Material
C1 [Feingersch, Roi; Beja, Oded] Technion Israel Inst Technol, Fac Biol, Haifa, Israel.
RP Feingersch, R (corresponding author), Technion Israel Inst Technol, Fac Biol, Haifa, Israel.
EM beja@tx.technion.ac.il
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NR 19
TC 12
Z9 12
PD OCT
PY 2009
VL 3
IS 10
BP 1117
EP 1119
DI 10.1038/ismej.2009.80
UT WOS:000270783100001
DA 2025-07-30
ER

PT J
AU Malmstrom, RR
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AF Malmstrom, Rex R.
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TI Diversity, abundance, and biomass production of bacterial groups in the
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SO AQUATIC MICROBIAL ECOLOGY
DT Article
AB To better understand links between the diversity and activity of bacterial communities in the Arctic Ocean, the surface waters of the Chukchi Sea were examined by clone library analysis and by a combination of fluorescence in situ hybridization (FISH) and microautoradiography. About 60% of the 16S rRNA sequences from the library had closest BLAST hits to bacteria found previously in the Arctic, and some of these sequences appear to be restricted to polar waters. The number of operational taxonomic units in the library dropped by more than half when sequences were grouped at 99% sequence similarity, indicating that the library was composed of several bacterial clusters with high sequence similarity. Oligonucleotide probes were designed to enumerate some bacterial groups found in the clone library such as the Arctic96B-16 cluster, Roseobacter RCA cluster, AGG58 cluster, and Polaribacter clade. FISH analyses revealed that each of these groups typically accounted for 3 to 10% of prokaryotes, while well known cosmopolitan groups like the SAR86 and SAR11 clades made up 8 and 25% of the prokaryotic communities, respectively. Overall, > 60% of total prokaryotes belonged to 8 specific bacterial groups, of which the SAR11 clade was the most diverse (< 13% 16S rRNA sequence difference). Together the Arctic96B-16, Roseobacter RCA, Polaribacter, and SARI 1 clades also accounted for 25 to 82% of biomass production at 4 locations, as determined by a combination of FISH and microautoradiography of H-3-leucine assimilation. These results indicate that community composition and biomass production in the western Arctic Ocean are dominated by a few bacterial groups.
C1 Univ Delaware, Coll Marine & Earth Studies, Lewes, DE 19958 USA.
RP Kirchman, DL (corresponding author), Univ Delaware, Coll Marine & Earth Studies, Lewes, DE 19958 USA.
EM kirchman@udel.edu
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NR 42
TC 102
Z9 112
PD APR 3
PY 2007
VL 47
IS 1
BP 45
EP 55
DI 10.3354/ame047045
UT WOS:000246081700005
DA 2025-07-30
ER

PT J
AU Weinbauer, MG
   Kerros, ME
   Motegi, C
   Wilhartitz, IC
   Rassoulzadegan, F
   Torréton, JP
   Mari, X
AF Weinbauer, Markus G.
   Kerros, Marie-Emmanuelle
   Motegi, Chiaki
   Wilhartitz, Ines C.
   Rassoulzadegan, Fereidoun
   Torreton, Jean-Pascal
   Mari, Xavier
TI Bacterial community composition and potential controlling mechanisms
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SO AQUATIC MICROBIAL ECOLOGY
DT Article
AB Bacterial abundance and community composition were investigated along trophic gradients in the barrier reef lagoon of Noumea, New Caledonia. Bacterial abundance and the percentage of high nucleic acid (%HNA) bacteria (a potential indicator for bacterial production) increased from offshore waters towards the head of the bays. 16S rRNA gene PCR and denaturing gradient gel electrophoresis (DGGE) were used as genetic fingerprints for assessing differences in bacterial community composition. Sequences of DGGE bands were assigned to (1) the genera Rugeria and Roseobacter (Rhodobacteriaceae), (2) the SAR11 cluster, (3) other Alphaproteobacteria, and (4) the genus Alteromonas. Removal of the operationally defined attached bacteria by prefiltration did not affect community profiles in offshore waters but had a strong influence in the bays, probably clue to the much higher particle load and thus, attached bacteria in the bays. For the free-living community, the number of bands decreased linearly with increasing water residence time, chlorophyll a concentration, and viral abundance. Specific bands were found for offshore waters and the 2 investigated semi-enclosed bays, whereas the lagoon showed no specific bands. A similarity analysis showed specific clusters for offshore water, the lagoon, and the bays. A principle component analysis together with cluster and correlation analysis indicated that water residence time, viruses, and a complex top-down cascading effect of ciliate grazers on flagellates influenced community composition. Also, data from fingerprints of the total and free-living communities suggest that the free-living and the attached community are controlled by different mechanisms.
C1 [Weinbauer, Markus G.; Kerros, Marie-Emmanuelle; Motegi, Chiaki; Rassoulzadegan, Fereidoun] Univ Paris 06, Microbial Ecol & Biogeochem Grp, Lab Oceanog Villefranche, F-06230 Villefranche Sur Mer, France.
   [Weinbauer, Markus G.; Kerros, Marie-Emmanuelle; Motegi, Chiaki; Rassoulzadegan, Fereidoun] CNRS, Lab Oceanog Villefranche, F-06230 Villefranche Sur Mer, France.
   [Wilhartitz, Ines C.] EAWAG Swiss Fed Inst Aquat Sci & Technol, CH-8600 Dubendorf, Switzerland.
   [Torreton, Jean-Pascal; Mari, Xavier] IRD, Noumea Ctr, Noumea 98848, New Caledonia.
RP Weinbauer, MG (corresponding author), Univ Paris 06, Microbial Ecol & Biogeochem Grp, Lab Oceanog Villefranche, F-06230 Villefranche Sur Mer, France.
EM wein@obs-vlfr.fr
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NR 74
TC 20
Z9 21
PY 2010
VL 60
IS 1
BP 15
EP 28
DI 10.3354/ame01411
UT WOS:000278021400002
DA 2025-07-30
ER

PT J
AU Williams, TJ
   Ertan, H
   Ting, L
   Cavicchioli, R
AF Williams, Timothy J.
   Ertan, Haluk
   Ting, Lily
   Cavicchioli, Ricardo
TI Carbon and nitrogen substrate utilization in the marine bacterium
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SO ISME JOURNAL
DT Article
AB Sphingopyxis alaskensis is a marine member of the Alphaproteobacteria that is adapted to heterotrophic growth under nutrient-depleted (oligotrophic) conditions. S. alaskensis strain RB2256 is an ultramicrobacterium (cell volume <0.1 mu m(3)), and has a genome size larger than that of the ultramicrobacterium 'Candidatus Pelagibacter ubique' HTCC1062 (SAR11 clade of Alphaproteobacteria): 3.35 versus 1.31 Mbp. In this study, we investigate the carbon and nitrogen metabolism of strain RB2256 using an integrated approach that combines growth and enzyme assays, proteomics and genome analysis. S. alaskensis is able to use specific amino acids and putrescine as a sole carbon and nitrogen source, and higher energy-yielding substrates such as glucose and trehalose as carbon sources. Alanine, in particular, emerges as a very important substrate in S. alaskensis metabolism. In an oligotrophic environment where competition for nutrients is intense, our data support a simplified metabolism for S. alaskensis in which the fate of certain substrates is constrained, especially at the intersections of central carbon and nitrogen metabolism, in order to ensure optimal disposition of scarce resources. This is the first investigation of central metabolism for an oligotrophic ultramicrobacterium that possesses a relatively large genome size. In contrast to the behavior so far observed for SAR11 oligotrophic bacteria, S. alaskensis shows a physiological capacity to exploit increases in ambient nutrient availability and thereby achieve high-population densities. The ISME Journal (2009) 3, 1036-1052; doi:10.1038/ismej.2009.52; published online 21 May 2009
C1 [Williams, Timothy J.; Ertan, Haluk; Ting, Lily; Cavicchioli, Ricardo] Univ New S Wales, Sch Biotechnol & Biomol Sci, Sydney, NSW 2052, Australia.
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RP Cavicchioli, R (corresponding author), Univ New S Wales, Sch Biotechnol & Biomol Sci, Sydney, NSW 2052, Australia.
EM r.cavicchioli@unsw.edu.au
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NR 95
TC 36
Z9 44
PD SEP
PY 2009
VL 3
IS 9
BP 1036
EP 1052
DI 10.1038/ismej.2009.52
UT WOS:000269618300004
DA 2025-07-30
ER

PT J
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SO SYSTEMATIC AND APPLIED MICROBIOLOGY
DT Article
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C1 Netherlands Inst Ecol, Ctr Limnol, NL-3631 AC Nieuwersluis, Netherlands.
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RP Zwart, G (corresponding author), Netherlands Inst Ecol, Ctr Limnol, Rijksstraatweg 6, NL-3631 AC Nieuwersluis, Netherlands.
EM zwart@cl.nioo.knaw.nl
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NR 38
TC 158
Z9 165
PD DEC
PY 1998
VL 21
IS 4
BP 546
EP 556
DI 10.1016/S0723-2020(98)80067-2
UT WOS:000078011000010
DA 2025-07-30
ER

PT J
AU Wang, Y
   Wang, B
   Dann, LM
   Mitchell, JG
   Hu, XK
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   Zhang, H
   Sheng, YQ
AF Wang, Yibo
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   Dann, Lisa M.
   Mitchell, James G.
   Hu, Xiaoke
   Tang, Haitian
   Zhang, Hua
   Sheng, Yanqing
TI Bacterial community structure in the Bohai Strait provides insights into
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SO CONTINENTAL SHELF RESEARCH
DT Article
AB The Bohai Strait is a crucial pathway for water exchange between the Bohai Sea and the Yellow Sea, and exhibits a robust spatiotemporal pattern of hydrodynamic conditions. 16S rRNA amplicon sequencing was applied to study the spatiotemporal patterns of bacterial community composition and diversity in the Bohai Strait. Physical and chemical parameters were measured in order to explain what might control the observed patterns in community composition and diversity. In response to environmental changes between seasons, especially the dramatic changes of temperature and nutrient (NO2-N and PO4-P) levels, Synechococcus and unclassified genera in Family I predominated in summer while some oligotrophic taxa (e.g., Pelagibacter, OM43 Glade) are more abundant in winter. The spatial heterogeneity and overall patchiness of bacterial assemblages in the Bohai Strait could not be well explained by the measured factors. However, the taxa with the most spatially variable presence and absence, e.g. Vibrionaceae, SAR11 and Sva0996 marine group, possess differentiated niches for utilization of organic matter (OM) and display a close relationship with the distribution of OM sources in this area, which may indicate the significance of OM sources to bacterial community structure. Our results suggest that local factors rather than regional factors, such as dispersal limited by hydrodynamics, structure the bacterial communities in the Bohai Strait.
C1 [Wang, Yibo; Wang, Bin; Hu, Xiaoke] Chinese Acad Sci, Key Lab Coastal Biol & Bioresource Utilizat, Yantai Inst Coastal Zone Res, Yantai 264003, Peoples R China.
   [Wang, Yibo; Wang, Bin; Hu, Xiaoke] Qingdao Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao 266237, Peoples R China.
   [Wang, Yibo; Wang, Bin] Univ Chinese Acad Sci, Beijing 100049, Peoples R China.
   [Dann, Lisa M.; Mitchell, James G.] Flinders Univ S Australia, Sch Biol Sci, Adelaide, SA 5042, Australia.
   [Tang, Haitian] State Ocean Adm Peoples Republ China, Yantai Monitoring Ctr Marine Environm, Yantai 264003, Peoples R China.
   [Zhang, Hua] Chinese Acad Sci, Yantai Inst Coastal Zone Res, Key Lab Coastal Zone Environm Proc & Ecol Remedia, Yantai 264003, Peoples R China.
   [Sheng, Yanqing] Chinese Acad Sci, Res Ctr Coastal Environm Engn Technol Shandong Pr, Yantai Inst Coastal Zone Res, Yantai 264003, Peoples R China.
RP Hu, XK (corresponding author), Chinese Acad Sci, Key Lab Coastal Biol & Bioresource Utilizat, Yantai Inst Coastal Zone Res, Yantai 264003, Peoples R China.
EM xkhu@yic.ac.cn
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DA 2025-07-30
ER

PT J
AU Dadon-Pilosof, A
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AF Dadon-Pilosof, Ayelet
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DT Correction
CR Dadon-Pilosof A, 2017, NAT MICROBIOL, V2, P1608, DOI 10.1038/s41564-017-0030-5
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TC 1
Z9 1
PD DEC
PY 2017
VL 2
IS 12
BP 1696
EP 1696
DI 10.1038/s41564-017-0064-8
UT WOS:000417976600021
DA 2025-07-30
ER

PT J
AU Dupont, CL
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AF Dupont, Chris L.
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TI Genomic insights to SAR86, an abundant and uncultivated marine bacterial
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DT Article
AB Bacteria in the 16S rRNA clade SAR86 are among the most abundant uncultivated constituents of microbial assemblages in the surface ocean for which little genomic information is currently available. Bioinformatic techniques were used to assemble two nearly complete genomes from marine metagenomes and single-cell sequencing provided two more partial genomes. Recruitment of metagenomic data shows that these SAR86 genomes substantially increase our knowledge of non-photosynthetic bacteria in the surface ocean. Phylogenomic analyses establish SAR86 as a basal and divergent lineage of gamma-proteobacteria, and the individual genomes display a temperature-dependent distribution. Modestly sized at 1.25-1.7 Mbp, the SAR86 genomes lack several pathways for amino-acid and vitamin synthesis as well as sulfate reduction, trends commonly observed in other abundant marine microbes. SAR86 appears to be an aerobic chemoheterotroph with the potential for proteorhodopsin-based ATP generation, though the apparent lack of a retinal biosynthesis pathway may require it to scavenge exogenously-derived pigments to utilize proteorhodopsin. The genomes contain an expanded capacity for the degradation of lipids and carbohydrates acquired using a wealth of tonB-dependent outer membrane receptors. Like the abundant planktonic marine bacterial clade SAR11, SAR86 exhibits metabolic streamlining, but also a distinct carbon compound specialization, possibly avoiding competition. The ISME Journal (2012) 6, 1186-1199; doi:10.1038/ismej.2011.189; published online 15 December 2011
C1 [Dupont, Chris L.; Yooseph, Shibu; Lombardo, Mary-Jane; Richter, R. Alexander; Valas, Ruben; Novotny, Mark; Yee-Greenbaum, Joyclyn; Lasken, Roger S.; Nealson, Kenneth; Friedman, Robert; Venter, J. Craig] J Craig Venter Inst, San Diego, CA 92121 USA.
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RP Dupont, CL (corresponding author), J Craig Venter Inst, 10355 Sci Ctr Dr, San Diego, CA 92121 USA.
EM cdupont@jcvi.org
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PD JUN
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BP 1186
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DI 10.1038/ismej.2011.189
UT WOS:000304047800011
DA 2025-07-30
ER

PT J
AU Luria, CM
   Amaral-Zettler, LA
   Ducklow, HW
   Rich, JJ
AF Luria, Catherine M.
   Amaral-Zettler, Linda A.
   Ducklow, Hugh W.
   Rich, Jeremy J.
TI Seasonal Succession of Free-Living Bacterial Communities in Coastal
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SO FRONTIERS IN MICROBIOLOGY
DT Article
AB The marine ecosystem along the Western Antarctic Peninsula undergoes a dramatic seasonal transition every spring, from almost total darkness to almost continuous sunlight, resulting in a cascade of environmental changes, including phytoplankton blooms that support a highly productive food web. Despite having important implications for the movement of energy and materials through this ecosystem, little is known about how these changes impact bacterial succession in this region. Using 16S rRNA gene amplicon sequencing, we measured changes in free-living bacterial community composition and richness during a 9-month period that spanned winter to the end of summer. Chlorophyll a concentrations were relatively low until summer when a major phytoplankton bloom occurred, followed 3 weeks later by a high peak in bacterial production. Richness in bacterial communities varied between similar to 1,200 and 1,800 observed operational taxonomic units (OTUs) before the major phytoplankton bloom (out of similar to 43,000 sequences per sample). During peak bacterial production, OTU richness decreased to similar to 700 OTUs. The significant decrease in OTU richness only lasted a few weeks, after which time OTU richness increased again as bacterial production declined toward pre-bloom levels. OTU richness was negatively correlated with bacterial production and chlorophyll a concentrations. Unlike the temporal pattern in OTU richness, community composition changed from winter to spring, prior to onset of the summer phytoplankton bloom. Community composition continued to change during the phytoplankton bloom, with increased relative abundance of several taxa associated with phytoplankton blooms, particularly Polaribacter. Bacterial community composition began to revert toward pre-bloom conditions as bacterial production declined. Overall, our findings clearly demonstrate the temporal relationship between phytoplankton blooms and seasonal succession in bacterial growth and community composition. Our study highlights the importance of high-resolution time series sampling, especially during the relatively under-sampled Antarctic winter and spring, which enabled us to discover seasonal changes in bacterial community composition that preceded the summertime phytoplankton bloom.
C1 [Luria, Catherine M.] Brown Univ, Dept Ecol & Evolutionary Biol, Providence, RI 02912 USA.
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RP Amaral-Zettler, LA (corresponding author), Marine Biol Lab, Josephine Bay Paul Ctr Comparat Mol Biol & Evolut, Woods Hole, MA 02543 USA.; Amaral-Zettler, LA (corresponding author), Brown Univ, Dept Earth Environm & Planetary Sci, Providence, RI 02912 USA.; Rich, JJ (corresponding author), Univ Maine, Sch Marine Sci, Walpole, ME 04573 USA.; Rich, JJ (corresponding author), Univ Maine, Darling Marine Ctr, Walpole, ME 04573 USA.
EM amaral@mbl.edu; jeremy.rich@maine.edu
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NR 103
TC 52
Z9 59
PD NOV 3
PY 2016
VL 7
AR 1731
DI 10.3389/fmicb.2016.01731
UT WOS:000388683600001
DA 2025-07-30
ER

PT J
AU Henson, MW
   Lanclos, VC
   Faircloth, BC
   Thrash, JC
AF Henson, Michael W.
   Lanclos, V. Celeste
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   Thrash, J. Cameron
TI Cultivation and genomics of the first freshwater SAR11 (LD12) isolate
   (vol 12, pg 1846, 2019)
SO ISME JOURNAL
DT Correction
EM thrashc@lsu.edu
CR Henson MW, 2018, ISME J, V12, P1846, DOI 10.1038/s41396-018-0092-2
NR 1
TC 0
Z9 0
PD MAR
PY 2020
VL 14
IS 3
BP 877
EP 877
DI 10.1038/s41396-019-0569-7
UT WOS:000514576800020
DA 2025-07-30
ER

PT J
AU Sun, J
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AF Sun, Jing
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TI The abundant marine bacterium Pelagibacter simultaneously catabolizes
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SO Nature Microbiology
DT Letter
NR 0
TC 4
Z9 4
PD NOV
PY 2016
VL 1
IS 11
DI 10.1038/NMICROBIOL.2016.210
UT WOS:000389139500020
DA 2025-07-30
ER

PT J
AU Steele, JA
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   Caron, DA
   Fuhrman, JA
AF Steele, Joshua A.
   Countway, Peter D.
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   Vigil, Patrick D.
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   Kim, Diane Y.
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   Schwalbach, Michael S.
   Rose, Julie M.
   Hewson, Ian
   Patel, Anand
   Sun, Fengzhu
   Caron, David A.
   Fuhrman, Jed A.
TI Marine bacterial, archaeal and protistan association networks reveal
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SO ISME JOURNAL
DT Article
AB Microbes have central roles in ocean food webs and global biogeochemical processes, yet specific ecological relationships among these taxa are largely unknown. This is in part due to the dilute, microscopic nature of the planktonic microbial community, which prevents direct observation of their interactions. Here, we use a holistic (that is, microbial system-wide) approach to investigate time-dependent variations among taxa from all three domains of life in a marine microbial community. We investigated the community composition of bacteria, archaea and protists through cultivation-independent methods, along with total bacterial and viral abundance, and physicochemical observations. Samples and observations were collected monthly over 3 years at a well-described ocean time-series site of southern California. To find associations among these organisms, we calculated time-dependent rank correlations (that is, local similarity correlations) among relative abundances of bacteria, archaea, protists, total abundance of bacteria and viruses and physico-chemical parameters. We used a network generated from these statistical correlations to visualize and identify time-dependent associations among ecologically important taxa, for example, the SAR11 cluster, stramenopiles, alveolates, cyanobacteria and ammonia-oxidizing archaea. Negative correlations, perhaps suggesting competition or predation, were also common. The analysis revealed a progression of microbial communities through time, and also a group of unknown eukaryotes that were highly correlated with dinoflagellates, indicating possible symbioses or parasitism. Possible 'keystone' species were evident. The network has statistical features similar to previously described ecological networks, and in network parlance has non-random, small world properties (that is, highly interconnected nodes). This approach provides new insights into the natural history of microbes. The ISME Journal (2011) 5, 1414-1425; doi:10.1038/ismej.2011.24; published online 24 March 2011
C1 Univ So Calif, Dept Biol Sci, Los Angeles, CA 90089 USA.
   Univ So Calif, Wrigley Inst Environm Studies, Los Angeles, CA USA.
RP Steele, JA (corresponding author), CALTECH, Div Geol & Planetary Sci, Mail Code 100-23, Pasadena, CA 91125 USA.
EM josh.a.steele@gmail.com
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NR 60
TC 511
Z9 587
PD SEP
PY 2011
VL 5
IS 9
BP 1414
EP 1425
DI 10.1038/ismej.2011.24
UT WOS:000295782900003
DA 2025-07-30
ER

PT J
AU Liang, YT
   Wang, L
   Wang, ZM
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AF Liang, Yantao
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   Wang, Zengmeng
   Zhao, Jiulong
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   Zhang, Lihua
   Jiao, Nianzhi
   Zhang, Yongyu
TI Metagenomic Analysis of the Diversity of DNA Viruses in the Surface and
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SO FRONTIERS IN MICROBIOLOGY
DT Article
AB A metagenomic analysis of the viral community from five surface and five deep sea water (>2000 m below the surface, mbs) samples collected from the central basin of the South China Sea and adjacent Northwest Pacific Ocean during July-August 2017 was conducted herein. We builded up a South China Sea DNA virome (SCSV) dataset of 29,967 viral Operational Taxonomic Units (vOTUs), which is comparable to the viral populations from the original Tara Ocean and Malaspina expeditions. The most abundant and widespread viral populations were from the uncultivated viruses annotated from the viral metagenomics. Only 74 and 37 vOTUs have similarity with the reported genomes from the cultivated viruses and the single-virus genomics, respectively. The community structures of deep sea viromes in the SCSV were generally different from the surface viromes. The carbon flux and nutrients (PO4 and NOx) were related to the surface and deep sea viromes in the SCSV, respectively. In the SCSV, the annotated vOTUs could be affiliated to the cultivated viruses mainly including Pelagibacter (SAR11) phage HTVC010P, Prochlorococcus phages (P-GSP1, P-SSM4, and P-TIM68), Cyanophages (MED4-184 and MED4-117) and Mycobacterium phages (Sparky and Squirty). It indicated that phage infection to the SAR11 cluster may occur ubiquitously and has significant impacts on bathypelagic SAR11 communities in the deep sea. Meanwhile, as Prochlorococcus is prominently distributed in the euphotic ocean, the existence of their potential phages in the deep sea suggested the sedimentation mechanism might contribute to the formation of the deep sea viromes. Intriguingly, the presence of Mycobacterium phages only in the deep sea viromes, suggests inhabitance of endemic viral populations in the deep sea viromes in the SCSV. This study provided an insight of the viral community in the South China Sea and for the first time uncovered the deep sea viral diversity in the central basin of the South China Sea.
C1 [Liang, Yantao; Wang, Long; Wang, Zengmeng; Zhao, Jiulong; Zhang, Yongyu] Chinese Acad Sci, Qingdao Inst Bioenergy & Bioproc Technol, Key Lab Biofuels, Shandong Prov Key Lab Energy Genet, Qingdao, Shandong, Peoples R China.
   [Liang, Yantao; Yang, Qingwei; Wang, Min] Ocean Univ China, Coll Marine Life Sci, Inst Evolut & Manne Biodivers, Qingdao, Shandong, Peoples R China.
   [Liang, Yantao; Jiao, Nianzhi] Xiamen Univ, Inst Marine Microbes & Ecospheres, State Key Lab Marine Environm Sci, Xiamen, Fujian, Peoples R China.
   [Yang, Kaiguang; Zhang, Lihua] Chinese Acad Sci, Dalian Inst Chem Phys, Dalian, Peoples R China.
RP Zhang, YY (corresponding author), Chinese Acad Sci, Qingdao Inst Bioenergy & Bioproc Technol, Key Lab Biofuels, Shandong Prov Key Lab Energy Genet, Qingdao, Shandong, Peoples R China.
EM zhangyy@qibebt.ac.cn
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NR 69
TC 42
Z9 44
PD AUG 23
PY 2019
VL 10
AR 1951
DI 10.3389/fmicb.2019.01951
UT WOS:000482413400001
DA 2025-07-30
ER

PT J
AU Qin, F
   Du, S
   Zhang, ZF
   Ying, HQ
   Wu, Y
   Zhao, GY
   Yang, MY
   Zhao, YL
AF Qin, Fang
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   Ying, Hanqi
   Wu, Ying
   Zhao, Guiyuan
   Yang, Mingyu
   Zhao, Yanlin
TI Newly identified HMO-2011-type phages reveal genomic diversity and
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SO ISME JOURNAL
DT Article
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C1 [Qin, Fang; Du, Sen; Zhang, Zefeng; Ying, Hanqi; Wu, Ying; Zhao, Guiyuan; Yang, Mingyu; Zhao, Yanlin] Fujian Agr & Forestry Univ, Coll Life Sci, Fujian Prov Key Lab Agroecol Proc & Safety Monito, Fuzhou, Peoples R China.
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RP Zhao, YL (corresponding author), Fujian Agr & Forestry Univ, Coll Life Sci, Fujian Prov Key Lab Agroecol Proc & Safety Monito, Fuzhou, Peoples R China.; Zhao, YL (corresponding author), Fujian Agr & Forestry Univ, Inst Oceanol, Key Lab Marine Biotechnol Fujian Prov, Fuzhou, Peoples R China.
EM yanlinzhao@fafu.edu.cn
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NR 81
TC 11
Z9 11
PD MAY
PY 2022
VL 16
IS 5
BP 1363
EP 1375
DI 10.1038/s41396-021-01183-7
EA JAN 2022
UT WOS:000741916300002
DA 2025-07-30
ER

PT J
AU Reji, L
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AF Reji, Linta
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SO FRONTIERS IN MICROBIOLOGY
DT Article
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RP Francis, CA (corresponding author), Stanford Univ, Dept Earth Syst Sci, Stanford, CA 94305 USA.
EM caf@stanford.edu
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NR 73
TC 19
Z9 20
PD MAY 25
PY 2020
VL 11
AR 1075
DI 10.3389/fmicb.2020.01075
UT WOS:000540565100001
DA 2025-07-30
ER

PT J
AU Thingstad, TF
   Ovreås, L
   Vadstein, O
AF Thingstad, Tron Frede
   Ovreas, Lise
   Vadstein, Olav
TI Mechanisms Generating Dichotomies in the Life Strategies of
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SO DIVERSITY-BASEL
DT Article
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C1 [Thingstad, Tron Frede; Ovreas, Lise] Univ Bergen, Dept Biol Sci, N-5007 Bergen, Norway.
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RP Thingstad, TF (corresponding author), Univ Bergen, Dept Biol Sci, N-5007 Bergen, Norway.
EM frede.thingstad@uib.no; lise.ovreas@uib.no; olav.vadstein@ntnu.no
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NR 92
TC 6
Z9 7
PD MAR
PY 2022
VL 14
IS 3
AR 217
DI 10.3390/d14030217
UT WOS:000775751900001
DA 2025-07-30
ER

PT J
AU Focardi, A
   Moore, LR
   Raina, JB
   Seymour, JR
   Paulsen, IT
   Tetu, SG
AF Focardi, Amaranta
   Moore, Lisa R.
   Raina, Jean-Baptiste
   Seymour, Justin R.
   Paulsen, Ian T.
   Tetu, Sasha G.
TI Plastic leachates impair picophytoplankton and dramatically reshape the
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SO MICROBIOME
DT Article
AB Background: Each year, approximately 9.5 million metric tons of plastic waste enter the ocean with the potential to adversely impact all trophic levels. Until now, our understanding of the impact of plastic pollution on marine microorganisms has been largely restricted to the microbial assemblages that colonize plastic particles. However, plastic debris also leaches considerable amounts of chemical additives into the water, and this has the potential to impact key groups of planktonic marine microbes, not just those organisms attached to plastic surfaces.
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C1 [Focardi, Amaranta; Raina, Jean-Baptiste; Seymour, Justin R.] Univ Technol Sydney, Climate Change Cluster C3, Sydney, NSW, Australia.
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RP Focardi, A (corresponding author), Univ Technol Sydney, Climate Change Cluster C3, Sydney, NSW, Australia.; Tetu, SG (corresponding author), Macquarie Univ, Sch Nat Sci, Sydney, NSW, Australia.; Tetu, SG (corresponding author), Macquarie Univ, ARC Ctr Excellence Synthet Biol, Sydney, NSW, Australia.
EM amaranta.focardi@uts.edu.au; sasha.tetu@mq.edu.au
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TC 25
Z9 28
PD OCT 24
PY 2022
VL 10
IS 1
AR 179
DI 10.1186/s40168-022-01369-x
UT WOS:000873827400001
DA 2025-07-30
ER

PT J
AU Aldunate, M
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AF Aldunate, Montserrat
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   Ulloa, Osvaldo
TI Oxygen modulates bacterial community composition in the coastal
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SO DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY
DT Article; Proceedings Paper
CT International Symposium on Microbial Responses to Ocean Deoxygenation
CY DEC, 2016
CL Natl Inst Oceanog, Council Sci & Ind Res, INDIA
HO Natl Inst Oceanog, Council Sci & Ind Res
AB Bacterial community composition and its relationship to oxygen were investigated in the non-sulfidic shelf waters exposed to seasonal upwelling and oxygen deficiency off central Chile. Using 16S rRNA gene clone libraries, terminal restriction fragment length polymorphism (T-RFLP) and iTAG sequencing analyses of nearly 4 years of monthly sampling through the water column (5-80 m depth), we found a clear partitioning of community composition that could be attributed to dissolved oxygen (Spearman correlation coefficient = 0.578) in comparison to other environmental variables, such as light, fluorescence, temperature, salinity, microbial abundance or nutrients. Bacteroidetes (orders Sphingobacteriales and Flavobacteriales), SAR11 (subclades Ia - Candidatus Pelagibacter ubique and II), an unclassified group of Alphaproteobacteria, and SAR86 dominated in waters containing dissolved oxygen concentrations >= 70 mu M. In contrast, taxonomic groups associated with capabilities of either oxidative or reductive cycling of inorganic sulfur dominated in waters with dissolved oxygen from similar to 70 mu M to undetectable levels. The dominant groups were Arctic96BD-19, SUP05 and SAR324 (sulfur oxidation) and Desulfobacterales (sulfate reduction). Desulfobacterales are known to come primarily from sulfidic, nitrate/nitrite-depleted waters and sediments. Their presence, therefore, provides taxonomic evidence for pelagic dissimilatory sulfate reduction within oxygen-depleted coastal environments.
C1 [Aldunate, Montserrat; Bertagnolli, Anthony D.; Ulloa, Osvaldo] Univ Concepcion, Dept Oceanog, Casilla 160-C, Concepcion 4070386, Chile.
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RP Ulloa, O (corresponding author), Univ Concepcion, Dept Oceanog, Casilla 160-C, Concepcion 4070386, Chile.; Ulloa, O (corresponding author), Univ Concepcion, Inst Milenio Oceanog, Casilla 160-C, Concepcion 4070386, Chile.
EM oulloa@udec.cl
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Z9 74
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SI SI
BP 68
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DA 2025-07-30
ER

PT J
AU Meziti, A
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AF Meziti, Alexandra
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DT Article
AB Studies focusing on the temporal and spatial dynamics of bacterioplankton communities within littoral areas undergoing direct influences from the coast are quite limited. In addition, they are more complicated to resolve compared to communities in the open ocean. In order to elucidate the effects of spatial vs. temporal variability on bacterial communities in a highly land-influenced semi-enclosed gulf, surface bacterioplankton communities from five coastal sites in Igoumenitsa Gulf (Ionian Sea, Greece) were analyzed over a nine-month period using 16S rDNA 454-pyrosequencing. Temporal differences were more pronounced than spatial ones, with lower diversity indices observed during the summer months. During winter and early spring, bacterial communities were dominated by SARI 1 representatives, while this pattern changed in May when they were abruptly replaced by members of Flavobacteriales, Pseudomonadales, and Alteromonadales. Additionally, correlation analysis showed high negative correlations between the presence of SAR11 OTUs in relation to temperature and sunlight that might have driven, directly or indirectly, the disappearance of these OTUs in the summer months. The dominance of SARI 1 during the winter months further supported the global distribution of the clade, not only in the open-sea, but also in coastal systems. This study revealed that specific bacteria exhibited distinct succession patterns in an anthropogenic-impacted coastal system. The major bacterioplankton component was represented by commonly found marine bacteria exhibiting seasonal dynamics, while freshwater and terrestrial-related phylotypes were absent. (C) 2015 Elsevier GmbH. All rights reserved.
C1 [Meziti, Alexandra; Karayanni, Hera] Univ Ioannina, Dept Biol Applicat & Technol, GR-45110 Ioannina, Greece.
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RP Karayanni, H (corresponding author), Univ Ioannina, Dept Biol Applicat & Technol, GR-45110 Ioannina, Greece.
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PT J
AU Suh, SS
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DT Article
AB High-resolution 16S rRNA tag pyrosequencing was used to obtain seasonal snapshots of the bacterial diversity and community structure at two locations in Gosung Bay (South Sea, Korea) over a one year period. Seasonal sampling from the water column at each site revealed highly diverse bacterial communities containing up to 900 estimated Operational Taxonomic Units (OTUs). The Alphaproteobacteria and Gammaproteobacteria were the most abundant groups, and the most frequently recorded OTUs were members of Pelagibacter and Glaciecola. In particular, it was observed that Arcobacter, a genus of the Epsilonproteobacteria, dominated during summer. In addition, Psedoalteromonadaceae, Vibrionaceae and SAR11-1 were predominant members of the OTUs found in all sampling seasons. Environmental factors significantly influenced the bacterial community structure among season, with the phosphate and nitrate concentrations contributing strongly to the spatial distribution of the Alphaproteobacteria; the Gammaproteobacteria, Flavobacteria, and Actinobacteria all showed marked negative correlations with all measured nutrients, particularly silicon dioxide and chlorophyll-a. The results suggest that seasonal changes in environmental variables contribute to the dynamic structure of the bacterial community in the study area.
C1 [Suh, Sung-Suk; Park, Mirye; Hwang, Jinik; Jung, Seung Won; Lee, Taek-Kyun] Korea Inst Ocean Sci & Technol, South Sea Environm Res Dept, Geoje 656830, South Korea.
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RP Lee, TK (corresponding author), Korea Inst Ocean Sci & Technol, South Sea Environm Res Dept, Geoje 656830, South Korea.
EM tklee@kiost.ac
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NR 43
TC 59
Z9 63
PD JUN 29
PY 2015
VL 10
IS 6
AR e0131633
DI 10.1371/journal.pone.0131633
UT WOS:000358150400132
DA 2025-07-30
ER

PT J
AU Cao, SN
   He, JF
   Zhang, F
   Lin, L
   Gao, Y
   Zhou, QM
AF Cao, Shunan
   He, Jianfeng
   Zhang, Fang
   Lin, Ling
   Gao, Yuan
   Zhou, Qiming
TI Diversity and community structure of bacterioplankton in surface waters
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SO POLAR RESEARCH
DT Article
AB Global climate change is significantly affecting marine life off the northern tip of the Antarctic Peninsula, but little is known about microbial ecology in this area. The main goal of this study was to investigate the bacterioplankton community structure in surface waters using pyrosequencing and to determine factors influencing this community. Pelagibacterales and Rhodobacterales (Alphaproteobacteria), Oceanospirillales and Alteromonadales (Gammaproteobacteria), and Flavobacteriales (Bacteroidetes) were the core taxa in our samples, and the five most relatively abundant genera were Pelagibacter, Polaribacter, Octadecabacter, group HTCC2207 and Sulfitobacter. Although nutrients and chlorophyll a (chl a) contributed more to bacterioplankton community structure than water masses or depth, only 30.39% of the variance could be explained by the investigated environmental factors, as revealed by RDA and pRDA. No significant difference with respect to nutrients and chl a was observed among water masses or depth, as indicated by ANOVA. Furthermore, significant correlations among the dominant bacterial genera were more common than correlations between dominant genera and environmental factors, as revealed by Spearman analysis. We conclude that nutrients and chl a become homogeneous and that interpopulation interactions may have a central role in influencing the bacterial community structure in surface waters off the northern tip of the Antarctic Peninsula during the summer.
C1 [Cao, Shunan; He, Jianfeng; Zhang, Fang; Lin, Ling; Gao, Yuan] State Ocean Adm, Key Lab Polar Sci, Polar Res Inst China, 451 Jinqiao Rd, Shanghai 200136, Peoples R China.
   [Gao, Yuan] Xiamen Univ, Coll Ocean & Earth Sci, Xiamen, Fujian, Peoples R China.
   [Zhou, Qiming] Harbin Inst Technol, Sch Life Sci & Technol, Harbin, Heilongjiang, Peoples R China.
   [Zhou, Qiming] ChosenMed Technol Beijing Co Ltd, Beijing, Peoples R China.
RP He, JF (corresponding author), State Ocean Adm, Key Lab Polar Sci, Polar Res Inst China, 451 Jinqiao Rd, Shanghai 200136, Peoples R China.
EM hejianfeng@pric.org.cn
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NR 96
TC 9
Z9 12
PD MAR 21
PY 2019
VL 38
AR 3491
DI 10.33265/polar.v38.3491
UT WOS:000474230600001
DA 2025-07-30
ER

PT J
AU Martinez-Hernandez, F
   Diop, A
   Garcia-Heredia, I
   Bobay, LM
   Martinez-Garcia, M
AF Martinez-Hernandez, Francisco
   Diop, Awa
   Garcia-Heredia, Inmaculada
   Bobay, Louis-Marie
   Martinez-Garcia, Manuel
TI Unexpected myriad of co-occurring viral strains and species in one of
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SO ISME JOURNAL
DT Article
AB Viral genetic microdiversity drives adaptation, pathogenicity, and speciation and has critical consequences for the viral-host arms race occurring at the strain and species levels, which ultimately impact microbial community structure and biogeochemical cycles. Despite the fact that most efforts have focused on viral macrodiversity, little is known about the microdiversity of ecologically important viruses on Earth. Recently, single-virus genomics discovered the putatively most abundant ocean virus in temperate and tropical waters: the uncultured dsDNA virus vSAG 37-F6 infecting Pelagibacter, the most abundant marine bacteria. In this study, we report the cooccurrence of up to approximate to 1,500 different viral strains (>95% nucleotide identity) and approximate to 30 related species (80-95% nucleotide identity) in a single oceanic sample. Viral microdiversity was maintained over space and time, and most alleles were the result of synonymous mutations without any apparent adaptive benefits to cope with host translation codon bias and efficiency. Gene flow analysis used to delimitate species according to the biological species concept (BSC) revealed the impact of recombination in shaping vSAG 37-F6 virus and Pelagibacter speciation. Data demonstrated that this large viral microdiversity somehow mirrors the host species diversity since approximate to 50% of the 926 analyzed Pelagibacter genomes were found to belong to independent BSC species that do not significantly engage in gene flow with one another. The host range of this evolutionarily successful virus revealed that a single viral species can infect multiple Pelagibacter BSC species, indicating that this virus crosses not only formal BSC barriers but also biomes since viral ancestors are found in freshwater.
C1 [Martinez-Hernandez, Francisco; Garcia-Heredia, Inmaculada; Martinez-Garcia, Manuel] Univ Alicante, Dept Physiol Genet & Microbiol, Alicante, Spain.
   [Diop, Awa; Bobay, Louis-Marie] Univ North Carolina Greensboro, Dept Biol, Greensboro, NC USA.
RP Martinez-Garcia, M (corresponding author), Univ Alicante, Dept Physiol Genet & Microbiol, Alicante, Spain.
EM m.martinez@ua.es
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NR 83
TC 11
Z9 11
PD APR
PY 2022
VL 16
IS 4
BP 1025
EP 1035
DI 10.1038/s41396-021-01150-2
EA NOV 2021
UT WOS:000718076600001
DA 2025-07-30
ER

PT J
AU Stingl, U
   Desiderio, RA
   Cho, JC
   Vergin, KL
   Giovannoni, SJ
AF Stingl, Ulrich
   Desiderio, Russell A.
   Cho, Jang-Cheon
   Vergin, Kevin L.
   Giovannoni, Stephen J.
TI The SAR92 clade: an abundant coastal clade of culturable marine bacteria
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Proteorhodopsin (PR) is a protein that is abundant in marine bacterioplankton. PR is hypothesized to be a light-dependent proton pump, thus creating a proton gradient that can be used for energy production without electron transport. Currently, the only culture that has been reported to possesses PR is the highly abundant alphaproteobacterium "Candidatus Pelagibacter ubique" (SAR11 clade), but surprisingly, its growth in batch culture was not enhanced by light. Here, we present the first cultured gammaproteobacterium that possesses a PR gene. Genome sequencing and analysis of HTCC2207 showed that the PR gene is present as a lone transcriptional unit directly followed by an operon containing genes that are presumably involved in the synthesis of retinal, the chromophore of PR. Half-time decay times of different PR intermediates in native HTCC2207 cells ranged between 2 and 15 ms, and the absorbance maximum of PR was determined to be 528 run. Proteorhodopsin was identified in three additional strains, using a specific PCR assay on other cultured members of the SAR92 clade. Phylogenetic analyses of the PR genes determined that they form a deeply rooting cluster not closely related to any PR genes recovered so far. Fluorescence in situ hybridization and RNA blots showed that the SAR92 clade reaches up to 10% of the total bacterial population in surface waters close to the Oregon coast and decreases over depth and distance from the shore. Although the growth of HTCC2207 is limited by the amount of available carbon that is present in the medium applied, these cultures do not grow at higher rates nor do they have higher growth yields when incubated under light.
C1 Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
   Inha Univ, Div Life & Marine Sci, Inchon 402751, South Korea.
RP Stingl, U (corresponding author), Oregon State Univ, Dept Microbiol, Nash Hall 220, Corvallis, OR 97331 USA.
EM stinglu@science.oregonstate.edu
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NR 30
TC 122
Z9 133
PD APR
PY 2007
VL 73
IS 7
BP 2290
EP 2296
DI 10.1128/AEM.02559-06
UT WOS:000245576300031
DA 2025-07-30
ER

PT J
AU Jing, XY
   Gou, HL
   Gong, YH
   Su, XL
   Xu, L
   Ji, YT
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   Thompson, IP
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   Huang, WE
AF Jing, Xiaoyan
   Gou, Honglei
   Gong, Yanhai
   Su, Xiaolu
   Xu, La
   Ji, Yuetong
   Song, Yizhi
   Thompson, Ian P.
   Xu, Jian
   Huang, Wei E.
TI Raman-activated cell sorting and metagenomic sequencing revealing
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB It is of great significance to understand CO2 fixation in the oceans. Using single cell Raman spectra (SCRS) as biochemical profiles, Raman activated cell ejection (RACE) was able to link phenotypes and genotypes of cells. Here, we show that mini-metagenomic sequences from RACE can be used as a reference to reconstruct nearly complete genomes of key functional bacteria by binning shotgun metagenomic sequencing data. By applying this approach to C-13 bicarbonate spiked seawater from euphotic zone of the Yellow Sea of China, the dominant bacteria Synechococcus spp. and Pelagibacter spp. were revealed and both of them contain carotenoid and were able to incorporate C-13 into the cells at the same time. Genetic analysis of the reconstructed genomes suggests that both Synechococcus spp. and Pelagibacter spp. contained all genes necessary for carotenoid synthesis, light energy harvesting and CO2 fixation. Interestingly, the reconstructed genome indicates that Pelagibacter spp. harbored intact sets of genes for -carotene (precursor of retional), proteorhodopsin synthesis and anaplerotic CO2 fixation. This novel approach shines light on the role of marine microbial dark matter' in global carbon cycling, by linking yet-to-be-cultured Synechococcus spp. and Pelagibacter spp. to carbon fixation and flow activities in situ.
C1 [Jing, Xiaoyan; Gou, Honglei; Gong, Yanhai; Su, Xiaolu; Ji, Yuetong; Xu, Jian] Chinese Acad Sci, Qingdao Inst BioEnergy & Bioproc Technol, Single Cell Ctr, Key Lab Biofuels, Qingdao, Shandong, Peoples R China.
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   [Jing, Xiaoyan; Gou, Honglei; Gong, Yanhai; Su, Xiaolu; Ji, Yuetong; Xu, Jian] Univ Chinese Acad Sci, Beijing, Peoples R China.
   [Xu, La] Marine Biol Inst Shandong Prov, Dis & Fishery Drugs Res Ctr, Qingdao, Shandong, Peoples R China.
RP Xu, J (corresponding author), Chinese Acad Sci, Qingdao Inst BioEnergy & Bioproc Technol, Single Cell Ctr, Key Lab Biofuels, Qingdao, Shandong, Peoples R China.; Xu, J (corresponding author), Chinese Acad Sci, Qingdao Inst BioEnergy & Bioproc Technol, Shandong Key Lab Energy Genet, Qingdao, Shandong, Peoples R China.; Huang, WE (corresponding author), Univ Oxford, Dept Engn Sci, Parks Rd, Oxford OX1 3PJ, England.; Xu, J (corresponding author), Univ Chinese Acad Sci, Beijing, Peoples R China.
EM xujian@qibebt.ac.cn; wei.huang@eng.ox.ac.uk
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NR 66
TC 71
Z9 81
PD JUN
PY 2018
VL 20
IS 6
SI SI
BP 2241
EP 2255
DI 10.1111/1462-2920.14268
UT WOS:000441876900036
DA 2025-07-30
ER

PT J
AU Clifton, BE
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   Uechi, GI
   Jackson, CJ
   Laurino, P
AF Clifton, Ben E.
   Alcolombri, Uria
   Uechi, Gen-Ichiro
   Jackson, Colin J.
   Laurino, Paola
TI The ultra-high affinity transport proteins of ubiquitous marine bacteria
SO NATURE
DT Article
AB SAR11 bacteria are the most abundant microorganisms in the surface ocean(1) and have global biogeochemical importance(2-4). To thrive in their competitive oligotrophic environment, these bacteria rely heavily on solute-binding proteins that facilitate uptake of specific substrates via membrane transporters(5,6). The functions and properties of these transport proteins are key factors in the assimilation of dissolved organic matter and biogeochemical cycling of nutrients in the ocean, but they have remained largely inaccessible to experimental investigation. Here we performed genome-wide experimental characterization of all solute-binding proteins in a prototypical SAR11 bacterium, revealing specific functions and general trends in their properties that contribute to the success of SAR11 bacteria in oligotrophic environments. We found that the solute-binding proteins of SAR11 bacteria have extremely high binding affinity (dissociation constant >20 pM) and high binding specificity, revealing molecular mechanisms of oligotrophic adaptation. Our functional data have uncovered new carbon sources for SAR11 bacteria and enable accurate biogeographical analysis of SAR11 substrate uptake capabilities throughout the ocean. This study provides a comprehensive view of the substrate uptake capabilities of ubiquitous marine bacteria, providing a necessary foundation for understanding their contribution to assimilation of dissolved organic matter in marine ecosystems.
C1 [Clifton, Ben E.; Uechi, Gen-Ichiro; Laurino, Paola] Okinawa Inst Sci & Technol Grad Univ, Prot Engn & Evolut Unit, Onna, Japan.
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   [Jackson, Colin J.] Australian Natl Univ, Res Sch Chem, Canberra, ACT, Australia.
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   [Jackson, Colin J.] Australian Natl Univ, Res Sch Chem, ARC Ctr Excellence Synthet Biol, Canberra, ACT, Australia.
   [Laurino, Paola] Osaka Univ, Inst Prot Res, Suita, Osaka, Japan.
RP Clifton, BE; Laurino, P (corresponding author), Okinawa Inst Sci & Technol Grad Univ, Prot Engn & Evolut Unit, Onna, Japan.; Laurino, P (corresponding author), Osaka Univ, Inst Prot Res, Suita, Osaka, Japan.
EM benjamin.clifton@oist.jp; paola.laurino@oist.jp
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NR 91
TC 4
Z9 4
PD OCT 17
PY 2024
VL 634
IS 8034
BP 721
EP +
DI 10.1038/s41586-024-07924-w
EA SEP 2024
UT WOS:001336278700004
DA 2025-07-30
ER

PT J
AU Eiler, A
   Mondav, R
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AF Eiler, Alexander
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   Torrents, David
   McMahon, Katherine D.
   Andersson, Siv G. E.
   Stepanauskas, Ramunas
   Woyke, Tanja
   Bertilsson, Stefan
TI Tuning fresh: radiation through rewiring of central metabolism in
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SO ISME JOURNAL
DT Article
AB Most free-living planktonic cells are streamlined and in spite of their limitations in functional flexibility, their vast populations have radiated into a wide range of aquatic habitats. Here we compared the metabolic potential of subgroups in the Alphaproteobacteria lineage SAR11 adapted to marine and freshwater habitats. Our results suggest that the successful leap from marine to freshwaters in SAR11 was accompanied by a loss of several carbon degradation pathways and a rewiring of the central metabolism. Examples for these are C1 and methylated compounds degradation pathways, the Entner-Doudouroff pathway, the glyoxylate shunt and anapleuretic carbon fixation being absent from the freshwater genomes. Evolutionary reconstructions further suggest that the metabolic modules making up these important freshwater metabolic traits were already present in the gene pool of ancestral marine SAR11 populations. The loss of the glyoxylate shunt had already occurred in the common ancestor of the freshwater subgroup and its closest marine relatives, suggesting that the adaptation to freshwater was a gradual process. Furthermore, our results indicate rapid evolution of TRAP transporters in the freshwater clade involved in the uptake of low molecular weight carboxylic acids. We propose that such gradual tuning of metabolic pathways and transporters toward locally available organic substrates is linked to the formation of subgroups within the SAR11 clade and that this process was critical for the freshwater clade to find and fix an adaptive phenotype.
C1 [Eiler, Alexander; Mondav, Rhiannon; Sinclair, Lucas; Fernandez-Vidal, Leyden; Bertilsson, Stefan] Uppsala Univ, Dept Ecol & Genet, Limnol, Norbyvagen 18D, S-75236 Uppsala, Sweden.
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   [McMahon, Katherine D.] Univ Wisconsin, Dept Civil & Environm Engn, Madison, WI 53706 USA.
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   [Andersson, Siv G. E.] Uppsala Univ, Dept Cell & Mol Biol, Mol Evolut, Uppsala, Sweden.
   [Martinez-Garcia, Manuel] Univ Alicante, Alicante, Spain.
RP Eiler, A; Bertilsson, S (corresponding author), Uppsala Univ, Dept Ecol & Genet, Limnol, Norbyvagen 18D, S-75236 Uppsala, Sweden.; Eiler, A; Bertilsson, S (corresponding author), Uppsala Univ, Sci Life Lab, Norbyvagen 18D, S-75236 Uppsala, Sweden.
EM alexander.eiler@ebc.uu.se; stebe@ebc.uu.se
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TC 35
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PD AUG
PY 2016
VL 10
IS 8
BP 1902
EP 1914
DI 10.1038/ismej.2015.260
UT WOS:000380959800010
DA 2025-07-30
ER

PT J
AU Buchholz, HH
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   Temperton, B
AF Buchholz, Holger H.
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   Temperton, Ben
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DT Article
AB We present the genomes of two isolated bacteriophages infecting Pelagibacter ubique HTCC1062. Pelagibacter phage Mosig EXVC030M (Myoviridae) and Pelagibacter phage Lederberg EXVC029P (Podoviridae) were isolated by dilution-to-extinction culturing from the oxygen minimum zone at Devil's Hole (Harrington Sound, Bermuda).
C1 [Buchholz, Holger H.; Michelsen, Michelle; Temperton, Ben] Univ Exeter, Sch Biosci, Exeter, Devon, England.
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RP Temperton, B (corresponding author), Univ Exeter, Sch Biosci, Exeter, Devon, England.
EM b.temperton@exeter.ac.uk
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TC 4
Z9 4
PD FEB
PY 2021
VL 10
IS 7
AR e01325-20
DI 10.1128/MRA.01325-20
UT WOS:000620705900004
DA 2025-07-30
ER

PT J
AU Zubkov, MV
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AF Zubkov, Mikhail V.
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TI Dominant oceanic bacteria secure phosphate using a large extracellular
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SO NATURE COMMUNICATIONS
DT Article
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RP Zubkov, MV (corresponding author), Natl Oceanog Ctr, Ocean Biogeochem & Ecosyst Res Grp, European Way, Southampton SO14 3ZH, Hants, England.
EM mvz@noc.ac.uk
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NR 27
TC 21
Z9 22
PD JUL
PY 2015
VL 6
AR 7878
DI 10.1038/ncomms8878
UT WOS:000358862100005
DA 2025-07-30
ER

PT J
AU Rodríguez-Blanco, A
   Ghiglione, JF
   Catala, P
   Casamayor, EO
   Lebaron, P
AF Rodriguez-Blanco, Arturo
   Ghiglione, Jean-Francois
   Catala, Philippe
   Casamayor, Emilio O.
   Lebaron, Philippe
TI Spatial comparison of total vs. active bacterial populations by coupling
   genetic fingerprinting and clone library analyses in the NW
   Mediterranean Sea
SO FEMS MICROBIOLOGY ECOLOGY
DT Article
AB Spatial distributions of both total (i.e. 16S rDNA-based fingerprints) and active (i.e. 16S rRNA-based fingerprints) bacterial populations, together with total bacterial activity measured by H-3-leucine incorporation, were studied along a 98 km transect in the NW Mediterranean Sea. Capillary electrophoresis-single strand conformation polymorphism (CE-SSCP) fingerprinting was coupled to a clone library, allowing CE-SSCP peaks identification and the monitoring of the spatial variation of bacterial phylotypes. Up to 80% of the community peaks matched those obtained from clone library sequences, accounting for 86.7% of the total fingerprinting area. A good agreement was found between the relative abundance of Prochlorococcus in the CE-SSCP fingerprints and flow cytometry counts (r(2)=0.66, P < 0.05). The largest differences between total and active bacterial populations distribution were found at depths with higher bacterial activity (i.e. surface and deep chlorophyll maximum, DCM). SAR11 at the surface and Gammaproteobacteria at the DCM were the most abundant groups on the 16S rDNA-based fingerprints. However, their ratio of relative importance between rRNA : rDNA was < 1 in most cases. Conversely, ratios observed for Prochlorococcus, were consistently > 1 both at the surface and at the DCM. These results emphasize the need for combining rDNA- and rRNA-based analyses to better understand the functional role of individual bacterial populations in situ.
C1 [Ghiglione, Jean-Francois] Univ Paris 06, CNRS, UMR 7621, UPMC,Lab Oceanog Biol Banyuls, F-66650 Banyuls Sur Mer, France.
   [Rodriguez-Blanco, Arturo; Ghiglione, Jean-Francois; Catala, Philippe; Lebaron, Philippe] Univ Paris 06, UPMC, UMR 7621, Lab Arago, F-66650 Banyuls Sur Mer, France.
   [Casamayor, Emilio O.] CSIC, CEAB, Dept Continental Ecol, Limnol Grp, Girona, Spain.
RP Ghiglione, JF (corresponding author), Univ Paris 06, CNRS, UMR 7621, UPMC,Lab Oceanog Biol Banyuls, Ave Fontaule,BP44, F-66650 Banyuls Sur Mer, France.
EM ghiglione@obs-banyuls.fr
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NR 46
TC 29
Z9 30
PD JAN
PY 2009
VL 67
IS 1
BP 30
EP 42
DI 10.1111/j.1574-6941.2008.00591.x
UT WOS:000261622000004
DA 2025-07-30
ER

PT J
AU Lee, PO
   McLellan, SL
   Graham, LE
   Young, EB
AF Lee, Philip O.
   McLellan, Sandra L.
   Graham, Linda E.
   Young, Erica B.
TI Invasive dreissenid mussels and benthic algae in Lake Michigan:
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SO FEMS MICROBIOLOGY ECOLOGY
DT Article
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C1 [Lee, Philip O.; Young, Erica B.] Univ Wisconsin, Dept Biol Sci, Milwaukee, WI 53201 USA.
   [McLellan, Sandra L.; Young, Erica B.] Univ Wisconsin, Sch Freshwater Sci, Milwaukee, WI 53204 USA.
   [Graham, Linda E.] Univ Wisconsin, Dept Bot, Madison, WI 53706 USA.
RP Young, EB (corresponding author), Univ Wisconsin, Dept Biol Sci, 3209 N Maryland Ave, Milwaukee, WI 53201 USA.
EM ebyoung@uwm.edu
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NR 55
TC 14
Z9 18
PD JAN
PY 2015
VL 91
IS 1
BP 1
EP 12
DI 10.1093/femsec/fiu001
UT WOS:000352781000001
DA 2025-07-30
ER

PT J
AU Henson, MW
   Pitre, DM
   Weckhorst, JL
   Lanclos, VC
   Webber, AT
   Thrash, JC
AF Henson, Michael W.
   Pitre, David M.
   Weckhorst, Jessica Lee
   Lanclos, V. Celeste
   Webber, Austen T.
   Thrash, J. Cameron
TI Artificial Seawater Media Facilitate Cultivating Members of the
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SO MSPHERE
DT Article
AB High-throughput cultivation studies have been successful at bringing numerous important marine bacterioplankton lineages into culture, yet these frequently utilize natural seawater media that can hamper portability, reproducibility, and downstream characterization efforts. Here we report the results of seven experiments with a set of newly developed artificial seawater media and evaluation of cultivation success via comparison with community sequencing data from the inocula. Eighty-two new isolates represent highly important marine clades, including SAR116, OM60/NOR5, SAR92, Roseobacter, and SAR11. For many, isolation with an artificial seawater medium is unprecedented, and several organisms are also the first of their type from the Gulf of Mexico. Community analysis revealed that many isolates were among the 20 most abundant organisms in their source inoculum. This method will expand the accessibility of bacterioplankton cultivation experiments and improve repeatability by avoiding normal compositional changes in natural seawater.
   IMPORTANCE The difficulty in cultivating many microbial taxa vexes researchers intent on understanding the contributions of these organisms to natural systems, particularly when these organisms are numerically abundant, and many cultivation attempts recover only rare taxa. Efforts to improve this conundrum with marine bacterioplankton have been successful with natural seawater media, but that approach suffers from a number of drawbacks and there have been no comparable artificial alternatives created in the laboratory. This work demonstrates that a newly developed suite of artificial seawater media can successfully cultivate many of the most abundant taxa from seawater samples and many taxa previously only cultivated with natural seawater media. This methodology therefore significantly simplifies efforts to cultivate bacterioplankton and greatly improves our ability to perform physiological characterization of cultures postisolation.
C1 [Henson, Michael W.; Pitre, David M.; Weckhorst, Jessica Lee; Lanclos, V. Celeste; Webber, Austen T.; Thrash, J. Cameron] Louisiana State Univ, Dept Biol Sci, Baton Rouge, LA 70803 USA.
RP Thrash, JC (corresponding author), Louisiana State Univ, Dept Biol Sci, Baton Rouge, LA 70803 USA.
EM thrashc@lsu.edu
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NR 46
TC 54
Z9 58
PD MAR-APR
PY 2016
VL 1
IS 2
AR e00028-16
DI 10.1128/mSphere.00028-16
UT WOS:000392584700006
DA 2025-07-30
ER

PT J
AU Whittaker, GR
AF Whittaker, Geraint Rhys
TI A song for Pelagibacter. Using creative improvisation as a tool
   for novel science communication through the Ocean Science Jam
SO FRONTIERS IN MARINE SCIENCE
DT Article
AB Sharing complex oceanic research in an accessible way with the public is being identified by scientific institutions, universities, governmental departments, and NGOs as a critical intervention in promoting better engagement with the sea. Art-science collaborations play an integral role in this. Traditionally, these involve pairing artists and marine scientists to work on a project which is then presented to an audience. Increasingly however more interactive relationships with the public are being seen as a beneficial way to merge art and scientific data. The Ocean Science Jam is such a project that brings musicians, artists, dancers, performers, and the public together to respond creatively in real time to visual and audio cues based on a theme related to marine scientists' work. By mixing creativity with science in an integrative way the Ocean Science Jam not only acts as tool for public communication but also opens new ways for scientific data to be interpreted by non-scientists. This paper will explore this initiative from design to delivery highlighting the results of facilitating with the public moments where new responses to ocean science can be created through art. It will do so by combining the reflections of the creator of the Ocean Science Jam as well as feedback from the scientists and public who have participated. It will argue for the benefits of using improvisation and artistic co-creation for developing moments of embodied oceanic exchange and connection.
C1 [Whittaker, Geraint Rhys] Carl von Ossietzky Univ Oldenburg, Helmholtz Inst Funct Marine Biodivers, HIFMB, Oldenburg, Germany.
   [Whittaker, Geraint Rhys] Alfred Wegener Inst, Helmholtz Ctr Polar & Marine Res, Bremerhaven, Germany.
RP Whittaker, GR (corresponding author), Carl von Ossietzky Univ Oldenburg, Helmholtz Inst Funct Marine Biodivers, HIFMB, Oldenburg, Germany.; Whittaker, GR (corresponding author), Alfred Wegener Inst, Helmholtz Ctr Polar & Marine Res, Bremerhaven, Germany.
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NR 75
TC 0
Z9 0
PD NOV 5
PY 2024
VL 11
AR 1430701
DI 10.3389/fmars.2024.1430701
UT WOS:001357846300001
DA 2025-07-30
ER

PT J
AU Mausz, MA
   Airs, RL
   Dixon, JL
   Widdicombe, CE
   Tarran, GA
   Polimene, L
   Dashfield, S
   Beale, R
   Scanlan, DJ
   Chen, Y
AF Mausz, Michaela A.
   Airs, Ruth L.
   Dixon, Joanna L.
   Widdicombe, Claire E.
   Tarran, Glen A.
   Polimene, Luca
   Dashfield, Sarah
   Beale, Rachael
   Scanlan, David J.
   Chen, Yin
TI Microbial uptake dynamics of choline and glycine betaine in coastal
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SO LIMNOLOGY AND OCEANOGRAPHY
DT Article
AB Choline and glycine betaine (GBT) are utilized as osmolytes to counteract osmotic stress, but also constitute important nutrient sources for many marine microbes. Bacterial catabolism of these substrates can then lead to the production of climate active trace gases such as methylamine and methane. Using radiotracers, we investigated prokaryotic choline/GBT uptake and determined biotic and abiotic factors driving these processes in the Western English Channel, UK. Kinetic uptake parameters indicated high affinity (nM range) for both osmolytes and showed a seasonal pattern for choline uptake. Generalized linear modeling of uptake parameters suggested a significant influence of sea surface temperature and salinity on prokaryotic uptake of both osmolytes. The presence of diatoms significantly influenced prokaryotic choline/GBT uptake dynamics. Choline uptake was further related to the occurrence of Phaeocystis spp., which were highly abundant in the phytoplankton community during spring, and dinoflagellates abundance during summer. While Rhodobacteraceae were the most important bacterial drivers for prokaryotic choline uptake, prokaryotic GBT uptake was associated with various groups such as SAR11 (Pelagibacterales) and Gammaproteobacteria, suggesting a wider capacity for GBT catabolism than previously recognized. Furthermore, using a newly developed approach we determined the first available data for dissolved GBT concentrations in seawater and found both osmolytes to be at the sub-nanomolar range. Together, this study improves our understanding of the biogeochemical cycling of these environmentally important osmolytes and highlights how their cycles may be affected by a changing climate.
C1 [Mausz, Michaela A.; Scanlan, David J.; Chen, Yin] Univ Warwick, Sch Life Sci, Gibbet Hill Campus, Coventry, Warwick, England.
   [Airs, Ruth L.; Dixon, Joanna L.; Widdicombe, Claire E.; Tarran, Glen A.; Polimene, Luca; Dashfield, Sarah; Beale, Rachael] Plymouth Marine Lab, Plymouth, Devon, England.
RP Mausz, MA; Chen, Y (corresponding author), Univ Warwick, Sch Life Sci, Gibbet Hill Campus, Coventry, Warwick, England.
EM m.mausz@warwick.ac.uk; y.chen25@warwick.ac.uk
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PD MAY
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IS 5
BP 1052
EP 1064
DI 10.1002/lno.12056
EA MAR 2022
UT WOS:000765257500001
DA 2025-07-30
ER

PT J
AU Manrique, JM
   Jones, LR
AF Manrique, Julieta M.
   Jones, Leandro R.
TI Are ocean currents to slow to counteract SAR11 evolution? A
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SO MOLECULAR PHYLOGENETICS AND EVOLUTION
DT Correction
C1 Consejo Nacl Invest Cient & Tecn, Av Rivadavia 1917 C1083ACA, Buenos Aires, DF, Argentina.
   [Jones, Leandro R.] Univ Nacl Patagonia San Juan Bosco, Fac Ciencias Nat Sede Trelew, Lab Virol & Genet Mol, 9 Julio & Belgrano S-N 9100, Trelew, Chubut, Argentina.
RP Jones, LR (corresponding author), Univ Nacl Patagonia San Juan Bosco, Fac Ciencias Nat Sede Trelew, Lab Virol & Genet Mol, 9 Julio & Belgrano S-N 9100, Trelew, Chubut, Argentina.
EM ljones@conicet.gov.ar
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TC 0
Z9 0
PD MAY
PY 2017
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BP 150
EP 150
DI 10.1016/j.ympev.2017.03.001
UT WOS:000398877500015
DA 2025-07-30
ER

PT J
AU Mizuno, CM
   Ghai, R
   Saghaï, A
   López-García, P
   Rodriguez-Valera, F
AF Mizuno, Carolina Megumi
   Ghai, Rohit
   Saghai, Aurelien
   Lopez-Garcia, Purificacion
   Rodriguez-Valera, Francisco
TI Genomes of Abundant and Widespread Viruses from the Deep Ocean
SO MBIO
DT Article
AB The deep sea is a massive, largely oligotrophic ecosystem, stretched over nearly 65% of the planet's surface. Deep-sea planktonic communities are almost completely dependent upon organic carbon sinking from the productive surface, forming a vital component of global biogeochemical cycles. However, despite their importance, viruses from the deep ocean remain largely unknown. Here, we describe the first complete genomes of deep-sea viruses assembled from metagenomic fosmid libraries. "Candidatus Pelagibacter" (SAR11) phage HTVC010P and Puniceispirillum phage HMO-2011 are considered the most abundant cultured marine viruses known to date. Remarkably, some of the viruses described here recruited as many reads from deep waters as these viruses do in the photic zone, and, considering the gigantic scale of the bathypelagic habitat, these genomes provide information about what could be some of the most abundant viruses in the world at large. Their role in the viral shunt in the global ocean could be very significant. Despite the challenges encountered in inferring the identity of their hosts, we identified one virus predicted to infect members of the globally distributed SAR11 cluster. We also identified a number of putative proviruses from diverse taxa, including deltaproteobacteria, bacteroidetes, SAR11, and gammaproteobacteria. Moreover, our findings also indicate that lysogeny is the preferred mode of existence for deep-sea viruses inhabiting an energy-limited environment, in sharp contrast to the predominantly lytic lifestyle of their photic-zone counterparts. Some of the viruses show a widespread distribution, supporting the tenet "everything is everywhere" for the deep-ocean virome.
   IMPORTANCE The deep sea is among the largest known habitats and a critical cog in biogeochemical cycling but remains under-explored in its microbiology. Even more than is the case for its prokaryotic community, our knowledge of its viral component has remained limited by the paucity of information provided by studies dependent upon short sequence fragments. In this work, we attempt to fill this existing gap by using a combination of classical fosmid libraries with next-generation sequencing and assembly to recover long viral genomic fragments. We have sequenced ca. 6,000 fosmids from two metagenomics libraries made from prokaryotic biomass from the deep Mediterranean Sea and recovered twenty-eight complete viral genomes, all of them novel and quite distinct from all previously described viral genomes. They are preferentially found in deeper waters and are widely distributed all over the oceans. To our knowledge, this is the first report on complete and cosmopolitan viral genomes from the bathypelagic habitat.
C1 [Mizuno, Carolina Megumi; Rodriguez-Valera, Francisco] Univ Miguel Hernandez, Evolutionary Genom Grp, Alicante, Spain.
   [Mizuno, Carolina Megumi] Inst Pasteur, Dept Microbiol, Unit Mol Biol Gene Extremophiles, Paris, France.
   [Ghai, Rohit] Acad Sci Czech Republ, Inst Hydrobiol, Dept Aquat Microbial Ecol, Ctr Biol, Ceske Budejovice, Czech Republic.
   [Saghai, Aurelien; Lopez-Garcia, Purificacion] Univ Paris 11, CNRS UMR 8079, Unite Ecol Systemat & Evolut, Orsay, France.
RP Rodriguez-Valera, F (corresponding author), Univ Miguel Hernandez, Evolutionary Genom Grp, Alicante, Spain.
EM frvalera@umh.es
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NR 56
TC 73
Z9 79
PD JUL-AUG
PY 2016
VL 7
IS 4
AR e00805-16
DI 10.1128/mBio.00805-16
UT WOS:000383440500018
DA 2025-07-30
ER

PT J
AU Morris, RM
   Vergin, KL
   Cho, JC
   Rappé, MS
   Carlson, CA
   Giovannoni, SJ
AF Morris, RM
   Vergin, KL
   Cho, JC
   Rappé, MS
   Carlson, CA
   Giovannoni, SJ
TI Temporal and spatial response of bacterioplankton lineages to annual
   convective overturn at the Bermuda Atlantic Time-series Study site
SO LIMNOLOGY AND OCEANOGRAPHY
DT Article
AB We used terminal restriction fragment length polymorphism (T-RFLP), clone library, phylogenetic, and bulk nucleic acid hybridization analyses to identify and characterize spatial and temporal patterns in marine bacterioplankton communities at the Bermuda Atlantic Time-series Study (BATS) site. Nonmetric multidimensional scaling of monthly surface and 200-m bacterial 16S rDNA T-RFLP fragments from 1992 to 2002 revealed temporal trends in bacterial community structure in different depth horizons. A 200-m 16S IRNA gene clone library was used to identify fragments increasing in relative abundance following mixing events and to link observed terminal restriction fragments with those predicted from sequence data. T-RFLP fragments matching those of cloned OCS116, SAR11, and marine Actinobacteria rRNA genes exhibited the strongest increases at 200 In following convective overturn, and fragments attributable to SAR11, SAR86, and SAR116 rRNA genes exhibited the strongest increases at the ocean surface during summer time periods. Variability in the distribution and relative abundance of fragments assigned to different SAR11 and SAR86 subclusters was also evident. Quantitative hybridization of extracted 16S IRNA with radiolabeled, taxon-specific oligonucleotide probes provided additional data supporting spatial and temporal patterns of lineage distributions and abundances suggested by ordination. Overall increases in the relative abundance of T-RFLP fragments attributable to the OCS116, SAR11, and marine Actinobacteria clusters following convective overturn suggest that members of these groups may play important roles in dissolved organic carbon dynamics at BATS.
C1 Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
   Inha Univ, Dept Oceanog, Inchon 402751, South Korea.
   Univ Hawaii Manoa, Sch Ocean & Environm Sci & Technol, Hawaii Inst Marine Biol, Kaneohe, HI 96744 USA.
   Univ Calif Santa Barbara, Dept Ecol Evolut & Marine Biol, Santa Barbara, CA 93106 USA.
RP Cornell Univ, Dept Microbiol, Ithaca, NY 14851 USA.
EM rm352@cornell.edu
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NR 42
TC 214
Z9 240
PD SEP
PY 2005
VL 50
IS 5
BP 1687
EP 1696
DI 10.4319/lo.2005.50.5.1687
UT WOS:000231932800033
DA 2025-07-30
ER

PT J
AU Labbé, M
   Thaler, M
   Pitot, TM
   Rapp, JZ
   Vincent, WF
   Culley, A
AF Labbe, Myriam
   Thaler, Mary
   Pitot, Thomas M.
   Rapp, Josephine Z.
   Vincent, Warwick F.
   Culley, Alexander, I
TI Climate-Endangered Arctic Epishelf Lake Harbors Viral Assemblages with
   Distinct Genetic Repertoires
SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Viruses are key to understanding polar aquatic ecosystems, which are dominated by microorganisms. However, studies of viral communities are challenging to interpret because the vast majority of viruses are known only from sequence fragments, and their taxonomy, hosts, and genetic repertoires are unknown.
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C1 [Labbe, Myriam; Thaler, Mary; Pitot, Thomas M.; Rapp, Josephine Z.; Culley, Alexander, I] Univ Laval, Dept Biochim Microbiol & Bioinformat, Quebec City, PQ, Canada.
   [Labbe, Myriam; Thaler, Mary; Pitot, Thomas M.; Rapp, Josephine Z.; Vincent, Warwick F.; Culley, Alexander, I] Univ Laval, Inst Biol Integrat & Syst IBIS, Quebec City, PQ, Canada.
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RP Culley, A (corresponding author), Univ Laval, Dept Biochim Microbiol & Bioinformat, Quebec City, PQ, Canada.; Culley, A (corresponding author), Univ Laval, Inst Biol Integrat & Syst IBIS, Quebec City, PQ, Canada.; Culley, A (corresponding author), Univ Laval, Ctr Etud Nordiques CEN, Quebec City, PQ, Canada.
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NR 77
TC 4
Z9 4
PD SEP 13
PY 2022
VL 88
IS 17
DI 10.1128/aem.00228-22
EA AUG 2022
UT WOS:000846759500001
DA 2025-07-30
ER

PT J
AU Saini, P
   Wani, SI
   Kumar, R
   Chhabra, R
   Chimni, SS
   Sareen, D
AF Saini, Priya
   Wani, Shadil Ibrahim
   Kumar, Ranjai
   Chhabra, Ravneet
   Chimni, Swapandeep Singh
   Sareen, Dipti
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SO PROTEIN EXPRESSION AND PURIFICATION
DT Correction
C1 [Saini, Priya; Wani, Shadil Ibrahim; Kumar, Ranjai; Chhabra, Ravneet; Sareen, Dipti] Panjab Univ, Dept Biochem, Chandigarh 160014, India.
   [Chimni, Swapandeep Singh] Guru Nanak Dev Univ, Dept Chem, Amritsar 143005, Punjab, India.
RP Sareen, D (corresponding author), Panjab Univ, Dept Biochem, Sect 14, Chandigarh 160014, India.
EM diptsare@pu.ac.in
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NR 1
TC 0
Z9 0
PD AUG
PY 2015
VL 112
BP 50
EP 50
DI 10.1016/j.pep.2014.10.011
UT WOS:000355572200008
DA 2025-07-30
ER

PT J
AU Teira, E
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   Lonborg, C
   Alvarez-Salgado, XA
AF Teira, Eva
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TI Growth rates of different phylogenetic bacterioplankton groups in a
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SO ENVIRONMENTAL MICROBIOLOGY REPORTS
DT Article
AB Microbial degradation of dissolved organic matter (DOM) in planktonic ecosystems is carried out by diverse prokaryotic communities, whose growth rates and patterns of DOM utilization modulate carbon and nutrient biogeochemical cycles at local and global scales. Nine dilution experiments (September 2007 to June 2008) were conducted with surface water from the highly productive coastal upwelling system of the R a de Vigo (NW Iberian Peninsula) to estimate bacterial growth rates of six relevant marine bacterial groups: Roseobacter, SAR11, Betaproteobacteria, Gammaproteobacteria, SAR86 and Bacteroidetes. Surprisingly, SAR11 dominated over the other bacterial groups in autumn, likely associated to the entry of nutrient-rich, DOC-poor Eastern North Atlantic Central Water (ENACW) into the embayment. Roseobacter and SAR11 showed significantly opposing growth characteristics. SAR11 consistently grows at low rates (range 0.19-0.71 day(-1)), while Roseobacter has a high growth potential (range 0.70-1.64 day(-1)). In contrast, Betaproteobacteria, Bacteroidetes, SAR86 and Gammaproteobacteria growth rates widely varied among experiments. Regardless of such temporal variability, mean SAR86 growth rate (range 0.1-1.4 day(-1)) was significantly lower than that of Gammaproteobacteria (range 0.3-2.1 day(-1)). Whereas the relative abundance of different bacterial groups showed strong correlations with several environmental variables, group-specific bacterial growth rates did not co-vary with ambient conditions. Our results suggest that different bacterial groups exhibit characteristic growth rates, and, consequently, distinct competitive abilities to succeed under contrasting environmental conditions.
C1 [Teira, Eva; Martinez-Garcia, Sandra] Univ Vigo, Dept Ecol & Biol Anim, Vigo 36310, Spain.
   [Lonborg, Christian; Alvarez-Salgado, Xose A.] CSIC, Inst Invest Marinas, Vigo 36208, Spain.
   [Lonborg, Christian] Scottish Assoc Marine Sci, Oban PA37 1QA, Argyll, Scotland.
RP Teira, E (corresponding author), Univ Vigo, Dept Ecol & Biol Anim, Vigo 36310, Spain.
EM teira@uvigo.es
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NR 59
TC 70
Z9 71
PD DEC
PY 2009
VL 1
IS 6
BP 545
EP 554
DI 10.1111/j.1758-2229.2009.00079.x
UT WOS:000279517400010
DA 2025-07-30
ER

PT J
AU Reisch, CR
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AF Reisch, Chris R.
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TI Novel pathway for assimilation of dimethylsulphoniopropionate widespread
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SO NATURE
DT Article
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C1 [Reisch, Chris R.; Varaljay, Vanessa A.; Whitman, William B.] Univ Georgia, Dept Microbiol, Athens, GA 30602 USA.
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RP Whitman, WB (corresponding author), Univ Georgia, Dept Microbiol, Athens, GA 30602 USA.
EM whitman@uga.edu
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TC 123
Z9 143
PD MAY 12
PY 2011
VL 473
IS 7346
BP 208
EP +
DI 10.1038/nature10078
UT WOS:000290487200037
DA 2025-07-30
ER

PT J
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AF Bullock, Hannah A.
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DT Article
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C1 [Bullock, Hannah A.; Reisch, Chris R.; Whitman, William B.] Univ Georgia, Dept Microbiol, Athens, GA 30602 USA.
   [Burns, Andrew S.; Moran, Mary Ann] Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
RP Whitman, WB (corresponding author), Univ Georgia, Dept Microbiol, Athens, GA 30602 USA.
EM whitman@uga.edu
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PT J
AU Nakai, R
AF Nakai, Ryosuke
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C1 [Nakai, Ryosuke] Natl Inst Adv Ind Sci & Technol, Appl Mol Microbiol Res Grp, Bioprod Res Inst, 2-17-2-1 Tsukisamu Higashi, Sapporo, Hokkaido 0628517, Japan.
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RP Nakai, R (corresponding author), Natl Inst Adv Ind Sci & Technol, Appl Mol Microbiol Res Grp, Bioprod Res Inst, 2-17-2-1 Tsukisamu Higashi, Sapporo, Hokkaido 0628517, Japan.; Nakai, R (corresponding author), Natl Inst Adv Ind Sci & Technol, Microbial Ecol & Technol Res Grp, Bioprod Res Inst, 2-17-2-1 Tsukisamu Higashi, Sapporo, Hokkaido 0628517, Japan.
EM nakai-ryosuke@aist.go.jp
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NR 115
TC 55
Z9 59
PY 2020
VL 35
IS 2
AR ME20025
DI 10.1264/jsme2.ME20025
UT WOS:000585925800001
DA 2025-07-30
ER

PT J
AU Needham, DM
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AF Needham, David M.
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TI Ecological dynamics and co-occurrence among marine phytoplankton,
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DT Article
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C1 [Needham, David M.; Sachdeva, Rohan; Fuhrman, Jed A.] Univ Soouthern Calif, Dept Biol Sci, 3616 Trousdale Pkwy,AHF 107, Los Angeles, CA 90089 USA.
RP Fuhrman, JA (corresponding author), Univ Soouthern Calif, Dept Biol Sci, 3616 Trousdale Pkwy,AHF 107, Los Angeles, CA 90089 USA.
EM fuhrman@usc.edu
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NR 77
TC 139
Z9 158
PD JUL
PY 2017
VL 11
IS 7
BP 1614
EP 1629
DI 10.1038/ismej.2017.29
UT WOS:000403675200010
DA 2025-07-30
ER

PT J
AU Jackson, CR
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AF Jackson, Colin R.
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
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C1 [Jackson, Colin R.; Millar, Justin J.; Payne, Jason T.; Ochs, Clifford A.] Univ Mississippi, Dept Biol, University, MS 38677 USA.
RP Jackson, CR (corresponding author), Univ Mississippi, Dept Biol, University, MS 38677 USA.
EM cjackson@olemiss.edu
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NR 54
TC 52
Z9 64
PD DEC
PY 2014
VL 80
IS 23
BP 7186
EP 7195
DI 10.1128/AEM.01844-14
UT WOS:000344163700008
DA 2025-07-30
ER

PT J
AU Reza, MS
   Kobiyama, A
   Yamada, Y
   Ikeda, Y
   Ikeda, D
   Mizusawa, N
   Ikeo, K
   Sato, S
   Ogata, T
   Jimbo, M
   Kudo, T
   Kaga, S
   Watanabe, S
   Naiki, K
   Kaga, Y
   Mineta, K
   Bajic, V
   Gojobori, T
   Watabe, S
AF Reza, Md Shaheed
   Kobiyama, Atsushi
   Yamada, Yuichiro
   Ikeda, Yuri
   Ikeda, Daisuke
   Mizusawa, Nanami
   Ikeo, Kazuho
   Sato, Shigeru
   Ogata, Takehiko
   Jimbo, Mitsuru
   Kudo, Toshiaki
   Kaga, Shinnosuke
   Watanabe, Shiho
   Naiki, Kimiaki
   Kaga, Yoshimasa
   Mineta, Katsuhiko
   Bajic, Vladimir
   Gojobori, Takashi
   Watabe, Shugo
TI Taxonomic profiles in metagenomic analyses of free-living microbial
   communities in the Ofunato Bay
SO GENE
DT Article
AB The Ofunato Bay in Iwate Prefecture, Japan is a deep coastal bay located at the center of the Sanriku Rias Coast and considered an economically and environmentally important asset. Here, we describe the first whole genome sequencing (WGS) study on the microbial community of the bay, where surface water samples were collected from three stations along its length to cover the entire bay; we preliminarily sequenced a 0.2 pm filter fraction among sequentially size-fractionated samples of 20.0, 5.0, 0.8 and 0.2 pm filters, targeting the free-living fraction only. From the 0.27-0.34 Gb WGS library, 0.9 x 10(6)-1.2 x 10(6) reads from three sampling stations revealed 29 bacterial phyla (similar to 80% of assigned reads), 3 archaeal phyla (similar to 4%) and 59 eukaryotic phyla (similar to 15%). Microbial diversity obtained from the WGS approach was compared with 16S rRNA gene results by mining WGS metagenomes, and we found similar estimates. The most frequently recovered bacterial sequences were Proteobacteria, predominantly comprised of 18.0-19.6% Planktomarina (Family Rhodobacteraceae) and 13.7-17.5% Candidatus Pelagibacter (Family Pelagibacterales). Other dominant bacterial genera, including Polaribacter (3.5-6.1%), Flavobacterium (1.8-2.6%), Sphingobacterium (1.4-1.6%) and Cellulophaga (1.4-2.0%), were members of Bacteroidetes and likely associated with the degradation and turnover of organic matter. The Marine Group I Archaea Nitrosopumilus was also detected. Remarkably, eukaryotic green alga Bathycoccus, Ostreococcus and Micromonas accounted for 8.8 15.2%, 3.6 4.9% and 2.1-3.1% of total read counts, respectively, highlighting their potential roles in the phytoplankton bloom after winter mixing.
C1 [Reza, Md Shaheed; Kobiyama, Atsushi; Yamada, Yuichiro; Ikeda, Yuri; Ikeda, Daisuke; Mizusawa, Nanami; Ikeo, Kazuho; Sato, Shigeru; Ogata, Takehiko; Jimbo, Mitsuru; Kudo, Toshiaki; Watabe, Shugo] Kitasato Univ, Sch Marine Biosci, Minami Ku, Sagamihara, Kanagawa 2520373, Japan.
   [Kaga, Shinnosuke; Watanabe, Shiho; Naiki, Kimiaki; Kaga, Yoshimasa] Iwate Fisheries Technol Ctr, Kamaishi, Iwate 0260001, Japan.
   [Mineta, Katsuhiko; Bajic, Vladimir; Gojobori, Takashi] KAUST, Computat Biosci Res Ctr, Thuwal 239556900, Saudi Arabia.
   [Reza, Md Shaheed] Bangladesh Agr Univ, Dept Fisheries Technol, Mymensingh 2202, Bangladesh.
   [Ikeo, Kazuho] Natl Inst Genet, Mishima, Shizuoka 4118540, Japan.
   [Kaga, Shinnosuke] Iwate Prefectural Govt, Ofunato Fisheries Promot Ctr, Ofunato, Iwate 0228502, Japan.
RP Gojobori, T (corresponding author), King Abdullah Univ Sci & Technol, Biol & Environm Sci & Engn, Computat Biosci Res Ctr, Thuwal 239556900, Saudi Arabia.; Watabe, S (corresponding author), Kitasato Univ, Sch Marine Biosci, Dept Marine Biochem, Minami Ku, Sagamihara, Kanagawa 2520373, Japan.
EM takashi.gojobori@kaust.edu.sa; swatabe@kitasato-u.ac.jp
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NR 94
TC 10
Z9 10
PD JUL 30
PY 2018
VL 665
BP 192
EP 200
DI 10.1016/j.gene.2018.04.075
UT WOS:000435621900024
DA 2025-07-30
ER

PT J
AU [Anonymous]
AF [Anonymous]
TI SAR11 clade microdiversity and activity during the early spring blooms
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SO ENVIRONMENTAL MICROBIOLOGY REPORTS
DT Correction
CR Dinasquet J, 2022, ENV MICROBIOL REP, V14, P907, DOI 10.1111/1758-2229.13117
NR 1
TC 0
Z9 0
PD JUN
PY 2023
VL 15
IS 3
BP 239
EP 239
DI 10.1111/1758-2229.13151
EA APR 2023
UT WOS:000978817600001
DA 2025-07-30
ER

PT J
AU Paver, SF
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AF Paver, Sara F.
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SO MSYSTEMS
DT Article
AB Marine and freshwater microbial communities are phylogenetically distinct, and transitions between habitat types are thought to be infrequent. We compared the phylogenetic diversity of marine and freshwater microorganisms and identified specific lineages exhibiting notably high or low similarity between marine and freshwater ecosystems using a meta-analysis of 16S rRNA gene tag-sequencing data sets. As expected, marine and freshwater microbial communities differed in the relative abundance of major phyla and contained habitat-specific lineages. At the same time, and contrary to expectations, many shared taxa were observed in both habitats. Based on several metrics, we found that Gammaproteobacteria, Alphaproteobacteria, Bacteroidetes, and Betaproteobacteria contained the highest number of closely related marine and freshwater sequences, suggesting comparatively recent habitat transitions in these groups. Using the abundant alphaproteobacterial group SAR11 as an example, we found evidence that new lineages, beyond the recognized LD12 Glade, are detected in freshwater at low but reproducible abundances; this evidence extends beyond the 16S rRNA locus to core genes throughout the genome. Our results suggest that shared taxa are numerous, but tend to occur sporadically and at low relative abundance in one habitat type, leading to an underestimation of transition frequency between marine and freshwater habitats. Rare taxa with abundances near or below detection, including lineages that appear to have crossed the salty divide relatively recently, may possess adaptations enabling them to exploit opportunities for niche expansion when environments are disturbed or conditions change.
   IMPORTANCE The distribution of microbial diversity across environments yields insight into processes that create and maintain this diversity as well as potential to infer how communities will respond to future environmental changes. We integrated data sets from dozens of freshwater lake and marine samples to compare diversity across open water habitats differing in salinity. Our novel combination of sequence-based approaches revealed lineages that likely experienced a recent transition across habitat types. These taxa are promising targets for studying physiological constraints on salinity tolerance. Our findings contribute to understanding the ecological and evolutionary controls on microbial distributions, and open up new questions regarding the plasticity and adaptability of particular lineages.
C1 [Paver, Sara F.; Muratore, Daniel; Coleman, Maureen L.] Univ Chicago, Dept Geophys Sci, 5734 S Ellis Ave, Chicago, IL 60637 USA.
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RP Coleman, ML (corresponding author), Univ Chicago, Dept Geophys Sci, 5734 S Ellis Ave, Chicago, IL 60637 USA.
EM mlcoleman@uchicago.edu
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NR 85
TC 36
Z9 38
PD NOV-DEC
PY 2018
VL 3
IS 6
AR e00232-18
DI 10.1128/mSystems.00232-18
UT WOS:000455120400017
DA 2025-07-30
ER

PT J
AU Arandia-Gorostidi, N
   Huete-Stauffer, TM
   Alonso-Sáez, L
   Morán, XAG
AF Arandia-Gorostidi, Nestor
   Megan Huete-Stauffer, Tamara
   Alonso-Saez, Laura
   Moran, Xose Anxelu G.
TI Testing the metabolic theory of ecology with marine bacteria: different
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
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C1 [Arandia-Gorostidi, Nestor; Megan Huete-Stauffer, Tamara; Alonso-Saez, Laura] Inst Espanol Oceanog, Ctr Oceanog Gijon Xixon, Plankton Ecol & Pelag Ecosyst Dynam Div, Gijon Xixon, Asturias, Spain.
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RP Arandia-Gorostidi, N (corresponding author), Inst Espanol Oceanog, Ctr Oceanog Gijon Xixon, Plankton Ecol & Pelag Ecosyst Dynam Div, Gijon Xixon, Asturias, Spain.
EM n.arandia86@gmail.com
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NR 108
TC 31
Z9 33
PD NOV
PY 2017
VL 19
IS 11
BP 4493
EP 4505
DI 10.1111/1462-2920.13898
UT WOS:000416149000009
DA 2025-07-30
ER

PT J
AU Thingstad, TF
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AF Thingstad, T. Frede
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TI A theoretical analysis of how strain-specific viruses can control
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SO PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
   AMERICA
DT Article
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C1 [Thingstad, T. Frede] Univ Bergen, Dept Biol, N-5020 Bergen, Norway.
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RP Thingstad, TF (corresponding author), Univ Bergen, Dept Biol, N-5020 Bergen, Norway.
EM frede.thingstad@bio.uib.no
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NR 33
TC 124
Z9 144
PD MAY 27
PY 2014
VL 111
IS 21
BP 7813
EP 7818
DI 10.1073/pnas.1400909111
UT WOS:000336411300069
DA 2025-07-30
ER

PT J
AU Hartmann, M
   Zubkov, MV
   Scanlan, DJ
   Lepère, C
AF Hartmann, Manuela
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   Lepere, Cecile
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SO ENVIRONMENTAL MICROBIOLOGY REPORTS
DT Article
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C1 [Hartmann, Manuela; Zubkov, Mikhail V.] Natl Oceanog Ctr, Ocean Biogeochem & Ecosyst Res Grp, Southampton SO14 3ZH, Hants, England.
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RP Lepère, C (corresponding author), Univ Blaise Pascal, Univ Clermont Ferrand 2, Lab Microorganismes Genome & Environm, BP 10448, F-63000 Clermont Ferrand, France.
EM cecile.lepere@univ-bpclermont.fr
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NR 31
TC 70
Z9 73
PD DEC
PY 2013
VL 5
IS 6
BP 835
EP 840
DI 10.1111/1758-2229.12084
UT WOS:000326891500007
DA 2025-07-30
ER

PT J
AU Campbell, BJ
   Yu, L
   Straza, TRA
   Kirchman, DL
AF Campbell, B. J.
   Yu, L.
   Straza, T. R. A.
   Kirchman, D. L.
TI Temporal changes in bacterial rRNA and rRNA genies in Delaware (USA)
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SO AQUATIC MICROBIAL ECOLOGY
DT Article
AB The diversity and abundance of bacterial 16S rRNA genes (rDNA) and associated 16S rRNA were assessed to examine community structure and potential activity in a 2 yr seasonal study of marine surface waters along the Delaware (USA) coast. The majority of the ribotypes appearing as rRNA or rDNA were present at least 50% of the time, and their variation over time was less than that of most biotic and abiotic factors. Even though there were no predictable seasonal patterns in community structure, environmental parameters explained between 40 and 50% of the observed variation in community structure, In general, summer communities correlated positively with temperature, light, bacterial production, and phosphate levels, while winter communities correlated with dissolved organic carbon concentrations. The abundance of 3 select ribotypes (SAR11, a Cytophaga subgroup, SAR116-like) varied some over time as measured by quantitative PCR (qPCR). The SAR11 clade was 10 times more abundant than the other 2 groups. However, the 16S rRNA to rDNA ratios, as measured by qPCR and reverse transcription-qPCR, varied greatly over time and were highest in the SAR11 population and the Cytophaga subgroup. The rRNA to rDNA ratio of the Cytophaga subgroup and SAR116-like group significantly correlated with some environmental parameters. Taken together, these results suggest that the community composition of the major members does not change much over time, but individual members do vary in abundance and activity and can be influenced by environmental factors.
C1 [Campbell, B. J.; Yu, L.; Straza, T. R. A.; Kirchman, D. L.] Univ Delaware, Sch Marine Sci & Policy, Lewes, DE 19958 USA.
RP Kirchman, DL (corresponding author), Univ Delaware, Sch Marine Sci & Policy, 700 Pilottown Rd, Lewes, DE 19958 USA.
EM kirchman@udel.edu
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NR 75
TC 35
Z9 42
PY 2009
VL 57
IS 2
BP 123
EP 135
DI 10.3354/ame01335
UT WOS:000272197000002
DA 2025-07-30
ER

PT J
AU Ferla, MP
   Thrash, JC
   Giovannoni, SJ
   Patrick, WM
AF Ferla, Matteo P.
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   Patrick, Wayne M.
TI New rRNA Gene-Based Phylogenies of the Alphaproteobacteria
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SO PLOS ONE
DT Article
AB Bacteria in the class Alphaproteobacteria have a wide variety of lifestyles and physiologies. They include pathogens of humans and livestock, agriculturally valuable strains, and several highly abundant marine groups. The ancestor of mitochondria also originated in this clade. Despite significant effort to investigate the phylogeny of the Alphaproteobacteria with a variety of methods, there remains considerable disparity in the placement of several groups. Recent emphasis on phylogenies derived from multiple protein-coding genes remains contentious due to disagreement over appropriate gene selection and the potential influences of systematic error. We revisited previous investigations in this area using concatenated alignments of the small and large subunit (SSU and LSU) rRNA genes, as we show here that these loci have much lower GC bias than whole genomes. This approach has allowed us to update the canonical 16S rRNA gene tree of the Alphaproteobacteria with additional important taxa that were not previously included, and with added resolution provided by concatenating the SSU and LSU genes. We investigated the topological stability of the Alphaproteobacteria by varying alignment methods, rate models, taxon selection and RY-recoding to circumvent GC content bias. We also introduce RYMK-recoding and show that it avoids some of the information loss in RY-recoding. We demonstrate that the topology of the Alphaproteobacteria is sensitive to inclusion of several groups of taxa, but it is less affected by the choice of alignment and rate methods. The majority of topologies and comparative results from Approximately Unbiased tests provide support for positioning the Rickettsiales and the mitochondrial branch within a clade. This composite clade is a sister group to the abundant marine SAR11 clade (Pelagibacterales). Furthermore, we add support for taxonomic assignment of several recently sequenced taxa. Accordingly, we propose three subclasses within the Alphaproteobacteria: the Caulobacteridae, the Rickettsidae, and the Magnetococcidae.
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RP Patrick, WM (corresponding author), Univ Otago, Dept Biochem, Dunedin, New Zealand.
EM wayne.patrick@otago.ac.nz
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NR 37
TC 79
Z9 91
PD DEC 11
PY 2013
VL 8
IS 12
AR e83383
DI 10.1371/journal.pone.0083383
UT WOS:000328730300146
DA 2025-07-30
ER

PT J
AU Zhong, KX
   Wirth, JF
   Chan, AM
   Suttle, CA
AF Zhong, Kevin Xu
   Wirth, Jennifer F.
   Chan, Amy M.
   Suttle, Curtis A.
TI Mortality by ribosomal sequencing (MoRS) provides a window into
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SO ISME JOURNAL
DT Article
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C1 [Zhong, Kevin Xu; Wirth, Jennifer F.; Chan, Amy M.; Suttle, Curtis A.] Univ British Columbia, Dept Earth Ocean & Atmospher Sci, Vancouver, BC, Canada.
   [Suttle, Curtis A.] Univ British Columbia, Dept Microbiol & Immunol, Vancouver, BC, Canada.
   [Suttle, Curtis A.] Univ British Columbia, Dept Bot, Vancouver, BC, Canada.
   [Suttle, Curtis A.] Univ British Columbia, Inst Oceans & Fisheries, Vancouver, BC, Canada.
   [Wirth, Jennifer F.] Montana State Univ, Dept Plant Sci & Plant Pathol, Bozeman, MT 59717 USA.
RP Zhong, KX; Suttle, CA (corresponding author), Univ British Columbia, Dept Earth Ocean & Atmospher Sci, Vancouver, BC, Canada.; Suttle, CA (corresponding author), Univ British Columbia, Dept Microbiol & Immunol, Vancouver, BC, Canada.; Suttle, CA (corresponding author), Univ British Columbia, Dept Bot, Vancouver, BC, Canada.; Suttle, CA (corresponding author), Univ British Columbia, Inst Oceans & Fisheries, Vancouver, BC, Canada.
EM xzhong@eoas.ubc.ca; suttle@science.ubc.ca
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ER

PT J
AU Zhao, WZ
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AF Zhao, Weizhou
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DT Editorial Material
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RP Andersson, SGE (corresponding author), Uppsala Univ, Biomed Ctr, Dept Mol Evolut Cell & Mol Biol, Uppsala, Sweden.
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PT J
AU Luo, HW
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DT Article
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RP Luo, HW (corresponding author), Chinese Univ Hong Kong, Sch Life Sci, Shatin, Hong Kong, Peoples R China.
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DA 2025-07-30
ER

PT J
AU Parada, AE
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AF Parada, Alma E.
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
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C1 [Parada, Alma E.; Needham, David M.; Fuhrman, Jed A.] Univ So Calif, Los Angeles, CA USA.
RP Fuhrman, JA (corresponding author), Univ So Calif, Los Angeles, CA USA.
EM fuhrman@usc.edu
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BP 1403
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HP N
DA 2025-07-30
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SO FRONTIERS IN MICROBIOLOGY
DT Article
AB Canopy-forming seaweed species of the genus Cystoseira form diverse and productive habitats along temperate rocky coasts of the Mediterranean Sea. Despite numerous studies on the rich macrofauna and flora associated with Cystoseira spp., there is little knowledge about the epiphytic bacteria. We analyzed bacterial populations associated with canopies of Cystoseira compressa, over an annual vegetative cycle (May-October), and their relationships with the bacterial populations in the surrounding seawater, at intertidal rocky shores in Vasto (Chieti-Italy). The bacterial diversity was assessed using Illumina Miseq sequences of V1-V3 hypervariable regions of 16S rRNA gene. C. compressa bacterial community was dominated by sequences of Proteobacteria and Bacteroidetes, Verrucomicrobia, Actinobacteria. and Cyanobactena especially of the Rhodobactenaceae, Flayobactenaceae, Sapropiraceae, Verrucomicrobiaceae, and Phyllobactenaceae families. Seawater libraries were also dominated by Proteobacteria and Bacteroidetes sequences, especially of the Candidatus Pelagibacter (SAR11) and Rhodobacteriaceae families, but were shown to be clearly distinct from C. compressa libraries with only few species in common between the two habitats. We observed a clear successional pattern in the epiphytic bacteria of C. compressa over time. These variations were characterized by gradual addition of OTUs (Verrucomicrobia, Actinobacteria and SR1) to the community over a growing season, indicative of a temporal gradient, rather than a radical reorganization of the bacterial community. Moreover, we also found an increase in abundance over time of Rhodobacteraceae, comprising six potential pathogenic genera, Ruegena, Nautella, Aquimarina, Loktanella, Saprospira, and Phaeobacter which seemed to be associated to aged thalli of C. compressa. These bacteria could have the potential to affect the health and ecology of the algae, suggesting the hypothesis of a possible, but still unexplored, role of the microbial communities in contributing to the extensive ongoing declines of populations of Cystoseira spp. in the Mediterranean Sea.
C1 [Mancuso, Francesco P.; Airoldi, Laura] Univ Bologna, Ctr Interdipartimentale Ric Sci Ambientali, Dipartimento Sci Biol Geol & Ambientali, UO CoNISMa, Ravenna, Italy.
   [Mancuso, Francesco P.; D'Hondt, Sofie; De Clerck, Olivier] Univ Ghent, Phycol Res Grp, B-9000 Ghent, Belgium.
   [Mancuso, Francesco P.; D'Hondt, Sofie; De Clerck, Olivier] Univ Ghent, Ctr Mol Phylogenet & Evolut, B-9000 Ghent, Belgium.
   [Willems, Anne] Univ Ghent, Dept Biochem & Microbiol, Lab Microbiol, B-9000 Ghent, Belgium.
RP Mancuso, FP; Airoldi, L (corresponding author), Univ Bologna, Ctr Interdipartimentale Ric Sci Ambientali, Dipartimento Sci Biol Geol & Ambientali, UO CoNISMa, Ravenna, Italy.; Mancuso, FP (corresponding author), Univ Ghent, Phycol Res Grp, B-9000 Ghent, Belgium.; Mancuso, FP (corresponding author), Univ Ghent, Ctr Mol Phylogenet & Evolut, B-9000 Ghent, Belgium.
EM laura.airoldi@unibo.it; laura.airoldi@unibo.it
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TC 89
Z9 98
PD APR 8
PY 2016
VL 7
AR 476
DI 10.3389/fmicb.2016.00476
UT WOS:000373594400001
DA 2025-07-30
ER

PT J
AU Herlemann, DPR
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AF Herlemann, Daniel P. R.
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   Juergens, Klaus
TI Phylogenetic Signals of Salinity and Season in Bacterial Community
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SO FRONTIERS IN MICROBIOLOGY
DT Article
AB Understanding the key processes that control bacterial community composition has enabled predictions of bacterial distribution and function within ecosystems. In this study, we used the Baltic Sea as a model system to quantify the phylogenetic signal of salinity and season with respect to bacterioplankton community composition. The abundances of 16S rRNA gene amplicon sequencing reads were analyzed from samples obtained from similar geographic locations in July and February along a brackish to marine salinity gradient in the Baltic Sea. While there was no distinct pattern of bacterial richness at different salinities, the number of bacterial phylotypes in winter was significantly higher than in summer. Bacterial community composition in brackish vs. marine conditions, and in July vs. February was significantly different. Non-metric multidimensional scaling showed that bacterial community composition was primarily separated according to salinity and secondly according to seasonal differences at all taxonomic ranks tested. Similarly, quantitative phylogenetic clustering implicated a phylogenetic signal for both salinity and seasonality. Our results suggest that global patterns of bacterial community composition with respect to salinity and season are the result of phylogenetically clustered ecological preferences with stronger imprints from salinity.
C1 [Herlemann, Daniel P. R.; Labrenz, Matthias; Juergens, Klaus] Leibniz Inst Balt Sea Res, Warnemunde, Germany.
   [Lundin, Daniel] Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, Kalmar, Sweden.
   [Andersson, Anders F.] KTH Royal Inst Technol, Sch Biotechnol, Div Gene Technol, Sci Life Lab, Stockholm, Sweden.
RP Herlemann, DPR (corresponding author), Leibniz Inst Balt Sea Res, Warnemunde, Germany.
EM daniel.herlemann@io-warnemuende.de
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UT WOS:000388761400001
DA 2025-07-30
ER

PT J
AU Mena, C
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   Santiago, R
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AF Mena, Catalina
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   Santiago, Rocio
   Sintes, Eva
TI Dynamics of actively dividing prokaryotes in the western Mediterranean
   Sea
SO SCIENTIFIC REPORTS
DT Article
AB Microbial community metabolism and functionality play a key role modulating global biogeochemical processes. However, the metabolic activities and contribution of actively growing prokaryotes to ecosystem energy fluxes remain underexplored. Here we describe the temporal and spatial dynamics of active prokaryotes in the different water masses of the Mediterranean Sea using a combination of bromodeoxyuridine labelling and 16S rRNA gene Illumina sequencing. Bulk and actively dividing prokaryotic communities were drastically different and depth stratified. Alteromonadales were rare in bulk communities (contributing 0.1% on average) but dominated the actively dividing community throughout the overall water column (28% on average). Moreover, temporal variability of actively dividing Alteromonadales oligotypes was evinced. SAR86, Actinomarinales and Rhodobacterales contributed on average 3-3.4% each to the bulk and 11, 8.4 and 8.5% to the actively dividing communities in the epipelagic zone, respectively. SAR11 and Nitrosopumilales contributed less to the actively dividing than to the bulk communities during all the study period. Noticeably, the large contribution of these two taxa to the total prokaryotic communities (23% SAR11 and 26% Nitrosopumilales), especially in the meso- and bathypelagic zones, results in important contributions to actively dividing communities (11% SAR11 and 12% Nitrosopumilales). The intense temporal and spatial variability of actively dividing communities revealed in this study strengthen the view of a highly dynamic deep ocean. Our results suggest that some rare or low abundant phylotypes from surface layers down to the deep sea can disproportionally contribute to the activity of the prokaryotic communities, exhibiting a more dynamic response to environmental changes than other abundant phylotypes, emphasizing the role they might have in community metabolism and biogeochemical processes.
C1 [Mena, Catalina; Reglero, Patricia; Balbin, Rosa; Martin, Melissa; Santiago, Rocio; Sintes, Eva] Inst Espanol Oceanog, Ctr Oceanog Balears, Ecosyst Oceanog Grp GRECO, Palma De Mallorca, Spain.
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RP Mena, C (corresponding author), Inst Espanol Oceanog, Ctr Oceanog Balears, Ecosyst Oceanog Grp GRECO, Palma De Mallorca, Spain.; Mena, C (corresponding author), IFREMER Ctr Bretagne ZI, Technopole Brest Iroise Pointe du Diable,BP70, F-29280 Plouzane, France.
EM Catalina.Mena.Oliyer@ifremer.fr
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NR 93
TC 4
Z9 4
PD FEB 8
PY 2022
VL 12
IS 1
AR 2064
DI 10.1038/s41598-022-06120-y
UT WOS:000756832600033
DA 2025-07-30
ER

PT J
AU Kanellopoulos, P
   Bezverkhniaia, E
   Abouzayed, A
   Rosenström, U
   Tolmachev, V
   Orlova, A
AF Kanellopoulos, Panagiotis
   Bezverkhniaia, Ekaterina
   Abouzayed, Ayman
   Rosenstro''m, Ulrika
   Tolmachev, Vladimir
   Orlova, Anna
TI Two Novel [<SUP>68</SUP>Ga]Ga-Labeled Radiotracers Based on
   Metabolically Stable [Sar<SUP>11</SUP>]RM26 Antagonistic Peptide for
   Diagnostic Positron Emission Tomography Imaging of GRPR-Positive
   Prostate Cancer
SO ACS OMEGA
DT Article
AB Gastrin releasing peptide receptor (GRPR) is overexpressed in prostate cancer (PC-3) and can be used for diagnostic purposes. We herein present the design and preclinical evaluation of two novel NOTA/NODAGA-containing peptides suitable for labeling with the positron emission tomography (PET) radionuclide Ga-68. These analogs are based on the previously reported GRPR-antagonist DOTAGA-PEG2-[Sar(11)]RM26, developed for targeted radiotheraostic applications. Both NOTA-PEG2-[Sar(11)]RM26 and NODAGA-PEG2-[Sar(11)]RM26 were successfully labeled with Ga-68 and evaluated in vitro and in vivo using PC-3 cell models. Both, [Ga-68]Ga-NOTA-PEG2-[Sar(11)]RM26 and [Ga-68]Ga-NODAGA-PEG2-[Sar(11)]RM26 displayed high metal-chelate stability in phosphate buffered saline and against the EDTA-challenge. The two [Ga-68]Ga-labeled conjugates demonstrated highly GRPR-mediated uptake in vitro and in vivo and exhibited a slow internalization over time, typical for radioantagonistis. The [Ga-nat]Ga-loaded peptides displayed affinity in the low nanomole range for GRPR in competition binding experiments. The new radiotracers demonstrated biodistribution profiles suitable for diagnostic imaging shortly after administration with fast background clearance. Their high tumor uptake (13 +/- 1 and 15 +/- 3% IA/g for NOTA and NODAGA conjugates, respectively) and high tumor-to-blood ratios (60 +/- 10 and 220 +/- 70, respectively) 3 h pi renders them promising PET tracers for use in patients. Tumor-to-normal organ ratios were higher for [Ga-68]Ga-NODAGA-PEG2-[Sar(11)]RM26 than for the NOTA-containing counterpart. The performance of the two radiopeptides was further supported with the PET/CT images. In conclusion, [Ga-68]Ga-NODAGA-PEG2-[Sar(11)]RM26 is a promising PET imaging tracer for visualization of GRPR-expressing lesions with high imaging contrast shortly after administration.
C1 [Kanellopoulos, Panagiotis; Bezverkhniaia, Ekaterina; Abouzayed, Ayman; Rosenstro''m, Ulrika; Orlova, Anna] Uppsala Univ, Dept Med Chem, S-75123 Uppsala, Sweden.
   [Tolmachev, Vladimir] Uppsala Univ, Dept Immunol Genet & Pathol, S-75237 Uppsala, Sweden.
   [Orlova, Anna] Uppsala Univ, Sci Life Lab, S-75237 Uppsala, Sweden.
RP Orlova, A (corresponding author), Uppsala Univ, Dept Med Chem, S-75123 Uppsala, Sweden.; Orlova, A (corresponding author), Uppsala Univ, Sci Life Lab, S-75237 Uppsala, Sweden.
EM anna.orlova@ilk.uu.se
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NR 34
TC 1
Z9 1
PD APR 10
PY 2024
VL 9
IS 16
BP 18608
EP 18616
DI 10.1021/acsomega.4c01348
EA APR 2024
UT WOS:001200269900001
DA 2025-07-30
ER

PT J
AU Suzuki, MT
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   Taylor, LT
   DeLong, EF
AF Suzuki, MT
   Béjà, O
   Taylor, LT
   DeLong, EF
TI Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Analyses of small subunit ribosomal RNA genes (SSU rDNAs) have significantly influenced our understanding of the composition of aquatic microbial assemblages. Unfortunately, SSU rDNA sequences often do not have sufficient resolving power to differentiate closely related species. To address this general problem for uncultivated bacterioplankton taxa, we analysed and compared sequences of polymerase chain reaction (PCR)-generated and bacterial artificial chromosome (BAC)-derived clones that contained most of the SSU rDNAs, the internal transcribed spacer (ITS) and the large subunit ribosomal RNA gene (LSU rDNA). The phylogenetic representation in the rRNA operon PCR library was similar to that reported previously in coastal bacterioplankton SSU rDNA libraries. We observed good concordance between the phylogenetic relationships among coastal bactetioplankton inferred from SSU or LSU rDNA sequences. ITS sequences confirmed the close intragroup relationships among members of the SAR11, SAR116 and SAR86 clades that were predicted by SSU and LSU rDNA sequence analyses. We also found strong support for homologous recombination between the ITS regions of operons from the SAR11 clade.
C1 Monterey Bay Aquarium Res Inst, Moss Landing, CA 95039 USA.
RP DeLong, EF (corresponding author), Monterey Bay Aquarium Res Inst, 7700 Sandholdt Rd, Moss Landing, CA 95039 USA.
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NR 40
TC 135
Z9 152
PD MAY
PY 2001
VL 3
IS 5
BP 323
EP 331
DI 10.1046/j.1462-2920.2001.00198.x
UT WOS:000169352900004
DA 2025-07-30
ER

PT J
AU Selje, N
   Simon, M
   Brinkhoff, T
AF Selje, N
   Simon, M
   Brinkhoff, T
TI A newly discovered Roseobacter cluster in temperate and polar
   oceans
SO NATURE
DT Article
AB Bacterioplankton phylotypes of alpha-Proteobacteria have been detected in various marine regions, but systematic biogeographical studies of their global distribution are missing. alpha-Proteobacteria comprise one of the largest fractions of heterotrophic marine bacteria(1,2) and include two clades, SAR11 and Roseobacter, which account for 26 and 16% of 16S ribosomal RNA gene clones retrieved from marine bacterioplankton(3). The SAR11 clade attracted much interest because related 16S rRNA gene clones were among the first groups of marine bacteria to be identified by cultivation-independent approaches(4) and appear to dominate subtropical surface bacterioplankton communities(5). Here we report on the global distribution of a newly discovered cluster affiliated to the Roseobacter clade, comprising only as-yet-uncultured phylotypes. Bacteria of this cluster occur from temperate to polar regions with highest abundance in the Southern Ocean, but not in tropical and subtropical regions. Between the south Atlantic subtropical front and Antarctica, we detected two distinct phylotypes, one north and one south of the polar front, indicating that two adjacent but different oceanic provinces allow the persistence of distinct but closely related phylotypes. These results suggest that the global distribution of major marine bacterioplankton components is related to oceanic water masses and controlled by their environmental and biogeochemical properties.
C1 Carl von Ossietzky Univ Oldenburg, Inst Chem & Biol Marine Environm, D-26111 Oldenburg, Germany.
RP Carl von Ossietzky Univ Oldenburg, Inst Chem & Biol Marine Environm, POB 2503, D-26111 Oldenburg, Germany.
EM m.simon@icbm.de
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   [No title captured]
NR 28
TC 220
Z9 240
PD JAN 29
PY 2004
VL 427
IS 6973
BP 445
EP 448
DI 10.1038/nature02272
UT WOS:000188470500044
DA 2025-07-30
ER

PT J
AU Zhang, R
   Wu, QL
   Piceno, YM
   Desantis, TZ
   Saunders, FM
   Andersen, GL
   Liu, WT
AF Zhang, Rui
   Wu, Qinglong
   Piceno, Yvette M.
   Desantis, Todd Z.
   Saunders, F. Michael
   Andersen, Gary L.
   Liu, Wen-Tso
TI Diversity of bacterioplankton in contrasting Tibetan lakes revealed by
   high-density microarray and clone library analysis
SO FEMS MICROBIOLOGY ECOLOGY
DT Article
AB Tibetan lakes represent a unique microbial environment and are a good ecosystem to investigate the microbial diversity of high mountain lakes and their relationship with environmental factors. The diversity and community structure of bacterioplankton in Tibetan lakes was determined using DNA fingerprinting analysis, high-density 16S rRNA gene microarray (PhyloChip) analysis, and extensive clone library analysis of bacterial 16S rRNA genes. A previously unseen high microbial diversity (1732 operational taxonomic units based on PhyloChip data) and numerous novel bacterial 16S rRNA gene sequences were observed. Abundant SAR11-like sequences retrieved from saline Lake Qinghai demonstrated a unique SAR11 phylogenetic sister clade related to the freshwater LD12 clade. Water chemistry (e.g. salinity) and altitude played important roles in the selection of bacterial taxa (both presence and relative abundance) in Tibetan lakes. The ubiquity and uniqueness of bacterial taxa, as well as the correlation between environmental factors and bacterial taxa, was observed to vary gradually with different phylogenetic levels. Our study suggested high microbial cosmopolitanism and high endemicity observed at higher and lower phylogenetic levels, respectively.
C1 [Zhang, Rui; Wu, Qinglong; Saunders, F. Michael; Liu, Wen-Tso] Natl Univ Singapore, Div Environm Sci & Engn, Singapore 117548, Singapore.
   [Zhang, Rui] Xiamen Univ, State Key Lab Marine Environm Sci, Xiamen, Peoples R China.
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RP Liu, WT (corresponding author), Univ Illinois, Dept Civil & Environm Engn, Urbana, IL 61801 USA.
EM wtliu@illinois.edu
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NR 41
TC 36
Z9 41
PD NOV
PY 2013
VL 86
IS 2
BP 277
EP 287
DI 10.1111/1574-6941.12160
UT WOS:000325986500010
DA 2025-07-30
ER

PT J
AU Hogle, SL
   Thrash, JC
   Dupont, CL
   Barbeau, KA
AF Hogle, Shane L.
   Thrash, J. Cameron
   Dupont, Chris L.
   Barbeau, Katherine A.
TI Trace Metal Acquisition by Marine Heterotrophic Bacterioplankton with
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
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C1 [Hogle, Shane L.; Barbeau, Katherine A.] Univ Calif San Diego, Scripps Inst Oceanog, Geosci Res Div, La Jolla, CA 92093 USA.
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   [Dupont, Chris L.] J Craig Venter Inst, La Jolla, CA USA.
RP Hogle, SL (corresponding author), Univ Calif San Diego, Scripps Inst Oceanog, Geosci Res Div, La Jolla, CA 92093 USA.
EM shogle@ucsd.edu
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NR 92
TC 38
Z9 41
PD MAR
PY 2016
VL 82
IS 5
BP 1613
EP 1624
DI 10.1128/AEM.03128-15
UT WOS:000373338800025
DA 2025-07-30
ER

PT J
AU Santic, D
   Stojan, I
   Tomas, AV
   Roje, BM
   Mujakic, I
   Villena-Alemany, C
   Koblízek, M
   Jozic, S
   Solic, M
   Sestanovic, S
AF Santic, Danijela
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   Mujakic, Izabela
   Villena-Alemany, Cristian
   Koblizek, Michal
   Jozic, Slaven
   Solic, Mladen
   Sestanovic, Stefanija
TI Contribution of different bacterial groups in the carbon flow through
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SO ESTUARINE COASTAL AND SHELF SCIENCE
DT Article
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C1 [Santic, Danijela; Tomas, Ana Vrdoljak; Roje, Blanka Milic; Jozic, Slaven; Solic, Mladen; Sestanovic, Stefanija] Inst Oceanog & Fisheries, Setaliste Ivana Mestrovica 63, Split 21000, Croatia.
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RP Santic, D (corresponding author), Setaliste Ivana Mestrovica 63, Split 21000, Croatia.
EM segvic@izor.hr; ivastojan77@gmail.com; ana.vrdoljak@izor.hr;
   broje@izor.hr; mujakic@alga.cz; villena@alga.cz; I.koblizek@alga.cz;
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NR 102
TC 0
Z9 0
PD JUL 15
PY 2025
VL 318
AR 109228
DI 10.1016/j.ecss.2025.109228
EA MAR 2025
UT WOS:001448531900001
DA 2025-07-30
ER

PT J
AU Brown, MV
   Fuhrman, JA
AF Brown, MV
   Fuhrman, JA
TI Marine bacterial microdiversity as revealed by internal transcribed
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SO AQUATIC MICROBIAL ECOLOGY
DT Article
AB A growing body of evidence suggests analysis of 16S rRNA gene sequences provides only a conservative estimate of the actual genetic diversity existing within microbial communities. We examined the less conserved internal transcribed spacer (ITS) region of the ribosomal operon to determine the impact microdiversity may have on our view of marine microbial consortia. Analysis of over 500 ITS sequences and 250 associated 16S rRNA gene sequences from an oceanic time series station in the San Pedro Channel, California, USA, revealed that the community in this region is composed of large numbers of distinct lineages, with more than 1000 lineages estimated from 3 clusters alone (the SAR11 clade, the Prochlorococcus low-B/A clade 1, and the Roseobacter NAC11-7 clade). Although we found no instances where divergent ITS sequences were associated with identical 16S rRNA gene sequences, the ITS region showed much greater pairwise divergence between clones. By comparison to our 16S rRNA gene-ITS region linked database, we were able to place an ITS sequences into a phylogenetic framework, allowing them to act as an alternative molecular marker with enhanced resolution. Comparison of SAR11 clade ITS sequences with those available in GenBank indicated phylogenetic groupings based not only on depth but also on geography, potentially indicating localized differentiation or adaptation.
C1 Univ So Calif, Wrigley Inst Environm Studies, Los Angeles, CA 90089 USA.
   Univ So Calif, Dept Biol Sci, Los Angeles, CA 90089 USA.
RP Univ Hawaii, NASA, Astrobiol Inst, Honolulu, HI 96822 USA.
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NR 31
TC 101
Z9 112
PD NOV 11
PY 2005
VL 41
IS 1
BP 15
EP 23
DI 10.3354/ame041015
UT WOS:000233696000002
DA 2025-07-30
ER

PT J
AU Lefort, T
   Gasol, JM
AF Lefort, Thomas
   Gasol, Josep M.
TI Global-scale distributions of marine surface bacterioplankton groups
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DT Article
AB We used literature data on marine bacterial (sub) group abundances, as determined by fluorescence in situ hybridization, to test whether the ecological variability of the different subgroups was similar to that of the bacterial community as a whole. Patterns of 6 major groups are described (Alpha-, Beta-, Gammaproteobacteria and Bacteroidetes, as well as Rhodobacteraceae and SAR11) and related to environmental variables such as chlorophyll a (chl a) concentration, salinity, and temperature, distinguishing between coastal or open-ocean environments. Coastal ecosystems exhibited higher relative abundances (average % of DAPI counts) of Bacteroidetes (23 %), Beta- (11 %) and Gammaproteobacteria (10 %), and Rhodobacteraceae (6%), while significantly higher contributions of Alphaproteobacteria and SAR11 (32 %) were on average enumerated offshore. Multiple regression analyses showed significant explanatory power of chl a and temperature on total and SAR11 absolute abundances (expressed as cells ml(-1)), and of chl a and salinity levels on absolute abundances of Betaproteobacteria and Rhodobacteraceae. Other analyses revealed increasing contribution of Gammaproteobacteria for increasing temperatures and high temperature avoidance for Betaproteobacteria. Significantly different log-log regression slopes were found between bacterial group absolute abundances and chl a concentration at a global scale, ranging from 0.13 +/- 0.04 (SE) for SAR11 to 0.53 +/- 0.08 for Betaproteobacteria. The different patterns observed for the different groups, in coastal and open-ocean environments, suggest different niche preferences by each group as well as a coherent response to environmental factors.
C1 [Lefort, Thomas; Gasol, Josep M.] CSIC, Inst Ciencies Mar, Dept Marine Biol & Oceanog, Barcelona, Catalonia, Spain.
RP Lefort, T (corresponding author), CSIC, Inst Ciencies Mar, Dept Marine Biol & Oceanog, Barcelona, Catalonia, Spain.
EM thlefort@icm.csic.es
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Z9 34
PY 2013
VL 70
IS 2
BP 111
EP 130
DI 10.3354/ame01643
UT WOS:000323492600002
DA 2025-07-30
ER

PT J
AU Philosof, A
   Béjà, O
AF Philosof, Alon
   Beja, Oded
TI Bacterial, archaeal and viral-like rhodopsins from the Red Sea
SO ENVIRONMENTAL MICROBIOLOGY REPORTS
DT Article
AB The Gulf of Aqaba, extending north to the Red Sea, is an oligotrophic basin with typical open ocean gyre characteristics. Here we report on the existence of diverse microbial rhodopsins in the Gulf of Aqaba, based on 454-pyrosequencing-generated metagenome and metatranscriptome data sets, obtained from the microbial fraction smaller than 1.6m. Bacterial SAR11, SAR86 and archaeal proteorhodopsins as well as viral-like rhodopsins were detected on the DNA level. On the RNA level, only SAR11 and SAR86 proteorhodopsin transcripts were detected. Our results add to the growing evidence that microbial rhodopsins are a diverse, abundant and widespread protein family.
C1 [Philosof, Alon; Beja, Oded] Technion Israel Inst Technol, Fac Biol, IL-32000 Haifa, Israel.
RP Béjà, O (corresponding author), Technion Israel Inst Technol, Fac Biol, IL-32000 Haifa, Israel.
EM beja@tx.technion.ac.il
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NR 57
TC 51
Z9 55
PD JUN
PY 2013
VL 5
IS 3
SI SI
BP 475
EP 482
DI 10.1111/1758-2229.12037
UT WOS:000318111500016
DA 2025-07-30
ER

PT J
AU Harbeitner, RC
   Wittmers, F
   Yung, CCM
   Eckmann, CA
   Hehenberger, E
   Blum, M
   Needham, DM
   Worden, AZ
AF Harbeitner, Rachel C.
   Wittmers, Fabian
   Yung, Charmaine C. M.
   Eckmann, Charlotte A.
   Hehenberger, Elisabeth
   Blum, Marguerite
   Needham, David M.
   Worden, Alexandra Z.
TI Gradients of bacteria in the oceanic water column reveal finely-resolved
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SO PLOS ONE
DT Article
AB Bacterial communities directly influence ecological processes in the ocean, and depth has a major influence due to the changeover in primary energy sources between the sunlit photic zone and dark ocean. Here, we examine the abundance and diversity of bacteria in Monterey Bay depth profiles collected from the surface to just above the sediments (e.g., 2000 m). Bacterial abundance in these Pacific Ocean samples decreased by >1 order of magnitude, from 1.22 +/- 0.69 x10(6) cells ml(-1) in the variable photic zone to 1.44 +/- 0.25 x10(5) and 6.71 +/- 1.23 x10(4) cells ml(-1) in the mesopelagic and bathypelagic, respectively. V1-V2 16S rRNA gene profiling showed diversity increased sharply between the photic and mesopelagic zones. Weighted Gene Correlation Network Analysis clustered co-occurring bacterial amplicon sequence variants (ASVs) into seven subnetwork modules, of which five strongly correlated with depth-related factors. Within surface-associated modules there was a clear distinction between a 'copiotrophic' module, correlating with chlorophyll and dominated by e.g., Flavobacteriales and Rhodobacteraceae, and an 'oligotrophic' module dominated by diverse Oceanospirillales (such as uncultured JL-ETNP-Y6, SAR86) and Pelagibacterales. Phylogenetic reconstructions of Pelagibacterales and SAR324 using full-length 16S rRNA gene data revealed several additional subclades, expanding known microdiversity within these abundant lineages, including new Pelagibacterales subclades Ia.B, Id, and IIc, which comprised 4-10% of amplicons depending on the subclade and depth zone. SAR324 and Oceanospirillales dominated in the mesopelagic, with SAR324 clade II exhibiting its highest relative abundances (17 +/- 4%) in the lower mesopelagic (300-750 m). The two newly-identified SAR324 clades showed highest relative abundances in the photic zone (clade III), while clade IV was extremely low in relative abundance, but present across dark ocean depths. Hierarchical clustering placed microbial communities from 900 m samples with those from the bathypelagic, where Marinimicrobia was distinctively relatively abundant. The patterns resolved herein, through high resolution and statistical replication, establish baselines for marine bacterial abundance and taxonomic distributions across the Monterey Bay water column, against which future change can be assessed.
C1 [Harbeitner, Rachel C.; Eckmann, Charlotte A.; Worden, Alexandra Z.] Univ Calif Santa Cruz, Dept Ocean Sci, Santa Cruz, CA 95064 USA.
   [Harbeitner, Rachel C.; Wittmers, Fabian; Yung, Charmaine C. M.; Hehenberger, Elisabeth; Needham, David M.; Worden, Alexandra Z.] GEOMAR Helmholtz Ctr Ocean Res Kiel, Ocean EcoSyst Biol Unit, RD3, Kiel, DE, Germany.
   [Wittmers, Fabian; Eckmann, Charlotte A.; Worden, Alexandra Z.] Marine Biol Lab, Woods Hole, MA 02543 USA.
   [Blum, Marguerite] Monterey Bay Aquarium Res Inst, Moss Landing, CA USA.
RP Worden, AZ (corresponding author), Univ Calif Santa Cruz, Dept Ocean Sci, Santa Cruz, CA 95064 USA.; Worden, AZ (corresponding author), GEOMAR Helmholtz Ctr Ocean Res Kiel, Ocean EcoSyst Biol Unit, RD3, Kiel, DE, Germany.; Worden, AZ (corresponding author), Marine Biol Lab, Woods Hole, MA 02543 USA.
EM azworden@mbl.edu
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NR 45
TC 3
Z9 3
PD APR 2
PY 2024
VL 19
IS 4
AR e0298139
DI 10.1371/journal.pone.0298139
UT WOS:001196120400041
DA 2025-07-30
ER

PT J
AU Shi, YM
   Tyson, GW
   DeLong, EF
AF Shi, Yanmei
   Tyson, Gene W.
   DeLong, Edward F.
TI Metatranscriptomics reveals unique microbial small RNAs in the ocean's
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SO NATURE
DT Article
AB Microbial gene expression in the environment has recently been assessed via pyrosequencing of total RNA extracted directly from natural microbial assemblages. Several such 'metatranscriptomic' studies(1,2) have reported that many complementary DNA sequences shared no significant homology with known peptide sequences, and so might represent transcripts from uncharacterized proteins. Here we report that a large fraction of cDNA sequences detected in microbial metatranscriptomic data sets are comprised of well-known small RNAs ( sRNAs) 3, as well as new groups of previously unrecognized putative sRNAs ( psRNAs). These psRNAs mapped specifically to intergenic regions of microbial genomes recovered from similar habitats, displayed characteristic conserved secondary structures and were frequently flanked by genes that indicated potential regulatory functions. Depth-dependent variation of psRNAs generally reflected known depth distributions of broad taxonomic groups(4), but fine-scale differences in the psRNAs within closely related populations indicated potential roles in niche adaptation. Genome-specific mapping of a subset of psRNAs derived from predominant planktonic species such as Pelagibacter revealed recently discovered as well as potentially new regulatory elements. Our analyses show that metatranscriptomic data sets can reveal new information about the diversity, taxonomic distribution and abundance of sRNAs in naturally occurring microbial communities, and indicate their involvement in environmentally relevant processes including carbon metabolism and nutrient acquisition.
C1 [Shi, Yanmei; Tyson, Gene W.; DeLong, Edward F.] MIT, Dept Civil & Environm Engn, Cambridge, MA 02139 USA.
   [DeLong, Edward F.] MIT, Dept Biol Engn, Cambridge, MA 02139 USA.
RP DeLong, EF (corresponding author), MIT, Dept Civil & Environm Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA.
EM delong@mit.edu
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NR 46
TC 201
Z9 230
PD MAY 14
PY 2009
VL 459
IS 7244
BP 266
EP U154
DI 10.1038/nature08055
UT WOS:000266036100044
DA 2025-07-30
ER

PT J
AU Bruwer, JD
   Orellana, LH
   Sidhu, C
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AF Bru''wer, Jan D.
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   Boersma, Maarten
   Wiltshire, Karen H.
   Amann, Rudolf
   Fuchs, Bernhard M.
TI E "In situ cell division and mortality rates of SAR11, SAR86,
   Bacteroidetes, and Aurantivirga during phytoplankton
   blooms reveal differences in population controls" (vol 8, e01287-22,
   2023)
SO MSYSTEMS
DT Correction
EM bfuchs@mpi-bremen.de
CR Bruewer JD, 2023, MSYSTEMS, V8, DOI 10.1128/msystems.01287-22
NR 1
TC 0
Z9 0
PD JAN 23
PY 2024
VL 9
IS 1
DI 10.1128/msystems.01196-23
EA DEC 2023
UT WOS:001128115300001
DA 2025-07-30
ER

PT J
AU Han, D
   Kang, HY
   Kang, CK
   Unno, T
   Hur, HG
AF Han, Dukki
   Kang, Hee Yoon
   Kang, Chang-Keun
   Unno, Tatsuya
   Hur, Hor-Gil
TI Seasonal Mixing-Driven System in Estuarine-Coastal Zone Triggers an
   Ecological Shift in Bacterial Assemblages Involved in
   Phytoplankton-Derived DMSP Degradation
SO MICROBIAL ECOLOGY
DT Article
AB The coastal zone has distinguishable but tightly connected ecosystems from rivers to the ocean and globally contributes to nutrient cycling including phytoplankton-derived organic matter. Particularly, bacterial contributions to phytoplankton-derived dimethylsulfoniopropionate (DMSP) degradation have been recently evaluated by using advanced sequencing technologies to understand their role in the marine microbial food web. Here, we surveyed the bacterial diversity and community composition under seasonal water mixing in the bay of Gwangyang (GW), a semi-enclosed estuary at the southern tip of the Korea Peninsula. We detected phylogenetic dissimilarities among season-specific habitats in GW and their specific bacterial taxa. Additionally, bacterial contribution to degradation of phytoplankton-derived DMSP from estuarine to coastal waters at euphotic depths in GW was investigated as the presence or absence of DMSP demethylation gene, encoded by dmdA. Among the operational taxonomic units (OTUs) in GW bacterial communities, the most dominant and ubiquitous OTU1 was affiliated with the SAR11 clade (SAR11-OTU). The population dynamics of SAR11-OTU in dmdA-detected GW waters suggest that water mass mixing plays a major role in shaping bacterial communities involved in phytoplankton-derived DMSP demethylation.
C1 [Han, Dukki; Unno, Tatsuya] Jeju Natl Univ, Jeju Special Self Governing Prov, Jeju 63243, South Korea.
   [Kang, Hee Yoon; Kang, Chang-Keun; Hur, Hor-Gil] Gwangju Inst Sci & Technol, Sch Earth Sci & Environm Engn, Gwangju 61005, South Korea.
RP Hur, HG (corresponding author), Gwangju Inst Sci & Technol, Sch Earth Sci & Environm Engn, Gwangju 61005, South Korea.
EM hghur@gist.ac.kr
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NR 49
TC 5
Z9 5
PD JAN
PY 2020
VL 79
IS 1
BP 12
EP 20
DI 10.1007/s00248-019-01392-w
UT WOS:000513239900002
DA 2025-07-30
ER

PT J
AU Piwosz, K
   Salcher, MM
   Zeder, M
   Ameryk, A
   Pernthaler, J
AF Piwosz, Kasia
   Salcher, Michaela M.
   Zeder, Michael
   Ameryk, Anetta
   Pernthaler, Jakob
TI Seasonal dynamics and activity of typical freshwater bacteria in
   brackish waters of the Gulf of Gdansk
SO LIMNOLOGY AND OCEANOGRAPHY
DT Article
AB While typical freshwater and marine bacteria have been found to co-occur in brackish habitats, it is unknown if they are active members of the local bacterial assemblages or if their presence is the result of passive transport only. We followed the seasonal dynamics of typical freshwater bacteria (R-BT lineage of Betaproteobacteria; Ac1 Actinobacteria; LD12 Alphaproteobacteria) and of marine SAR11 Alphaproteobacteria in the brackish water of the Gulf of Gdansk (southern Baltic Sea), and we assessed their incorporation of thymidine and leucine at three distinct environmental conditions. The temporal development of bacteria was driven not only by local conditions but also by phenomena resulting from the dynamic hydrology of the site. Both temperature and salinity were important factors influencing bacterial community composition, as reflected by the clear distinction of three assemblages in spring and summer and during a period of enhanced freshwater influx. During spring, high proportions of R-BT Betaproteobacteria and Ac1 Actinobacteria incorporated the radiolabeled tracers, and all three freshwater lineages were most active during the subsequent phase of low salinity. The summer period was characterized by highest abundances of Ac1 Actinobacteria and of both alphaproteobacterial lineages. All studied freshwater lineages were active members of the brackish water communities at specific environmental conditions, including LD12 Alphaproteobacteria, which have so far been considered to thrive exclusively in freshwater habitats. By contrast, the presence of the typical marine SAR11 bacteria seemed to result from passive inflow with more saline waters from the Baltic proper.
C1 [Piwosz, Kasia; Ameryk, Anetta] Natl Marine Fisheries Res Inst, Gdynia, Poland.
   [Salcher, Michaela M.; Zeder, Michael; Pernthaler, Jakob] Univ Zurich, Inst Plant Biol, Limnol Stn, Kilchberg, Switzerland.
RP Pernthaler, J (corresponding author), Univ Zurich, Inst Plant Biol, Limnol Stn, Kilchberg, Switzerland.
EM pernthaler@limnol.uzh.ch
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NR 40
TC 27
Z9 29
PD MAY
PY 2013
VL 58
IS 3
BP 817
EP 826
DI 10.4319/lo.2013.58.3.0817
UT WOS:000322491100005
DA 2025-07-30
ER

PT J
AU Chronopoulou, PM
   Sanni, GO
   Silas-Olu, DI
   van der Meer, JR
   Timmis, KN
   Brussaard, CPD
   McGenity, TJ
AF Chronopoulou, Panagiota-Myrsini
   Sanni, Gbemisola O.
   Silas-Olu, Daniel I.
   van der Meer, Jan Roelof
   Timmis, Kenneth N.
   Brussaard, Corina P. D.
   McGenity, Terry J.
TI Generalist hydrocarbon-degrading bacterial communities in the
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SO MICROBIAL BIOTECHNOLOGY
DT Article
AB The aim of this work was to determine the effect of light crude oil on bacterial communities during an experimental oil spill in the North Sea and in mesocosms (simulating a heavy, enclosed oil spill), and to isolate and characterize hydrocarbon-degrading bacteria from the water column. No oil-induced changes in bacterial community (3m below the sea surface) were observed 32h after the experimental spill at sea. In contrast, there was a decrease in the dominant SAR11 phylotype and an increase in Pseudoalteromonas spp. in the oiled mesocosms (investigated by 16S rRNA gene analysis using denaturing gradient gel electrophoresis), as a consequence of the longer incubation, closer proximity of the samples to oil, and the lack of replenishment with seawater. A total of 216 strains were isolated from hydrocarbon enrichment cultures, predominantly belonging to the genus Pseudoaltero monas; most strains grew on PAHs, branched and straight-chain alkanes, as well as many other carbon sources. No obligate hydrocarbonoclastic bacteria were isolated or detected, highlighting the potential importance of cosmopolitan marine generalists like Pseudoalteromonas spp. in degrading hydrocarbons in the water column beneath an oil slick, and revealing the susceptibility to oil pollution of SAR11, the most abundant bacterial clade in the surface ocean.
C1 [Chronopoulou, Panagiota-Myrsini; Sanni, Gbemisola O.; Silas-Olu, Daniel I.; McGenity, Terry J.] Univ Essex, Sch Biol Sci, Colchester CO4 3SQ, Essex, England.
   [van der Meer, Jan Roelof] Univ Lausanne, Dept Fundamental Microbiol, Lausanne, Switzerland.
   [Timmis, Kenneth N.] Tech Univ Carolo Wilhelmina Braunschweig, Inst Microbiol, D-38106 Braunschweig, Germany.
   [Brussaard, Corina P. D.] Royal Netherlands Inst Sea Res NIOZ, Dept Biol Oceanog, Den Burg, Netherlands.
RP McGenity, TJ (corresponding author), Univ Essex, Sch Biol Sci, Wivenhoe Pk, Colchester CO4 3SQ, Essex, England.
EM tjmcgen@essex.ac.uk
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NR 75
TC 67
Z9 78
PD MAY
PY 2015
VL 8
IS 3
BP 434
EP 447
DI 10.1111/1751-7915.12176
UT WOS:000353236500007
DA 2025-07-30
ER

PT J
AU Huanca-Valenzuela, P
   Cram, JA
   Fuchsman, CA
AF Huanca-Valenzuela, Paulina
   Cram, Jacob A.
   Fuchsman, Clara A.
TI Niche differentiation in microorganisms capable of using alternative
   reduced nitrogen sources studied across depth and between oxic and
   anoxic ocean regions
SO FRONTIERS IN MARINE SCIENCE
DT Article
AB Introduction: Assimilation of reduced nitrogen is less energetically costly than assimilation of oxidized forms. In the open ocean, ammonium is generally absent from the water column, including in oxygen-deficient zones (ODZs). Some microorganisms can use alternative organic reduced nitrogen forms like urea and cyanate, as indicated by the presence of cyanase (cynS) and urease (ureC) genes.
   Methods: Here we examine the Hawaii Ocean Time series, two stations in the Eastern Tropical South Pacific ODZ and one in the Eastern Tropical North Pacific ODZ, using phylogenetic read placement of metagenomic reads to define the proportion of each taxon capable of using cyanate and/or urea in oxic and anoxic environments.
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C1 [Huanca-Valenzuela, Paulina; Cram, Jacob A.; Fuchsman, Clara A.] Univ Maryland, Ctr Environm Sci, Horn Point Lab, Cambridge, MD 21613 USA.
RP Fuchsman, CA (corresponding author), Univ Maryland, Ctr Environm Sci, Horn Point Lab, Cambridge, MD 21613 USA.
EM cfuchsman@umces.edu
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NR 117
TC 2
Z9 2
PD JUL 16
PY 2024
VL 11
AR 1386686
DI 10.3389/fmars.2024.1386686
UT WOS:001280178200001
DA 2025-07-30
ER

PT J
AU Landry, MR
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AF Landry, Michael R.
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DT Article
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C1 [Landry, Michael R.; Freibott, Alexandra L.; Rabines, Ariel; Allen, Andrew E.] Univ Calif San Diego, Scripps Inst Oceanog, La Jolla, CA 92093 USA.
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RP Landry, MR (corresponding author), Univ Calif San Diego, Scripps Inst Oceanog, La Jolla, CA 92093 USA.
EM mlandry@ucsd.edu
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NR 56
TC 0
Z9 0
PD FEB 29
PY 2024
VL 90
BP 23
EP 39
DI 10.3354/ame02006
UT WOS:001199767100001
DA 2025-07-30
ER

PT J
AU Qin, QL
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AF Qin, Qi-Long
   Li, Yi
   Sun, Lin-Lin
   Wang, Zhi-Bin
   Wang, Shi
   Chen, Xiu-Lan
   Oren, Aharon
   Zhang, Yu-Zhong
TI Trophic Specialization Results in Genomic Reduction in Free-Living
   Marine Idiomarina Bacteria
SO MBIO
DT Article
AB The streamlining hypothesis is generally used to explain the genomic reduction events related to the small genome size of free-living bacteria like marine bacteria SAR11. However, our current understanding of the correlation between bacterial genome size and environmental adaptation relies on too few species. It is still unclear whether there are other paths leading to genomic reduction in free-living bacteria. The genome size of marine free-living bacteria of the genus Idiomarina belonging to the order Alteromonadales (Gammaproteobacteria) is much smaller than the size of related genomes from bacteria in the same order. Comparative genomic and physiological analyses showed that the genomic reduction pattern in this genus is different from that of the classical SAR11 lineage. Genomic reduction reconstruction and substrate utilization profile showed that Idiomarina spp. lost a large number of genes related to carbohydrate utilization, and instead they specialized on using proteinaceous resources. Here we propose a new hypothesis to explain genomic reduction in this genus; we propose that trophic specialization increasing the metabolic efficiency for using one kind of substrate but reducing the substrate utilization spectrum could result in bacterial genomic reduction, which would be not uncommon in nature. This hypothesis was further tested in another free-living genus, Kangiella, which also shows dramatic genomic reduction. These findings highlight that trophic specialization is potentially an important path leading to genomic reduction in some marine free-living bacteria, which is distinct from the classical lineages like SAR11.
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C1 [Qin, Qi-Long; Li, Yi; Sun, Lin-Lin; Wang, Zhi-Bin; Chen, Xiu-Lan; Zhang, Yu-Zhong] Shandong Univ, Marine Biotechnol Res Ctr, State Key Lab Microbial Technol, Qingdao, Peoples R China.
   [Wang, Shi; Zhang, Yu-Zhong] Ocean Univ China, Coll Marine Life Sci, Qingdao, Peoples R China.
   [Chen, Xiu-Lan; Zhang, Yu-Zhong] Qingdao Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao, Peoples R China.
   [Oren, Aharon] Hebrew Univ Jerusalem, Alexander Silberman Inst Life Sci, Dept Plant & Environm Sci, Edmond J Safra Campus, Jerusalem, Israel.
RP Zhang, YZ (corresponding author), Shandong Univ, Marine Biotechnol Res Ctr, State Key Lab Microbial Technol, Qingdao, Peoples R China.; Zhang, YZ (corresponding author), Ocean Univ China, Coll Marine Life Sci, Qingdao, Peoples R China.; Zhang, YZ (corresponding author), Qingdao Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao, Peoples R China.; Oren, A (corresponding author), Hebrew Univ Jerusalem, Alexander Silberman Inst Life Sci, Dept Plant & Environm Sci, Edmond J Safra Campus, Jerusalem, Israel.
EM aharon.oren@mail.huji.ac.il; zhangyz@sdu.edu.cn
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NR 53
TC 20
Z9 21
PD JAN-FEB
PY 2019
VL 10
IS 1
AR e02545-18
DI 10.1128/mBio.02545-18
UT WOS:000460314300052
DA 2025-07-30
ER

PT J
AU Evans, C
   Gomez-Pereira, PR
   Martin, AP
   Scanlan, DJ
   Zubkov, MV
AF Evans, Claire
   Gomez-Pereira, Paola R.
   Martin, Adrian P.
   Scanlan, David J.
   Zubkov, Mikhail V.
TI Photoheterotrophy of bacterioplankton is ubiquitous in the surface
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SO PROGRESS IN OCEANOGRAPHY
DT Review
AB Accurate measurements in the Southern Hemisphere were obtained to test a hypothesis of the ubiquity of photoheterotrophy in the oligotrophic ocean. We present experimental results of light-enhanced uptake of methionine, leucine and ATP by bacterioplankton during two large-scale transects of the South Atlantic. Light increased the uptake of substrates by both dominant bacterioplankton groups, Prochlorococcus and SAR11, as well as for the bulk microbial community. Our consistent experimental evidence strongly indicates that photoheterotrophy is characteristic of dominant bacterioplankton populations in the global oligotrophic ocean. (C) 2015 Elsevier Ltd. All rights reserved.
C1 [Evans, Claire; Gomez-Pereira, Paola R.; Martin, Adrian P.; Zubkov, Mikhail V.] Natl Oceanog Ctr, Ocean Biogeochem & Ecosyst Res Grp, Southampton, Hants, England.
   [Scanlan, David J.] Univ Warwick, Sch Life Sci, Coventry CV4 7AL, W Midlands, England.
RP Zubkov, MV (corresponding author), Natl Oceanog Ctr, Ocean Biogeochem & Ecosyst Res Grp, European Way, Southampton, Hants, England.
EM mvz@noc.ac.uk
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NR 36
TC 14
Z9 16
PD JUN
PY 2015
VL 135
BP 139
EP 145
DI 10.1016/j.pocean.2015.04.014
UT WOS:000356552100010
DA 2025-07-30
ER

PT J
AU Buchholz, HH
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   Bell, AG
   Michelsen, ML
   Allen, MJ
   Temperton, B
AF Buchholz, Holger H.
   Bolanos, Luis M.
   Bell, Ashley G.
   Michelsen, Michelle L.
   Allen, Michael J.
   Temperton, Ben
TI A Novel and Ubiquitous Marine Methylophage Provides Insights into
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Isolation and cultivation of viruses are the foundations on which the mechanistic understanding of virus-host interactions and parameterization of bioinformatic tools for viral ecology are based. This study isolated and characterized the first myophage known to infect the OM43 clade, expanding our knowledge of this understudied group of microbes.
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C1 [Buchholz, Holger H.; Bolanos, Luis M.; Bell, Ashley G.; Michelsen, Michelle L.; Allen, Michael J.; Temperton, Ben] Univ Exeter, Sch Biosci, Exeter, Devon, England.
   [Allen, Michael J.] Plymouth Marine Lab, Plymouth, Devon, England.
RP Temperton, B (corresponding author), Univ Exeter, Sch Biosci, Exeter, Devon, England.
EM b.temperton@exeter.ac.uk
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NR 130
TC 5
Z9 5
PD APR 12
PY 2022
VL 88
IS 7
AR e00255-22
DI 10.1128/aem.00255-22
UT WOS:000782461400033
DA 2025-07-30
ER

PT J
AU Li, CY
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AF Li, Chun-Yang
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   Chen, Yin
   Zhang, Yu-Zhong
TI Ubiquitous occurrence of a dimethylsulfoniopropionate ABC transporter in
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SO ISME JOURNAL
DT Article
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C1 [Li, Chun-Yang; Wang, Shu-Yan; Fu, Hui-Hui; Chen, Yin; Zhang, Yu-Zhong] Ocean Univ China, Frontiers Sci Ctr Deep Ocean Multispheres & Earth, Qingdao, Peoples R China.
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RP Li, CY; Chen, Y; Zhang, YZ (corresponding author), Ocean Univ China, Frontiers Sci Ctr Deep Ocean Multispheres & Earth, Qingdao, Peoples R China.; Li, CY; Chen, Y; Zhang, YZ (corresponding author), Ocean Univ China, Coll Marine Life Sci, Qingdao, Peoples R China.; Li, CY; Zhang, YZ (corresponding author), Shandong Univ, Marine Biotechnol Res Ctr, State Key Lab Microbial Technol, Qingdao, Peoples R China.; Li, CY; Zhang, YZ (corresponding author), Pilot Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao, Peoples R China.; Chen, Y (corresponding author), Univ Warwick, Sch Life Sci, Coventry CV4 7AL, England.
EM Lcy@ouc.edu.cn; Y.Chen.25@warwick.ac.uk; zhangyz@sdu.edu.cn
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NR 56
TC 12
Z9 13
PD APR
PY 2023
VL 17
IS 4
BP 579
EP 587
DI 10.1038/s41396-023-01375-3
EA JAN 2023
UT WOS:000920980000001
DA 2025-07-30
ER

PT J
AU Mukhanov, VS
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AF Mukhanov, V. S.
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TI Transbiome invasions of femtoplankton
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DT Article
AB The results of ecological and phylogenetic studies of femtoplankton, the smallest size fraction of plankton formed by viruses and ultramicrobacteria (UMB), are overviewed to shed light on the problem of transbiome invasions by microbes. Phylogenetic lineages of viruses and UMB are shown to be associated with particular biomes, thus indicating infrequent transbiome transitions in the microbial world. An alternative hypothesis of widespread cross-colonization events requires a deeper analysis of the factors that form the barrier between biomes and are responsible for the adaptation of microorganisms to different environments.
C1 [Mukhanov, V. S.; Rylkova, O. A.; Sakhon, E. G.] Russian Acad Sci, Kovalevsky Inst Marine Biol Res, Pr Nakhimova 2, Sevastopol 299011, Russia.
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RP Mukhanov, VS (corresponding author), Russian Acad Sci, Kovalevsky Inst Marine Biol Res, Pr Nakhimova 2, Sevastopol 299011, Russia.
EM v.s.mukhanov@gmail.com
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NR 47
TC 2
Z9 2
PD MAY
PY 2016
VL 9
IS 3
BP 266
EP 271
DI 10.1134/S1995425516030112
UT WOS:000378901100003
DA 2025-07-30
ER

PT J
AU Geron, A
   Werner, J
   Lebaron, P
   Wattiez, R
   Matallana-Surget, S
AF Geron, Augustin
   Werner, Johannes
   Lebaron, Philippe
   Wattiez, Ruddy
   Matallana-Surget, Sabine
TI Diel Protein Regulation of Marine Picoplanktonic Communities Assessed by
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SO MICROORGANISMS
DT Article
AB The diel cycle is of enormous biological importance in that it imposes temporal structure on ecosystem productivity. In the world's oceans, microorganisms form complex communities that carry out about half of photosynthesis and the bulk of life-sustaining nutrient cycling. How the functioning of microbial communities is impacted by day and night periods in surface seawater remains to be elucidated. In this study, we compared the day and night metaproteomes of the free-living and the particle-attached bacterial fractions from picoplanktonic communities sampled from the northwest Mediterranean Sea surface. Our results showed similar taxonomic distribution of free-living and particle-attached bacterial populations, with Alphaproteobacteria, Gammaproteobacteria and Cyanobacteria being the most active members. Comparison of the day and night metaproteomes revealed that free-living and particle-attached bacteria were more active during the day and the night, respectively. Interestingly, protein diel variations were observed in the photoautotroph Synechococcales and in (photo)-heterotrophic bacteria such as Flavobacteriales, Pelagibacterales and Rhodobacterales. Moreover, our data demonstrated that diel cycle impacts light-dependent processes such as photosynthesis and UV-stress response in Synechococcales and Rhodobacterales, respectively, while the protein regulation from the ubiquitous Pelagibacterales remained stable over time. This study unravels, for the first time, the diel variation in the protein expression of major free-living and particle-attached microbial players at the sea surface, totaling an analysis of eight metaproteomes.
C1 [Geron, Augustin; Wattiez, Ruddy] Univ Mons, Prote & Microbiol Dept, B-7000 Mons, Belgium.
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RP Matallana-Surget, S (corresponding author), Univ Stirling, Div Biol & Environm Sci BES, Fac Nat Sci, Stirling FK9 4LA, Scotland.
EM augustin.geron@umons.ac.be; johannes.werner@uni-tuebingen.de;
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NR 58
TC 3
Z9 3
PD DEC
PY 2021
VL 9
IS 12
AR 2621
DI 10.3390/microorganisms9122621
UT WOS:000735903400001
DA 2025-07-30
ER

PT J
AU Kathuria, S
   Martiny, AC
AF Kathuria, Satish
   Martiny, Adam C.
TI Prevalence of a calcium-based alkaline phosphatase associated with the
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB P>Phosphate plays a key role in regulating primary productivity in several regions of the world's oceans and here dissolved organic phosphate can be an important phosphate source. A key enzyme for utilizing dissolved organic phosphate is alkaline phosphatase and the phoA-type of this enzyme has a zinc cofactor. As the dissolved zinc concentration is low in phosphate depleted environments, this has led to the hypothesis that some phytoplankton may be zinc-P co-limited. Recently, it was shown that many marine bacteria contain an alternative form of alkaline phosphatase called phoX, but it is unclear which marine lineages carry this enzyme. Here, we describe the occurrence in low phosphate environments of phoX that is associated with uncultured Prochlorococcus and SAR11 cells. Through heterologous expression, we demonstrate that phoX encodes an active phosphatase with a calcium cofactor. The enzyme also functions with magnesium and copper, whereas cobalt, manganese, nickel and zinc inhibit enzyme activity to various degrees. We also find that uncultured SAR11 cells and cyanophages contain a different alkaline phosphatase related to a variant present in several Prochlorococcus isolates. Overall, the results suggest that many bacterial lineages including Prochlorococcus and SAR11 may not be subject to zinc-P co-limitation.
C1 [Kathuria, Satish; Martiny, Adam C.] Univ Calif Irvine, Dept Earth Syst Sci, Irvine, CA 92697 USA.
   [Martiny, Adam C.] Univ Calif Irvine, Dept Ecol & Evolutionary Biol, Irvine, CA 92697 USA.
RP Martiny, AC (corresponding author), Univ Calif Irvine, Dept Earth Syst Sci, Irvine, CA 92697 USA.
EM amartiny@uci.edu
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NR 35
TC 99
Z9 110
PD JAN
PY 2011
VL 13
IS 1
BP 74
EP 83
DI 10.1111/j.1462-2920.2010.02310.x
UT WOS:000285876600007
DA 2025-07-30
ER

PT J
AU Laghdass, M
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AF Laghdass, Melissa
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   Batailler, Nicole
   Caparros, Jocelyne
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   Lebaron, Philippe
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TI Impact of lower salinity waters on bacterial heterotrophic production
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SO ENVIRONMENTAL MICROBIOLOGY REPORTS
DT Article
AB P>We investigated the impact of water masses originating from freshwater input on bacterial heterotrophic metabolism and community structure at an offshore site in the oligotrophic NW Mediterranean Sea in 2007 and 2008. By combining 16S rRNA gene clone libraries and MICRO-CARD-FISH we determined the dominant operational taxonomic units (OTU) and their contribution to bulk abundance and activity in the presence of buoyant water masses characterized by lower salinity (LSW, < 37.9) and compared these with the winter and spring phytoplankton blooms. We demonstrate that organic matter associated with LSW markedly stimulated bacterial heterotrophic production as determined by [3H]-leucine incorporation. The OTUs SAR11-IA, SAR11-IIB, SAR86-I and SAR86-III were dominant in all clone libraries, while the Roseobacter clade and the Bacteroidetes OTU NorSea72 were more specific to the spring phytoplankton bloom. The relative contribution of these OTUs to leucine incorporation varied between 23% and 69% for SAR11, 2% and 17% for Roseobacter and was up to 4% for NorSea72. Together, they accounted for roughly 50% of bulk abundance and leucine incorporation during the four situations investigated. Our results suggest that a few cosmopolitan OTUs respond to different DOM sources in the NW Mediterranean Sea.
C1 [Laghdass, Melissa; West, Nyree J.; Batailler, Nicole; Caparros, Jocelyne; Catala, Philippe; Lantoine, Francois; Oriol, Louise; Lebaron, Philippe; Obernosterer, Ingrid] Univ Paris 06, UMR 7621, LOMIC, Observ Oceanol, F-66651 Banyuls Sur Mer, France.
   [Laghdass, Melissa; West, Nyree J.; Batailler, Nicole; Caparros, Jocelyne; Catala, Philippe; Lantoine, Francois; Oriol, Louise; Lebaron, Philippe; Obernosterer, Ingrid] CNRS, UMR 7621, LOMIC, Observ Oceanol, F-66651 Banyuls Sur Mer, France.
RP Obernosterer, I (corresponding author), Univ Paris 06, UMR 7621, LOMIC, Observ Oceanol, F-66651 Banyuls Sur Mer, France.
EM ingrid.obernosterer@obs-banyuls.fr
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NR 53
TC 14
Z9 15
PD DEC
PY 2010
VL 2
IS 6
BP 761
EP 769
DI 10.1111/j.1758-2229.2010.00181.x
UT WOS:000284484700009
DA 2025-07-30
ER

PT J
AU Varaljay, VA
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   Wilson, ST
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   Karl, DM
   Moran, MA
AF Varaljay, Vanessa A.
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TI Bacterial Dimethylsulfoniopropionate Degradation Genes in the
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Dimethylsulfoniopropionate (DMSP) is an organic sulfur compound that is rapidly metabolized by marine bacteria either by cleavage to dimethylsulfide (DMS) or demethylation to 3-methiolpropionate. The abundance and diversity of genes encoding bacterial DMS production (dddP) and demethylation (dmdA) were measured in the North Pacific subtropical gyre (NPSG) between May 2008 and February 2009 at Station ALOHA (22 degrees 45'N, 158 degrees 00'W) at two depths: 25 m and the deep chlorophyll maximum (DCM; similar to 100 m). The highest abundance of dmdA genes was in May 2008 at 25 m, with similar to 16.5% of cells harboring a gene in one of the eight subclades surveyed, while the highest abundance of dddP genes was in July 2008 at 25 m, with similar to 2% of cells harboring a gene. The dmdA gene pool was consistently dominated by homologs from SAR11 subclades, which was supported by findings in metagenomic data sets derived from Station ALOHA. Expression of the SAR11 dmdA genes was low, with typical transcript: gene ratios between 1:350 and 1:1,400. The abundance of DMSP genes was statistically different between 25 m and the DCM and correlated with a number of environmental variables, including primary production, photosynthetically active radiation, particulate DMSP, and DMS concentrations. At 25 m, dddP abundance was positively correlated with pigments that are diagnostic of diatoms; at the DCM, dmdA abundance was positively correlated with temperature. Based on gene abundance, we hypothesize that SAR11 bacterioplankton dominate DMSP cycling in the oligotrophic NPSG, with lesser but consistent involvement of other members of the bacterioplankton community.
C1 [Gifford, Scott M.; Sharma, Shalabh; Moran, Mary Ann] Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
   [Varaljay, Vanessa A.] Univ Georgia, Dept Microbiol, Athens, GA 30602 USA.
   [Wilson, Samuel T.; Karl, David M.] Univ Hawaii, Ctr Microbial Oceanog Res & Educ, Honolulu, HI 96822 USA.
   [Wilson, Samuel T.; Karl, David M.] Univ Hawaii, Dept Oceanog, Honolulu, HI 96822 USA.
RP Moran, MA (corresponding author), Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
EM mmoran@uga.edu
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NR 66
TC 35
Z9 38
PD APR
PY 2012
VL 78
IS 8
BP 2775
EP 2782
DI 10.1128/AEM.07559-11
UT WOS:000302147300031
DA 2025-07-30
ER

PT J
AU Alamer, A
   Almutairi, AR
   Halloush, S
   Al-jedai, A
   Alrashed, A
   AlFaifi, M
   Mohzari, Y
   Almutairi, M
   AlHassar, F
   Howaidi, J
   Almutairi, W
   Abraham, I
   Alkhatib, N
AF Alamer, Ahmad
   Almutairi, Abdulaali R.
   Halloush, Shiraz
   Al-jedai, Ahmed
   Alrashed, Ahmed
   AlFaifi, Mashael
   Mohzari, Yahya
   Almutairi, Malak
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   Almutairi, Wedad
   Abraham, Ivo
   Alkhatib, Nimer
TI Cost-effectiveness of Favipiravir in moderately to severely ill COVID-19
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SO SAUDI PHARMACEUTICAL JOURNAL
DT Article
AB Purpose: We aimed to evaluate the cost effectiveness of Favipiravir treatment versus standard of care (SC) in moderately to severely ill COVID-19 patients from the Saudi healthcare payer perspective. Methods: We used the patient-level simulation method to simulate a cohort of 415 patients with mod-erate to severe COVID-19 disease who were admitted to two Saudi COVID-19 referral hospitals: 220 patients on Favipiravir and 195 patients on SC. We estimated the incremental cost-effectiveness ratio (ICER) of Favipiravir versus SC in terms of the probability to be discharged alive from hospital and the mean time in days to discharge one patient alive. The model was performed twice: first, using unweighted, and second, using weighted clinical and economic data. Weighting using the inverse weight probability method was performed to achieve balance in baseline characteristics. Results: In the unweighted model, base case (probabilistic) ICER estimates favored Favipiravir at savings of Saudi Riyal (SAR)1,611,511 (SAR1,998,948) per 1% increase in the probability of being discharged alive. As to mean time to discharging one patient alive, ICERs favored Favipiravir at savings of SAR11,498 (SAR11,125). Similar results were observed in the weighted model with savings using Favipiravir of SAR1,514,893 (SAR2,453,551) per 1% increase in the probability of being discharged alive, and savings of SAR11,989 (SAR11,277) for each day a patient is discharged alive. Conclusion: From the payer perspective, the addition of Favipiravir in moderately to severely ill COVID-19 patients was cost-savings over SC. Favipiravir was associated with a higher probability of discharging patients alive and lower daily spending on hospitalization than SC.(c) 2023 The Author(s). Published by Elsevier B.V. on behalf of King Saud University. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
C1 [Alamer, Ahmad] Prince Sattam Bin Abdulaziz Univ, Coll Pharm, Dept Clin Pharm, Alkharj, Saudi Arabia.
   [Alamer, Ahmad; Abraham, Ivo] Univ Arizona, Ctr Hlth Outcomes & Pharmacoecon Res, Tucson, AZ USA.
   [Almutairi, Abdulaali R.] Saudi Food & Drug Author, Drug Sect, Riyadh, Saudi Arabia.
   [Halloush, Shiraz] Appl Sci Private Univ, Fac Pharm, Dept Clin Pharm & Therapeut, Amman, Jordan.
   [Al-jedai, Ahmed] Deputyship Therapeut Affairs, Minist Hlth, Riyadh, Saudi Arabia.
   [Al-jedai, Ahmed] Al Faisal Univ, Coll Pharm, Riyadh, Saudi Arabia.
   [Alrashed, Ahmed; Howaidi, Jude] King Fahad Med City, Dept Clin Pharm, Riyadh, Saudi Arabia.
   [AlFaifi, Mashael; Mohzari, Yahya] King Fahad Med City, Riyadh, Saudi Arabia.
   [Almutairi, Malak] Almaarefa Univ, Coll Pharm, Dept Pharm Practice, Riyadh, Saudi Arabia.
   [AlHassar, Fatimah; Almutairi, Wedad] Imam Abdulrahman Bin Faisal Univ, Dept Clin Pharm, Dammam, Saudi Arabia.
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RP Almutairi, AR (corresponding author), Saudi Food & Drug Author, Drug Sect, Riyadh, Saudi Arabia.
EM armutairi@sfda.gov.sa
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TC 4
Z9 5
PD APR
PY 2023
VL 31
IS 4
BP 510
EP 516
DI 10.1016/j.jsps.2023.02.003
EA MAR 2023
UT WOS:000994669900001
DA 2025-07-30
ER

PT J
AU Schattenhofer, M
   Fuchs, BM
   Amann, R
   Zubkov, MV
   Tarran, GA
   Pernthaler, J
AF Schattenhofer, Martha
   Fuchs, Bernhard M.
   Amann, Rudolf
   Zubkov, Mikhail V.
   Tarran, Glen A.
   Pernthaler, Jakob
TI Latitudinal distribution of prokaryotic picoplankton populations in the
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB P>Members of the prokaryotic picoplankton are the main drivers of the biogeochemical cycles over large areas of the world's oceans. In order to ascertain changes in picoplankton composition in the euphotic and twilight zones at an ocean basin scale we determined the distribution of 11 marine bacterial and archaeal phyla in three different water layers along a transect across the Atlantic Ocean from South Africa (32.9 degrees S) to the UK (46.4 degrees N) during boreal spring. Depth profiles down to 500 m at 65 stations were analysed by catalysed reporter deposition fluorescence in situ hybridization (CARD-FISH) and automated epifluorescence microscopy. There was no obvious overall difference in microbial community composition between the surface water layer and the deep chlorophyll maximum (DCM) layer. There were, however, significant differences between the two photic water layers and the mesopelagic zone. SAR11 (35 +/- 9%) and Prochlorococcus (12 +/- 8%) together dominated the surface waters, whereas SAR11 and Crenarchaeota of the marine group I formed equal proportions of the picoplankton community below the DCM (both similar to 15%). However, due to their small cell sizes Crenarchaeota contributed distinctly less to total microbial biomass than SAR11 in this mesopelagic water layer. Bacteria from the uncultured Chloroflexi-related clade SAR202 occurred preferentially below the DCM (4-6%). Distinct latitudinal distribution patterns were found both in the photic zone and in the mesopelagic waters: in the photic zone, SAR11 was more abundant in the Northern Atlantic Ocean (up to 45%) than in the Southern Atlantic gyre (similar to 25%), the biomass of Prochlorococcus peaked in the tropical Atlantic Ocean, and Bacteroidetes and Gammaproteobacteria bloomed in the nutrient-rich northern temperate waters and in the Benguela upwelling. In mesopelagic waters, higher proportions of SAR202 were present in both central gyre regions, whereas Crenarchaeota were clearly more abundant in the upwelling regions and in higher latitudes. Other phylogenetic groups such as the Planctomycetes, marine group II Euryarchaeota and the uncultured clades SAR406, SAR324 and SAR86 rarely exceeded more than 5% of relative abundance.
C1 [Schattenhofer, Martha; Fuchs, Bernhard M.; Amann, Rudolf] Max Planck Inst Marine Microbiol, D-28359 Bremen, Germany.
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   [Tarran, Glen A.] Plymouth Marine Lab, Plymouth PL1 3DH, Devon, England.
   [Pernthaler, Jakob] Univ Zurich, Limnol Inst, Kilchberg, Switzerland.
RP Fuchs, BM (corresponding author), Max Planck Inst Marine Microbiol, Celsiusstr 1, D-28359 Bremen, Germany.
EM bfuchs@mpi-bremen.de
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BP 2078
EP 2093
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DA 2025-07-30
ER

PT J
AU Straza, TRA
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AF Straza, Tiffany R. A.
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TI Abundance and single-cell activity of bacterial groups in Antarctic
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SO LIMNOLOGY AND OCEANOGRAPHY
DT Article
AB We estimated the abundance and single-cell activity of bacterial groups in waters off the West Antarctic Peninsula (WAP) using a combination of microautoradiography and fluorescent in situ hybridization (FISH). The abundance of the Ant4D3 subgroup, detected by a new FISH probe, was 10% of the total community and half of the gammaproteobacterial population. The Ant4D3, Polaribacter, and SAR11 subgroups accounted for the majority of the Gammaproteobacteria, Sphingobacteria-Flavobacteria, and Alphaproteobacteria, respectively. Approximately 40% of the total microbial community actively incorporated leucine (added at 20 nmol L-1), while a smaller fraction (12-22%) used protein and an amino acid mixture (added at tracer concentrations). The fractions of SAR11, Polaribacter, and Ant4D3 that were active differed from each other and varied among substrates. SAR11 had the largest fraction of active cells incorporating leucine, while Polaribacter dominated the community using protein. The fraction of Ant4D3 using different compounds did not vary, but this group dominated the incorporation of amino acids, and was an abundant and active component of the bacterial community. Bacteria in the WAP region were as active as bacteria in the Mid-Atlantic Bight, even though total bacterial production was lower in the WAP. Though persistently cold (0-1 degrees C) and dominated by different bacterial taxa, the single-cell activity of this summertime Antarctic bacterial community was comparable to that of temperate communities.
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RP Kirchman, DL (corresponding author), Univ Delaware, Sch Marine Sci & Policy, Lewes, DE 19958 USA.
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NR 39
TC 43
Z9 48
PD NOV
PY 2010
VL 55
IS 6
BP 2526
EP 2536
DI 10.4319/lo.2010.55.6.2526
UT WOS:000287844700024
DA 2025-07-30
ER

PT J
AU Kobiyama, A
   Rashid, J
   Reza, MS
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   Yamada, Y
   Kudo, T
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   Watabe, S
AF Kobiyama, Atsushi
   Rashid, Jonaira
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   Kaga, Yoshimasa
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   Musashi, Tatsuya
   Mineta, Katsuhiko
   Gojobori, Takashi
   Watabe, Shugo
TI Seasonal and annual changes in the microbial communities of Ofunato Bay,
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SO SCIENTIFIC REPORTS
DT Article
AB Five years of datasets from 2015 to 2019 of whole genome shotgun sequencing for cells trapped on 0.2-mu m filters of seawater collected monthly from Ofunato Bay, an enclosed bay in Japan, were analysed, which included the 2015 data that we had reported previously. Nucleotide sequences were determined for extracted DNA from three locations for both the upper (1 m) and deeper (8 or 10 m) depths. The biotic communities analysed at the domain level comprised bacteria, eukaryotes, archaea and viruses. The relative abundance of bacteria was over 60% in most months for the five years. The relative abundance of the SAR86 cluster was highest in the bacterial group, followed by Candidatus Pelagibacter and Planktomarina. The relative abundance of Ca. Pelagibacter showed no relationship with environmental factors, and those of SAR86 and Planktomarina showed positive correlations with salinity and dissolved oxygen, respectively. The bacterial community diversity showed seasonal changes, with high diversity around September and low diversity around January for all five years. Nonmetric multidimensional scaling analysis also revealed that the bacterial communities in the bay were grouped in a season-dependent manner and linked with environmental variables such as seawater temperature, salinity and dissolved oxygen.
C1 [Kobiyama, Atsushi; Rashid, Jonaira; Reza, Md Shaheed; Ikeda, Yuri; Yamada, Yuichiro; Kudo, Toshiaki; Mizusawa, Nanami; Yanagisawa, Saki; Ikeda, Daisuke; Sato, Shigeru; Ogata, Takehiko; Ikeo, Kazuho; Watabe, Shugo] Kitasato Univ, Sch Marine Biosci, Minami Ku, Sagamihara, Kanagawa 2520373, Japan.
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   [Reza, Md Shaheed] Bangladesh Agr Univ, Dept Fisheries Technol, Mymensingh 2202, Bangladesh.
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   [Kaga, Shinnosuke; Watanabe, Shiho; Segawa, Satoshi; Tada, Yumiko] Iwate FisheriesTechnol Ctr, Kamaishi, Iwate 0260001, Japan.
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RP Watabe, S (corresponding author), Kitasato Univ, Sch Marine Biosci, Minami Ku, Sagamihara, Kanagawa 2520373, Japan.; Gojobori, T (corresponding author), King Abdullah Univ Sci & Technol, Computat Biosci Res Ctr, Thuwal 239556900, Saudi Arabia.
EM takashi.gojobori@kaust.edu.sa; swatabe@kitasato-u.ac.jp
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NR 74
TC 5
Z9 5
PD AUG 26
PY 2021
VL 11
IS 1
AR 17277
DI 10.1038/s41598-021-96641-9
UT WOS:000691021200089
DA 2025-07-30
ER

PT J
AU Nowinski, B
   Motard-Côté, J
   Landa, M
   Preston, CM
   Scholin, CA
   Birch, JM
   Kiene, RP
   Moran, MA
AF Nowinski, Brent
   Motard-Cote, Jessie
   Landa, Marine
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   Moran, Mary Ann
TI Microdiversity and temporal dynamics of marine bacterial
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Dimethylsulfoniopropionate (DMSP) is an abundant organic sulfur metabolite produced by many phytoplankton species and degraded by bacteria via two distinct pathways with climate-relevant implications. We assessed the diversity and abundance of bacteria possessing these pathways in the context of phytoplankton community composition over a 3-week time period spanning September-October, 2014 in Monterey Bay, CA. The dmdA gene from the DMSP demethylation pathway dominated the DMSP gene pool and was harboured mostly by members of the alphaproteobacterial SAR11 clade and secondarily by the Roseobacter group, particularly during the second half of the study. Novel members of the DMSP-degrading community emerged from dmdA sequences recovered from metagenome assemblies and single-cell sequencing, including largely uncharacterized gammaproteobacteria and alphaproteobacteria taxa. In the DMSP cleavage pathway, the SAR11 gene dddK was the most abundant early in the study, but was supplanted by dddP over time. SAR11 members, especially those harbouring genes for both DMSP degradation pathways, had a strong positive relationship with the abundance of dinoflagellates, and DMSP-degrading gammaproteobacteria co-occurred with haptophytes. This in situ study of the drivers of DMSP fate in a coastal ecosystem demonstrates for the first time correlations between specific groups of bacterial DMSP degraders and phytoplankton taxa.
C1 [Nowinski, Brent; Landa, Marine; Moran, Mary Ann] Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
   [Motard-Cote, Jessie; Kiene, Ronald P.] Univ S Alabama, Dept Marine Sci, Mobile, AL 36688 USA.
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   [Landa, Marine] Univ Calif Santa Cruz, Ocean Sci Dept, Santa Cruz, CA 95064 USA.
RP Moran, MA (corresponding author), Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
EM mmoran@uga.edu
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NR 54
TC 26
Z9 30
PD MAY
PY 2019
VL 21
IS 5
BP 1687
EP 1701
DI 10.1111/1462-2920.14560
UT WOS:000471715900013
DA 2025-07-30
ER

PT J
AU Williams, KP
   Sobral, BW
   Dickerman, AW
AF Williams, Kelly P.
   Sobral, Bruno W.
   Dickerman, Allan W.
TI A robust species tree for the Alphaproteobacteria
SO JOURNAL OF BACTERIOLOGY
DT Article
AB The branching order and coherence of the alphaproteobacterial orders have not been well established, and not all studies have agreed that mitochondria arose from within the Rickettsiales. A species tree for 72 alphaproteobacteria was produced from a concatenation of alignments for 104 well-behaved protein families. Coherence was upheld for four of the five orders with current standing that were represented here by more than one species. However, the family Hyphomonadaceae was split from the other Rhodobacterales, forming an expanded group with Caulobacterales that also included Parvularcula. The three earliest-branching alphaproteobacterial orders were the Rickettsiales, followed by the Rhodospirillales and then the Sphingomonaddles. The principal uncertainty is whether the expanded Caulobacterales group is more closely associated with the Rhodobacterales or the Rhizobiales. The mitochondrial branch was placed within the Rickettsiales as a sister to the combined Anaplasmataceae and Rickettsiaceae, all subtended by the Pelagibacter branch. Pelagibacter genes will serve as useful additions to the bacterial outgroup in future evolutionary studies of mitochondrial genes, including those that have transferred to the eukaryotic nucleus.
C1 Inst Poliomyelitis & Viral Encephalitis, Virginia Bioinformat Inst, Blacksburg, VA 24061 USA.
RP Williams, KP (corresponding author), Inst Poliomyelitis & Viral Encephalitis, Virginia Bioinformat Inst, Blacksburg, VA 24061 USA.
EM kellwill@vt.edu
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NR 32
TC 203
Z9 242
PD JUL
PY 2007
VL 189
IS 13
BP 4578
EP 4586
DI 10.1128/JB.00269-07
UT WOS:000247612100004
DA 2025-07-30
ER

PT J
AU Braakman, R
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   Longnecker, K
   Hogle, SL
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   Dooley, K
   Arellano, A
   Soule, MCK
   Kujawinski, EB
   Chisholm, SW
AF Braakman, Rogier
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   O'Keefe, Tyler J.
   Longnecker, Krista
   Hogle, Shane L.
   Becker, Jamie W.
   Li, Robert C.
   Dooley, Keven
   Arellano, Aldo
   Soule, Melissa C. Kido
   Kujawinski, Elizabeth B.
   Chisholm, Sallie W.
TI Global niche partitioning of purine and pyrimidine cross-feeding among
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SO SCIENCE ADVANCES
DT Article
AB Cross-feeding involves microbes consuming exudates of other surrounding microbes, mediating elemental cycling. Characterizing the diversity of cross-feeding pathways in ocean microbes illuminates evolutionary forces driving self-organization of ocean ecosystems. Here, we uncover a purine and pyrimidine cross-feeding network in globally abundant groups. The cyanobacterium Prochlorococcus exudes both compound classes, which metabolic reconstructions suggest follows synchronous daily genome replication. Co-occurring heterotrophs differentiate into purine- and pyrimidine-using generalists or specialists that use compounds for different purposes. The most abundant heterotroph, SAR11, is a specialist that uses purines as sources of energy, carbon, and/or nitrogen, with subgroups differentiating along ocean-scale gradients in the supply of energy and nitrogen, in turn producing putative cryptic nitrogen cycles that link many microbes. Last, in an SAR11 subgroup that dominates where Prochlorococcus is abundant, adenine additions to cultures inhibit DNA synthesis, poising cells for replication. We argue that this subgroup uses inferred daily adenine pulses from Prochlorococcus to synchronize to the daily photosynthate supply from surrounding phytoplankton.
C1 [Braakman, Rogier; Li, Robert C.] MIT, Dept Earth Atmospher & Planetary Sci, Cambridge, MA 02139 USA.
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   [Chisholm, Sallie W.] MIT, Dept Biol, Cambridge, MA USA.
   [Satinsky, Brandon] Dyno Therapeut, Watertown, MA USA.
   [O'Keefe, Tyler J.] Univ North Carolina, Inst Marine Sci, Morehead City, NC USA.
   [Hogle, Shane L.] Univ Turku, Dept Biol, Turku, Finland.
   [Becker, Jamie W.] Alvernia Univ, Dept Sci, Reading, PA USA.
   [Dooley, Keven] Natl Renewable Energy Lab, Renewable Resources & Enabling Sci Ctr, Golden, CO USA.
   [Arellano, Aldo] Univ Wisconsin, Dept Bacteriol, Madison, WI USA.
RP Braakman, R (corresponding author), MIT, Dept Earth Atmospher & Planetary Sci, Cambridge, MA 02139 USA.
EM braakman@mit.edu
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NR 85
TC 1
Z9 1
PD JAN 3
PY 2025
VL 11
IS 1
AR eadp1949
DI 10.1126/sciadv.adp1949
UT WOS:001389489200020
DA 2025-07-30
ER

PT J
AU Kudo, T
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AF Kudo, Toshiaki
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TI Seasonal changes in the abundance of bacterial genes related to
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SO GENE
DT Article
AB Ofunato Bay is located in the northeastern Pacific Ocean area of Japan, and it has the highest biodiversity of marine organisms in the world, primarily due to tidal influences from the cold Oyashio and warm Kuroshio Currents. Our previous results from performing shotgun metagenomics indicated that Candidatus Pelagibacter ubique and Planktomarina temperata were the dominant bacteria (Reza et al., 2018a, 2018b). These bacteria are reportedly able to catabolize dimethylsulfoniopropionate (DMSP) produced from phytoplankton into dimethyl sulfide (DMS) or methanethiol (MeSH). This study was focused on seasonal changes in the abundances of bacterial genes (dddP, dmdA) related to DMSP catabolism in the seawater of Ofunato Bay by BLAST + analysis using shotgun metagenomic datasets. We found seasonal changes among the Candidatus Pelagibacter ubique strains, including those of the HTCC1062 type and the Red Sea type. A good correlation was observed between the chlorophyll a concentrations and the abundances of the catabolic genes, suggesting that the bacteria directly interact with phytoplankton in the marine material cycle system and play important roles in producing DMS and MeSH from DMSP as signaling molecules for the possible formation of the scent of the tidewater or as fish attractants.
C1 [Kudo, Toshiaki; Kobiyama, Atsushi; Rashid, Jonaira; Reza, Md Shaheed; Yamada, Yuichiro; Ikeda, Yuri; Ikeda, Daisuke; Mizusawa, Nanami; Ikeoa, Kazuho; Sato, Shigeru; Ogata, Takehiko; Jimbo, Mitsuru; Watabe, Shugo] Kitasato Univ, Sch Marine Biosci, Minami Ku, Sagamihara, Kanagawa 2520373, Japan.
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   [Kaga, Shinnosuke] Iwate Prefectural Govt, Ofunato Fisheries Promot Ctr, Ofunato, Iwate 0228502, Japan.
RP Gojobori, T (corresponding author), King Abdullah Univ Sci & Technol, Computat Biosci Res Ctr, Biol & Environm Sci & Engn, Thuwal 239556900, Saudi Arabia.; Watabe, S (corresponding author), Kitasato Univ, Sch Marine Biosci, Dept Marine Biochem, Minami Ku, Sagamihara, Kanagawa 2520373, Japan.
EM takashi.gojobori@kaust.edu.sa; swatabe@kitasato-u.ac.jp
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PD JUL 30
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VL 665
BP 174
EP 184
DI 10.1016/j.gene.2018.04.072
UT WOS:000435621900022
DA 2025-07-30
ER

PT J
AU Tada, Y
   Shiozaki, T
   Ogawa, H
   Suzuki, K
AF Tada, Yuya
   Shiozaki, Takuhei
   Ogawa, Hiroshi
   Suzuki, Koji
TI Basin-scale distribution of prokaryotic phylotypes in the epipelagic
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SO JOURNAL OF OCEANOGRAPHY
DT Article
AB In the present study, we used catalyzed reporter deposition-fluorescence in situ hybridization to quantify the abundance of five bacterial (Alphaproteobacteria, SAR11, Gammaproteobacteria, SAR86, and Bacteroidetes) and two archaeal (Crenarchaeota and Euryarchaeota) phylotypes in the epipelagic layer (0-200 m) of the Central South Pacific Ocean along 170A degrees W from 0A degrees to 40A degrees S. We found that the distribution patterns of these phylotypes differed from each other. All phylotypes except Gammaproteobacteria were particularly abundant at the surface water of the equatorial region, whereas Gammaproteobacteria was relatively abundant in the area from the southern part of the South Pacific Ocean. SAR11, affiliated with Alphaproteobacteria was the dominant phylotype at all depths, throughout the study area. The abundance of SAR11 significantly increased with chlorophyll a concentration, suggesting that phytoplankton could affect their distribution pattern. There was a positive correlation between Bacteroidetes abundance and water temperature, suggesting that the temperature gradient could be a critical factor determining their distribution in the South Pacific Ocean. Crenarchaeota and Euryarchaeota were more abundant at the equatorial region than in other study areas. Euryarchaeota abundance significantly decreased with depth, and increased with chlorophyll a concentration. This suggests that there was ecological interaction between Euryarchaeota and phytoplankton in the equatorial surface. Our data indicate that distinct hydrographic properties such as seawater temperature, salinity, and the concentrations of chlorophyll a and nutrients can principally control the basin-scale distribution of different prokaryotic phylotypes in the epipelagic layer of the Central South Pacific Ocean.
C1 [Tada, Yuya; Suzuki, Koji] Hokkaido Univ, Fac Environm Earth Sci, Kita Ku, North 10 West 5, Sapporo, Hokkaido 0600810, Japan.
   [Shiozaki, Takuhei; Ogawa, Hiroshi] Univ Tokyo, Atmosphere & Ocean Res Inst, 5-1-5 Kashiwanoha, Kashiwa, Chiba 2778564, Japan.
   [Shiozaki, Takuhei] Japan Agcy Marine Earth Sci & Technol, Res & Dev Ctr Global Change, 2-15 Natsushima Cho, Yokosuka, Kanagawa 2330061, Japan.
RP Tada, Y (corresponding author), Hokkaido Univ, Fac Environm Earth Sci, Kita Ku, North 10 West 5, Sapporo, Hokkaido 0600810, Japan.
EM yuyatada@ees.hokudai.ac.jp
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NR 76
TC 1
Z9 1
PD APR
PY 2017
VL 73
IS 2
BP 145
EP 158
DI 10.1007/s10872-016-0391-z
UT WOS:000395621000001
DA 2025-07-30
ER

PT J
AU Ruiz-González, C
   Galí, M
   Gasol, JM
   Simó, R
AF Ruiz-Gonzalez, Clara
   Gali, Marti
   Gasol, Josep M.
   Simo, Rafel
TI Sunlight effects on the DMSP-sulfur and leucine assimilation activities
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SO BIOGEOCHEMISTRY
DT Article; Proceedings Paper
CT 5th International Symposium on Biological and Environmental Chemistry of
   DMS(P) and Related Compounds
CY OCT 19-22, 2010
CL Natl Inst Oceanography (NIO), INDIA
HO Natl Inst Oceanography (NIO)
AB The influence of solar ultraviolet radiation and photosynthetically active radiation (PAR) on summertime marine bacterial uptake and assimilation of sulfur from radiolabeled dimethlysulfoniopropionate (S-35-DMSP) was studied at four Arctic and two Antarctic stations. Incubations with H-3-leucine were also conducted for comparative purposes as a measurement of bacterial activity. Arctic waters were characterized by large numbers of colonial Phaeocystis pouchetii and higher DMSP concentrations than in the two diatom-dominated Antarctic samples. Exposure to full sunlight radiation (280-700 nm), and to a lesser extent to PAR + UVA (320-700 nm), generally decreased the bacterial assimilation of H-3-leucine with respect to darkness, and caused variable effects on S-35-DMSP assimilation. By using a single-cell approach involving microautoradiography we found high percentages of sulfur assimilating cells within the bacterial groups Gammaproteobacteria, Bacteroidetes, SAR11 and Roseobacter despite the varying DMSP concentrations between Arctic and Antarctic samples. The dominant SAR11 clade contributed 50-70% of the cells assimilating both substrates in the Arctic stations, whereas either Gammaproteobacteria or SAR11 were the largest contributors to H-3-leucine uptake in samples from the two Antarctic stations. Only one station was analyzed for single-cell S-35-DMSP assimilation in Antarctica, and Gammaproteobacteria were major contributors to its uptake, providing the first evidence for Antarctic bacteria actively taking up S-35-DMSP. PAR + UVA repeatedly increased the number of SAR11 cells assimilating H-3-leucine. This pattern also occurred with other S-35-DMSP assimilating groups, though not so consistently. Our results support a widespread capability of polar bacteria to assimilate DMSP-sulfur during the season of maximum DMSP concentrations, and show for the first time that all major polar taxa can be highly active at this assimilation under the appropriate circumstances. Our findings further confirm the role of sunlight as a modulator of heterotrophic carbon and sulfur fluxes in the surface ocean.
C1 [Ruiz-Gonzalez, Clara; Gali, Marti; Gasol, Josep M.; Simo, Rafel] CSIC, Inst Ciencies Mar, E-08003 Barcelona, Catalunya, Spain.
RP Ruiz-González, C (corresponding author), CSIC, Inst Ciencies Mar, Pg Maritim Barceloneta 37-49, E-08003 Barcelona, Catalunya, Spain.
EM clara.ruiz.glez@gmail.com
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NR 86
TC 16
Z9 17
PD SEP
PY 2012
VL 110
IS 1-3
SI SI
BP 57
EP 74
DI 10.1007/s10533-012-9699-y
UT WOS:000309227400006
DA 2025-07-30
ER

PT J
AU Munson-McGee, JH
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AF Munson-McGee, Jacob H.
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   Stepanauskas, Ramunas
TI Decoupling of respiration rates and abundance in marine prokaryoplankton
SO NATURE
DT Article
AB The ocean-atmosphere exchange of CO2 largely depends on the balance between marine microbial photosynthesis and respiration. Despite vast taxonomic and metabolic diversity among marine planktonic bacteria and archaea (prokaryoplankton)(1-3), their respiration usually is measured in bulk and treated as a 'black box' in global biogeochemical models(4); this limits the mechanistic understanding of the global carbon cycle. Here, using a technology for integrated phenotype analyses and genomic sequencing of individual microbial cells, we show that cell-specific respiration rates differ by more than 1,000x among prokaryoplankton genera. The majority of respiration was found to be performed by minority members of prokaryoplankton (including the Roseobacter cluster), whereas cells of the most prevalent lineages (including Pelagibacter and SAR86) had extremely low respiration rates. The decoupling of respiration rates from abundance among lineages, elevated counts of proteorhodopsin transcripts in Pelagibacter and SAR86 cells and elevated respiration of SAR86 at night indicate that proteorhodopsin-based phototrophy(3,5-7) probably constitutes an important source of energy to prokaryoplankton and may increase growth efficiency. These findings suggest that the dependence of prokaryoplankton on respiration and remineralization of phytoplankton-derived organic carbon into CO2 for its energy demands and growth may be lower than commonly assumed and variable among lineages.
C1 [Munson-McGee, Jacob H.; Lindsay, Melody R.; Brown, Julia M.; D'Angelo, Timothy; Brown, Joe; Lubelczyk, Laura C.; Emerson, David; Orcutt, Beth N.; Poulton, Nicole J.; Stepanauskas, Ramunas] Bigelow Lab Ocean Sci, East Boothbay, ME 04544 USA.
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RP Stepanauskas, R (corresponding author), Bigelow Lab Ocean Sci, East Boothbay, ME 04544 USA.
EM rstepanauskas@bigelow.org
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NR 79
TC 39
Z9 39
PD DEC 22
PY 2022
VL 612
IS 7941
BP 764
EP +
DI 10.1038/s41586-022-05505-3
EA DEC 2022
UT WOS:000895213100006
DA 2025-07-30
ER

PT J
AU Cui, YS
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   Kaneko, R
   Kameyama, S
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AF Cui, Yingshun
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   Omori, Yuko
   Wong, Shu-Kuan
   Ijichi, Minoru
   Kaneko, Ryo
   Kameyama, Sohiko
   Tanimoto, Hiroshi
   Hamasaki, Koji
TI Abundance and Distribution of Dimethylsulfoniopropionate Degradation
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Dimethylsulfoniopropionate (DMSP) is mainly produced by marine phytoplankton but is released into the microbial food web and degraded by marine bacteria to dimethyl sulfide (DMS) and other products. To reveal the abundance and distribution of bacterial DMSP degradation genes and the corresponding bacterial communities in relation to DMS and DMSP concentrations in seawater, we collected surface seawater samples from DMS hot spot sites during a cruise across the Pacific Ocean. We analyzed the genes encoding DMSP lyase (dddP) and DMSP demethylase (dmdA), which are responsible for the transformation of DMSP to DMS and DMSP assimilation, respectively. The averaged abundance (+/- standard deviation) of these DMSP degradation genes relative to that of the 16S rRNA genes was 33% +/- 12%. The abundances of these genes showed large spatial variations. dddP genes showed more variation in abundances than dmdA genes. Multidimensional analysis based on the abundances of DMSP degradation genes and environmental factors revealed that the distribution pattern of these genes was influenced by chlorophyll a concentrations and temperatures. dddP genes, dmdA subclade C/2 genes, and dmdA subclade D genes exhibited significant correlations with the marine Roseobacter clade, SAR11 subgroup Ib, and SAR11 subgroup Ia, respectively. SAR11 subgroups Ia and Ib, which possessed dmdA genes, were suggested to be the main potential DMSP consumers. The Roseobacter clade members possessing dddP genes in oligotrophic subtropical regions were possible DMS producers. These results suggest that DMSP degradation genes are abundant and widely distributed in the surface seawater and that the marine bacteria possessing these genes influence the degradation of DMSP and regulate the emissions of DMS in subtropical gyres of the Pacific Ocean.
C1 [Cui, Yingshun; Suzuki, Shotaro; Wong, Shu-Kuan; Ijichi, Minoru; Kaneko, Ryo; Hamasaki, Koji] Univ Tokyo, Atmosphere & Ocean Res Inst, Div Marine Life Sci, Marine Microbiol,Dept Marine Ecosyst Dynam, Kashiwa, Chiba, Japan.
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RP Cui, YS (corresponding author), Univ Tokyo, Atmosphere & Ocean Res Inst, Div Marine Life Sci, Marine Microbiol,Dept Marine Ecosyst Dynam, Kashiwa, Chiba, Japan.
EM yscui415@aori.u-tokyo.ac.jp
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NR 51
TC 35
Z9 41
PD JUN
PY 2015
VL 81
IS 12
BP 4184
EP 4194
DI 10.1128/AEM.03873-14
UT WOS:000354864000028
DA 2025-07-30
ER

PT J
AU Williams, TJ
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   DeMaere, MZ
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AF Williams, Timothy J.
   Wilkins, David
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TI The role of planktonic Flavobacteria in processing algal organic
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Heterotrophic marine bacteria play key roles in remineralizing organic matter generated from primary production. However, far more is known about which groups are dominant than about the cellular processes they perform in order to become dominant. In the Southern Ocean, eukaryotic phytoplankton are the dominant primary producers. In this study we used metagenomics and metaproteomics to determine how the dominant bacterial and archaeal plankton processed bloom material. We examined the microbial community composition in 14 metagenomes and found that the relative abundance of Flavobacteria (dominated by Polaribacter) was positively correlated with chlorophyll a fluorescence, and the relative abundance of SAR11 was inversely correlated with both fluorescence and Flavobacteria abundance. By performing metaproteomics on the sample with the highest relative abundance of Flavobacteria (Newcomb Bay, East Antarctica) we defined how Flavobacteria attach to and degrade diverse complex organic material, how they make labile compounds available to Alphaproteobacteria (especially SAR11) and Gammaproteobacteria, and how these heterotrophic Proteobacteria target and utilize these nutrients. The presence of methylotrophic proteins for archaea and bacteria also indicated the importance of metabolic specialists. Overall, the study provides functional data for the microbial mechanisms of nutrient cycling at the surface of the coastal Southern Ocean.
C1 [Williams, Timothy J.; Wilkins, David; Long, Emilie; Evans, Flavia; DeMaere, Mathew Z.; Cavicchioli, Ricardo] Univ New S Wales, Sch Biotechnol & Biomol Sci, Sydney, NSW 2052, Australia.
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RP Cavicchioli, R (corresponding author), Univ New S Wales, Sch Biotechnol & Biomol Sci, Sydney, NSW 2052, Australia.
EM r.cavicchioli@unsw.edu.au
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NR 83
TC 241
Z9 276
PD MAY
PY 2013
VL 15
IS 5
SI SI
BP 1302
EP 1317
DI 10.1111/1462-2920.12017
UT WOS:000318041800006
DA 2025-07-30
ER

PT J
AU Ghai, R
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   Picazo, A
   Camacho, A
   Rodriguez-Valera, F
AF Ghai, Rohit
   Mizuno, Carolina Megumi
   Picazo, Antonio
   Camacho, Antonio
   Rodriguez-Valera, Francisco
TI Metagenomics uncovers a new group of low GC and ultra-small marine
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SO SCIENTIFIC REPORTS
DT Article
AB We describe a deep-branching lineage of marine Actinobacteria with very low GC content (33%) and the smallest free living cells described yet (cell volume ca. 0.013 mu m(3)), even smaller than the cosmopolitan marine photoheterotroph, 'Candidatus Pelagibacter ubique'. These microbes are highly related to 16S rRNA sequences retrieved by PCR from the Pacific and Atlantic oceans 20 years ago. Metagenomic fosmids allowed a virtual genome reconstruction that also indicated very small genomes below 1 Mb. A new kind of rhodopsin was detected indicating a photoheterotrophic lifestyle. They are estimated to be, similar to 4% of the total numbers of cells found at the site studied (the Mediterranean deep chlorophyll maximum) and similar numbers were estimated in all tropical and temperate photic zone metagenomes available. Their geographic distribution mirrors that of picocyanobacteria and there appears to be an association between these microbial groups. A new sub-class, 'Candidatus Actinomarinidae' is proposed to designate these microbes.
C1 [Ghai, Rohit; Mizuno, Carolina Megumi; Rodriguez-Valera, Francisco] Univ Miguel Hernandez, Evolutionary Genom Grp, Dept Prod Vegetal & Microbiol, Alicante 03550, Spain.
   [Picazo, Antonio; Camacho, Antonio] Univ Valencia, Cavanilles Inst Biodivers & Evolutionary Biol, E-46100 Burjassot, Spain.
RP Rodriguez-Valera, F (corresponding author), Univ Miguel Hernandez, Evolutionary Genom Grp, Dept Prod Vegetal & Microbiol, Alicante 03550, Spain.
EM frvalera@umh.es
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NR 75
TC 148
Z9 162
PD AUG 20
PY 2013
VL 3
AR 2471
DI 10.1038/srep02471
UT WOS:000323243400002
DA 2025-07-30
ER

PT J
AU Sargeant, SL
   Murrell, JC
   Nightingale, PD
   Dixon, JL
AF Sargeant, Stephanie L.
   Murrell, J. Colin
   Nightingale, Philip D.
   Dixon, Joanna L.
TI Basin-scale variability of microbial methanol uptake in the Atlantic
   Ocean
SO BIOGEOSCIENCES
DT Article
AB Methanol is a climate-active gas and the most abundant oxygenated volatile organic compound (OVOC) in the atmosphere and seawater. Marine methylotrophs are aerobic bacteria that utilise methanol from seawater as a source of carbon (assimilation) and/or energy (dissimilation). A few spatially limited studies have previously reported methanol oxidation rates in seawater; however, the basin-wide ubiquity of marine microbial methanol utilisation remains unknown. This study uniquely combines seawater C-14 labelled methanol tracer studies with 16S rRNA "pyrosequencing" to investigate variability in microbial methanol dissimilation and known methanol-utilising bacteria throughout a meridional transect of the Atlantic Ocean between 47 degrees N to 39 degrees S. Microbial methanol dissimilation varied between 0.05 and 1.68 nmol L-1 h(-1) in the top 200 m of the Atlantic Ocean and showed significant variability between biogeochemical provinces. The highest rates of methanol dissimilation were found in the northern subtropical gyre (average 0.99 +/- 0.41 nmol L-1 h(-1)), which were up to 8 times greater than other Atlantic regions. Microbial methanol dissimilation rates displayed a significant inverse correlation with heterotrophic bacterial production (determined using H-3-leucine). Despite significant depth stratification of bacterial communities, methanol dissimilation rates showed much greater variability between oceanic provinces compared to depth. There were no significant differences in rates between samples collected under light and dark environmental conditions. The variability in the numbers of SAR11 (16S rRNA gene sequences) were estimated to explain approximately 50 % of the changes in microbial methanol dissimilation rates. We estimate that SAR11 cells in the Atlantic Ocean account for between 0.3 % and 59 % of the rates of methanol dissimilation in Atlantic waters, compared to < 0.01 %-2.3 % for temperate coastal waters. These results make a substantial contribution to our current knowledge and understanding of the utilisation of methanol by marine microbial communities, but highlight the lack of understanding of in situ methanol production mechanisms.
C1 [Sargeant, Stephanie L.; Nightingale, Philip D.; Dixon, Joanna L.] Plymouth Marine Lab, Prospect Pl, Plymouth PL1 3DH, Devon, England.
   [Murrell, J. Colin] Univ East Anglia, Sch Environm Sci, Norwich Res Pk, Norwich NR4 7TJ, Norfolk, England.
   [Sargeant, Stephanie L.] Univ West England, Ctr Res Biosci, Frenchay Campus,Coldharbour Lane, Bristol BS16 1QY, Avon, England.
RP Dixon, JL (corresponding author), Plymouth Marine Lab, Prospect Pl, Plymouth PL1 3DH, Devon, England.
EM jod@pml.ac.uk
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NR 42
TC 8
Z9 8
PD AUG 28
PY 2018
VL 15
IS 16
BP 5155
EP 5167
DI 10.5194/bg-15-5155-2018
UT WOS:000442943600001
DA 2025-07-30
ER

PT J
AU Seong, HJ
   Roux, S
   Hwang, CY
   Sul, WJ
AF Seong, Hoon Je
   Roux, Simon
   Hwang, Chung Yeon
   Sul, Woo Jun
TI Marine DNA methylation patterns are associated with microbial community
   composition and inform virus-host dynamics
SO MICROBIOME
DT Article
AB Background: DNA methylation in prokaryotes is involved in many different cellular processes including cell cycle regulation and defense against viruses. To date, most prokaryotic methylation systems have been studied in culturable microorganisms, resulting in a limited understanding of DNA methylation from a microbial ecology perspective. Here, we analyze the distribution patterns of several microbial epigenetics marks in the ocean microbiome through genome-centric metagenomics across all domains of life.
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   Conclusions: Overall, this study elucidates that DNA methylation patterns are associated with ecological changes and virus-host dynamics in the ocean microbiome.
C1 [Seong, Hoon Je; Sul, Woo Jun] Chung Ang Univ, Dept Syst Biotechnol, Anseong, South Korea.
   [Roux, Simon] Lawrence Berkeley Natl Lab, DOE Joint Genome Inst, Berkeley, CA USA.
   [Hwang, Chung Yeon] Seoul Natl Univ, Sch Earth & Environm Sci, Seoul, South Korea.
   [Hwang, Chung Yeon] Seoul Natl Univ, Res Inst Oceanog, Seoul, South Korea.
RP Sul, WJ (corresponding author), Chung Ang Univ, Dept Syst Biotechnol, Anseong, South Korea.
EM sulwj@cau.ac.kr
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NR 89
TC 14
Z9 14
PD SEP 28
PY 2022
VL 10
IS 1
AR 157
DI 10.1186/s40168-022-01340-w
UT WOS:000860681700001
DA 2025-07-30
ER

PT J
AU Lim, YK
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AF Lim, Young Kyun
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DT Article
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C1 [Lim, Young Kyun; Kim, Jin Ho; Baek, Seung Ho] KIOST Korea Inst Ocean Sci & Technol, Risk Assessment Res Ctr, Geoje 53201, South Korea.
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RP Baek, SH (corresponding author), KIOST Korea Inst Ocean Sci & Technol, Risk Assessment Res Ctr, Geoje 53201, South Korea.; Baek, SH (corresponding author), Univ Sci & Technol, Dept Ocean Sci, Daejeon 34113, South Korea.
EM baeksh@kiost.ac.kr
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ER

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NR 70
TC 8
Z9 9
PD OCT
PY 2013
VL 5
IS 5
BP 686
EP 696
DI 10.1111/1758-2229.12068
UT WOS:000325142700008
DA 2025-07-30
ER

PT J
AU Chow, CET
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   Fuhrman, JA
AF Chow, Cheryl-Emiliane T.
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   Cram, Jacob A.
   Steele, Joshua A.
   Needham, David M.
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   Parada, Alma E.
   Fuhrman, Jed A.
TI Temporal variability and coherence of euphotic zone bacterial
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SO ISME JOURNAL
DT Article
AB Time-series are critical to understanding long-term natural variability in the oceans. Bacterial communities in the euphotic zone were investigated for over a decade at the San Pedro Ocean Time-series station (SPOT) off southern California. Community composition was assessed by Automated Ribosomal Intergenic Spacer Analysis (ARISA) and coupled with measurements of oceanographic parameters for the surface ocean (0-5 m) and deep chlorophyll maximum (DCM, average depth similar to 30 m). SAR11 and cyanobacterial ecotypes comprised typically more than one-third of the measured community; diversity within both was temporally variable, although a few operational taxonomic units (OTUs) were consistently more abundant. Persistent OTUs, mostly Alphaproteobacteria (SAR11 clade), Actinobacteria and Flavobacteria, tended to be abundant, in contrast to many rarer yet intermittent and ephemeral OTUs. Association networks revealed potential niches for key OTUs from SAR11, cyanobacteria, SAR86 and other common clades on the basis of robust correlations. Resilience was evident by the average communities drifting only slightly as years passed. Average Bray-Curtis similarity between any pair of dates was similar to 40%, with a slight decrease over the decade and obvious near-surface seasonality; communities 8-10 years apart were slightly more different than those 1-4 years apart with the highest rate of change at 0-5m between communities <4 years apart. The surface exhibited more pronounced seasonality than the DCM. Inter-depth Bray-Curtis similarities repeatedly decreased as the water column stratified each summer. Environmental factors were better predictors of shifts in community composition than months or elapsed time alone; yet, the best predictor was community composition at the other depth (that is, 0-5m versus DCM).
C1 [Chow, Cheryl-Emiliane T.; Sachdeva, Rohan; Cram, Jacob A.; Steele, Joshua A.; Needham, David M.; Patel, Anand; Parada, Alma E.; Fuhrman, Jed A.] Univ So Calif, Dept Biol Sci, Los Angeles, CA 90089 USA.
RP Chow, CET (corresponding author), Univ British Columbia, Dept Earth Ocean & Atmospher Sci, 2020-2207 Main Mall, Vancouver, BC V6T 1Z4, Canada.
EM cheryltchow@alumni.usc.edu
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TC 125
Z9 148
PD DEC
PY 2013
VL 7
IS 12
BP 2259
EP 2273
DI 10.1038/ismej.2013.122
UT WOS:000327451800003
DA 2025-07-30
ER

PT J
AU Sutherland, KM
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   Suffridge, CP
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AF Sutherland, Kevin M.
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   Plummer, Sydney
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TI Extracellular superoxide production by key microbes in the global ocean
SO LIMNOLOGY AND OCEANOGRAPHY
DT Article
AB Bacteria and eukaryotes produce the reactive oxygen species superoxide both within and outside the cell. Although superoxide is typically associated with the detrimental and sometimes fatal effects of oxidative stress, it has also been shown to be involved in a range of essential biochemical processes, including cell signaling, growth, differentiation, and defense. Light-independent extracellular superoxide production has been shown to be widespread among many marine heterotrophs and phytoplankton, but the extent to which this trait is relevant to marine microbial physiology and ecology throughout the global ocean is unknown. Here, we investigate the dark extracellular superoxide production of five groups of organisms that are geographically widespread and represent some of the most abundant organisms in the global ocean. These include Prochlorococcus, Synechococcus, Pelagibacter, Phaeocystis, and Geminigera. Cell-normalized net extracellular superoxide production rates ranged seven orders of magnitude, from undetectable to 14,830 amol cell(-1) h(-1), with the cyanobacterium Prochlorococcus being the lowest producer and the cryptophyte Geminigera being the most prolific producer. Extracellular superoxide production exhibited a strong inverse relationship with cell number, pointing to a potential role in cell signaling. We demonstrate that rapid, cell-number-dependent changes in the net superoxide production rate by Synechococcus and Pelagibacter arose primarily from changes in gross production of extracellular superoxide, not decay. These results expand the relevance of dark extracellular superoxide production to key marine microbes of the global ocean, suggesting that superoxide production in marine waters is regulated by a diverse suite of marine organisms in both dark and sunlit waters.
C1 [Sutherland, Kevin M.; Wankel, Scott D.; Hansel, Colleen M.] Woods Hole Oceanog Inst, Dept Marine Chem & Geochem, Woods Hole, MA 02543 USA.
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RP Hansel, CM (corresponding author), Woods Hole Oceanog Inst, Dept Marine Chem & Geochem, Woods Hole, MA 02543 USA.
EM chansel@whoi.ediu
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PD NOV
PY 2019
VL 64
IS 6
BP 2679
EP 2693
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EA JUL 2019
UT WOS:000477223800001
DA 2025-07-30
ER

PT J
AU Hanson, BT
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AF Hanson, Buck T.
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   Madsen, Eugene L.
TI Metaproteomic Survey of Six Aquatic Habitats: Discovering the Identities
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SO MICROBIAL ECOLOGY
DT Article
AB Our goal is to strengthen the foundations of metaproteomics as a microbial community analysis tool that links the functional identity of actively expressed gene products with host phylogeny. We used shotgun metaproteomics to survey waters in six disparate aquatic habitats (Cayuga Lake, NY; Oneida Lake, NY; Gulf of Maine; Chesapeake Bay, MD; Gulf of Mexico; and the South Pacific). Peptide pools prepared from filter-gathered microbial biomass, analyzed by nano-liquid chromatography-mass spectrometry (MS/MS) generating 9,693 +/- 1,073 mass spectra identified 326 +/- 107 bacterial proteins per sample. Distribution of proteobacterial (Alpha and Beta) and cyanobacterial (Prochlorococcus and Synechococcus spp.) protein hosts across all six samples was consistent with the previously published biogeography for these microorganisms. Marine samples were enriched in transport proteins (TRAP-type for dicarboxylates and ATP binding cassette (ABC)-type for amino acids and carbohydrates) compared with the freshwater samples. We were able to match in situ expression of many key proteins catalyzing C-, N-, and S-cycle processes with their bacterial hosts across all six habitats. Pelagibacter was identified as the host of ABC-type sugar-, organic polyanion-, and glycine betaine-transport proteins; this extends previously published studies of Pelagibacter's in situ biogeochemical role in marine C- and N-metabolism. Proteins matched to Ruegeria confirmed these organism's role in marine waters oxidizing both carbon monoxide and sulfide. By documenting both processes expressed in situ and the identity of host cells, metaproteomics tested several existing hypotheses about ecophysiological processes and provided fodder for new ones.
C1 [Hanson, Buck T.; Hewson, Ian; Madsen, Eugene L.] Cornell Univ, Dept Microbiol, Ithaca, NY 14853 USA.
RP Madsen, EL (corresponding author), Cornell Univ, Dept Microbiol, B57A Wing Hall, Ithaca, NY 14853 USA.
EM elm3@cornell.edu
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NR 100
TC 31
Z9 33
PD APR
PY 2014
VL 67
IS 3
BP 520
EP 539
DI 10.1007/s00248-013-0346-5
UT WOS:000333348900003
DA 2025-07-30
ER

PT J
AU Bergen, B
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AF Bergen, Benjamin
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   Juergens, Klaus
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SO FRONTIERS IN MICROBIOLOGY
DT Article
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C1 [Bergen, Benjamin; Herlemann, Daniel P. R.; Juergens, Klaus] Leibniz Inst Balt Sea Res Wamemunde, D-18119 Rostock, Germany.
RP Jürgens, K (corresponding author), Leibniz Inst Balt Sea Res Wamemunde, Seestr 15, D-18119 Rostock, Germany.
EM klaus.juergens@io-warnemuende.de
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NR 69
TC 16
Z9 17
PD JUN 18
PY 2015
VL 6
AR 621
DI 10.3389/fmicb.2015.00621
UT WOS:000356939700001
DA 2025-07-30
ER

PT J
AU Buchholz, HH
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AF Buchholz, Holger H.
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DT Article
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C1 [Buchholz, Holger H.; Michelsen, Michelle L.; Bolanos, Luis M.; Browne, Emily; Allen, Michael J.; Temperton, Ben] Univ Exeter, Sch Biosci, Exeter, Devon, England.
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RP Temperton, B (corresponding author), Univ Exeter, Sch Biosci, Exeter, Devon, England.
EM b.temperton@exeter.ac.uk
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NR 80
TC 28
Z9 31
PD JUN
PY 2021
VL 15
IS 6
BP 1585
EP 1598
DI 10.1038/s41396-020-00872-z
EA JAN 2021
UT WOS:000611448600001
DA 2025-07-30
ER

PT J
AU Luo, Y
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AF Luo, Yu
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SO SENSORS AND ACTUATORS B-CHEMICAL
DT Article
AB In order to develop a simple, convenient and economic method to detect and quantify the level of sarcosine in human urine samples, we have selected DNA aptamers for sarcosine through a modified affinity chromatography SELEX (Systematic Evolution of Ligands by Exponential Enrichment), which is based on the aptamer sequences bound by the target molecules would be released from the DNA hybridizations coupled on streptavidin-agarose beads. 4 aptamer candidates were obtained after 12 rounds of selection, and their affinities were preliminarily checked by SYBR green I staining. The best of them is Sar11, which with the dissociation constant (K-d) of 134.8 nM was further modified and used to design a fluorescence sensor to quantify sarcosine. The detection limit of sarcosine by this sensor is 55 nM, while its quantitative range is 100 to 2000 nM. Also, the aptamer Sar11 shows good selectivity for sarcosine to its analogues. Moreover, the fluorescent aptasensor obtains a satisfying result for the detection of sarcosine in human urine samples.
C1 [Luo, Yu; Wang, Jine; Yang, Luyan; Gao, Tian; Pei, Renjun] Chinese Acad Sci, CAS Key Lab Nanobio Interface, Suzhou Inst Nanotech & Nanobion, Suzhou 215123, Peoples R China.
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RP Pei, RJ (corresponding author), Chinese Acad Sci, CAS Key Lab Nanobio Interface, Suzhou Inst Nanotech & Nanobion, Suzhou 215123, Peoples R China.
EM rjpei2011@sinano.ac.cn
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TC 41
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PD DEC 10
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VL 276
BP 128
EP 135
DI 10.1016/j.snb.2018.08.105
UT WOS:000444637600018
DA 2025-07-30
ER

PT J
AU Straza, TRA
   Kirchman, DL
AF Straza, Tiffany R. A.
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DT Article
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C1 [Straza, Tiffany R. A.; Kirchman, David L.] Univ Delaware, Sch Marine Sci & Policy, Lewes, DE 19958 USA.
RP Kirchman, DL (corresponding author), Univ Delaware, Sch Marine Sci & Policy, 700 Pilottown Rd, Lewes, DE 19958 USA.
EM kirchman@udel.edu
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NR 64
TC 15
Z9 17
PY 2011
VL 62
IS 3
BP 267
EP U81
DI 10.3354/ame01469
UT WOS:000287203900005
DA 2025-07-30
ER

PT J
AU Bano, N
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AF Bano, N
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TI Phylogenetic composition of bacterioplankton assemblages from the Arctic
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
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C1 Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
RP Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
EM aquadoc@uga.edu
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NR 66
TC 259
Z9 308
PD FEB
PY 2002
VL 68
IS 2
BP 505
EP 518
DI 10.1128/AEM.68.2.505-518.2002
UT WOS:000173588600008
DA 2025-07-30
ER

PT J
AU Zha, H
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AF Zha, Hua
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   Chang, Kevin
   Li, Lanjuan
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SO CHEMOSPHERE
DT Article
AB Microplastics (MP) and nanoplastics (NP) have been found in multiple environments and creatures. However, their effects on the airway microbiota still remain poorly understood. In this study, a series of bioinformatic and statistical analyses were carried out to explore the influence of airborne MP and NP on the nasal and lung microbiota in mice. Both MP and NP were capable of inducing nasal microbial dysbiosis, and MP had a stronger influence on the lung microbiota than NP. Multiple nasal and lung bacteria were associated with MP and NP groups, among which nasal Staphylococcus and lung Roseburia were most associated with MP group, while nasal Prevotella and lung unclassified_Muribaculaceae were most associated with NP group. The nasal Staphylococcus, lung Roseburia, lung Eggerthella and lung Corynebacterium were associated with both MP and NP groups, which were potential biomarkers of micro/nanoplastics-induced airway dysbiosis. SAR11_Clade_Ia and SAR11_Clade_II were associated with both nasal and lung microbiota in MP group, while no such bacterium was determined in NP group. The relevant results suggest that both airborne MP and NP could induce nasal and lung microbial dysbiosis, and the relevant preventative and curable strategies deserve further investigations.
C1 [Zha, Hua; Xia, Jiafeng; Li, Shengjie; Lv, Jiawen; Zhuge, Aoxiang; Tang, Ruiqi; Wang, Shuting; Wang, Kaiceng; Li, Lanjuan] Zhejiang Univ, Affiliated Hosp 1, Collaborat Innovat Ctr Diag & Treatment Infect Dis, Sch Med,Natl Clin Res Ctr Infect Dis,State Key Lab, Hangzhou, Peoples R China.
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RP Li, LJ (corresponding author), Zhejiang Univ, Affiliated Hosp 1, Collaborat Innovat Ctr Diag & Treatment Infect Dis, Sch Med,Natl Clin Res Ctr Infect Dis,State Key Lab, 79 Qingchun Rd, Hangzhou 310000, Peoples R China.
EM ljli@zju.edu.cn
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TC 44
Z9 49
PD JAN
PY 2023
VL 310
AR 136764
DI 10.1016/j.chemosphere.2022.136764
EA OCT 2022
UT WOS:000937987500001
DA 2025-07-30
ER

PT J
AU Ortmann, AC
   Santos, TTL
AF Ortmann, Alice C.
   Santos, Thays T. L.
TI Spatial and temporal patterns in the Pelagibacteraceae across an
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SO FEMS MICROBIOLOGY ECOLOGY
DT Article
AB Marine bacterial communities show strong spatial and seasonal patterns, often characterized by changes at high taxonomic levels. The Pelagibacteraceae are common members of bacterial communities, with well-documented biogeography at the subclade level. To identify patterns within the subclades, the abundance and diversity of Pelagibacteraceae were analyzed over a two-year period at four stations across an estuarine gradient. Pelagibacteraceae was the most abundant bacterial family, averaging 27% of the community, but varying from 1% to 57% in any one sample. Highest abundances were detected in autumn and winter. Pelagibacteraceae richness was lowest at the most inshore site, and highest in autumn and winter at all sites. Shannon diversity decreased in winter, when a few OTUs dominated the community. Dissolved oxygen, dissolved silicate and prokaryote abundance explained most of the variability in the Pelagibacteraceae communities, with salinity differentiating low salinity communities. The 10 most abundant OTUs included OTUs that varied across sites, with little seasonality as well as those with small site effects, but strong seasonal patterns indicating differences in the niches of individual OTUs. While salinity was important in structuring low salinity communities, higher salinity communities appear to be responding to additional environmental parameters including oxygen, nutrients and other organisms.Closely related Pelagibacteraceae OTUs vary spatially and temporally across an estuary due to differences in salinity as well as oxygen, nutrients and the abundance of other organisms.Closely related Pelagibacteraceae OTUs vary spatially and temporally across an estuary due to differences in salinity as well as oxygen, nutrients and the abundance of other organisms.
C1 [Ortmann, Alice C.] Univ S Alabama, Dept Marine Sci, Mobile, AL 36688 USA.
   [Ortmann, Alice C.] Dauphin Isl Sea Lab, Dauphin Isl, AL 36528 USA.
   [Santos, Thays T. L.] Univ Fed Maranhao, Dept Oceanog & Limnol, BR-65080805 Sao Luis, MA, Brazil.
   [Santos, Thays T. L.] Univ Maine, Sch Marine Sci, Orono, ME 04469 USA.
RP Ortmann, AC (corresponding author), Bedford Inst Oceanog, Ctr Offshore Oil Gas & Energy Res, Dept Fisheries & Ocean Canada, Dartmouth, NS B2Y 4A2, Canada.
EM ortmannalice@gmail.com
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TC 20
Z9 21
PD SEP
PY 2016
VL 92
IS 9
AR fiw133
DI 10.1093/femsec/fiw133
UT WOS:000383898400008
DA 2025-07-30
ER

PT J
AU Henson, MW
   Lanclos, VC
   Pitre, DM
   Weckhorst, JL
   Lucchesi, AM
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   Ben Temperton
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AF Henson, Michael W.
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   Pitre, David M.
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   Ben Temperton
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TI Expanding the Diversity of Bacterioplankton Isolates and Modeling
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Cultivated bacterioplankton representatives from diverse lineages and locations are essential for microbiology, but the large majority of taxa either remain uncultivated or lack isolates from diverse geographic locales. We paired large-scale dilution-to-extinction (DTE) cultivation with microbial community analysis and modeling to expand the phylogenetic and geographic diversity of cultivated bacterioplankton and to evaluate DTE cultivation success. Here, we report results from 17 DTE experiments totaling 7,820 individual incubations over 3 years, yielding 328 repeatably transferable isolates. Comparison of isolates to microbial community data for source waters indicated that we successfully isolated 5% of the observed bacterioplankton community throughout the study; 43% and 26% of our isolates matched operational taxonomic units and amplicon single-nucleotide variants, respectively, within the top 50 most abundant taxa. Isolates included those from previously uncultivated clades such as SAR 1 LD12 and Actinobacteria aclV, as well as geographically novel members from other ecologically important groups like SAR11 subclade IIla, SAR116, and others, providing isolates in eight putatively new genera and seven putatively new species. Using a newly developed DTE cultivation model, we evaluated taxon viability by comparing relative abundance with cultivation success. The model (i) revealed the minimum attempts required for successful isolation of taxa amenable to growth on our media and (ii) identified possible subpopulation viability variation in abundant taxa such as SAR11 that likely impacts cultivation success. By incorporating viability in experimental design, we can now statistically constrain the effort necessary for successful cultivation of specific taxa on a defined medium.
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C1 [Henson, Michael W.; Lanclos, V. Celeste; Cheng, Chuankai; Thrash, J. Cameron] Univ Southern Calif, Dept Biol Sci, Los Angeles, CA 90007 USA.
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   [Henson, Michael W.] Univ Chicago, Dept Geol Sci, Chicago, IL 60637 USA.
   [Weckhorst, Jessica Lee] Baylor Coll Med, Quantitat & Computat Biosci Program, Houston, TX 77030 USA.
RP Thrash, JC (corresponding author), Univ Southern Calif, Dept Biol Sci, Los Angeles, CA 90007 USA.; Ben Temperton (corresponding author), Univ Exeter, Sch Biosci, Exeter, Devon, England.
EM b.temperton@exeter.ac.uk; thrash@usc.edu
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NR 140
TC 33
Z9 41
PD SEP
PY 2020
VL 86
IS 17
AR e00943-20
DI 10.1128/AEM.00943-20
UT WOS:000566697600011
DA 2025-07-30
ER

PT J
AU Mishra, A
   Mcnichol, J
   Fuhrman, J
   Blei, D
   Mueller, CL
AF Mishra, Aditya
   Mcnichol, Jesse
   Fuhrman, Jed
   Blei, David
   Mueller, Christian L.
TI Variational inference for microbiome survey data with application to
   global ocean data
SO ISME COMMUNICATIONS
DT Article
AB Linking sequence-derived microbial taxa abundances to host (patho-)physiology or habitat characteristics in a reproducible and interpretable manner has remained a formidable challenge for the analysis of microbiome survey data. Here, we introduce a flexible probabilistic modeling framework, VI-MIDAS (variational inference for microbiome survey data analysis), that enables joint estimation of context-dependent drivers and broad patterns of associations of microbial taxon abundances from microbiome survey data. VI-MIDAS comprises mechanisms for direct coupling of taxon abundances with covariates and taxa-specific latent coupling, which can incorporate spatio-temporal information and taxon-taxon interactions. We leverage mean-field variational inference for posterior VI-MIDAS model parameter estimation and illustrate model building and analysis using Tara Ocean Expedition survey data. Using VI-MIDAS' latent embedding model and tools from network analysis, we show that marine microbial communities can be broadly categorized into five modules, including SAR11-, nitrosopumilus-, and alteromondales-dominated communities, each associated with specific environmental and spatiotemporal signatures. VI-MIDAS also finds evidence for largely positive taxon-taxon associations in SAR11 or Rhodospirillales clades, and negative associations with Alteromonadales and Flavobacteriales classes. Our results indicate that VI-MIDAS provides a powerful integrative statistical analysis framework for discovering broad patterns of associations between microbial taxa and context-specific covariate data from microbiome survey data.
C1 [Mishra, Aditya] Univ Georgia, Dept Stat, Athens, GA 30606 USA.
   [Mcnichol, Jesse] St Francis Xavier Univ, Dept Biol, Antigonish, NS B2G 2W5, Canada.
   [Mcnichol, Jesse; Fuhrman, Jed] Univ Southern Calif, Dept Biol Sci, Los Angeles, CA 90007 USA.
   [Blei, David; Mueller, Christian L.] Flatiron Inst, Ctr Computat Math, New York, NY 10010 USA.
   [Blei, David] Columbia Univ, Dept Stat & Comp Sci, New York, NY 10027 USA.
   [Mueller, Christian L.] Helmholtz Zentrum Munchen, Computat Hlth Ctr, D-85764 Munich, Germany.
   [Mueller, Christian L.] LMU Munchen, Dept Stat, D-80539 Munich, Germany.
RP Mishra, A (corresponding author), Univ Georgia, Dept Stat, Athens, GA 30606 USA.
EM aditya.mishra@uga.edu
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NR 80
TC 0
Z9 0
PD JAN
PY 2025
VL 5
IS 1
AR ycaf062
DI 10.1093/ismeco/ycaf062
UT WOS:001484463100001
DA 2025-07-30
ER

PT J
AU Fuchsman, CA
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   Brazelton, WJ
   Murray, JW
   Staley, JT
AF Fuchsman, Clara A.
   Kirkpatrick, John B.
   Brazelton, William J.
   Murray, James W.
   Staley, James T.
TI Metabolic strategies of free-living and aggregate-associated bacterial
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   Sea suboxic zone
SO FEMS MICROBIOLOGY ECOLOGY
DT Article
AB The Black Sea is a permanently anoxic basin with a well-defined redox gradient. We combine environmental 16S rRNA gene data from clone libraries, terminal restriction fragment length polymorphisms, and V6 hypervariable region pyrosequences to provide the most detailed bacterial survey to date. Furthermore, this data set is informed by comprehensive geochemical data; using this combination of information, we put forward testable hypotheses regarding possible metabolisms of uncultured bacteria from the Black Sea's suboxic zone (microaerophily, nitrate reduction, manganese cycling, and oxidation of methane, ammonium, and sulfide). Dominant bacteria in the upper suboxic zone included members of the SAR11, SAR324, and Microthrix groups and in the deep suboxic zone included members of BS-GSO-2, Marine Group A, and SUP05. A particulate fraction (30 mu m filter) was used to distinguish between free-living and aggregate-attached communities in the suboxic zone. The particulate fraction contained greater diversity of V6 tag sequences than the bulk water samples. Lentisphaera, Epsilonproteobacteria, WS3, Planctomycetes, and Deltaproteobacteria were enriched in the particulate fraction, whereas SAR11 relatives dominated the free-living fraction. On the basis of the bacterial assemblages and simple modeling, we find that in suboxic waters, the interior of sinking aggregates potentially support manganese reduction, sulfate reduction, and sulfur oxidation.
C1 [Fuchsman, Clara A.; Kirkpatrick, John B.; Brazelton, William J.; Murray, James W.] Univ Washington, Sch Oceanog, Seattle, WA 98195 USA.
   [Staley, James T.] Univ Washington, Dept Microbiol, Seattle, WA 98195 USA.
RP Fuchsman, CA (corresponding author), Univ Washington, Sch Oceanog, Box 355351, Seattle, WA 98195 USA.
EM cfuchsm1@u.washington.edu
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NR 79
TC 89
Z9 105
PD DEC
PY 2011
VL 78
IS 3
BP 586
EP 603
DI 10.1111/j.1574-6941.2011.01189.x
UT WOS:000297156300015
DA 2025-07-30
ER

PT J
AU Wei, B
AF Wei, Bo
TI Diversity and distribution of proteorhodopsin-containing microorganisms
   in marine environments
SO FRONTIERS OF ENVIRONMENTAL SCIENCE & ENGINEERING
DT Article
AB Proteorhodopsin (PR) is a recently discovered protein involved in the utilization of light energy. Several studies have shown that PR-containing microorganisms are widespread and compose a large proportion of the biomass in marine ecosystems. A better understanding of the ecological role of PR will help clarify the effect of the global flow of energy and the carbon cycle on marine communities. In this study, a bioinformatical database of PR codon sequences, the Global Distribution Database of Proteorhodopsin (GDDP), as a tool for analyzing the diversity and distribution of PR-containing microorganisms in marine environments throughout the world was designed. The community structure of PR microorganisms were also compared using PCR assays and UniFrac analyses of 12 samples collected from three water layers (0, 75, and 200 m) at four representative sites in the Pacific, Atlantic, and Indian Oceans. The results indicate that PRcontaining microorganisms can be grouped into two distribution types: widespread and location-specific. Representative cases of the former include SAR11-PR and HOT2C01-PR. Interestingly, PR communities cluster by geographic locale but not by water depth.
C1 Xiamen Univ, Sch Life Sci, Xiamen 361005, Peoples R China.
RP Wei, B (corresponding author), Xiamen Univ, Sch Life Sci, Xiamen 361005, Peoples R China.
EM weibo88@gmail.com
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NR 32
TC 0
Z9 0
PD FEB
PY 2012
VL 6
IS 1
BP 98
EP 106
DI 10.1007/s11783-010-0278-y
UT WOS:000299521200012
DA 2025-07-30
ER

PT J
AU Gu, BW
   Liu, JX
   Cheung, SY
   Ho, NHE
   Tan, YH
   Xia, XM
AF Gu, Bowei
   Liu, Jiaxing
   Cheung, Shunyan
   Ho, Ngai Hei Ernest
   Tan, Yehui
   Xia, Xiaomin
TI Insights into Prokaryotic Community and Its Potential Functions in
   Nitrogen Metabolism in the Bay of Bengal, a Pronounced Oxygen Minimum
   Zone
SO MICROBIOLOGY SPECTRUM
DT Article
AB Ocean oxygen minimum zones (OMZs) around the global ocean are expanding both horizontally and vertically. Multiple studies have identified the significant influence of anoxic conditions (<= 1 mu M O-2) on marine prokaryotic communities and biogeochemical cycling of elements. However, little attention has been paid to the expanding low-oxygen zones where the oxygen level is still above the anoxic level. Here, we studied the abundance and taxonomic and functional profiles of prokaryotic communities in the Bay of Bengal (BoB), where the oxygen concentration is barely above suboxic level (5 mu M O-2). We found the sinking of Trichodesmium into deep water was far more efficient than that of Prochlorococcus, suggesting Trichodesmium blooms might be an essential carbon and nitrogen source for the maintenance of the BoB OMZ. In addition to the shift in the prokaryotic community composition, the abundance of some functional genes also changed with the change of oxygen concentration. Compared to oxic (>60 mu M O-2) Tara Ocean and high-hypoxic (>20 to <= 60 mu M O-2) BoB samples, we found more SAR11-nar sequences (responsible for reducing nitrate to nitrite) in low-hypoxic (>5 to <= 20 mu M O-2) BoB waters. This suggested SAR11-nar genes would be more widespread due to the expansion of OMZs. It seems that the nitrite-N was not further reduced to nitrogen through denitrification but likely oxidized to nitrate by Nitrospinae in the BoB OMZ and then accumulated in the form of nitrate-N. However, the lack of N-2 production in the BoB would change if the BoB OMZ became anoxic. Together, these results suggested that reduction of oxygen concentration and OMZ expansion may increase the use of nitrate by SAR11 and N-2 production in the BoB. IMPORTANCE Recognizing the prokaryotic community and its functions in hypoxic (>5 to <= 60 mu M O-2) environments before further expansion of OMZs is critical. We demonstrate the prokaryotic community and its potential functions in nitrogen metabolism in the Bay of Bengal (BoB), where oxygen concentration is barely above suboxic level. This study highlighted that Trichodesmium might be an essential carbon and nitrogen source in the maintenance of the BoB OMZ. Additionally, we suggest that the lack of N-2 production in the BoB would change if the BoB OMZ became anoxic, and the expansion of OMZs in the global ocean may potentially increase the use of nitrate by SAR11.
   Recognizing the prokaryotic community and its functions in hypoxic (>5 to <= 60 mu M O-2) environments before further expansion of OMZs is critical. We demonstrate the prokaryotic community and its potential functions in nitrogen metabolism in the Bay of Bengal (BoB), where oxygen concentration is barely above suboxic level.
C1 [Gu, Bowei; Liu, Jiaxing; Tan, Yehui; Xia, Xiaomin] Chinese Acad Sci, South China Sea Inst Oceanol, Key Lab Trop Marine Bioresources & Ecol, Guangzhou, Peoples R China.
   [Gu, Bowei; Liu, Jiaxing; Tan, Yehui; Xia, Xiaomin] Univ Chinese Acad Sci, Beijing, Peoples R China.
   [Gu, Bowei; Liu, Jiaxing; Tan, Yehui; Xia, Xiaomin] Southern Marine Sci & Engn Guangdong Lab Guangzh, Guangzhou, Peoples R China.
   [Cheung, Shunyan; Ho, Ngai Hei Ernest] Hong Kong Univ Sci & Technol, Dept Ocean Sci, Hong Kong, Peoples R China.
   [Cheung, Shunyan] Hong Kong Univ Sci & Technol, Southern Marine Sci & Engn Guangdong Lab, Hong Kong Branch, Hong Kong, Peoples R China.
RP Xia, XM (corresponding author), Chinese Acad Sci, South China Sea Inst Oceanol, Key Lab Trop Marine Bioresources & Ecol, Guangzhou, Peoples R China.; Xia, XM (corresponding author), Univ Chinese Acad Sci, Beijing, Peoples R China.; Xia, XM (corresponding author), Southern Marine Sci & Engn Guangdong Lab Guangzh, Guangzhou, Peoples R China.
EM xxia@connect.ust.hk
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NR 92
TC 18
Z9 18
PD JUN
PY 2022
VL 10
IS 3
DI 10.1128/spectrum.00892-21
EA MAY 2022
UT WOS:000799829100003
DA 2025-07-30
ER

PT J
AU Reintjes, G
   Tegetmeyer, HE
   Bürgisser, M
   Orlic, S
   Tews, I
   Zubkov, M
   Voss, D
   Zielinski, O
   Quast, C
   Glöckner, FO
   Amann, R
   Ferdelman, TG
   Fuchs, BM
AF Reintjes, Greta
   Tegetmeyer, Halina E.
   Buergisser, Miriam
   Orlic, Sandi
   Tews, Ivo
   Zubkov, Mikhail
   Voss, Daniela
   Zielinski, Oliver
   Quast, Christian
   Gloeckner, Frank Oliver
   Amann, Rudolf
   Ferdelman, Timothy G.
   Fuchs, Bernhard M.
TI On-Site Analysis of Bacterial Communities of the Ultraoligotrophic South
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB The South Pacific Gyre (SPG) covers 10% of the ocean's surface and is often regarded as a marine biological desert. To gain an on-site overview of the remote, ultraoligotrophic microbial community of the SPG, we developed a novel on-board analysis pipeline, which combines next-generation sequencing with fluorescence in situ hybridization and automated cell enumeration. We tested the pipeline during the SO-245 "UltraPac" cruise from Chile to New Zealand and found that the overall microbial community of the SPG was highly similar to those of other oceanic gyres. The SPG was dominated by 20 major bacterial clades, including SAR11, SAR116, the AEGEAN-169 marine group, SAR86, Prochlorococcus, SAR324, SAR406, and SAR202. Most of the bacterial clades showed a strong vertical (20m to 5,000 m), but only a weak longitudinal (80 degrees W to 160 degrees W), distribution pattern. Surprisingly, in the central gyre, Prochlorococcus, the dominant photosynthetic organism, had only low cellular abundances in the upper waters (20 to 80 m) and was more frequent around the 1% irradiance zone (100 to 150 m). Instead, the surface waters of the central gyre were dominated by the SAR11, SAR86, and SAR116 clades known to harbor light-driven proton pumps. The alphaproteobacterial AEGEAN-169 marine group was particularly abundant in the surface waters of the central gyre, indicating a potentially interesting adaptation to ultraoligotrophic waters and high solar irradiance. In the future, the newly developed community analysis pipeline will allow for on-site insights into a microbial community within 35 h of sampling, which will permit more targeted sampling efforts and hypothesis-driven research.
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C1 [Reintjes, Greta; Tegetmeyer, Halina E.; Buergisser, Miriam; Quast, Christian; Gloeckner, Frank Oliver; Amann, Rudolf; Ferdelman, Timothy G.; Fuchs, Bernhard M.] Max Planck Inst Marine Microbiol, Bremen, Germany.
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   [Gloeckner, Frank Oliver] Jacobs Univ, Bremen, Germany.
RP Reintjes, G (corresponding author), Max Planck Inst Marine Microbiol, Bremen, Germany.
EM greintje@mpi-bremen.de
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NR 73
TC 29
Z9 30
PD JUL
PY 2019
VL 85
IS 14
AR e00184-19
DI 10.1128/AEM.00184-19
UT WOS:000476468600001
DA 2025-07-30
ER

PT J
AU Aylward, FO
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   DeLong, EF
AF Aylward, Frank O.
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SO PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
   AMERICA
DT Article
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C1 [Aylward, Frank O.; Eppley, John M.; DeLong, Edward F.] Univ Hawaii Manoa, Daniel K Inouye Ctr Microbial Oceanog Res & Educ, Honolulu, HI 96822 USA.
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   [DeLong, Edward F.] MIT, Dept Biol Engn, Cambridge, MA 02139 USA.
RP DeLong, EF (corresponding author), Univ Hawaii Manoa, Daniel K Inouye Ctr Microbial Oceanog Res & Educ, Honolulu, HI 96822 USA.
EM edelong@hawaii.edu
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NR 35
TC 140
Z9 161
PD APR 28
PY 2015
VL 112
IS 17
BP 5443
EP 5448
DI 10.1073/pnas.1502883112
UT WOS:000353554000058
DA 2025-07-30
ER

PT J
AU Wietz, M
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   Boetius, A
AF Wietz, Matthias
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   Wolf, Christian
   Janssen, Felix
   Salter, Ian
   Boetius, Antje
TI Impact of preservation method and storage period on ribosomal
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SO FRONTIERS IN MICROBIOLOGY
DT Article
AB Automated sampling technologies can enhance the temporal and spatial resolution of marine microbial observations, particularly in remote and inaccessible areas. A critical aspect of automated microbiome sampling is the preservation of nucleic acids over long-term autosampler deployments. Understanding the impact of preservation method on microbial metabarcoding is essential for implementing genomic observatories into existing infrastructure, and for establishing best practices for the regional and global synthesis of data. The present study evaluates the effect of two preservatives commonly used in autosampler deployments (mercuric chloride and formalin) and two extraction kits (PowerWater and NucleoSpin) on amplicon sequencing of 16S and 18S rRNA gene over 50 weeks of sample storage. Our results suggest the combination of mercuric chloride preservation and PowerWater extraction as most adequate for 16S and 18S rRNA gene amplicon-sequencing from the same seawater sample. This approach provides consistent information on species richness, diversity and community composition in comparison to control samples (nonfixed, filtered and frozen) when stored up to 50 weeks at in situ temperature. Preservation affects the recovery of certain taxa, with specific OTUs becoming overrepresented (SAR11 and diatoms) or underrepresented (Colwellia and pico-eukaryotes) after preservation. In case eukaryotic sequence information is the sole target, formalin preservation and NucleoSpin extraction performed best. Our study contributes to the design of long-term autonomous microbial observations in remote ocean areas, allowing cross-comparison of microbiome dynamics across sampling devices (e.g., water and particle samplers) and marine realms.
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RP Wietz, M (corresponding author), Helmholtz Ctr Polar & Marine Res, Alfred Wegener Inst, Deep Sea Ecol & Technol, Bremerhaven, Germany.; Wietz, M (corresponding author), Max Planck Inst Marine Microbiol, Bremen, Germany.
EM matthias.wietz@awi.de
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NR 67
TC 4
Z9 5
PD SEP 7
PY 2022
VL 13
AR 999925
DI 10.3389/fmicb.2022.999925
UT WOS:000860497900001
DA 2025-07-30
ER

PT J
AU Nelson, CE
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AF Nelson, Craig E.
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TI Community differentiation and population enrichment of Sargasso Sea
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
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C1 [Nelson, Craig E.; Carlson, Craig A.; Ewart, Courtney S.; Halewood, Elisa R.] Univ Calif Santa Barbara, Inst Marine Sci, Santa Barbara, CA 93106 USA.
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RP Nelson, CE (corresponding author), Univ Calif Santa Barbara, Inst Marine Sci, Santa Barbara, CA 93106 USA.
EM craig.nelson@hawaii.edu
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TC 52
Z9 60
PD MAR
PY 2014
VL 16
IS 3
BP 871
EP 887
DI 10.1111/1462-2920.12241
UT WOS:000332085400020
DA 2025-07-30
ER

PT J
AU Luo, HW
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AF Luo, Haiwei
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SO TRENDS IN MICROBIOLOGY
DT Review
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RP Moran, MA (corresponding author), Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
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NR 87
TC 57
Z9 68
PD SEP
PY 2015
VL 23
IS 9
BP 577
EP 584
DI 10.1016/j.tim.2015.05.004
UT WOS:000361413900010
DA 2025-07-30
ER

PT J
AU Herlemann, DPR
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AF Herlemann, Daniel P. R.
   Labrenz, Matthias
   Juergens, Klaus
   Bertilsson, Stefan
   Waniek, Joanna J.
   Andersson, Anders F.
TI Transitions in bacterial communities along the 2000 km salinity gradient
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SO ISME JOURNAL
DT Article
AB Salinity is a major factor controlling the distribution of biota in aquatic systems, and most aquatic multicellular organisms are either adapted to life in saltwater or freshwater conditions. Consequently, the saltwater-freshwater mixing zones in coastal or estuarine areas are characterized by limited faunal and floral diversity. Although changes in diversity and decline in species richness in brackish waters is well documented in aquatic ecology, it is unknown to what extent this applies to bacterial communities. Here, we report a first detailed bacterial inventory from vertical profiles of 60 sampling stations distributed along the salinity gradient of the Baltic Sea, one of world's largest brackish water environments, generated using 454 pyrosequencing of partial (400 bp) 16S rRNA genes. Within the salinity gradient, bacterial community composition altered at broad and finer-scale phylogenetic levels. Analogous to faunal communities within brackish conditions, we identified a bacterial brackish water community comprising a diverse combination of freshwater and marine groups, along with populations unique to this environment. As water residence times in the Baltic Sea exceed 3 years, the observed bacterial community cannot be the result of mixing of fresh water and saltwater, but our study represents the first detailed description of an autochthonous brackish microbiome. In contrast to the decline in the diversity of multicellular organisms, reduced bacterial diversity at brackish conditions could not be established. It is possible that the rapid adaptation rate of bacteria has enabled a variety of lineages to fill what for higher organisms remains a challenging and relatively unoccupied ecological niche. The ISME Journal (2011) 5, 1571-1579; doi: 10.1038/ismej.2011.41; published online 7 April 2011
C1 [Andersson, Anders F.] KTH Royal Inst Technol, Sci Life Lab, Sch Biotechnol, SE-10450 Stockholm, Sweden.
   [Herlemann, Daniel P. R.; Labrenz, Matthias; Juergens, Klaus; Waniek, Joanna J.] Leibniz Inst Baltic Sea Res, Dept Biol Oceanog, Rostock, Germany.
   [Bertilsson, Stefan] Uppsala Univ, Dept Ecol & Genet, Uppsala, Sweden.
RP Andersson, AF (corresponding author), KTH Royal Inst Technol, Sci Life Lab, Sch Biotechnol, Box 24075, SE-10450 Stockholm, Sweden.
EM doubleanders@gmail.com
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NR 59
TC 2165
Z9 2291
PD OCT
PY 2011
VL 5
IS 10
BP 1571
EP 1579
DI 10.1038/ismej.2011.41
UT WOS:000295783200003
DA 2025-07-30
ER

PT J
AU Molina-Pardines, C
   Haro-Moreno, JM
   López-Préez, M
AF Molina-Pardines, Carmen
   Haro-Moreno, Jose M.
   Lopez-Perez, Mario
TI Phosphate-related genomic islands as drivers of environmental adaptation
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SO MSYSTEMS
DT Article
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RP López-Préez, M (corresponding author), Univ Miguel Hernandez, Div Microbiol, Evolutionary Genom Grp, San Juan 03550, Alicante, Spain.
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NR 98
TC 4
Z9 4
PD DEC 21
PY 2023
VL 8
IS 6
DI 10.1128/msystems.00898-23
EA DEC 2023
UT WOS:001114832800001
DA 2025-07-30
ER

PT J
AU Campbell, BJ
   Yu, LY
   Heidelberg, JF
   Kirchman, DL
AF Campbell, Barbara J.
   Yu, Liying
   Heidelberg, John F.
   Kirchman, David L.
TI Activity of abundant and rare bacteria in a coastal ocean
SO PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
   AMERICA
DT Article
AB The surface layer of the oceans and other aquatic environments contains many bacteria that range in activity, from dormant cells to those with high rates of metabolism. However, little experimental evidence exists about the activity of specific bacterial taxa, especially rare ones. Here we explore the relationship between abundance and activity by documenting changes in abundance over time and by examining the ratio of 16S rRNA to rRNA genes (rDNA) of individual bacterial taxa. The V1-V2 region of 16S rRNA and rDNA was analyzed by tag pyrosequencing in a 3-y study of surface waters off the Delaware coast. Over half of the bacterial taxa actively cycled between abundant and rare, whereas about 12% always remained rare and potentially inactive. There was a significant correlation between the relative abundance of 16S rRNA and the relative abundance of 16S rDNA for most individual taxa. However, 16S rRNA: rDNA ratios were significantly higher in about 20% of the taxa when they were rare than when abundant. Relationships between 16S rRNA and rDNA frequencies were confirmed for five taxa by quantitative PCR. Our findings suggest that though abundance follows activity in the majority of the taxa, a significant portion of the rare community is active, with growth rates that decrease as abundance increases.
C1 [Campbell, Barbara J.; Yu, Liying; Kirchman, David L.] Univ Delaware, Sch Marine Sci & Policy, Lewes, DE 19958 USA.
   [Heidelberg, John F.] Univ So Calif, Wrigley Marine Sci Ctr, Avalon, CA 90704 USA.
RP Campbell, BJ (corresponding author), Univ Delaware, Sch Marine Sci & Policy, Lewes, DE 19958 USA.
EM bjc@udel.edu
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NR 39
TC 459
Z9 506
PD AUG 2
PY 2011
VL 108
IS 31
BP 12776
EP 12781
DI 10.1073/pnas.1101405108
UT WOS:000293385700050
DA 2025-07-30
ER

PT J
AU Biller, SJ
   Lundeen, RA
   Hmelo, LR
   Becker, KW
   Arellano, AA
   Dooley, K
   Heal, KR
   Carlson, LT
   Van Mooy, BAS
   Ingalls, AE
   Chisholm, SW
AF Biller, Steven J.
   Lundeen, Rachel A.
   Hmelo, Laura R.
   Becker, Kevin W.
   Arellano, Aldo A.
   Dooley, Keven
   Heal, Katherine R.
   Carlson, Laura T.
   Van Mooy, Benjamin A. S.
   Ingalls, Anitra E.
   Chisholm, Sallie W.
TI Prochlorococcus extracellular vesicles: molecular composition and
   adsorption to diverse microbes
SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Extracellular vesicles are small (similar to 50-200 nm diameter) membrane-bound structures released by cells from all domains of life. While vesicles are abundant in the oceans, their functions, both for cells themselves and the emergent ecosystem, remain a mystery. To better characterize these particles - a prerequisite for determining function - we analysed the lipid, protein, and metabolite content of vesicles produced by the marine cyanobacterium Prochlorococcus. We show that Prochlorococcus exports a diverse array of cellular compounds into the surrounding seawater enclosed within discrete vesicles. Vesicles produced by two different strains contain some materials in common, but also display numerous strain-specific differences, reflecting functional complexity within vesicle populations. The vesicles contain active enzymes, indicating that they can mediate extracellular biogeochemical reactions in the ocean. We further demonstrate that vesicles from Prochlorococcus and other bacteria associate with diverse microbes including the most abundant marine bacterium, Pelagibacter. Together, our data point toward hypotheses concerning the functional roles of vesicles in marine ecosystems including, but not limited to, possibly mediating energy and nutrient transfers, catalysing extracellular biochemical reactions, and mitigating toxicity of reactive oxygen species.
C1 [Biller, Steven J.; Arellano, Aldo A.; Dooley, Keven; Chisholm, Sallie W.] MIT, Dept Civil & Environm Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA.
   [Biller, Steven J.] Wellesley Coll, Dept Biol Sci, Wellesley, MA 02181 USA.
   [Lundeen, Rachel A.; Hmelo, Laura R.; Heal, Katherine R.; Carlson, Laura T.; Ingalls, Anitra E.] Univ Washington, Sch Oceanog, Seattle, WA 98195 USA.
   [Becker, Kevin W.; Van Mooy, Benjamin A. S.] Woods Hole Oceanog Inst, Dept Marine Chem & Geochem, Woods Hole, MA 02543 USA.
   [Becker, Kevin W.] GEOMAR Helmholtz Ctr Ocean Res Kiel, Kiel, Germany.
   [Heal, Katherine R.] Integral Consulting Inc, Seattle, WA USA.
   [Chisholm, Sallie W.] MIT, Dept Biol, Cambridge, MA USA.
RP Biller, SJ (corresponding author), MIT, Dept Civil & Environm Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA.; Biller, SJ (corresponding author), Wellesley Coll, Dept Biol Sci, Wellesley, MA 02181 USA.
EM sbiller@wellesley.edu
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NR 91
TC 29
Z9 32
PD JAN
PY 2022
VL 24
IS 1
BP 420
EP 435
DI 10.1111/1462-2920.15834
EA NOV 2021
UT WOS:000717518600001
DA 2025-07-30
ER

PT J
AU Braakman, R
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   Chisholm, SW
AF Braakman, Rogier
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   Chisholm, Sallie W.
TI Metabolic evolution and the self-organization of ecosystems
SO PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
   AMERICA
DT Article
AB Metabolism mediates the flow of matter and energy through the biosphere. We examined how metabolic evolution shapes ecosystems by reconstructing it in the globally abundant oceanic phytoplankter Prochlorococcus. To understand what drove observed evolutionary patterns, we interpreted them in the context of its population dynamics, growth rate, and light adaptation, and the size and macromolecular and elemental composition of cells. This multilevel view suggests that, over the course of evolution, there was a steady increase in Prochlorococcus' metabolic rate and excretion of organic carbon. We derived a mathematical framework that suggests these adaptations lower the minimal subsistence nutrient concentration of cells, which results in a drawdown of nutrients in oceanic surface waters. This, in turn, increases total ecosystem biomass and promotes the coevolution of all cells in the ecosystem. Additional reconstructions suggest that Prochlorococcus and the dominant cooccurring heterotrophic bacterium SAR11 form a coevolved mutualism that maximizes their collective metabolic rate by recycling organic carbon through complementary excretion and uptake pathways. Moreover, the metabolic codependencies of Prochlorococcus and SAR11 are highly similar to those of chloroplasts and mitochondria within plant cells. These observations lead us to propose a general theory relating metabolic evolution to the self-amplification and self-organization of the biosphere. We discuss the implications of this framework for the evolution of Earth's biogeochemical cycles and the rise of atmospheric oxygen.
C1 [Braakman, Rogier; Chisholm, Sallie W.] MIT, Dept Civil & Environm Engn, Cambridge, MA 02139 USA.
   [Braakman, Rogier; Follows, Michael J.] MIT, Dept Earth Atmospher & Planetary Sci, Cambridge, MA 02139 USA.
   [Chisholm, Sallie W.] MIT, Dept Biol, Cambridge, MA 02139 USA.
RP Braakman, R; Chisholm, SW (corresponding author), MIT, Dept Civil & Environm Engn, Cambridge, MA 02139 USA.; Braakman, R (corresponding author), MIT, Dept Earth Atmospher & Planetary Sci, Cambridge, MA 02139 USA.; Chisholm, SW (corresponding author), MIT, Dept Biol, Cambridge, MA 02139 USA.
EM rogierbraakman@gmail.com; chisholm@mit.edu
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NR 163
TC 100
Z9 117
PD APR 11
PY 2017
VL 114
IS 15
BP E3091
EP E3100
DI 10.1073/pnas.1619573114
UT WOS:000398789800014
DA 2025-07-30
ER

PT J
AU McNally, SP
   Parsons, RJ
   Santoro, AE
   Apprill, A
AF McNally, Sean P.
   Parsons, Rachel J.
   Santoro, Alyson E.
   Apprill, Amy
TI Multifaceted impacts of the stony coral Porites astreoides on
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SO LIMNOLOGY AND OCEANOGRAPHY
DT Article
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C1 [McNally, Sean P.; Apprill, Amy] Woods Hole Oceanog Inst, Woods Hole, MA 02543 USA.
   [McNally, Sean P.; Parsons, Rachel J.] Bermuda Inst Ocean Sci, Ferry Reach, Bermuda.
   [Santoro, Alyson E.] Univ Maryland, Ctr Environm Sci, Horn Point Lab, Cambridge, MD USA.
   [McNally, Sean P.] Univ Massachusetts, Boston, MA 02125 USA.
   [Santoro, Alyson E.] Univ Calif Santa Barbara, Dept Ecol Evolut & Marine Biol, Santa Barbara, CA 93106 USA.
RP Apprill, A (corresponding author), Woods Hole Oceanog Inst, Woods Hole, MA 02543 USA.
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NR 99
TC 35
Z9 45
PD JAN
PY 2017
VL 62
IS 1
BP 217
EP 234
DI 10.1002/lno.10389
UT WOS:000393804600015
DA 2025-07-30
ER

PT J
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AF Costas-Selas, Cecilia
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SO MICROBIAL ECOLOGY
DT Article
AB We present here the first detailed description of the seasonal patterns in bacterial community composition (BCC) in shelf waters off the Ria de Vigo (Spain), based on monthly samplings during 2 years. Moreover, we studied the relationship between bacterial and small-sized eukaryotic community composition to identify potential biotic interactions among components of these two communities. Bacterial operational taxonomic unit (OTU) richness and diversity systematically peaked in autumn-winter, likely related to low resource availability during this period. BCC showed seasonal and vertical patterns, with Rhodobacteraceae and Flavobacteriaceae families dominating in surface waters, and SAR11 clade dominating at the base of the photic zone (30 m depth). BCC variability was significantly explained by environmental variables (e.g., temperature of water, solar radiation, or dissolved organic matter). Interestingly, a strong and significant correlation was found between BCC and small-sized eukaryotic community composition (ECC), which suggests that biotic interactions may play a major role as structuring factors of the microbial plankton in this productive area. In addition, co-occurrence network analyses revealed strong and significant, mostly positive, associations between bacteria and small-sized phytoplankton. Positive associations likely result from mutualistic relationships (e.g., between Dinophyceae and Rhodobacteraceae), while some negative correlations suggest antagonistic interactions (e.g., between Pseudo-nitzchia sp. and SAR11). These results support the key role of biotic interactions as structuring factors of the small-sized eukaryotic community, mostly driven by positive associations between small-sized phytoplankton and bacteria.
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   [Logares, Ramiro] CSIC, Dept Biol Marina & Oceanog, Inst Ciencies Mar ICM, Barcelona, Catalonia, Spain.
RP Costas-Selas, C (corresponding author), Univ Vigo, Ctr Invest Marina, Dept Ecol & Biol Anim, Vigo 36310, Spain.
EM cecilia.costas.selas@uvigo.es; sandra@uvigo.es;
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NR 93
TC 12
Z9 13
PD AUG
PY 2023
VL 86
IS 2
BP 777
EP 794
DI 10.1007/s00248-022-02125-2
EA OCT 2022
UT WOS:000875609500001
DA 2025-07-30
ER

PT J
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SO ENVIRONMENTAL MICROBIOLOGY
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NR 78
TC 6
Z9 7
PD JUN
PY 2017
VL 19
IS 6
SI SI
BP 2379
EP 2390
DI 10.1111/1462-2920.13748
UT WOS:000404007700023
DA 2025-07-30
ER

PT J
AU Sánchez, O
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   Gasol, JM
   Ferrera, I
AF Sanchez, Olga
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   Ferrera, Isabel
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SO ENVIRONMENTAL MICROBIOLOGY REPORTS
DT Article
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C1 [Sanchez, Olga] Univ Autonoma Barcelona, Dept Genet & Microbiol, Bellaterra 08193, Catalunya, Spain.
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RP Ferrera, I (corresponding author), CSIC, Inst Ciencies Mar, Dept Biol Marina & Oceanog, E-08003 Barcelona, Catalunya, Spain.
EM iferrera@icm.csic.es
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NR 48
TC 20
Z9 22
PD JUN
PY 2017
VL 9
IS 3
BP 300
EP 309
DI 10.1111/1758-2229.12535
UT WOS:000401193800014
DA 2025-07-30
ER

PT J
AU Obernosterer, I
   Catala, P
   Lebaron, P
   West, NJ
AF Obernosterer, Ingrid
   Catala, Philippe
   Lebaron, Philippe
   West, Nyree J.
TI Distinct bacterial groups contribute to carbon cycling during a
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SO LIMNOLOGY AND OCEANOGRAPHY
DT Article
AB We investigated the contribution of distinct bacterial groups to bulk abundance and leucine incorporation during a spring phytoplankton bloom induced by natural iron fertilization in the Southern Ocean (Kerguelen Ocean and Plateau Compared Study, January-February 2005). Oligonucleotide probes were designed to target five operational taxonomic units (OTUs) at a narrow phylogenetic level (>= 99% identity of the 16S ribosomal ribonucleic acid [rRNA] gene). During the peak of the phytoplankton bloom, the Roseobacter groups NAC11-7 and RCA, the OTUs SAR92 belonging to Gammaproteobacteria, and the Bacteroidetes OTU Agg58 dominated bulk abundance and leucine incorporation. These four OTUs disappeared with the decline of the bloom, when the cosmopolitan groups SAR11 and SAR86 became dominant. In high-nutrient, low-chlorophyll waters and at a site characterized by transient high phytoplankton biomass, the SAR11 and SAR86 clusters and a Polaribacter OTU dominated abundance and leucine incorporation in the upper 100 m. Our results demonstrate that a few distinct bacterial groups identified on a relatively narrow phylogenetic level account for 47% to 82% of bulk abundance and leucine incorporation during the spring phytoplankton bloom in the naturally fertilized region off Kerguelen. The major role of these bacterial groups in carbon cycling in response to natural iron fertilization in the Southern Ocean suggests they could play an important role in the coupling of the biogeochemical cycles of carbon and iron.
C1 [Obernosterer, Ingrid; Catala, Philippe; Lebaron, Philippe; West, Nyree J.] Univ Paris 06, Observ Oceanol, Lab Oceanog Microbienne, UMR 7621,UMS 2348, Banyuls Sur Mer, France.
   [Obernosterer, Ingrid; Catala, Philippe; Lebaron, Philippe] CNRS, Observ Oceanol, Lab Oceanog Microbienne, UMR 7621, Banyuls Sur Mer, France.
   [Lebaron, Philippe; West, Nyree J.] CNRS, Observ Oceanol, UMS 2348, Banyuls Sur Mer, France.
RP Obernosterer, I (corresponding author), Univ Paris 06, Observ Oceanol, Lab Oceanog Microbienne, UMR 7621,UMS 2348, Banyuls Sur Mer, France.
EM ingrid.obernosterer@obs-banyuls.fr
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NR 38
TC 29
Z9 30
PD NOV
PY 2011
VL 56
IS 6
BP 2391
EP 2401
DI 10.4319/lo.2011.56.6.2391
UT WOS:000299349700035
DA 2025-07-30
ER

PT J
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AF Olson, Daniel K.
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DT Article
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C1 [Olson, Daniel K.; Boeuf, Dominique; DeLong, Edward F.] Univ Hawaii, Dept Oceanog, Daniel K Inouye Ctr Microbial Oceanog Res & Educ, Honolulu, HI 96822 USA.
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RP DeLong, EF (corresponding author), Univ Hawaii, Dept Oceanog, Daniel K Inouye Ctr Microbial Oceanog Res & Educ, Honolulu, HI 96822 USA.
EM edelong@hawaii.edu
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TC 44
Z9 49
PD APR
PY 2018
VL 12
IS 4
BP 1047
EP 1060
DI 10.1038/s41396-018-0074-4
UT WOS:000427917700010
DA 2025-07-30
ER

PT J
AU Topping, JN
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AF Topping, Juliette N.
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TI Bacterioplankton composition in the Scotia Sea, Antarctica, during the
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DT Article
AB Physical ocean processes (ice-melt, island run-off and upwelling of nutrients) were hypothesised to affect the bacterioplankton composition in the surface mixed layer of the Scotia Sea during the austral summer of 2003, and this was investigated using flow cytometry and catalysed reporter deposition fluorescence in situ hybridisation (CARD-FISH) techniques. The bacterioplankton was composed predominantly of Alphaproteobacteria (PB), comprising SAR11, Roseobacter spp. and SAR116 groups, followed by Sphingobacteria/Flavobacteria and Gammaproteobacteria, including SAR86. Two distinct bacterioplankton communities were identified, largely based on bacterioplankton abundance, which varied from 0.3 +/- 0.06 x 10(6) cells ml(-1) in the west to 0.8 +/- 0.3 x 10(6) cells ml(-1) in the east, and a corresponding difference in SAR11 percentages of 30 +/- 15% in the west compared to 5 +/- 5% in the east. The western community was present in waters that were largely in an over-wintered, pre-bloom condition. The eastern bacterioplankton community was associated with phytoplankton blooms developed within the eastern Scotia Sea nutrient upwelling zone, where the Antarctic Circumpolar Current (ACC) encounters the shallow bathymetry associated with the Scotia Arc, in combination with seasonal ice-melt and island effects that enabled surface water stratification.
C1 Natl Oceanog Ctr, Southampton SO14 3ZH, Hants, England.
   British Antarctic Survey, NERC, Cambridge CB3 0ET, England.
RP Topping, JN (corresponding author), Natl Oceanog Ctr, European Way, Southampton SO14 3ZH, Hants, England.
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NR 35
TC 14
Z9 17
PD DEC 21
PY 2006
VL 45
IS 3
BP 229
EP 235
DI 10.3354/ame045229
UT WOS:000243607700003
DA 2025-07-30
ER

PT J
AU BRITSCHGI, TB
   GIOVANNONI, SJ
AF BRITSCHGI, TB
   GIOVANNONI, SJ
TI PHYLOGENETIC ANALYSIS OF A NATURAL MARINE BACTERIOPLANKTON POPULATION BY
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
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TC 194
Z9 209
PD JUN
PY 1991
VL 57
IS 6
BP 1707
EP 1713
DI 10.1128/AEM.57.6.1707-1713.1991
UT WOS:A1991FP56400021
DA 2025-07-30
ER

PT J
AU Xie, ZX
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AF Xie, Zhang-Xian
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TI Dissecting microbial community structure and metabolic activities at an
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DT Article
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RP Wang, DZ (corresponding author), Xiamen Univ, State Key Lab Marine Environm Sci, Coll Environm & Ecol, Xiamen 361005, Peoples R China.
EM dzwang@xmu.edu.cn
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TC 4
Z9 5
PD OCT
PY 2020
VL 188
AR 102439
DI 10.1016/j.pocean.2020.102439
UT WOS:000582696800018
DA 2025-07-30
ER

PT J
AU DeWall, MT
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AF DeWall, Michael Thomas
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TI The minimal genome-a metabolic and environmental comparison
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DT Article
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RP Cheng, DW (corresponding author), Calif State Univ Fresno, Dept Biol, Res Infrastruct Minor Inst, Fresno, CA 93740 USA.
EM dcheng@csufresno.edu
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PD SEP
PY 2011
VL 10
IS 5
BP 312
EP 315
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UT WOS:000295886400006
DA 2025-07-30
ER

PT J
AU Cram, JA
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AF Cram, Jacob A.
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DT Article
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RP Cram, JA (corresponding author), Univ So Calif, Dept Biol Sci, Los Angeles, CA 90089 USA.; Cram, JA (corresponding author), Univ Washington, Sch Oceanog, Seattle, WA 98195 USA.
EM cramjaco@gmail.com
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NR 61
TC 42
Z9 46
PD MAY
PY 2016
VL 61
IS 3
BP 889
EP 905
DI 10.1002/lno.10259
UT WOS:000375748400007
DA 2025-07-30
ER

PT J
AU Thiele, S
   Fuchs, BM
   Ramaiah, N
   Amann, R
AF Thiele, Stefan
   Fuchs, Bernhard M.
   Ramaiah, Nagappa
   Amann, Rudolf
TI Microbial Community Response during the Iron Fertilization Experiment
   LOHAFEX
SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Iron fertilization experiments in high-nutrient, low-chlorophyll areas are known to induce phytoplankton blooms. However, little is known about the response of the microbial community upon iron fertilization. As part of the LOHAFEX experiment in the southern Atlantic Ocean, Bacteria and Archaea were monitored within and outside an induced bloom, dominated by Phaeocystis- like nanoplankton, during the 38 days of the experiment. The microbial production increased 1.6-fold (thymidine uptake) and 2.1-fold (leucine uptake), while total cell numbers increased only slightly over the course of the experiment. 454 tag pyrosequencing of partial 16S rRNA genes and catalyzed reporter deposition fluorescence in situ hybridization (CARD FISH) showed that the composition and abundance of the bacterial and archaeal community in the iron-fertilized water body were remarkably constant without development of typical bloom-related succession patterns. Members of groups usually found in phytoplankton blooms, such as Roseobacter and Gammaproteobacteria, showed no response or only a minor response to the bloom. However, sequence numbers and total cell numbers of the SAR11 and SAR86 clades increased slightly but significantly toward the end of the experiment. It seems that although microbial productivity was enhanced within the fertilized area, a succession-like response of the microbial community upon the algal bloom was averted by highly effective grazing. Only small-celled members like the SAR11 and SAR86 clades could possibly escape the grazing pressure, explaining a net increase of those clades in numbers.
C1 [Thiele, Stefan; Fuchs, Bernhard M.; Amann, Rudolf] Max Planck Inst Marine Microbiol, Bremen, Germany.
   [Ramaiah, Nagappa] Natl Inst Oceanog, Panaji, Goa, India.
RP Fuchs, BM (corresponding author), Max Planck Inst Marine Microbiol, Bremen, Germany.
EM bfuchs@mpi-bremen.de
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NR 68
TC 41
Z9 44
PD DEC
PY 2012
VL 78
IS 24
BP 8803
EP 8812
DI 10.1128/AEM.01814-12
UT WOS:000311213200034
DA 2025-07-30
ER

PT J
AU Luo, HW
   Cusros, M
   Hughes, AL
   Moran, MA
AF Luo, Haiwei
   Cusros, Miklos
   Hughes, Austin L.
   Moran, Mary Ann
TI Evolution of Divergent Life History Strategies in Marine
   Alphaproteobacteria
SO MBIO
DT Article
AB Marine bacteria in the Roseobacter and SAR11 lineages successfully exploit the ocean habitat, together accounting for similar to 40% of bacteria in surface waters, yet have divergent life histories that exemplify patch-adapted versus free-living ecological roles. Here, we use a phylogenetic birth-and-death model to understand how genome content supporting different life history strategies evolved in these related alphaproteobacterial taxa, showing that the streamlined genomes of free-living SAR11 were gradually downsized from a common ancestral genome only slightly larger than the extant members (similar to 2,000 genes), while the larger and variably sized genomes of roseobacters evolved along dynamic pathways from a sizeable common ancestor (similar to 8,000 genes). Genome changes in the SAR11 lineage occurred gradually over similar to 800 million years, whereas Roseobacter genomes underwent more substantial modifications, including major periods of expansion, over similar to 260 million years. The timing of the first Roseobacter genome expansion was coincident with the predicted radiation of modern marine eukaryotic phytoplankton of sufficient size to create nutrient-enriched microzones and is consistent with present-day ecological associations between these microbial groups. We suggest that diversification of red-lineage phytoplankton is an important driver of divergent life history strategies among the heterotrophic bacterioplankton taxa that dominate the present-day ocean.
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C1 [Luo, Haiwei; Moran, Mary Ann] Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
   [Cusros, Miklos] Univ Montreal, Dept Comp Sci & Operat Res, Montreal, PQ, Canada.
   [Hughes, Austin L.] Univ S Carolina, Dept Biol Sci, Columbia, SC 29208 USA.
RP Moran, MA (corresponding author), Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
EM mmoran@uga.edu
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NR 64
TC 87
Z9 96
PD JUL-AUG
PY 2013
VL 4
IS 4
AR e00373-13
DI 10.1128/mBio.00373-13
UT WOS:000326881100020
DA 2025-07-30
ER

PT J
AU Wilhelm, LJ
   Tripp, HJ
   Givan, SA
   Smith, DP
   Giovannoni, SJ
AF Wilhelm, Larry J.
   Tripp, H. James
   Givan, Scott A.
   Smith, Daniel P.
   Giovannoni, Stephen J.
TI Natural variation in SARII marine bacterioplankton genomes inferred from
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SO BIOLOGY DIRECT
DT Article
AB Background: One objective of metagenomics is to reconstruct information about specific uncultured organisms from fragmentary environmental DNA sequences. We used the genome of an isolate of the marine alphaproteobacterium SARII ('Candidatus Pelagibacter ubique'; strain HTCC1062), obtained from the cold, productive Oregon coast, as a query sequence to study variation in SARII metagenome sequence data from the Sargasso Sea, a warm, oligotrophic ocean gyre. Results: The average amino acid identity of SARII genes encoded by the metagenomic data to the query genome was only 71%, indicating significant evolutionary divergence between the coastal isolates and Sargasso Sea populations. However, an analysis of gene neighbors indicated that SARII genes in the Sargasso Sea metagenomic data match the gene order of the HTCC1062 genome in 96% of cases (> 85,000 observations), and that rearrangements are most frequent at predicted operon boundaries. There were no conserved examples of genes with known functions being found in the coastal isolates, but not the Sargasso Sea metagenomic data, or vice versa, suggesting that core regions of these diverse SARII genomes are relatively conserved in gene content. However, four hypervariable regions were observed, which may encode properties associated with variation in SARII ecotypes. The largest of these, HVR2, is a 48 kb region flanked by the sole 5S and 23S genes in the HTCC1062 genome, and mainly encodes genes that determine cell surface properties. A comparison of two closely related 'Candidatus Pelagibacter' genomes (HTCC1062 and HTCC1002) revealed a number of "gene indels" in core regions. Most of these were found to be polymorphic in the metagenomic data and showed evidence of purifying selection, suggesting that the same "polymorphic gene indels" are maintained in physically isolated SARII populations. Conclusion: These findings suggest that natural selection has conserved many core features of SARII genomes across broad oceanic scales, but significant variation was found associated with four hypervariable genome regions. The data also led to the hypothesis that some gene insertions and deletions might be polymorphisms, similar to allelic polymorphisms.
C1 [Wilhelm, Larry J.; Tripp, H. James; Smith, Daniel P.; Giovannoni, Stephen J.] Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
   [Givan, Scott A.] Oregon State Univ, Ctr Genome Res & Bioinformat, Corvallis, OR 97331 USA.
RP Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
EM wilhelml@science.oregonstate.edu; tripph@onid.orst.edu;
   givans@cgrb.oregonstate.edu; dansmith@orst.edu;
   steve.giovannoni@oregonstate.edu
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NR 48
TC 89
Z9 101
PD NOV 7
PY 2007
VL 2
AR 27
DI 10.1186/1745-6150-2-27
UT WOS:000252923600001
DA 2025-07-30
ER

PT J
AU León-Zayas, R
   Novotny, M
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AF Leon-Zayas, Rosa
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TI Single Cells within the Puerto Rico Trench Suggest Hadal Adaptation of
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
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RP Bartlett, DH (corresponding author), Univ Calif San Diego, Scripps Inst Oceanog, Div Marine Biol Res, La Jolla, CA 92093 USA.
EM dbartlett@ucsd.edu
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NR 78
TC 34
Z9 37
PD DEC
PY 2015
VL 81
IS 24
BP 8265
EP 8276
DI 10.1128/AEM.01659-15
UT WOS:000365212800003
DA 2025-07-30
ER

PT J
AU Bolaños, LM
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AF Bolanos, Luis M.
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TI Seasonality of the Microbial Community Composition in the North Atlantic
SO FRONTIERS IN MARINE SCIENCE
DT Article
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RP Bolaños, LM; Giovannoni, S (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
EM bolanosi@oregonstate.edu; Steve.giovannoni@oregonstate.edu
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NR 81
TC 30
Z9 34
PD FEB 5
PY 2021
VL 8
AR 624164
DI 10.3389/fmars.2021.624164
UT WOS:000617914300001
DA 2025-07-30
ER

PT J
AU Lindh, MV
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   Pinhassi, J
AF Lindh, Markus V.
   Sjostedt, Johanna
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   Andersson, Agneta
   Legrand, Catherine
   Pinhassi, Jarone
TI Local Environmental Conditions Shape Generalist But Not Specialist
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DT Article
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C1 [Lindh, Markus V.; Sjostedt, Johanna; Legrand, Catherine; Pinhassi, Jarone] Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, Kalmar, Sweden.
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   [Lindh, Markus V.] Lund Univ, Dept Biol, Lund, Sweden.
   [Sjostedt, Johanna] Lund Univ, Dept Biol Aquat Ecol, Lund, Sweden.
   [Sjostedt, Johanna] Tech Univ Denmark, Inst Aquat Resources, Ctr Ocean Life, Charlottenlund, Denmark.
RP Lindh, MV (corresponding author), Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, Kalmar, Sweden.; Lindh, MV (corresponding author), Lund Univ, Dept Biol, Lund, Sweden.
EM markusvlindh@gmail.com
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VL 7
AR 2078
DI 10.3389/fmicb.2016.02078
UT WOS:000390658700001
DA 2025-07-30
ER

PT J
AU Pontiller, B
   Martínez-García, S
   Joglar, V
   Amnebrink, D
   Pérez-Martínez, C
   González, JM
   Lundin, D
   Fernández, E
   Teira, E
   Pinhassi, J
AF Pontiller, Benjamin
   Martinez-Garcia, Sandra
   Joglar, Vanessa
   Amnebrink, Dennis
   Perez-Martinez, Clara
   Gonzalez, Jose M.
   Lundin, Daniel
   Fernandez, Emilio
   Teira, Eva
   Pinhassi, Jarone
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SO ISME JOURNAL
DT Article
AB Coastal upwelling zones are hotspots of oceanic productivity, driven by phytoplankton photosynthesis. Bacteria, in turn, grow on and are the principal remineralizers of dissolved organic matter (DOM) produced in aquatic ecosystems. However, the molecular processes that key bacterial taxa employ to regulate the turnover of phytoplankton-derived DOM are not well understood. We therefore carried out comparative time-series metatranscriptome analyses of bacterioplankton in the Northwest Iberian upwelling system, using parallel sampling of seawater and mesocosms with in situ-like conditions. The mesocosm experiment uncovered a taxon-specific progression of transcriptional responses from bloom development (characterized by a diverse set of taxa in the orders Cellvibrionales, Rhodobacterales, and Pelagibacterales), over early decay (mainly taxa in the Alteromonadales and Flavobacteriales), to senescence phases (Flavobacteriales and Saprospirales taxa). Pronounced order-specific differences in the transcription of glycoside hydrolases, peptidases, and transporters were found, supporting that functional resource partitioning is dynamically structured by temporal changes in available DOM. In addition, comparative analysis of mesocosm and field samples revealed a high degree of metabolic plasticity in the degradation and uptake of carbohydrates and nitrogen-rich compounds, suggesting these gene systems critically contribute to modulating the stoichiometry of the labile DOM pool. Our findings suggest that cascades of transcriptional responses in gene systems for the utilization of organic matter and nutrients largely shape the fate of organic matter on the time scales typical of upwelling-driven phytoplankton blooms.
C1 [Pontiller, Benjamin; Amnebrink, Dennis; Perez-Martinez, Clara; Lundin, Daniel; Pinhassi, Jarone] Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, S-39182 Kalmar, Sweden.
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   [Gonzalez, Jose M.] Univ La Laguna, Dept Microbiol, San Cristobal la Laguna 38200, Spain.
RP Pinhassi, J (corresponding author), Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, S-39182 Kalmar, Sweden.
EM jarone.pinhassi@lnu.se
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NR 100
TC 29
Z9 31
PD OCT
PY 2022
VL 16
IS 10
BP 2360
EP 2372
DI 10.1038/s41396-022-01273-0
EA JUL 2022
UT WOS:000822288300001
DA 2025-07-30
ER

PT J
AU Laas, P
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   Metsis, M
AF Laas, Peeter
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TI Spatial variability of winter bacterioplankton community composition in
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SO JOURNAL OF MARINE SYSTEMS
DT Article
AB The microbial communities in the Baltic Sea are extremely diverse and highly dynamic and undergoing shifts in dominant phylotypes in response to spatial and temporal environmental gradients. We present the first study of wintertime bacterioplankton with a high-throughput sequencing approach. Using barcoded pyrosequencing of the 16S rRNA gene we investigated the bacterial diversity and spatial distribution of winter picoplankton communities in the Gulf of Finland. We analyzed ten samples and identified 609 OTUs (operational taxanomic units), mostly members of Proteobacteria, Actinobacteria, Bacteroidetes and Cyanobacteria. Most abundant OTUs of the dataset were identified as Sulfurimonas and Pelagibacter, which dominated the near-bottom and surface layers, respectively. Surface communities yielded about the same species richness estimates than a previous study conducted in same area during springtime. (c) 2013 Elsevier B.V. All rights reserved.
C1 [Laas, Peeter; Lips, Inga] Tallinn Univ Technol, Marine Syst Inst, EE-12618 Tallinn, Estonia.
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RP Laas, P (corresponding author), Tallinn Univ Technol, Marine Syst Inst, Akad Tee 15A, EE-12618 Tallinn, Estonia.
EM peeter.laas@msi.ttu.ee
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NR 64
TC 16
Z9 17
PD JAN
PY 2014
VL 129
BP 127
EP 134
DI 10.1016/j.jmarsys.2013.07.016
UT WOS:000329881600013
DA 2025-07-30
ER

PT J
AU Mandal, M
   Mandal, S
AF Mandal, Manisha
   Mandal, Shyamapada
TI Cross-biome metagenomic analyses of the impact of pollutants on
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SO GENE REPORTS
DT Article
AB Due to anthropogenic activities, a large number of pollutants are disposed into the environment. The microbial communities in the environment are immensely diverse and critical mediators of various ecosystem processes. But it is not clearly known to what extent xenobiotics effect the composition and functionality of environmental microorganisms, across biomes in different geographic locations, with varying contaminating sources, categories of chemical pollutants, and their application types. Here, we investigated the impact of xenobiotics by meta-genomic analysis of 16S rRNA from seawater, soil, sludge and sediment, for deciphering microbial diversity, community structure, functional enrichment and metabolic potentiality in relation to the application of pesticide (metaldehyde), herbicide (2,4-dichlorophenoxyacetic acid; DCPAA), insecticide (chlordecone) and flame retar-dant additives (organophosphate triesters; OPT and tris 2 chloroethyl phosphate; TCEP). Firmicutes was the most abundant phylum consisting of Clostridia, in association with DCPAA (Lutispora sp.), metaldehyde and TCEP treatments. The next two abundant phyla were Proteobacteria [class Deltaproteobacteria, Alphaproteobacteria (Pelagibacter ubique with OPT treatment) and Gammaproteobacteria], and Euryarchaeota consisting mostly of Methanobacteria with chlordecone and DCPAA. Both Desulfomicrobium and Sedimentibacter were predominant in the subtropical moist forest sediment, while Synechococcus and Pelagibacter dominated the temperate Mediterranean Sea. Ruminococcus and Lutispora were more abundant in rain forest compared to waste water solid, while Anaerovorax predominated subtropical moist forest. Sequences involved in house-keeping genes comprised the most abundant hits. The genes involved in environmental information processing such as ABC transporters catalyzing carbohydrate uptake, membrane transport and quorum sensing were over-represented with TCEP, DCPAA, OPT and metaldehyde. Exposure to different classes of xenobiotics revealed major differ-ences in microbial structure and function abundances, mainly driven by environmental sources and biomes. Preponderance of core metabolic functional genes across all the metagenomes analysed is indicative of microbial community responding and adjusting itself to deal with these treatments and maintain its balance.
C1 [Mandal, Manisha] MGM Med Coll, Dept Physiol, Kishanganj 855107, India.
   [Mandal, Shyamapada] Univ Gour Banga, Dept Zool, Malda 732103, India.
RP Mandal, S (corresponding author), Univ Gour Banga, Dept Zool, Malda 732103, India.
EM samtropmed@gmail.com
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NR 44
TC 4
Z9 5
PD DEC
PY 2022
VL 29
AR 101690
DI 10.1016/j.genrep.2022.101690
EA OCT 2022
UT WOS:000869762500004
DA 2025-07-30
ER

PT J
AU Mary, I
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AF Mary, Isabelle
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DT Article
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C1 Natl Oceanog Ctr, Southampton SO17 3ZH, Hants, England.
   Plymouth Marine Lab, Plymouth, Devon, England.
   Univ Southampton, Sch Biol Sci, Southampton SO9 5NH, Hants, England.
   Univ Warwick, Dept Sci Biol, Coventry CV4 7AL, W Midlands, England.
   Sir Alister Hardy Fdn Ocean Sci, Plymouth, Devon, England.
   Univ Plymouth, Inst Marine, Plymouth, Devon, England.
RP Zubkov, MV (corresponding author), Natl Oceanog Ctr, European Way, Southampton SO17 3ZH, Hants, England.
EM mvz@noc.soton.ac.uk
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TC 81
Z9 85
PD JAN
PY 2008
VL 63
IS 1
BP 36
EP 45
DI 10.1111/j.1574-6941.2007.00414.x
UT WOS:000251504000005
DA 2025-07-30
ER

PT J
AU Norris, N
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AF Norris, Noele
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DT Article
AB Marine bacterial diversity is immense and believed to be driven in part by trade-offs in metabolic strategies. Here we consider heterotrophs that rely on organic carbon as an energy source and present a molecular-level model of cell metabolism that explains the dichotomy between copiotrophs-which dominate in carbon-rich environments-and oligotrophs-which dominate in carbon-poor environments-as the consequence of trade-offs between nutrient transport systems. While prototypical copiotrophs, like Vibrios, possess numerous phosphotransferase systems (PTS), prototypical oligotrophs, such as SAR11, lack PTS and rely on ATP-binding cassette (ABC) transporters, which use binding proteins. We develop models of both transport systems and use them in proteome allocation problems to predict the optimal nutrient uptake and metabolic strategy as a function of carbon availability. We derive a Michaelis-Menten approximation of ABC transport, analytically demonstrating how the half-saturation concentration is a function of binding protein abundance. We predict that oligotrophs can attain nanomolar half-saturation concentrations using binding proteins with only micromolar dissociation constants and while closely matching transport and metabolic capacities. However, our model predicts that this requires large periplasms and that the slow diffusion of the binding proteins limits uptake. Thus, binding proteins are critical for oligotrophic survival yet severely constrain growth rates. We propose that this trade-off fundamentally shaped the divergent evolution of oligotrophs and copiotrophs.
   Author summary Marine bacteria utilize carbon as a building block and an energy source and thus exert an important control on the amount of carbon that is sequestered in the ocean versus respired into the atmosphere. They use a spectrum of strategies to consume carbon: while copiotrophic bacteria dominate in nutrient-rich environments, oligotrophic bacteria dominate in nutrient-poor environments and are typically smaller, nonmotile, and slower growing. Yet the paragon oligotroph SAR11 is the planet's most abundant organism. Despite this, most of our understanding of bacteria derives from research on copiotrophs. Here we use molecular-level models to understand how an oligotroph's physiology enables it to outperform copiotrophs in nutrient-poor but not in nutrient-rich environments. We contrast copiotrophs' prevalent method of sugar transport with oligotrophs' reliance on binding proteins, which trap nutrients in the periplasm. Binding proteins allow cells to attain affinities that are much higher than the transport proteins' intrinsic affinities. However, our model predicts that attaining such high affinities requires large periplasms with high abundances of the slowly diffusing binding proteins, which precludes high growth rates. By quantifying the benefits and costs of binding proteins, we provide a mechanistic explanation for the divergent evolution of oligotrophs and copiotrophs.
C1 [Norris, Noele] MIT, Dept Elect Engn & Comp Sci, Cambridge, MA 02139 USA.
   [Norris, Noele; Levine, Naomi M.] Univ Southern Calif, Dept Biol Sci, Los Angeles, CA 90007 USA.
   [Norris, Noele; Fernandez, Vicente I.; Stocker, Roman] Swiss Fed Inst Technol, Dept Civil Environm & Geomat Engn, Inst Environm Engn, Zurich, Switzerland.
RP Norris, N (corresponding author), MIT, Dept Elect Engn & Comp Sci, Cambridge, MA 02139 USA.; Norris, N (corresponding author), Univ Southern Calif, Dept Biol Sci, Los Angeles, CA 90007 USA.; Norris, N; Stocker, R (corresponding author), Swiss Fed Inst Technol, Dept Civil Environm & Geomat Engn, Inst Environm Engn, Zurich, Switzerland.
EM noelen@alum.mit.edu
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NR 64
TC 27
Z9 29
PD MAY
PY 2021
VL 17
IS 5
AR e1009023
DI 10.1371/journal.pcbi.1009023
UT WOS:000664309400001
DA 2025-07-30
ER

PT J
AU Zhang, ZF
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   Chu, X
   Luo, HW
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   Du, S
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AF Zhang, Zefeng
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DT Article
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RP Zhao, YL (corresponding author), Fujian Agr & Forestry Univ, Coll Life Sci, Fujian Prov Key Lab Agroecol Proc & Safety Monito, Fuzhou, Fujian, Peoples R China.
EM yanlinzhao@fafu.edu.cn
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TC 27
Z9 28
PD FEB
PY 2021
VL 23
IS 2
BP 1145
EP 1161
DI 10.1111/1462-2920.15272
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UT WOS:000579318200001
DA 2025-07-30
ER

PT J
AU Jiao, NZ
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AF Jiao, Nianzhi
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DT Review
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RP Jiao, NZ (corresponding author), Xiamen Univ, State Key Lab Marine Environm Sci, Xiamen 361005, Peoples R China.
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NR 67
TC 78
Z9 101
PD NOV
PY 2011
VL 77
IS 21
BP 7439
EP 7444
DI 10.1128/AEM.05640-11
UT WOS:000296568200001
DA 2025-07-30
ER

PT J
AU Zeng, DN
   Fan, ZY
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   Quan, ZX
AF Zeng, Dan-Ning
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   Quan, Zhe-Xue
TI Analysis of the bacterial communities associated with different drinking
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SO WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY
DT Article
AB A drinking water plant was surveyed to determine the bacterial composition of different drinking water treatment processes (DWTP). Water samples were collected from different processing steps in the plant (i.e., coagulation, sedimentation, sand filtration, and chloramine disinfection) and from distantly piped water. The samples were pyrosequensed using sample-specific oligonucleotide barcodes. The taxonomic composition of the microbial communities of different DWTP and piped water was dominated by the phylum Proteobacteria. Additionally, a large proportion of the sequences were assigned to the phyla Actinobacteria and Bacteroidetes. The piped water exhibited increasing taxonomic diversity, including human pathogens such as the Mycobacterium, which revealed a threat to the safety of drinking water. Surprisingly, we also found that a sister group of SAR11 (LD12) persisted throughout the DWTP, which was always detected in freshwater aquatic systems. Moreover, Polynucleobacter, Rhodoferax, and a group of Actinobacteria, hgcI clade, were relatively consistent throughout the processes. It is concluded that smaller-size microorganisms tended to survive against the present treatment procedure. More improvement should be made to ensure the long-distance transmission drinking water.
C1 [Zeng, Dan-Ning; Fan, Zhen-Yu; Chi, Liang; Quan, Zhe-Xue] Fudan Univ, Sch Life Sci, Dept Microbiol & Microbial Engn, Shanghai 200433, Peoples R China.
   [Wang, Xia; Qu, Wei-Dong] Fudan Univ, Sch Publ Hlth, Dept Environm Hlth, Key Lab Publ Hlth & Safety,Minist Educ, Shanghai 200032, Peoples R China.
RP Quan, ZX (corresponding author), Fudan Univ, Sch Life Sci, Dept Microbiol & Microbial Engn, Shanghai 200433, Peoples R China.
EM quanzx@fudan.edu.cn
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ER

PT J
AU Shi, YM
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AF Shi, Yanmei
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   DeLong, Edward F.
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DT Article
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C1 [Shi, Yanmei; Tyson, Gene W.; Eppley, John M.; DeLong, Edward F.] MIT, Dept Civil & Environm Engn, Cambridge, MA 02139 USA.
   [Tyson, Gene W.] Univ Queensland, Adv Water Management Ctr, Brisbane, Qld, Australia.
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RP DeLong, EF (corresponding author), MIT, Dept Civil & Environm Engn, 15 Vassar St, Cambridge, MA 02139 USA.
EM delong@mit.edu
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DA 2025-07-30
ER

PT J
AU Crump, BC
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AF Crump, Byron C.
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C1 Univ Maryland, Ctr Environm Sci, Horn Point Lab, Cambridge, MD 21613 USA.
RP Crump, BC (corresponding author), Univ Maryland, Ctr Environm Sci, Horn Point Lab, 2020 Horns Point Rd, Cambridge, MD 21613 USA.
EM bcrump@hpl.umces.edu
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NR 64
TC 78
Z9 94
PD NOV
PY 2007
VL 73
IS 21
BP 6802
EP 6810
DI 10.1128/AEM.00648-07
UT WOS:000250700600012
DA 2025-07-30
ER

PT J
AU Feng, SS
   Xiao, WW
   Yu, YY
   Liu, GF
   Zhang, YL
   Chen, T
   Lu, CR
AF Feng, Shanshan
   Xiao, Wenwen
   Yu, Yingying
   Liu, Guangfeng
   Zhang, Yunlong
   Chen, Ting
   Lu, Changrui
TI Linker-Mediated Inactivation of the SAM-II Domain in the Tandem
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SO INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
DT Article
AB Tandem SAM-II/SAM-V riboswitch belongs to a class of riboswitches found in the marine bacterium 'Candidatus Pelagibacter ubique'. Previous studies have demonstrated that these riboswitches have the potential for digital modulation of gene expression at both the transcriptional and translational levels. In this study, we investigate the conformational changes in the tandem SAM-II/SAM-V riboswitch binding to S-adenosylmethionine (SAM) using selective 2 '-hydroxyl acylation analyzed by the primer extension (SHAPE) assay, small-angle X-ray scattering (SAXS), and oligos depressing probing. Our findings reveal that the linker between SAM-II/SAM-V aptamers blocks the SAM response of the SAM-II domain. This result proposes a new mechanism for gene expression regulation, where the ligand-binding functions of tandem riboswitches can be selectively masked or released through a linker.
C1 [Feng, Shanshan; Xiao, Wenwen; Yu, Yingying; Zhang, Yunlong; Chen, Ting; Lu, Changrui] Donghua Univ, Coll Biol Sci & Med Engn, Shanghai 201620, Peoples R China.
   [Liu, Guangfeng] Chinese Acad Sci, Shanghai Adv Res Inst, Natl Ctr Prot Sci Shanghai, Shanghai 201204, Peoples R China.
RP Lu, CR (corresponding author), Donghua Univ, Coll Biol Sci & Med Engn, Shanghai 201620, Peoples R China.
EM sandyfss@163.com; wenwen_xiao@yeah.net; yingyingyu0312@163.com;
   liuguangfeng@sari.ac.cn; zhyl@dhu.edu.cn; chenting@dhu.edu.cn;
   crlu@dhu.edu.cn
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NR 86
TC 0
Z9 0
PD OCT
PY 2024
VL 25
IS 20
AR 11288
DI 10.3390/ijms252011288
UT WOS:001341601300001
DA 2025-07-30
ER

PT J
AU Chen, Y
   Patel, NA
   Crombie, A
   Scrivens, JH
   Murrell, JC
AF Chen, Yin
   Patel, Nisha A.
   Crombie, Andrew
   Scrivens, James H.
   Murrell, J. Colin
TI Bacterial flavin-containing monooxygenase is trimethylamine
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SO PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
   AMERICA
DT Article
AB Flavin-containing monooxygenases (FMOs) are one of the most important monooxygenase systems in Eukaryotes and have many important physiological functions. FMOs have also been found in bacteria; however, their physiological function is not known. Here, we report the identification and characterization of trimethylamine (TMA) monooxygenase, termed Tmm, from Methylocella silvestris, using a combination of proteomic, biochemical, and genetic approaches. This bacterial FMO contains the FMO sequence motif (FXGXXXHXXXF/Y) and typical flavin adenine dinucleotide and nicotinamide adenine dinucleotide phosphate-binding domains. The enzyme was highly expressed in TMA-grown M. silvestris and absent during growth on methanol. The gene, tmm, was expressed in Escherichia coli, and the purified recombinant protein had high Tmm activity. Mutagenesis of this gene abolished the ability of M. silvestris to grow on TMA as a sole carbon and energy source. Close homologs of tmm occur in many Alphaproteobacteria, in particular Rhodobacteraceae (marine Roseobacter clade, MRC) and the marine SAR11 clade (Pelagi-bacter ubique). We show that the ability of MRC to use TMA as a sole carbon and/or nitrogen source is directly linked to the presence of tmm in the genomes, and purified Tmm of MRC and SAR11 from recombinant E. coli showed Tmm activities. The tmm gene is highly abundant in the metagenomes of the Global Ocean Sampling expedition, and we estimate that 20% of the bacteria in the surface ocean contain tmm. Taken together, our results suggest that Tmm, a bacterial FMO, plays an important yet overlooked role in the global carbon and nitrogen cycles.
C1 [Chen, Yin; Patel, Nisha A.; Crombie, Andrew; Scrivens, James H.; Murrell, J. Colin] Univ Warwick, Sch Life Sci, Coventry CV4 7AL, W Midlands, England.
RP Chen, Y (corresponding author), Univ Warwick, Sch Life Sci, Coventry CV4 7AL, W Midlands, England.
EM cheny98@gmail.com; j.c.murrell@warwick.ac.uk
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Z9 134
PD OCT 25
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VL 108
IS 43
BP 17791
EP 17796
DI 10.1073/pnas.1112928108
UT WOS:000296378100051
DA 2025-07-30
ER

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SO JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY
DT Article
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C1 [Oh, Hyun-Myung] Pukyong Natl Univ, Inst Liberal Arts Educ, Busan 48547, South Korea.
   [Lee, Ji Hyen] Ewha Womans Univ, Sch Med, Dept Pediat, Seoul 07804, South Korea.
   [Choi, Ahyoung] Nakdonggang Natl Inst Biol Resources, Sangju 37242, South Korea.
   [Yang, Sung-Hyun; Kang, Sung Gyun] Korea Inst Ocean Sci & Technol, Busan 49111, South Korea.
   [Shin, Gyung-Hoon; Kwon, Kae-Kyoung] Hanyang Univ ERICA, Ansan 15588, South Korea.
   [Cho, Jang-Cheon] Inha Univ, Div Biol & Ocean Sci, Incheon 22212, South Korea.
   [Kim, Hak Jun] Pukyong Natl Univ, Dept Chem, Busan 48547, South Korea.
RP Kwon, KK (corresponding author), Hanyang Univ ERICA, Ansan 15588, South Korea.; Kim, HJ (corresponding author), Pukyong Natl Univ, Dept Chem, Busan 48547, South Korea.
EM kimhj@pknu.ac.kr; kkkwon@kordi.re.kr
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TC 0
Z9 0
PY 2025
VL 35
AR e2410034
DI 10.4014/jmb.2410.10034
UT WOS:001398736600003
DA 2025-07-30
ER

PT J
AU Korlevic, M
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RP Korlevic, M (corresponding author), Rudjer Boskovic Inst, Ctr Marine Res, Rovinj, Croatia.
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TC 13
Z9 13
PD OCT 7
PY 2022
VL 12
IS 1
AR 16859
DI 10.1038/s41598-022-20954-6
UT WOS:000865124900050
DA 2025-07-30
ER

PT J
AU Piccini, C
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AF Piccini, Claudia
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
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   Inst Ecol, Lab Aquat Photobiol & Plankton Ecol, Innsbruck, Austria.
RP Pernthaler, J (corresponding author), Univ Zurich, Limnol Stn, Dept Plant Biol, Inst Plant Biol, Seestr 187, CH-8802 Kilchberg, Switzerland.
EM pernthaler@limnol.unizh.ch
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NR 62
TC 66
Z9 67
PD OCT
PY 2006
VL 72
IS 10
BP 6560
EP 6568
DI 10.1128/AEM.01089-06
UT WOS:000241170300017
DA 2025-07-30
ER

PT J
AU Born, DA
   Ulrich, EC
   Ju, KS
   Peck, SC
   van der Donk, WA
   Drennan, CL
AF Born, David A.
   Ulrich, Emily C.
   Ju, Kou-San
   Peck, Spencer C.
   van der Donk, Wilfred A.
   Drennan, Catherine L.
TI Structural basis for methylphosphonate biosynthesis
SO SCIENCE
DT Article
AB Methylphosphonate synthase (MPnS) produces methylphosphonate, a metabolic precursor to methane in the upper ocean. Here, we determine a 2.35-angstrom resolution structure of MPnS and discover that it has an unusual 2-histidine-1-glutamine iron-coordinating triad. We further solve the structure of a related enzyme, hydroxyethylphosphonate dioxygenase from Streptomyces albus (SaHEPD), and find that it displays the same motif. SaHEPD can be converted into an MPnS by mutation of glutamine-adjacent residues, identifying the molecular requirements for methylphosphonate synthesis. Using these sequence markers, we find numerous putative MPnSs in marine microbiomes and confirm that MPnS is present in the abundant Pelagibacter ubique. The ubiquity of MPnS-containing microbes supports the proposal that methylphosphonate is a source of methane in the upper, aerobic ocean, where phosphorus-starved microbes catabolize methylphosphonate for its phosphorus.
C1 [Born, David A.] Harvard Univ, Grad Program Biophys, Cambridge, MA 02138 USA.
   [Born, David A.; Drennan, Catherine L.] MIT, Dept Biol, Cambridge, MA USA.
   [Ulrich, Emily C.; Peck, Spencer C.; van der Donk, Wilfred A.] Univ Illinois, Dept Chem, Urbana, IL USA.
   [Ulrich, Emily C.; Ju, Kou-San; Peck, Spencer C.; van der Donk, Wilfred A.] Univ Illinois, Carl R Woese Inst Genom Biol, Urbana, IL USA.
   [Ju, Kou-San] Ohio State Univ, Dept Microbiol, 484 W 12th Ave, Columbus, OH 43210 USA.
   [Ju, Kou-San] Ohio State Univ, Div Med Chem & Pharmacognosy, Columbus, OH 43210 USA.
   [van der Donk, Wilfred A.] Univ Illinois, Howard Hughes Med Inst, Urbana, IL USA.
   [Drennan, Catherine L.] MIT, Dept Chem, Cambridge, MA 02139 USA.
   [Drennan, Catherine L.] MIT, Howard Hughes Med Inst, Cambridge, MA USA.
   [Peck, Spencer C.] Harvard Univ, Dept Chem & Chem Biol, Cambridge, MA 02138 USA.
RP Drennan, CL (corresponding author), MIT, Dept Biol, Cambridge, MA USA.; van der Donk, WA (corresponding author), Univ Illinois, Dept Chem, Urbana, IL USA.; van der Donk, WA (corresponding author), Univ Illinois, Carl R Woese Inst Genom Biol, Urbana, IL USA.; van der Donk, WA (corresponding author), Univ Illinois, Howard Hughes Med Inst, Urbana, IL USA.; Drennan, CL (corresponding author), MIT, Dept Chem, Cambridge, MA 02139 USA.; Drennan, CL (corresponding author), MIT, Howard Hughes Med Inst, Cambridge, MA USA.
EM vddonk@illinois.edu; cdrennan@mit.edu
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NR 20
TC 39
Z9 43
PD DEC 8
PY 2017
VL 358
IS 6368
BP 1336
EP 1338
DI 10.1126/science.aao3435
UT WOS:000417254700066
DA 2025-07-30
ER

PT J
AU Lidbury, I
   Murrell, JC
   Chen, Y
AF Lidbury, Ian
   Murrell, J. Colin
   Chen, Yin
TI Trimethylamine N-oxide metabolism by abundant marine
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SO PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
   AMERICA
DT Article
AB Trimethylamine N-oxide (TMAO) is a common osmolyte found in a variety of marine biota and has been detected at nanomolar concentrations in oceanic surface waters. TMAO can serve as an important nutrient for ecologically important marine heterotrophic bacteria, particularly the SAR11 clade and marine Roseobacter clade (MRC). However, the enzymes responsible for TMAO catabolism and the membrane transporter required for TMAO uptake into microbial cells have yet to be identified. We show here that the enzyme TMAO demethylase (Tdm) catalyzes the first step in TMAO degradation. This enzyme represents a large group of proteins with an uncharacterized domain (DUF1989). The function of TMAO demethylase in a representative from the SAR11 clade (strain HIMB59) and in a representative of the MRC (Ruegeria pomeroyi DSS-3) was confirmed by heterologous expression of tdm (the gene encoding Tdm) in Escherichia coli. In R. pomeroyi, mutagenesis experiments confirmed that tdm is essential for growth on TMAO. We also identified a unique ATP-binding cassette transporter (TmoXWV) found in a variety of marine bacteria and experimentally confirmed its specificity for TMAO through marker exchange mutagenesis and lacZ reporter assays of the promoter for genes encoding this transporter. Both Tdm and TmoXWV are particularly abundant in natural seawater assemblages and actively expressed, as indicated by a number of recent metatranscriptomic and metaproteomic studies. These data suggest that TMAO represents a significant, yet overlooked, nutrient for marine bacteria.
C1 [Lidbury, Ian; Chen, Yin] Univ Warwick, Sch Life Sci, Coventry CV4 7AL, W Midlands, England.
   [Murrell, J. Colin] Univ E Anglia, Sch Environm Sci, Norwich NR4 7TJ, Norfolk, England.
RP Chen, Y (corresponding author), Univ Warwick, Sch Life Sci, Coventry CV4 7AL, W Midlands, England.
EM y.chen.25@warwick.ac.uk
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NR 53
TC 132
Z9 155
PD FEB 18
PY 2014
VL 111
IS 7
BP 2710
EP 2715
DI 10.1073/pnas.1317834111
UT WOS:000331396500064
DA 2025-07-30
ER

PT J
AU Howard, EC
   Sun, SL
   Reisch, CR
   del Valle, DA
   Bürgmann, H
   Kiene, RP
   Moran, MA
AF Howard, Erinn C.
   Sun, Shulei
   Reisch, Christopher R.
   del Valle, Daniela A.
   Buergmann, Helmut
   Kiene, Ronald P.
   Moran, Mary Ann
TI Changes in Dimethylsulfoniopropionate Demethylase Gene Assemblages in
   Response to an Induced Phytoplankton Bloom
SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Over half of the bacterioplankton cells in ocean surface waters are capable of carrying out a demethylation of the phytoplankton metabolite dimethylsulfoniopropionate (DMSP) that routes the sulfur moiety away from the climatically active gas dimethylsulfide (DMS). In this study, we tracked changes in dmdA, the gene responsible for DMSP demethylation, over the course of an induced phytoplankton bloom in Gulf of Mexico seawater microcosms. Analysis of >91,000 amplicon sequences indicated 578 different dmdA sequence clusters at a conservative clustering criterion of >= 90% nucleotide sequence identity over the 6-day study. The representation of the major clades of dmdA, several of which are linked to specific taxa through genomes of cultured marine bacterioplankton, remained fairly constant. However, the representation of clusters within these major clades shifted significantly in response to the bloom, including two Roseobacter-like clusters and a SAR11-like cluster, and the best correlate with shifts of the dominant dmdA clades was chlorophyll a concentration. Concurrent 16S rRNA amplification and sequencing indicated the presence of Roseobacter, SAR11, OM60, and marine Rhodospirillales populations, all of which are known to harbor dmdA genes, although the largest taxonomic change was an increase in Flavobacteriaceae, a group not yet demonstrated to have DMSP-demethylating capabilities. Sequence heterogeneity in dmdA and other functional gene populations is becoming increasingly evident with the advent of high-throughput sequencing technologies, and understanding the ecological implications of this heterogeneity is a major challenge for marine microbial ecology.
C1 [Howard, Erinn C.; Sun, Shulei; Moran, Mary Ann] Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
   [Reisch, Christopher R.] Univ Georgia, Dept Microbiol, Athens, GA 30602 USA.
   [del Valle, Daniela A.; Kiene, Ronald P.] Univ S Alabama, Dept Marine Sci, Mobile, AL 36688 USA.
   [Buergmann, Helmut] Eawag, Swiss Fed Inst Aquat Sci & Technol, Dept Surface Waters Res & Management, CH-6047 Kastanienbaum, Switzerland.
RP Moran, MA (corresponding author), Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
EM mmoran@uga.edu
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NR 39
TC 40
Z9 43
PD JAN
PY 2011
VL 77
IS 2
BP 524
EP 531
DI 10.1128/AEM.01457-10
UT WOS:000286147300017
DA 2025-07-30
ER

PT J
AU Ardell, DH
AF Ardell, David H.
TI Computational analysis of tRNA identity
SO FEBS LETTERS
DT Review
AB I review recent developments in computational analysis of tRNA identity. I suggest that the tRNA-protein interaction network is hierarchically organized, and coevolutionarily flexible. Its functional specificity of recognition and discrimination persists despite generic structural constraints and perturbative evolutionary forces. This flexibility comes from its arbitrary nature as a self-recognizing shape code. A revisualization of predicted Proteobacterial tRNA identity highlights open research problems. tRNA identity elements and their coevolution with proteins must be mapped structurally over the Tree of Life. These traits can also resolve deep roots in the Tree. I show that histidylation identity elements phylogenetically reposition Pelagibacter ubique within alpha-Proteobacteria. (C) 2009 Published by Elsevier B. V. on behalf of the Federation of European Biochemical Societies.
C1 [Ardell, David H.] Univ Calif, Sch Nat Sci, Merced, CA 95343 USA.
   [Ardell, David H.] Univ Calif, UC Merced Ctr Computat Biol, Merced, CA 95343 USA.
RP Ardell, DH (corresponding author), Univ Calif, Sch Nat Sci, Merced, CA 95343 USA.
EM dardell@ucmerced.edu
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NR 69
TC 23
Z9 31
PD JAN 21
PY 2010
VL 584
IS 2
BP 325
EP 333
DI 10.1016/j.febslet.2009.11.084
UT WOS:000273209600011
DA 2025-07-30
ER

PT J
AU Tada, Y
   Taniguchi, A
   Sato-Takabe, Y
   Hamasaki, K
AF Tada, Yuya
   Taniguchi, Akito
   Sato-Takabe, Yuki
   Hamasaki, Koji
TI Growth and succession patterns of major phylogenetic groups of marine
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SO JOURNAL OF OCEANOGRAPHY
DT Article
AB Our objective was to track microbial processes associated with serial degradation of organic matter derived from algal blooms. To do this, we analyzed population fluctuations and growth responses of major phylogenetic groups of free-living marine bacteria. We used bromodeoxyuridine immunocytochemistry-fluorescence in situ hybridization methodology to examine marine bacterial community development during and after a diatom bloom in a mesocosm. We revealed that the Roseobacter/Rhodobacter, SAR11, Alteromonas, and Bacteroidetes groups were clearly major phylotypes responsible for most free-living bacterial biomass and production throughout the experiment. The clearest bacterial response was a proliferation of the Alteromonas group (cells with large volumes) during development of the bloom (up to 30 % of actively growing cells). Populations of these bacteria declined sharply thereafter, likely due to grazing. Alteromonas group responses suggest that these bacteria strongly influenced the flux of organic matter at an early bloom stage. The growth potential of Bacteroidetes was relatively large as the bloom peaked; this early development probably contributed to the initial stage of bloom decomposition. In contrast, the contribution of Roseobacter/Rhodobacter to total bacterial production increased at a late stage of decomposing of the bloom. The contributions of Betaproteobacteria, SAR11, and SAR86 groups to total bacterial abundance and production were relatively minor throughout the experiment. These results imply that the ability to utilize organic matter derived from diatoms varies among bacterial phylotypes, and, frequently, less abundant but ecological specialist taxa such as Alteromonas may play major roles in the flux of organic matter during diatom blooms.
C1 [Tada, Yuya; Hamasaki, Koji] Univ Tokyo, Atmosphere & Ocean Res Inst, Kashiwa, Chiba 2778564, Japan.
   [Taniguchi, Akito] Kinki Univ, Grad Sch Agr, Naka 6318505, Japan.
   [Sato-Takabe, Yuki] Hokkaido Univ, Grad Sch Environm Sci, Kita Ku, Sapporo, Hokkaido 0600810, Japan.
RP Hamasaki, K (corresponding author), Univ Tokyo, Atmosphere & Ocean Res Inst, 5-1-5 Kashiwanoha, Kashiwa, Chiba 2778564, Japan.
EM hamasaki@aori.u-tokyo.ac.jp
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NR 40
TC 25
Z9 28
PD AUG
PY 2012
VL 68
IS 4
BP 509
EP 519
DI 10.1007/s10872-012-0114-z
UT WOS:000307295700003
DA 2025-07-30
ER

PT J
AU Mannen, K
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   Rozenberg, A
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AF Mannen, Kentaro
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   Uchihashi, Takayuki
   Inoue, Keiichi
TI Multiple Roles of a Conserved Glutamate Residue for Unique Biophysical
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   Rhodopsin
SO JOURNAL OF MOLECULAR BIOLOGY
DT Article
AB TAT rhodopsin, a microbial rhodopsin found in the marine SAR11 bacterium HIMB114, uniquely possesses a Thr-Ala-Thr (TAT) motif in the third transmembrane helix. Because of a low pKa value of the retinal Schiff base (RSB), TAT rhodopsin exhibits both a visible light -absorbing state with the protonated RSB and a UV -absorbing state with the deprotonated RSB at a neutral pH. The UV -absorbing state, in contrast to the visible light -absorbing one, converts to a long-lived photointermediate upon light absorption, implying that TAT rhodopsin functions as a pH -dependent light sensor. Despite detailed biophysical characterization and mechanistic studies on the TAT rhodopsin, it has been unknown whether other proteins with similarly unusual features exist. Here, we identified several new rhodopsin genes homologous to the TAT rhodopsin of HIMB114 (TATHIMB) from metagenomic data. Based on the absorption spectra of expressed proteins from these genes with visible and UV peaks similar to that of TATHIMB, they were classified as Twin -peaked Rhodopsin (TwR) family. TwR genes form a gene cluster with a set of 13 ORFs conserved in subclade IIIa of SAR11 bacteria. A glutamic acid in the second transmembrane helix, Glu54, is conserved in all of the TwRs. We investigated E54Q mutants of two TwRs and revealed that Glu54 plays critical roles in regulating the RSB pKa, oligomer formation, and the efficient photoreaction of the UV -absorbing state. The discovery of novel TwRs enables us to study the universality and individuality of the characteristics revealed so far in the original TATHIMB and contributes to further studies on mechanisms of unique properties of TwRs. (c) 2023 Elsevier Ltd. All rights reserved.
C1 [Mannen, Kentaro; Nagata, Takashi; Konno, Masae; Inoue, Keiichi] Univ Tokyo, Inst Solid State Phys, Room A401,5-1-5 Kashiwanoha, Kashiwa, Chiba 2778581, Japan.
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   [Uchihashi, Takayuki] Nagoya Univ, Dept Phys, Nagoya 4648602, Japan.
   [Uchihashi, Takayuki] Natl Inst Nat Sci, Exploratory Res Ctr Life & Living Syst, Okazaki, Aichi 4448787, Japan.
   [Uchihashi, Takayuki] Nagoya Univ, Inst Glycocore Res, Nagoya 4648602, Japan.
   [Marin, Maria del Carmen] Israel Inst Technol, IL-3200003 Haifa, Israel.
   [Bagherzadeh, Reza] RIKEN Ctr Integrat Med Sci, Yokohama, Kanagawa 2300045, Japan.
RP Inoue, K (corresponding author), Univ Tokyo, Inst Solid State Phys, Room A401,5-1-5 Kashiwanoha, Kashiwa, Chiba 2778581, Japan.
EM inoue@issp.u-tokyo.ac.jp
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NR 48
TC 6
Z9 6
PD MAR 1
PY 2024
VL 436
IS 5
AR 168331
DI 10.1016/j.jmb.2023.168331
EA MAR 2024
UT WOS:001258400700001
DA 2025-07-30
ER

PT J
AU Ma, YF
   Allen, LZ
   Palenik, B
AF Ma, Yingfei
   Allen, Lisa Zeigler
   Palenik, Brian
TI Diversity and genome dynamics of marine cyanophages using metagenomic
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SO ENVIRONMENTAL MICROBIOLOGY REPORTS
DT Article
AB Cyanophages are abundant in the oceanic environment and directly impact cyanobacterial distributions, physiological processes and evolution. Two samples collected from coastal Maine in July and September 2009 were enriched for Synechococcus cells using flow cytometry and examined through metagenomic sequencing. Homology-based sequence prediction indicated cyanophages, largely myoviruses, accounted for almost half the reads and provided insights into environmental infection events. T4-phage core-gene phylogenetic reconstruction revealed unique diversity among uncultured cyanophages and reference isolates resulting in identification of a new phylogenetic cluster. Genomic comparison of reference cyanophage strains S-SM2 and Syn1 with putative homologous contigs recovered from metagenomes provided evidence that gene insertion, deletion and recombination have occurred among, and are likely important for diversification of, natural populations. Identification of putative genetic exchange between cyanophage and non-cyanophage viruses, i.e. Micromonas virus and Pelagibacter phage, supports hypotheses related to a significant role for viruses in mediating transfer of genetic material between taxonomically diverse organisms with overlapping ecological niches.
C1 [Ma, Yingfei; Palenik, Brian] Univ Calif San Diego, Scripps Inst Oceanog, Div Marine Biol Res, La Jolla, CA 92093 USA.
   [Allen, Lisa Zeigler] J Craig Venter Inst, Microbial & Environm Genom Dept, San Diego, CA USA.
RP Palenik, B (corresponding author), Univ Calif San Diego, Scripps Inst Oceanog, Div Marine Biol Res, La Jolla, CA 92093 USA.
EM bpalenik@ucsd.edu
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NR 68
TC 16
Z9 19
PD DEC
PY 2014
VL 6
IS 6
BP 583
EP 594
DI 10.1111/1758-2229.12160
UT WOS:000345702700006
DA 2025-07-30
ER

PT J
AU De Corte, D
   Sintes, E
   Yokokawa, T
   Herndl, GJ
AF De Corte, Daniele
   Sintes, Eva
   Yokokawa, Taichi
   Herndl, Gerhard J.
TI Comparison between MICRO-CARD-FISH and 16S rRNA gene clone libraries to
   assess the active versus total bacterial community in the coastal Arctic
SO ENVIRONMENTAL MICROBIOLOGY REPORTS
DT Article
AB We collected surface- and deep-water samples (maximum depth 300m) during the springsummer transition in the coastal Arctic along a transect in the Kongsfjorden (Ny-angstrom lesund, Spitsbergen, Norway) to determine the structure of the active versus total marine bacterioplankton community using different approaches. Catalysed reporter depositionfluorescence in situ hybridization combined with microautoradiography (MICROCARDFISH) was used to determine the abundance and activity of different bacterial groups. The bacterial communities were dominated by members of Alphaproteobacteria followed by Bacteroidetes, whereas Gammaproteobacteria were present at low abundance but exhibited a high percentage of active cells taking up leucine. The clone libraries of 16S rRNA genes (16S rDNA) and 16S rRNA from two different depths were used to decipher the bacterial community structure. Independently of the type of clone libraries analysed (16S rDNA- or 16S rRNA-based), four major and four minor taxonomic groups were detected. The bacterioplankton community was mainly dominated at both the DNA and the RNA levels by Alphaproteobacteria followed by Gammaproteobacteria. The Rhodobacteriaceae were the most abundant members of the Alphaproteobacteria in both DNA and RNA clone libraries, followed by the SAR11 clade, which was only detectable at the 16S rDNA level. Moreover, there was a general agreement between the results obtained with both techniques, although some specific phylogenetic groups, such as SAR11 and Roseobacter, deviated substantially from this relation. These discrepancies are most likely linked to different physiological states among members of the bacterioplankton community. Combined, MICROCARDFISH and DNA and RNA clone libraries, however, allowed for accurately quantifying different bacterial groups and their activity as well as a detailed phylogenetic insight into the fractions of present versus metabolically active bacterial groups.
C1 [De Corte, Daniele; Sintes, Eva; Yokokawa, Taichi; Herndl, Gerhard J.] Royal Netherlands Inst Sea Res NIOZ, Dept Biol Oceanog, NL-1790 AB Den Burg, Netherlands.
   [De Corte, Daniele] Univ Groningen, Ctr Ecol & Evolutionary Studies, NL-9700 CC Groningen, Netherlands.
   [Herndl, Gerhard J.] Univ Vienna, Dept Marine Biol, Fac Ctr Ecol, A-1090 Vienna, Austria.
RP Herndl, GJ (corresponding author), Royal Netherlands Inst Sea Res NIOZ, Dept Biol Oceanog, POB 59, NL-1790 AB Den Burg, Netherlands.
EM gerhard.herndl@univie.ac.at
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NR 41
TC 23
Z9 25
PD APR
PY 2013
VL 5
IS 2
BP 272
EP 281
DI 10.1111/1758-2229.12013
UT WOS:000315851200010
DA 2025-07-30
ER

PT J
AU Shilova, IN
   Robidart, JC
   DeLong, EF
   Zehr, JP
AF Shilova, Irina N.
   Robidart, Julie C.
   DeLong, Edward F.
   Zehr, Jonathan P.
TI Genetic Diversity Affects the Daily Transcriptional Oscillations of
   Marine Microbial Populations
SO PLOS ONE
DT Article
AB Marine microbial communities are genetically diverse but have robust synchronized daily transcriptional patterns at the genus level that are similar across a wide variety of oceanic regions. We developed a microarray-inspired gene-centric approach to resolve transcription of closely-related but distinct strains/ecotypes in high-throughput sequence data. Applying this approach to the existing metatranscriptomics datasets collected from two different oceanic regions, we found unique and variable patterns of transcription by individual taxa within the abundant picocyanobacteria Prochlorococcus and Synechococcus, the alpha Proteobacterium Pelagibacter and the eukaryotic picophytoplankton Ostreococcus. The results demonstrate that marine microbial taxa respond differentially to variability in space and time in the ocean. These intra-genus individual transcriptional patterns underlie whole microbial community responses, and the approach developed here facilitates deeper insights into microbial population dynamics.
C1 [Shilova, Irina N.; Robidart, Julie C.; Zehr, Jonathan P.] Univ Calif Santa Cruz, Dept Ocean Sci, Santa Cruz, CA 95064 USA.
   [DeLong, Edward F.] Univ Hawaii Manoa, Sch Ocean & Earth Sci & Technol, Honolulu, HI USA.
RP Zehr, JP (corresponding author), Univ Calif Santa Cruz, Dept Ocean Sci, Santa Cruz, CA 95064 USA.
EM zehrj@ucsc.edu
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NR 53
TC 7
Z9 7
PD JAN 11
PY 2016
VL 11
IS 1
AR e0146706
DI 10.1371/journal.pone.0146706
UT WOS:000367888100133
DA 2025-07-30
ER

PT J
AU Zhou, J
   Song, X
   Zhang, CY
   Chen, GF
   Lao, YM
   Jin, H
   Cai, ZH
AF Zhou, Jin
   Song, Xiao
   Zhang, Chun-Yun
   Chen, Guo-Fu
   Lao, Yong-Min
   Jin, Hui
   Cai, Zhong-Hua
TI Distribution Patterns of Microbial Community Structure Along a 7000-Mile
   Latitudinal Transect from the Mediterranean Sea Across the Atlantic
   Ocean to the Brazilian Coastal Sea
SO MICROBIAL ECOLOGY
DT Article
AB A central goal in marine microecology is to understand the ecological factors shaping spatiotemporal microbial patterns and the underlying processes. We hypothesized that abiotic and/or biotic interactions are probably more important for explaining the distribution patterns of marine bacterioplankton than environmental filtering. In this study, surface seawater samples were collected about 7000 miles from the Mediterranean Sea, transecting the North Atlantic Ocean, to the Brazilian marginal sea. In bacterial biosphere, SAR11, SAR86, Rhodobacteraceae, and Rhodospiriaceae were predominant in the Mediterranean Sea; Prochlorococcus was more frequent in Atlantic Ocean: whereas in the Brazilian coastal sea, the main bacterial members were Synechococcus and SAR11. With respect to archaea, Eloyarchaeota were predominant in the Atlantic Ocean and Thaumarchaeota in the Mediterranean Sea. With respect to the eukaryotes, Syndiniales, Spumellaria, Ciyomonadida, and Chlorodendrales were predominant in the open ocean, while diatoms and microzooplankton were dominant in the coastal sea. Distinct clusters of prokaryotes and eukaryotes displayed clear spatial heterogeneity. Among the environmental parameters measured, temperature and salinity were key factors controlling bacterial and archaeal community structure, respectively, whereas N/P/Si contributed to eukaryotic variation. The relative contribution of environmental parameters to the microbial distribution pattern was 45.2%. Interaction analysis showed that Gammaproteobacteria, Alphaproteobacteria, and 1.7avobacteriia were the keystone taxa within the positive-correlation network, while Thermoplasmata was the main contributor in the negativecorrelation network. Our study demonstrated that microbial communities are co-governed by environmental filtering and biotic interactions, which are the main deterministic driving factors modulating the spatiotemporal patterns of marine plankton synergistically at the regional or global levels.
C1 [Zhou, Jin; Lao, Yong-Min; Jin, Hui; Cai, Zhong-Hua] Shenzhen Univ Town, Tsinghua Univ, Grad Sch Shenzhen, Shenzhen Publ Platform Screening & Applicat Marin, Room 905,Marine Bldg, Shenzhen 518055, Guangdong, Peoples R China.
   [Song, Xiao] Tsinghua Univ, Dept Life Sci, Beijing, Peoples R China.
   [Zhang, Chun-Yun; Chen, Guo-Fu] Harbin Inst Technol, Sch Marine Sci & Technol, Weihai, Shangdong, Peoples R China.
RP Cai, ZH (corresponding author), Shenzhen Univ Town, Tsinghua Univ, Grad Sch Shenzhen, Shenzhen Publ Platform Screening & Applicat Marin, Room 905,Marine Bldg, Shenzhen 518055, Guangdong, Peoples R China.; Chen, GF (corresponding author), Harbin Inst Technol, Sch Marine Sci & Technol, Weihai, Shangdong, Peoples R China.
EM chenguofu@hitch.edu.cn; caizh@sz.tsinghua.edu.cn
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NR 108
TC 34
Z9 39
PD OCT
PY 2018
VL 76
IS 3
BP 592
EP 609
DI 10.1007/s00248-018-1150-z
UT WOS:000443567600004
DA 2025-07-30
ER

PT J
AU González, JM
   Simó, R
   Massana, R
   Covert, JS
   Casamayor, EO
   Pedrós-Alió, C
   Moran, MA
AF González, JM
   Simó, R
   Massana, R
   Covert, JS
   Casamayor, EO
   Pedrós-Alió, C
   Moran, MA
TI Bacterial community structure associated with a
   dimethylsulfoniopropionate-producing North Atlantic algal bloom
SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB The bacteria associated with oceanic algal blooms are acknowledged to play important roles in carbon, nitrogen, and sulfur cycling, yet little information is available on their identities or phylogenetic affiliations. Three culture-independent methods were used to characterize bacteria from a dimethylsulfoniopropionate (DMSP)-producing algal bloom in the North Atlantic, Group-specific 165 rRNA-targeted oligonucleotides, 16S ribosomal DNA (rDNA) clone libraries, and terminal restriction fragment length polymorphism analysis all indicated that the marine Roseobacter lineage was numerically important in the heterotrophic bacterial community, averaging >20% of the 16S rDNA sampled. Two other groups of heterotrophic bacteria, the SAR86 and SAR11 clades, were also shown by the three 16S rRNA-based methods to be abundant in the bloom community. In surface waters, the Roseobacter, SAR86, and SAR11 lineages together accounted for over 50% of the bacterial rDNA and showed little spatial variability in abundance despite variations in the dominant algal species. Depth profiles indicated that Roseobacter phylotype abundance decreased with depth and was positively correlated with chlorophyll a, DMSP, and total organic sulfur (dimethyl sulfide plus DMSP plus dimethyl sulfoxide) concentrations. Based on these data and previous physiological studies of cultured Roseobacter strains, we hypothesize that this lineage plays a role in cycling organic sulfur compounds produced within the bloom. Three other abundant bacterial phylotypes (representing a cyanobacterium and two members of the or Proteobacteria) were primarily associated with chlorophyll-rich surface waters of the bloom Ill to 50 m), while two others (representing Cytophagales and delta Proteobacteria) were primarily found in deeper waters (200 to 500 m).
C1 Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
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RP Moran, MA (corresponding author), Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
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NR 49
TC 368
Z9 417
PD OCT
PY 2000
VL 66
IS 10
BP 4237
EP 4246
DI 10.1128/AEM.66.10.4237-4246.2000
UT WOS:000089649700010
DA 2025-07-30
ER

PT J
AU López-Pérez, M
   Haro-Moreno, JM
   Iranzo, J
   Rodriguez-Valera, F
AF Lopez-Perez, Mario
   Haro-Moreno, Jose M.
   Iranzo, Jaime
   Rodriguez-Valera, Francisco
TI Genomes of the "Candidatus Actinomarinales" Order: Highly
   Streamlined Marine Epipelagic Actinobacteria
SO MSYSTEMS
DT Article
AB "Candidatus Actinomarinales" was defined as a subclass of exclusively marine Actinobacteria with small cells and genomes. We have collected all the available genomes in databases to assess the diversity included in this group and analyzed it by comparative genomics. We have found the equivalent of five genera and 18 genomospecies. They have genome reduction parameters equal to those of freshwater actinobacterial "Candidatus Nanopelagicales" or marine alphaproteobacterial Pelagibacterales. Genome recruitment shows that they are found only in the photic zone and mainly in surface waters, with only one genus that is found preferentially at or below the deep chlorophyll maximum. "Ca. Actinomarinales" show a highly conserved core genome (80% of the gene families conserved for the whole order) with a saturation of genomic diversity of the flexible genome at the genomospecies level. We found only a flexible genomic island preserved throughout the order; it is related to the sugar decoration of the envelope and uses several tRNAs as hot spots to increase its genomic diversity. Populations had a discrete level of sequence diversity similar to other marine microbes but drastically different from the much higher levels found for Pelagibacterales. Genomic analysis suggests that they are all aerobic photoheterotrophs with one type 1 rhodopsin and a heliorhodopsin. Like other actinobacteria, they possess the F420 coenzyme biosynthesis pathway, and its lower reduction potential could provide access to an increased range of redox chemical transformations. Last, sequence analysis revealed the first "Ca. Actinomarinales" phages, including a prophage, with metaviromic islands related to sialic acid cleavage.
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C1 [Lopez-Perez, Mario; Haro-Moreno, Jose M.; Rodriguez-Valera, Francisco] Univ Miguel Hernandez, Div Microbiol, Evolutionary Genom Grp, Alicante, Spain.
   [Iranzo, Jaime] Univ Politecn Madrid UPM, Ctr Biotecnol & Genom Plantas, Inst Nacl Invest & Tecnol Agr & Alimentaria INIA, Madrid, Spain.
   [Iranzo, Jaime] Univ Zaragoza, Inst Biocomputat & Phys Complex Syst BIFI, Zaragoza, Spain.
   [Rodriguez-Valera, Francisco] Moscow Inst Phys & Technol, Res Ctr Mol Mech Aging & Agerelated Dis, Dolgoprudnyi, Russia.
RP Rodriguez-Valera, F (corresponding author), Univ Miguel Hernandez, Div Microbiol, Evolutionary Genom Grp, Alicante, Spain.; Rodriguez-Valera, F (corresponding author), Moscow Inst Phys & Technol, Res Ctr Mol Mech Aging & Agerelated Dis, Dolgoprudnyi, Russia.
EM frvalera@umh.es
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TC 40
Z9 42
PD NOV-DEC
PY 2020
VL 5
IS 6
AR e01041-20
DI 10.1128/mSystems.01041-20
UT WOS:000630974900022
DA 2025-07-30
ER

PT J
AU Tamayo-Leiva, J
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   Arroyo, JI
   Masotti, I
   Díez, B
AF Tamayo-Leiva, Javier
   Cifuentes-Anticevic, Jeronimo
   Aparicio-Rizzo, Pilar
   Arroyo, Jose Ignacio
   Masotti, Italo
   Diez, Beatriz
TI Influence of Estuarine Water on the Microbial Community Structure of
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SO FRONTIERS IN MARINE SCIENCE
DT Article
AB Fjords are sensitive areas affected by climate change and can act as a natural laboratory to study microbial ecological processes. The Chilean Patagonian fjords (41-56 degrees S), belonging to the Subantarctic ecosystem (46-60 degrees S), make up one of the world's largest fjord systems. In this region, Estuarine Water (EW) strongly influences oceanographic conditions, generating sharp gradients of oxygen, salinity and nutrients, the effects of which on the microbial community structure are poorly understood. During the spring of 2017 we studied the ecological patterns (dispersal and oceanographic factors) underlying the microbial community distribution in a linear span of 450 km along the estuarine-influenced Chilean Patagonian fjords. Our results show that widespread microbial dispersion existed along the fjords where bacterioplankton exhibited dependence on the eukaryotic phytoplankton community composition. This dependence was particularly observed under the low chlorophyll-a conditions of the Baker Channel area, in which a significant relationship was revealed between SAR11 Clade III and the eukaryotic families Pyrenomonadaceae (Cryptophyte) and Coccomyxaceae (Chlorophyta). Furthermore, dissolved oxygen and salinity were revealed as the main drivers influencing the surface marine microbial communities in these fjords. A strong salinity gradient resulted in the segregation of the Baker Channel prokaryotic communities from the rest of the Patagonian fjords. Likewise, Microbacteriaceae, Burkholderiaceae and SAR11 Clade III, commonly found in freshwater, were strongly associated with EW conditions in these fjords. The direct effect of EW on the microbial community structure and diversity of the fjords exemplifies the significance that climate change and, in particular, deglaciation have on this marine region and its productivity.
C1 [Tamayo-Leiva, Javier; Cifuentes-Anticevic, Jeronimo; Arroyo, Jose Ignacio; Diez, Beatriz] Pontificia Univ Catolica Chile, Fac Biol Sci, Dept Mol Genet & Microbiol, Santiago, Chile.
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   [Masotti, Italo] Univ Valparaiso, Ctr Observ Marino Estudios Riesgos Ambiente Coste, Vina Del Mar, Chile.
   [Diez, Beatriz] Ctr Genome Regulat CRG, Santiago, Chile.
RP Díez, B (corresponding author), Pontificia Univ Catolica Chile, Fac Biol Sci, Dept Mol Genet & Microbiol, Santiago, Chile.; Díez, B (corresponding author), Univ Chile, Ctr Climate & Resilience Res CR2, Santiago, Chile.; Díez, B (corresponding author), Ctr Genome Regulat CRG, Santiago, Chile.
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NR 87
TC 8
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PD JUL 23
PY 2021
VL 8
AR 611981
DI 10.3389/fmars.2021.611981
UT WOS:000684305400001
DA 2025-07-30
ER

PT J
AU Apprill, A
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   Rappe, MS
AF Apprill, Amy
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   Rappe, Michael S.
TI Specificity of Associations between Bacteria and the Coral
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Relationships between corals and specific bacterial associates are thought to play an important role in coral health. In this study, the specificity of bacteria associating with the coral Pocillopora meandrina was investigated by exposing coral embryos to various strains of cultured marine bacteria, sterile seawater, or raw seawater and examining the identity, density, and location of incorporated cells. The isolates utilized in this experiment included members of the Roseobacter and SAR11 clades of the Alpha-proteobacteria, a Pseudoalteromonas species of the Gammaproteobacteria, and a Synechococcus species of the Cyanobacteria phylum. Based on terminal restriction fragment length polymorphism analysis of small-subunit rRNA genes, similarities in bacterial communities associated with 170-h-old planulae were observed regardless of treatment, suggesting that bacteria may have been externally associated from the outset of the experiment. Microscopic examination of P. meandrina planulae by fluorescence in situ hybridization with bacterial and Roseobacter clade-specific oligonucleotide probes revealed differences in the densities and locations of planulae-associated cells. Planulae exposed to either raw seawater or strains of Pseudoalteromonas and Roseobacter harbored the highest densities of internally associated cells, of which 20 to 100% belonged to the Roseobacter clade. Planulae exposed to sterile seawater or strains of the SAR11 clade and Synechococcus did not show evidence of prominent bacterial associations. Additional analysis of the raw-seawater-exposed planulae via electron microscopy confirmed the presence of internally associated prokaryotic cells, as well as virus-like particles. These results suggest that the availability of specific microorganisms may be an important factor in the establishment of coral-bacterial relationships.
C1 [Apprill, Amy; Rappe, Michael S.] Univ Hawaii, SOEST, Hawaii Inst Marine Biol, Kaneohe, HI USA.
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RP Rappe, MS (corresponding author), Univ Hawaii, SOEST, Hawaii Inst Marine Biol, Kaneohe, HI USA.
EM rappe@hawaii.edu
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NR 63
TC 50
Z9 56
PD OCT
PY 2012
VL 78
IS 20
BP 7467
EP 7475
DI 10.1128/AEM.01232-12
UT WOS:000309328700034
DA 2025-07-30
ER

PT J
AU Fortunato, CS
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   Needoba, JA
   Peterson, TD
   Crump, BC
AF Fortunato, Caroline S.
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   Needoba, Joseph A.
   Peterson, Tawnya D.
   Crump, Byron C.
TI Determining indicator taxa across spatial and seasonal gradients in the
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SO ISME JOURNAL
DT Article
AB Bacterioplankton communities are deeply diverse and highly variable across space and time, but several recent studies demonstrate repeatable and predictable patterns in this diversity. We expanded on previous studies by determining patterns of variability in both individual taxa and bacterial communities across coastal environmental gradients. We surveyed bacterioplankton diversity across the Columbia River coastal margin, USA, using amplicon pyrosequencing of 16S rRNA genes from 596 water samples collected from 2007 to 2010. Our results showed seasonal shifts and annual reassembly of bacterioplankton communities in the freshwater-influenced Columbia River, estuary, and plume, and identified indicator taxa, including species from freshwater SAR11, Oceanospirillales, and Flavobacteria groups, that characterize the changing seasonal conditions in these environments. In the river and estuary, Actinobacteria and Betaproteobacteria indicator taxa correlated strongly with seasonal fluctuations in particulate organic carbon (rho = -0.664) and residence time (rho=0.512), respectively. In contrast, seasonal change in communities was not detected in the coastal ocean and varied more with the spatial variability of environmental factors including temperature and dissolved oxygen. Indicator taxa of coastal ocean environments included SAR406 and SUP05 taxa from the deep ocean, and Prochlorococcus and SAR11 taxa from the upper water column. We found that in the Columbia River coastal margin, freshwater-influenced environments were consistent and predictable, whereas coastal ocean community variability was difficult to interpret due to complex physical conditions. This study moves beyond beta-diversity patterns to focus on the occurrence of specific taxa and lends insight into the potential ecological roles these taxa have in coastal ocean environments.
C1 [Fortunato, Caroline S.; Crump, Byron C.] Univ Maryland, Ctr Environm Sci, Horn Point Lab, Cambridge, MD USA.
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RP Fortunato, CS (corresponding author), Josephine Bay Paul Ctr, Marine Biol Lab, Woods Hole, MA 02543 USA.
EM cfortunato@mbl.edu
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TC 128
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VL 7
IS 10
BP 1899
EP 1911
DI 10.1038/ismej.2013.79
UT WOS:000324869400003
DA 2025-07-30
ER

PT J
AU Brakstad, OG
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AF Brakstad, Odd G.
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DT Article
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EM odd.brakstad@sintef.no
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BP 989
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DA 2025-07-30
ER

PT J
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AF Yeh, Yi-Chun
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DT Article
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RP Fuhrman, JA (corresponding author), Univ Southern Calif, Dept Biol Sci, Los Angeles, CA 90089 USA.
EM fuhrman@usc.edu
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NR 89
TC 47
Z9 49
PD APR 13
PY 2022
VL 2
IS 1
AR 36
DI 10.1038/s43705-022-00121-8
UT WOS:001105679600001
DA 2025-07-30
ER

PT J
AU Landa, M
   Blain, S
   Harmand, J
   Monchy, S
   Rapaport, A
   Obernosterer, I
AF Landa, Marine
   Blain, Stephane
   Harmand, Jerome
   Monchy, Sebastien
   Rapaport, Alain
   Obernosterer, Ingrid
TI Major changes in the composition of a Southern Ocean bacterial community
   in response to diatom-derived dissolved organic matter
SO FEMS MICROBIOLOGY ECOLOGY
DT Article
AB In the Southern Ocean, natural iron fertilization in the wake of islands leads to annually occurring spring phytoplankton blooms associated with enhanced heterotrophic activity through the release of labile dissolved organic matter (DOM). The aim of this study was to investigate experimentally how diatom-derived DOM affects the composition of Southern Ocean winter water bacterial communities and to identify the most responsive taxa. A bacterial community collected in the naturally iron-fertilized region off Kerguelen Island (KEOPS2 October-November 2011) was grown onboard in continuous cultures, on winter water alone or amended with diatom-derived DOM supplied at identical DOC concentrations. 454 sequencing of 16S amplicons revealed that the two DOM sources sustained strikingly different bacterial communities, with higher relative abundances of Sulfitobacter, Colwellia and Methylophaga operational taxonomic units (OTUs) and lower relative abundances of Polaribacter, Marinobacter, NAC11-7 and SAR11 OTUs in diatom-DOM compared to winter water conditions. Using a modeling approach, we obtained growth rates for phylogenetically diverse taxa varying between 0.12 and 0.49 d(-1) under carbon-limited conditions. Our results identify diatom DOM as a key factor shaping Southern Ocean winter water bacterial communities and suggest a role for niche partitioning and microbial interactions in organic matter utilization.
C1 [Landa, Marine; Blain, Stephane; Obernosterer, Ingrid] UPMC Univ Paris 06, Sorbonne Univ, CNRS, Lab Oceanog Microbienne LOMIC,Observ Oceanol, F-66650 Banyuls Sur Mer, France.
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   [Rapaport, Alain] Univ Montpellier, INRA, MISTEA, Montpellier SupAgro, 2 Pl Viala, F-34060 Montpellier, France.
   [Landa, Marine] Univ Calif Santa Cruz, Ocean Sci Dept, Santa Cruz, CA 95064 USA.
RP Landa, M (corresponding author), 1156 High St, Santa Cruz, CA 95064 USA.; Landa, M (corresponding author), Univ Calif Santa Cruz, Ocean Sci Dept, Santa Cruz, CA 95064 USA.
EM mlandabe@ucsc.edu
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NR 117
TC 25
Z9 27
PD APR
PY 2018
VL 94
IS 4
AR fiy034
DI 10.1093/femsec/fiy034
UT WOS:000429481200014
DA 2025-07-30
ER

PT J
AU Kaur, C
   Vishnoi, A
   Ariyadasa, TU
   Bhattacharya, A
   Singla-Pareek, SL
   Sopory, SK
AF Kaur, Charanpreet
   Vishnoi, Anchal
   Ariyadasa, Thilini Udayangani
   Bhattacharya, Alok
   Singla-Pareek, Sneh Lata
   Sopory, Sudhir Kumar
TI Episodes of horizontal gene-transfer and gene-fusion led to co-existence
   of different metal-ion specific glyoxalase I
SO SCIENTIFIC REPORTS
DT Article
AB Glyoxalase pathway plays an important role in stress adaptation and many clinical disorders. The first enzyme of this pathway, glyoxalase I (GlxI), uses methylglyoxal as a substrate and requires either Ni(II)/Co(II) or Zn(II) for activity. Here we have investigated the origin of different metal ion specificities of GlxI and subsequent pattern of inheritance during evolution. Our results suggest a primitive origin of single-domain Ni dependent GlxI [Ni-GlxI]. This subsequently evolved into Zn activated GlxI [Zn-GlxI] in deltaproteobacteria. However, origin of eukaryotic Zn-GlxI is different and can be traced to GlxI from Candidatus pelagibacter and Sphingomonas. In eukaryotes GlxI has evolved as two-domain protein but the corresponding Zn form is lost in plants/higher eukaryotes. In plants gene expansion has given rise to multiple two-domain Ni-GlxI which are differentially regulated under abiotic stress conditions. Our results suggest that different forms of GlxI have evolved to help plants adapt to stress.
C1 [Kaur, Charanpreet; Ariyadasa, Thilini Udayangani; Singla-Pareek, Sneh Lata; Sopory, Sudhir Kumar] Int Ctr Genet Engn & Biotechnol, New Delhi 110067, India.
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   [Vishnoi, Anchal; Bhattacharya, Alok] Jawaharlal Nehru Univ, Sch Life Sci, New Delhi 110067, India.
RP Kaur, C (corresponding author), Int Ctr Genet Engn & Biotechnol, Aruna Asaf Ali Marg, New Delhi 110067, India.
EM charanpreet06@gmail.com; anchalv@gmail.com
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NR 49
TC 44
Z9 48
PD NOV 13
PY 2013
VL 3
AR 3076
DI 10.1038/srep03076
UT WOS:000327019600001
DA 2025-07-30
ER

PT J
AU Kim, KE
   Joo, HM
   Kim, YJ
   Kang, D
   Lee, TK
   Jung, SW
   Ha, SY
AF Kim, Kang Eun
   Joo, Hyoung Min
   Kim, Yu Jin
   Kang, Donhyug
   Lee, Taek-Kyun
   Jung, Seung Won
   Ha, Sun-Yong
TI Ecological Interaction between Bacteriophages and Bacteria in Sub-Arctic
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SO MICROORGANISMS
DT Article
AB Marine virus diversity and their relationships with their hosts in the marine environment remain unclear. This study investigated the co-occurrence of marine DNA bacteriophages (phages) and bacteria in the sub-Arctic area of Kongsfjorden Bay in Svalbard (Norway) in April and June 2018 using metagenomics tools. Of the marine viruses identified, 48-81% were bacteriophages of the families Myoviridae, Siphoviridae, and Podoviridae. Puniceispirillum phage HMO-2011 was dominant (7.61%) in April, and Puniceispirillum phage HMO-2011 (3.32%) and Pelagibacter phage HTVC008M (3.28%) were dominant in June. Gammaproteobacteria (58%), including Eionea flava (14.3%) and Pseudomonas sabulinigri (12.2%), were dominant in April, whereas Alphaproteobacteria (87%), including Sulfitobacter profundi (51.5%) and Loktanella acticola (32.4%), were dominant in June. The alpha diversity of the bacteriophages and bacterial communities exhibited opposite patterns. The diversity of the bacterial community was higher in April and lower in June. Changes in water temperature and light can influence the relationship between bacteria and bacteriophages.
C1 [Kim, Kang Eun; Kim, Yu Jin; Jung, Seung Won] Korea Inst Ocean Sci & Technol, Lib Marine Samples, Geoje 53201, South Korea.
   [Kim, Kang Eun; Kim, Yu Jin; Lee, Taek-Kyun; Jung, Seung Won] Univ Sci & Technol, Dept Ocean Sci, Daejeon 34113, South Korea.
   [Joo, Hyoung Min] Korea Polar Res Inst, Unit Next Generat IBRV Bldg Program, Incheon 21990, South Korea.
   [Kang, Donhyug] Korea Inst Ocean Sci & Technol, Marine Domain & Secur Res Dept, Pusan 49111, South Korea.
   [Lee, Taek-Kyun] Korea Inst Ocean Sci & Technol, Risk Assessment Res Ctr, Geoje 53201, South Korea.
   [Ha, Sun-Yong] Korea Polar Res Inst, Div Polar Ocean Sci, Incheon 21990, South Korea.
RP Jung, SW (corresponding author), Korea Inst Ocean Sci & Technol, Lib Marine Samples, Geoje 53201, South Korea.; Jung, SW (corresponding author), Univ Sci & Technol, Dept Ocean Sci, Daejeon 34113, South Korea.; Ha, SY (corresponding author), Korea Polar Res Inst, Div Polar Ocean Sci, Incheon 21990, South Korea.
EM rkddmssl@kiost.ac.kr; hmjoo77@kopri.re.kr; rladbwls06069@kiost.ac.kr;
   dhkang@kiost.ac.kr; tklee@kiost.ac.kr; diatoms@kiost.ac.kr;
   syha@kopri.re.kr
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NR 68
TC 2
Z9 2
PD FEB
PY 2024
VL 12
IS 2
AR 276
DI 10.3390/microorganisms12020276
UT WOS:001172354300001
DA 2025-07-30
ER

PT J
AU Nekrouf, NA
   Maestre-Carballa, L
   Lluesma-Gomez, M
   Martinez-Hernandez, F
   Martinez-Garcia, M
AF Nekrouf, Nadefa Adda
   Maestre-Carballa, Lucia
   Lluesma-Gomez, Monica
   Martinez-Hernandez, Francisco
   Martinez-Garcia, Manuel
TI Annual dynamics and metagenomics of marine vesicles: One more layer of
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SO LIMNOLOGY AND OCEANOGRAPHY
DT Article
AB Despite the role of extracellular vesicles (EVs) in genetic and biogeochemical exchange in the ocean, there is a notable dearth of studies delving into the seasonal annual dynamics of EVs in uncultured microbial communities. Here, quantitative data from the oligotrophic Mediterranean Sea revealed that EVs mL-1 ranged from 104 to 106 throughout the year and correlated with microbial abundances (correlation coefficient = 0.67). The ratio of EVs per cell ranged from 1 to 4. Vesicle metagenomics identified copiotrophic and oligotrophic prokaryotic species, such as Flavobacterium and Pelagibacter, putatively dominating the production of EVs containing DNA in the annual dataset. Micromonas spp. and others Mamiellophyceae emerged as the dominant eukaryotic producers of EVs containing DNA. Genes belonging to viruses were consistently identified in purified vesicles. The relative proportion of viral contigs found in the vesicle fraction (2.4-30.4%) suggested that the release of viral genomes in EVs could be more common than previously thought.
C1 [Nekrouf, Nadefa Adda; Maestre-Carballa, Lucia; Lluesma-Gomez, Monica; Martinez-Hernandez, Francisco; Martinez-Garcia, Manuel] Univ Alicante, Dept Physiol Genet & Microbiol, Alicante, Spain.
   [Nekrouf, Nadefa Adda; Maestre-Carballa, Lucia; Lluesma-Gomez, Monica; Martinez-Hernandez, Francisco; Martinez-Garcia, Manuel] Univ Alicante, Multidisciplinary Inst Environm Studies IMEM, Alicante, Spain.
RP Martinez-Garcia, M (corresponding author), Univ Alicante, Dept Physiol Genet & Microbiol, Alicante, Spain.; Martinez-Garcia, M (corresponding author), Univ Alicante, Multidisciplinary Inst Environm Studies IMEM, Alicante, Spain.
EM m.martinez@ua.es
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NR 59
TC 0
Z9 0
PD MAY
PY 2025
VL 70
IS 5
BP 1315
EP 1328
DI 10.1002/lno.70031
EA MAR 2025
UT WOS:001446774300001
DA 2025-07-30
ER

PT J
AU Coutinho, FH
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   Gregoracci, GB
   Thompson, CC
   Edwards, RA
   Brussaard, CPD
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   Thompson, FL
AF Coutinho, Felipe H.
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   Gregoracci, Gustavo B.
   Thompson, Cristiane C.
   Edwards, Robert A.
   Brussaard, Corina P. D.
   Dutilh, Bas E.
   Thompson, Fabiano L.
TI Marine viruses discovered via metagenomics shed light on viral
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SO NATURE COMMUNICATIONS
DT Article
AB Marine viruses are key drivers of host diversity, population dynamics and biogeochemical cycling and contribute to the daily flux of billions of tons of organic matter. Despite recent advancements in metagenomics, much of their biodiversity remains uncharacterized. Here we report a data set of 27,346 marine virome contigs that includes 44 complete genomes. These outnumber all currently known phage genomes in marine habitats and include members of previously uncharacterized lineages. We designed a new method for host prediction based on co-occurrence associations that reveals these viruses infect dominant members of the marine microbiome such as Prochlorococcus and Pelagibacter. A negative association between host abundance and the virus-to-host ratio supports the recently proposed Piggyback-the-Winner model of reduced phage lysis at higher host densities. An analysis of the abundance patterns of viruses throughout the oceans revealed how marine viral communities adapt to various seasonal, temperature and photic regimes according to targeted hosts and the diversity of auxiliary metabolic genes.
C1 [Coutinho, Felipe H.; Silveira, Cynthia B.; Thompson, Cristiane C.; Dutilh, Bas E.; Thompson, Fabiano L.] Univ Fed Rio de Janeiro, IB, BR-21944970 Rio de Janeiro, Brazil.
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   [Gregoracci, Gustavo B.] Univ Fed Sao Paulo UNIFESP, Dept Ciencias Mar, BR-11070100 Baixada Santista, Brazil.
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   [Brussaard, Corina P. D.] Univ Utrecht, POB 59, NL-1790 AB Den Burg, Netherlands.
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   [Thompson, Fabiano L.] Univ Fed Rio de Janeiro, COPPE, SAGE, BR-21941950 Rio de Janeiro, Brazil.
RP Thompson, FL (corresponding author), Univ Fed Rio de Janeiro, IB, BR-21944970 Rio de Janeiro, Brazil.; Thompson, FL (corresponding author), Univ Fed Rio de Janeiro, COPPE, SAGE, BR-21941950 Rio de Janeiro, Brazil.
EM fabianothompson1@gmail.com
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NR 77
TC 176
Z9 194
PD JUL 5
PY 2017
VL 8
AR 15955
DI 10.1038/ncomms15955
UT WOS:000404780000001
DA 2025-07-30
ER

PT J
AU Chiriac, MC
   Haber, M
   Salcher, MM
AF Chiriac, Maria-Cecilia
   Haber, Markus
   Salcher, Michaela M.
TI Adaptive genetic traits in pelagic freshwater microbes
SO ENVIRONMENTAL MICROBIOLOGY
DT Review
AB Pelagic microbes have adopted distinct strategies to inhabit the pelagial of lakes and oceans and can be broadly categorized in two groups: free-living, specialized oligotrophs and patch-associated generalists or copiotrophs. In this review, we aim to identify genomic traits that enable pelagic freshwater microbes to thrive in their habitat. To do so, we discuss the main genetic differences of pelagic marine and freshwater microbes that are both dominated by specialized oligotrophs and the difference to freshwater sediment microbes, where copiotrophs are more prevalent. We phylogenomically analysed a collection of >7700 metagenome-assembled genomes, classified habitat preferences on different taxonomic levels, and compared the metabolic traits of pelagic freshwater, marine, and freshwater sediment microbes. Metabolic differences are mainly associated with transport functions, environmental information processing, components of the electron transport chain, osmoregulation and the isoelectric point of proteins. Several lineages with known habitat transitions (Nitrososphaeria, SAR11, Methylophilaceae, Synechococcales, Flavobacteriaceae, Planctomycetota) and the underlying mechanisms in this process are discussed in this review. Additionally, the distribution, ecology and genomic make-up of the most abundant freshwater prokaryotes are described in details in separate chapters for Actinobacteriota, Bacteroidota, Burkholderiales, Verrucomicrobiota, Chloroflexota, and 'Ca. Patescibacteria'.
C1 [Chiriac, Maria-Cecilia; Haber, Markus; Salcher, Michaela M.] Biol Ctr CAS, Inst Hydrobiol, Ceske Budejovice, Czech Republic.
   [Salcher, Michaela M.] Biol Ctr CAS, Inst Hydrobiol, NaSadkach 7, Ceske Budejovice 37005, Czech Republic.
RP Salcher, MM (corresponding author), Biol Ctr CAS, Inst Hydrobiol, NaSadkach 7, Ceske Budejovice 37005, Czech Republic.
EM michaelasalcher@gmail.com
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NR 325
TC 28
Z9 30
PD MAR
PY 2023
VL 25
IS 3
BP 606
EP 641
DI 10.1111/1462-2920.16313
EA DEC 2022
UT WOS:000905443900001
DA 2025-07-30
ER

PT J
AU Teira, E
   Martínez-García, S
   Calvo-Diaz, A
   Morán, XAG
AF Teira, Eva
   Martinez-Garcia, Sandra
   Calvo-Diaz, Alejandra
   Moran, Xose Anxelu G.
TI Effects of inorganic and organic nutrient inputs on bacterioplankton
   community composition along a latitudinal transect in the Atlantic Ocean
SO AQUATIC MICROBIAL ECOLOGY
DT Article
AB Bacterioplankton are responsible for a large fraction of respiration and dissolved organic matter (DOM) remineralisation in the ocean; therefore, changes in their taxonomic composition due to changes in nutrient inputs may have important biogeochemical implications. The impact of nutrient loading will depend on the type of input and the initial environmental conditions. We conducted a set of 5 microcosm experiments along a broad latitudinal transect in the Atlantic Ocean (26 degrees N to 29 degrees S) in order to assess the effects of inorganic (nitrate, ammonium, phosphate, silica) and organic (glucose, amino acids) inputs, added separately as well as jointly, on the bacterioplankton community composition at the level of major groups. We followed changes in the relative abundance of important bacterial phylogenetic (Roseobacter spp., SAR11, Gammaproteobacteria, Bacteroidetes) and cytometric (low, high and very high nucleic acid content) groups. We observed that distinct groups responded differently to nutrient additions: SAR11 and Bacteroidetes responded negatively to organic and mixed additions, while Roseobacter spp. and Gammaproteobacteria responded positively. Only the group Roseobacter spp. responded positively to inorganic additions. The abundance of very high nucleic acid content bacteria was low in the control and the inorganic treatment; however, they reached very high numbers in the organic and mixed treatments. There was a clear increasing north to south gradient in the magnitude of response of Gammaproteobacteria to organic inputs (containing carbon and nitrogen), likely related to an increasing north to south gradient in phosphate concentration. The magnitude of response of Gammaproteobacteria explained 89% of the observed variability in the magnitude of bacterial production response, which suggests a strong link between bacterial community composition and carbon cycling in the oligotrophic ocean.
C1 [Teira, Eva; Martinez-Garcia, Sandra] Univ Vigo, Fac Ciencias, Dept Ecol & Biol Anim, Vigo 36310, Spain.
   [Calvo-Diaz, Alejandra; Moran, Xose Anxelu G.] Ctr Oceanog Xixon, Inst Espanol Oceanog, Xixon 33212, Spain.
RP Teira, E (corresponding author), Univ Vigo, Fac Ciencias, Dept Ecol & Biol Anim, Campus Lagoas Marcosende, Vigo 36310, Spain.
EM teira@uvigo.es
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NR 75
TC 25
Z9 26
PY 2010
VL 60
IS 3
BP 299
EP 313
DI 10.3354/ame01435
UT WOS:000280768400008
DA 2025-07-30
ER

PT J
AU Teira, E
   Logares, R
   Gutiérrez-Barral, A
   Ferrera, I
   Varela, MM
   Morán, XAG
   Gasol, JM
AF Teira, Eva
   Logares, Ramiro
   Gutierrez-Barral, Alberto
   Ferrera, Isabel
   Varela, Marta M.
   Moran, Xose Anxelu G.
   Gasol, Josep M.
TI Impact of grazing, resource availability and light on prokaryotic growth
   and diversity in the oligotrophic surface global ocean
SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB The impact of grazing, resource competition and light on prokaryotic growth and taxonomic composition in subtropical and tropical surface waters were studied through 10 microcosm experiments conducted between 30 degrees N and 30 degrees S in the Atlantic, Pacific and Indian oceans. Under natural sunlight conditions, significant changes in taxonomic composition were only observed after the reduction of grazing by sample filtration in combination with a decrease in resource competition by sample dilution. Sunlight exposure significantly reduced prokaryote growth (11 +/- 6%) and community richness (14 +/- 4%) compared to continuous darkness but did not significantly change community composition. The largest growth inhibition after sunlight exposure occurred at locations showing deep mixed layers. The reduction of grazing had an expected and significant positive effect on growth, but caused a significant decrease in community richness (16 +/- 6%), suggesting that the coexistence of many different OTUs is partly promoted by the presence of predators. Dilution of the grazer-free prokaryotic community significantly enhanced growth at the level of community, but consistently and sharply reduced the abundance of Prochlorococcus and SAR11 populations. The decline of these oligotrophic bacterial taxa following an increase in resource availability is consistent with their high specialization for exploiting the limited resources available in the oligotrophic warm ocean.
C1 [Teira, Eva; Gutierrez-Barral, Alberto] Univ Vigo, Dept Ecol & Biol Anim, Vigo, Spain.
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RP Teira, E (corresponding author), Univ Vigo, Dept Ecol & Biol Anim, Vigo, Spain.
EM teira@uvigo.es
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NR 104
TC 24
Z9 25
PD APR
PY 2019
VL 21
IS 4
BP 1482
EP 1496
DI 10.1111/1462-2920.14581
UT WOS:000464373000023
DA 2025-07-30
ER

PT J
AU Bakenhus, I
   Wemheuer, B
   Akyol, P
   Giebel, HA
   Dlugosch, L
   Daniel, R
   Simon, M
AF Bakenhus, Insa
   Wemheuer, Bernd
   Akyol, Pinar
   Giebel, Helge-Ansgar
   Dlugosch, Leon
   Daniel, Rolf
   Simon, Meinhard
TI Distinct relationships between fluorescence in situ hybridization
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SO SYSTEMATIC AND APPLIED MICROBIOLOGY
DT Article
AB Catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) and amplicon sequencing of the total (16S rRNA gene) and potentially active (16S rRNA transcripts), community are the major state of the art approaches for assessing the composition of bacterial communities in marine pelagic and other ecosystems. However, CARD-FISH and amplicon sequencing methods have not yet been directly compared to assess the composition of bacterioplankton communities. Therefore, these approaches were used to study the composition of bacterial communities in two North Sea seawater mesocosm experiments supplemented with diatom-derived organic matter (OM). All approaches revealed Proteobacteria and Bacteroidetes as major components of the bacterioplankton communities. The Roseobacter group and its RCA cluster, as well as Bacteroidetes and Gammaproteobacteria, responded most strongly to OM addition, whereas the SAR11 clade responded in only one of the two mesocosms. A correlation analysis showed that CARD-FISH and amplicon sequencing data of the SAR11 clade and the Roseobacter group, together with its RCA cluster, were highly significantly correlated, whereas Bacteroidetes did not yield any significant correlation and Gammaproteobacteria was only correlated with the potentially active fraction. However, subgroups of these phylogenetic groups, the SAR92 clade, the genera Pseudoalteromonas and Polaribacter, exhibited significant correlations in one of the two mesocosms. Correlations of CARD-FISH with amplicon sequencing data from the total and potentially active fractions of these lineages exhibited distinct differences. The study showed that CARD-FISH and amplicon sequencing data of distinct bacterioplankton groups and especially the phylogenetic lineages at a higher taxonomic level were correlated but reflected different aspects of their growth dynamics. (C) 2019 Elsevier GmbH. All rights reserved.
C1 [Bakenhus, Insa; Giebel, Helge-Ansgar; Dlugosch, Leon; Simon, Meinhard] Carl von Ossietzky Univ Oldenburg, Inst Chem & Biol Marine Environm, Carl von Ossietzky Str 9-11, D-26129 Oldenburg, Germany.
   [Wemheuer, Bernd; Akyol, Pinar; Daniel, Rolf] Georg August Univ Gottingen, Inst Microbiol & Genet, Dept Genom & Appl Microbiol, Grisebachstr 8, D-37077 Gottingen, Germany.
   [Wemheuer, Bernd; Akyol, Pinar; Daniel, Rolf] Georg August Univ Gottingen, Inst Microbiol & Genet, Gottingen Genom Lab, Grisebachstr 8, D-37077 Gottingen, Germany.
RP Simon, M (corresponding author), Carl von Ossietzky Univ Oldenburg, Inst Chem & Biol Marine Environm, Carl von Ossietzky Str 9-11, D-26129 Oldenburg, Germany.
EM m.simon@icbm.de
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NR 74
TC 5
Z9 5
PD SEP
PY 2019
VL 42
IS 5
AR 126000
DI 10.1016/j.syapm.2019.06.005
UT WOS:000484822400006
DA 2025-07-30
ER

PT J
AU Zemskaya, TI
   Cabello-Yeves, PJ
   Pavlova, ON
   Rodriguez-Valera, F
AF Zemskaya, Tamara, I
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   Pavlova, Olga N.
   Rodriguez-Valera, Francisco
TI Microorganisms of Lake Baikal-the deepest and most ancient lake on Earth
SO APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
DT Review
AB Lake Baikal (Russia) is the largest (by volume) and deepest lake on Earth. The lake remains relatively pristine due to the low population density around its basin. Being very distant from any marine water body but having a remarkable number of similarities to oceans (depth, oxygen content, oligotrophy) provides a unique model of pelagic microbiota that is submitted to marine-like conditions minus the salt content of the water. It is also a model of lakes located at high latitudes and submitted to yearly ice cover (from January to April). The analysis by different approaches has indeed provided a view of the microbiota of this lake. It contains novel microbes that are closely related to marine groups not known to be present in freshwater like Chloroflexi or Pelagibacter. The deep water mass contains large communities of chemolithotrophs that use ammonia generated in the photic zone or methane from the sediments.
C1 [Zemskaya, Tamara, I; Pavlova, Olga N.] Russian Acad Sci, Limnol Inst, Siberian Branch, Irkutsk, Russia.
   [Cabello-Yeves, Pedro J.; Rodriguez-Valera, Francisco] Univ Miguel Hernandez, Evolutionary Genom Grp, Dept Prod Vegetal & Microbiol, Alicante, Spain.
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RP Zemskaya, TI (corresponding author), Russian Acad Sci, Limnol Inst, Siberian Branch, Irkutsk, Russia.
EM tzema@lin.irk.ru
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NR 97
TC 14
Z9 16
PD JUL
PY 2020
VL 104
IS 14
BP 6079
EP 6090
DI 10.1007/s00253-020-10660-6
EA MAY 2020
UT WOS:000533813200002
DA 2025-07-30
ER

PT J
AU Sakami, T
   Watanabe, T
   Kakehi, S
   Taniuchi, Y
   Kuwata, A
AF Sakami, Tomoko
   Watanabe, Tsuyoshi
   Kakehi, Shigeho
   Taniuchi, Yukiko
   Kuwata, Akira
TI Spatial variation of bacterial community composition at the expiry of
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SO GENE
DT Article
AB In order to characterize how bacterial communities are propagated over spatial scales in a coastal area, the bacterial community composition was examined along with a transect line set in a bay at an expiry of spring phyto-plankton bloom. Four distinctive bacterial communities were found within the bay by a fingerprinting method of 16S rRNA gene amplicons. The most widely distributed one was distributed in the surface and middle layers at whole area of the bay. The water was characterized by low inorganic nutrients concentration and high bacterial abundance, suggesting that the bacterial community had been developed in the bloom. Pyrosequencing analyses of the gene amplicons indicated that Rhodobacteriaceae and Flavobacteriaceae were abundant in the bacterial community, though the most abundant bacterial taxon was SAR11. The second group was distributed in the bottom water at the coastal side of the bay where considerably high Chl. a concentration was observed, probably because of the sedimentation of phytoplankton bloom. The community diversity was high and Alteromonadaceae, Saprospiraceae, and some families of Actinobacter existed more in this community than the others. The third group was distributed in the deep water near the border with the outside of the bay. The ratio of SAR11 was the highest in this community; besides, Burkholdetianceae and Rhodospilliraceae existed in relatively high abundances. Another bacterial community having intermediate characters was observed in the middle to bottom layers around a central part of the bay where vertical water mixing was observed. These findings suggest that spatially different bacterial communities were formed under the influences of phytoplankton bloom and/or hydrographic events such as oceanic seawater intrusion of the bay. (C) 2015 The Authors. Published by Elsevier B.V.
C1 [Sakami, Tomoko; Watanabe, Tsuyoshi; Kakehi, Shigeho; Kuwata, Akira] Fisheries Res Agcy, Tohoku Natl Fisheries Res Inst, Shiogama, Miyagi 9850001, Japan.
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RP Sakami, T (corresponding author), Fisheries Res Agcy, Tohoku Natl Fisheries Res Inst, 3-27-5 Shinhama, Shiogama, Miyagi 9850001, Japan.
EM sakami@affrc.go.jp
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DA 2025-07-30
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PT J
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SO FRONTIERS IN MICROBIOLOGY
DT Article
AB The winter Arctic Ocean is one of the most unexplored marine environments from a microbiological perspective. Heterotrophic bacteria maintain their activity at a baseline level during the extremely low-energy conditions of the winter, but little is known about the specific phylotypes that have the potential to survive and grow in such harsh environment. In this study, we aimed at identifying actively growing ribotypes in winter Arctic Ocean seawater cultures by experimental incubations with the thymidine analog bromodeoxyuridine (BrdU), followed by immunocapturing, terminal restriction fragment length polymorphism fingerprinting, cloning, and sequencing the 16S rRNA gene. We incubated water collected at different months over the Arctic winter and showed that the actively growing bacterial fraction, taking up BrdU, represented only a subset of the total community. Among the BrdU-labeled bacterial taxa we identified the Flavobacteria Polaribacter, the Alphaproteobacteria SAR11, the Gammaproteobacteria Arctic 96B-16 cluster and, predominately, members of Colwellia spp. Interestingly, Colwellia sequences formed three clusters (93 and 97% pairwise 16S rRNA identity) that contributed in contrasting ways to the active communities in the incubations. Polanbacter, Arctic 96B-16 and one cluster of Colwellia were more abundant in the active community represented by the BrdU-labeled DNA. In contrast, SAR11 and two other Colwellia clusters were underrepresented in the BrdU-labeled community compared to total communities. Despite the limitation of the long incubations needed to label slow growing arctic communities, the BrdU approach revealed the potential for active growth in low-energy conditions in some relevant groups of polar bacteria, including Polaribacter and Arctic 96B-16. Moreover, under similar incubation conditions, the growth of different Colwellia ribotypes varied, suggesting that related clusters of Colwellia may have distinct metabolic features.
C1 [Galand, Pierre E.; Casamayor, Emilio O.] CSIC, Ctr Estudis Avancats Blanes, Biogeodynam & Biodivers Grp, Blanes, Spain.
   [Galand, Pierre E.] Univ Paris 06, F-75252 Paris 05, France.
   [Galand, Pierre E.] Observ Oceanol Banyuls, Lab Ecogeochim Environm Benth, CNRS, UMR 8222, F-66650 Banyuls Sur Mer, France.
   [Alonso-Saez, Laura; Bertilsson, Stefan] Uppsala Univ, Dept Ecol & Genet, Uppsala, Sweden.
   [Alonso-Saez, Laura] Inst Espanol Oceanog, Ctr Oceanog Gijon, Gijon, Spain.
   [Lovejoy, Connie] Univ Laval, Dept Biol, Inst Biol Integrat & Syst, Quebec City, PQ G1K 7P4, Canada.
RP Galand, PE (corresponding author), Observ Oceanol Banyuls, Lab Ecogeochim Environm Benth, Ave Fontaule, F-66650 Banyuls Sur Mer, France.
EM pierre.galand@obs-banyuls.fr
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NR 34
TC 14
Z9 16
PD MAY 20
PY 2013
VL 4
AR 118
DI 10.3389/fmicb.2013.00118
UT WOS:000331118900001
DA 2025-07-30
ER

PT J
AU Ferrera, I
   Gasol, JM
   Sebastián, M
   Hojerová, E
   Koblízek, M
AF Ferrera, Isabel
   Gasol, Josep M.
   Sebastian, Marta
   Hojerova, Eva
   Koblizek, Michal
TI Comparison of Growth Rates of Aerobic Anoxygenic Phototrophic Bacteria
   and Other Bacterioplankton Groups in Coastal Mediterranean Waters
SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Growth is one of the basic attributes of any living organism. Surprisingly, the growth rates of marine bacterioplankton are only poorly known. Current data suggest that marine bacteria grow relatively slowly, having generation times of several days. However, some bacterial groups, such as the aerobic anoxygenic phototrophic (AAP) bacteria, have been shown to grow much faster. Two manipulation experiments, in which grazing, viruses, and resource competition were reduced, were conducted in the coastal Mediterranean Sea (Blanes Bay Microbial Observatory). The growth rates of AAP bacteria and of several important phylogenetic groups (the Bacteroidetes, the alphaproteobacterial groups Roseobacter and SAR11, and the Gammaproteobacteria group and its subgroups the Alteromonadaceae and the NOR5/OM60 clade) were calculated from changes in cell numbers in the manipulation treatments. In addition, we examined the role that top-down (mortality due to grazers and viruses) and bottom-up (resource availability) factors play in determining the growth rates of these groups. Manipulations resulted in an increase of the growth rates of all groups studied, but its extent differed largely among the individual treatments and among the different groups. Interestingly, higher growth rates were found for the AAP bacteria (up to 3.71 day(-1)) and for the Alteromonadaceae (up to 5.44 day(-1)), in spite of the fact that these bacterial groups represented only a very low percentage of the total prokaryotic community. In contrast, the SAR11 clade, which was the most abundant group, was the slower grower in all treatments. Our results show that, in general, the least abundant groups exhibited the highest rates, whereas the most abundant groups were those growing more slowly, indicating that some minor groups, such the AAP bacteria, very likely contribute much more to the recycling of organic matter in the ocean than what their abundances alone would predict.
C1 [Ferrera, Isabel; Gasol, Josep M.; Sebastian, Marta] CSIC, Inst Ciencias Mar, Dept Biol Marina & Oceanog, E-08003 Barcelona, Catalunya, Spain.
   [Hojerova, Eva; Koblizek, Michal] Inst Microbiol CAS, Trebon 37981, Czech Republic.
   [Hojerova, Eva] Univ S Bohemia, Fac Sci, Ceske Budejovice 37005, Czech Republic.
RP Ferrera, I (corresponding author), CSIC, Inst Ciencias Mar, Dept Biol Marina & Oceanog, Pg Maritim de la Barceloneta 37-49, E-08003 Barcelona, Catalunya, Spain.
EM iferrera@icm.csic.es
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NR 46
TC 94
Z9 98
PD NOV
PY 2011
VL 77
IS 21
BP 7451
EP 7458
DI 10.1128/AEM.00208-11
UT WOS:000296568200003
DA 2025-07-30
ER

PT J
AU Biller, SJ
   Coe, A
   Arellano, AA
   Dooley, K
   Silvestri, SM
   Gong, JS
   Yeager, EA
   Becker, JW
   Chisholm, SW
AF Biller, Steven J.
   Coe, Allison
   Arellano, Aldo A.
   Dooley, Keven
   Silvestri, Samantha M.
   Gong, Jacqueline S.
   Yeager, Emily A.
   Becker, Jamie W.
   Chisholm, Sallie W.
TI Environmental and Taxonomic Drivers of Bacterial Extracellular Vesicle
   Production in Marine Ecosystems
SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Bacteria release extracellular vesicles that contain a wide variety of cellular compounds, including lipids, proteins, nucleic acids, and small molecules, into their surrounding environment. These structures are found in diverse microbial habitats, including the oceans, where their distributions vary throughout the water column and likely affect their functional impacts within microbial ecosystems.
   Extracellular vesicles are small (approximately 50 to 250 nm in diameter), membrane-bound structures that are released by cells into their surrounding environment. Heterogeneous populations of vesicles are abundant in the global oceans, and they likely play a number of ecological roles in these microbially dominated ecosystems. Here, we examine how vesicle production and size vary among different strains of cultivated marine microbes as well as explore the degree to which this is influenced by key environmental variables. We show that both vesicle production rates and vesicle sizes significantly differ among cultures of marine Proteobacteria, Cyanobacteria, and Bacteroidetes. Further, these properties vary within individual strains as a function of differences in environmental conditions, such as nutrients, temperature, and light irradiance. Thus, both community composition and the local abiotic environment are expected to modulate the production and standing stock of vesicles in the oceans. Examining samples from the oligotrophic North Pacific Gyre, we show depth-dependent changes in the abundance of vesicle-like particles in the upper water column in a manner that is broadly consistent with culture observations: the highest vesicle abundances are found near the surface, where the light irradiances and the temperatures are the greatest, and they then decrease with depth. This work represents the beginnings of a quantitative framework for describing extracellular vesicle dynamics in the oceans, which is essential as we begin to incorporate vesicles into our ecological and biogeochemical understanding of marine ecosystems.IMPORTANCE Bacteria release extracellular vesicles that contain a wide variety of cellular compounds, including lipids, proteins, nucleic acids, and small molecules, into their surrounding environment. These structures are found in diverse microbial habitats, including the oceans, where their distributions vary throughout the water column and likely affect their functional impacts within microbial ecosystems. Using a quantitative analysis of marine microbial cultures, we show that bacterial vesicle production in the oceans is shaped by a combination of biotic and abiotic factors. Different marine taxa release vesicles at rates that vary across an order of magnitude, and vesicle production changes dynamically as a function of environmental conditions. These findings represent a step forward in our understanding of bacterial extracellular vesicle production dynamics and provide a basis for the quantitative exploration of the factors that shape vesicle dynamics in natural ecosystems.
C1 [Biller, Steven J.; Coe, Allison; Arellano, Aldo A.; Dooley, Keven; Becker, Jamie W.; Chisholm, Sallie W.] MIT, Dept Civil & Environm Engn, Cambridge, MA 02139 USA.
   [Biller, Steven J.; Silvestri, Samantha M.; Gong, Jacqueline S.; Yeager, Emily A.] Wellesley Coll, Dept Biol Sci, Wellesley, MA USA.
   [Becker, Jamie W.] Alvernia Univ, Sci Dept, Reading, PA USA.
   [Chisholm, Sallie W.] MIT, Dept Biol, Cambridge, MA USA.
RP Biller, SJ (corresponding author), MIT, Dept Civil & Environm Engn, Cambridge, MA 02139 USA.
EM sbiller@wellesley.edu
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VL 89
IS 6
DI 10.1128/aem.00594-23
EA MAY 2023
UT WOS:000990236000001
DA 2025-07-30
ER

PT J
AU Galand, PE
   Potvin, M
   Casamayor, EO
   Lovejoy, C
AF Galand, Pierre E.
   Potvin, Marianne
   Casamayor, Emilio O.
   Lovejoy, Connie
TI Hydrography shapes bacterial biogeography of the deep Arctic Ocean
SO ISME JOURNAL
DT Article
AB It has been long debated as to whether marine microorganisms have a ubiquitous distribution or patterns of biogeography, but recently a consensus for the existence of microbial biogeography is emerging. However, the factors controlling the distribution of marine bacteria remain poorly understood. In this study, we combine pyrosequencing and traditional Sanger sequencing of the 16S rRNA gene to describe in detail bacterial communities from the deep Arctic Ocean. We targeted three separate water masses, from three oceanic basins and show that bacteria in the Arctic Ocean have a biogeography. The biogeographical distribution of bacteria was explained by the hydrography of the Arctic Ocean and subsequent circulation of its water masses. Overall, this first taxonomic description of deep Arctic bacteria communities revealed an abundant presence of SAR11 (Alphaproteobacteria), SAR406, SAR202 (Chloroflexi) and SAR324 (Deltaproteobacteria) clusters. Within each cluster, the abundance of specific phylotypes significantly varied among water masses. Water masses probably act as physical barriers limiting the dispersal and controlling the diversity of bacteria in the ocean. Consequently, marine microbial biogeography involves more than geographical distances, as it is also dynamically associated with oceanic processes. Our ocean scale study suggests that it is essential to consider the coupling between microbial and physical oceanography to fully understand the diversity and function of marine microbes. The ISME Journal (2010) 4, 564-576; doi:10.1038/ismej.2009.134; published online 10 December 2009
C1 [Galand, Pierre E.] CNRS, Observ Oceanol, UMR 7621, LOBB, F-66651 Banyuls Sur Mer, France.
   [Galand, Pierre E.; Casamayor, Emilio O.] CSIC, Limnol Unit, Ctr Estudis Avancats Blanes, Dept Continental Ecol, Blanes, Spain.
   [Potvin, Marianne; Lovejoy, Connie] Univ Laval, Dept Biol, Quebec City, PQ G1K 7P4, Canada.
   [Potvin, Marianne; Lovejoy, Connie] Univ Laval, Inst Biol Integrat & Syst, Quebec City, PQ, Canada.
   [Galand, Pierre E.] Univ Paris 06, UPMC, Paris, France.
RP Galand, PE (corresponding author), CNRS, Observ Oceanol Banyuls Sur Mer, UMR 7621, F-66651 Banyuls Sur Mer, France.
EM pierre.galand@obs-banyuls.fr
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NR 60
TC 151
Z9 165
PD APR
PY 2010
VL 4
IS 4
BP 564
EP 576
DI 10.1038/ismej.2009.134
UT WOS:000275851100011
DA 2025-07-30
ER

PT J
AU Ni, JY
   Chen, MM
   Shen, JM
   Liu, L
   Jiang, ZP
   Zhou, KB
   Li, XL
   Dai, MH
   Zhang, Y
AF Ni, Junyi
   Chen, Mingming
   Shen, Jiaming
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   Zhou, Kuanbo
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   Zhang, Yao
TI Elevated Heterotrophic Prokaryotic Production Supported by Low Nucleic
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SO JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS
DT Article
AB The cyclonic eddy uplifts nutrient-rich seawater into the euphotic zone, typically directly enhancing phytoplankton abundance and primary production. However, its impact on heterotrophic prokaryotic production (HPP) remains unclear due to the complex interplay of multiple indirect factors governing this process. Here, we conducted a comprehensive investigation of the distribution of picophytoplankton and heterotrophic prokaryotes, prokaryotic community structure, and HPP within a cyclonic eddy in the western North Pacific subtropical gyre. The results indicated that despite the higher abundance of picophytoplankton accompanied by nutrient upwelling at the eddy core compared to the edge, higher levels of HPP were observed at the eddy edge between 100 and 200 m, consistent with the distribution of the low nucleic acid content (LNA) prokaryotes. The significant positive correlation between HPP and the proportion of LNA group in total heterotrophic prokaryotes suggested a primary contribution from the LNA group over the high nucleic acid content (HNA) group. SAR11, a typical member of the LNA group, may primarily contribute to the elevated HPP observed at the eddy edge. The changes in temperature, nutrients, and light intensity induced by the cyclonic eddy may significantly influence the distribution and activity of HNA and LNA groups, potentially exerting a greater impact on HPP compared to phytoplankton-related factors. These findings contribute to understanding the underlying mechanisms of HPP responses to cyclonic eddies in the oligotrophic open ocean.
C1 [Ni, Junyi; Chen, Mingming; Shen, Jiaming; Liu, Li; Zhou, Kuanbo; Li, Xiaolin; Dai, Minhan; Zhang, Yao] Xiamen Univ, Coll Ocean & Earth Sci, State Key Lab Marine Environm Sci, Xiamen, Peoples R China.
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RP Zhang, Y (corresponding author), Xiamen Univ, Coll Ocean & Earth Sci, State Key Lab Marine Environm Sci, Xiamen, Peoples R China.
EM yaozhang@xmu.edu.cn
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NR 101
TC 0
Z9 0
PD NOV
PY 2024
VL 129
IS 11
AR e2024JC021414
DI 10.1029/2024JC021414
UT WOS:001370000700001
DA 2025-07-30
ER

PT J
AU Sieradzki, ET
   Fuhrman, JA
   Rivero-Calle, S
   Gómez-Consamau, L
AF Sieradzki, Ella T.
   Fuhrman, Jed A.
   Rivero-Calle, Sara
   Gomez-Consamau, Laura
TI Proteorhodopsins dominate the expression of phototrophic mechanisms in
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SO PEERJ
DT Article
AB The most abundant and ubiquitous microbes in the surface ocean use light as an energy source, capturing it via complex chlorophyll-based photosystems or simple retinal-based rhodopsins. Studies in various ocean regimes compared the abundance of these mechanisms, but few investigated their expression. Here we present the first full seasonal study of abundance and expression of light-harvesting mechanisms (proteorhodopsin, PR; aerobic anoxygenic photosynthesis, AAnP; and oxygenic photosynthesis, PSI) from deepsequenced metagenomes and metatranscriptomes of marine picoplankton (< 1 mu m) at three coastal stations of the San Pedro Channel in the Pacific Ocean. We show that, regardless of season or sampling location, the most common phototrophic mechanism in metagenomes of this dynamic region was PR (present in 65-104% of the genomes as estimated by single-copy recA), followed by PSI (5-104%) and AAnP (5-32%). Furthermore, the normalized expression (RNA to DNA ratio) of PR genes was higher than that of oxygenic photosynthesis (average +/- standard deviation 26.2 +/- 8.4 vs. 11 +/- 9.7), and the expression of the AAnP marker gene was significantly lower than both mechanisms (0.013 +/- 0.02). We demonstrate that PR expression was dominated by the SAR11-cluster year-round, followed by other Alphaproteobacteria, unknown-environmental clusters and Gammaproteobacteria. This highly dynamic system further allowed us to identify a trend for PR spectral tuning, in which blue-absorbing PR genes dominate in areas with low chlorophyll-a concentrations (< 0.25 mu gL(-1)). This suggests that PR phototrophy is not an accessory function but instead a central mechanism that can regulate photoheterotrophic population dynamics.
C1 [Sieradzki, Ella T.; Fuhrman, Jed A.; Rivero-Calle, Sara; Gomez-Consamau, Laura] Univ Southern Calif, Dept Biol Sci, Los Angeles, CA 90007 USA.
RP Sieradzki, ET (corresponding author), Univ Southern Calif, Dept Biol Sci, Los Angeles, CA 90007 USA.
EM ellasiera@berkeley.edu
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NR 71
TC 18
Z9 19
PD OCT 23
PY 2018
VL 6
AR e5798
DI 10.7717/peerj.5798
UT WOS:000448082800010
DA 2025-07-30
ER

PT J
AU Signori, CN
   Pellizari, VH
   Enrich-Prast, A
   Sievert, SM
AF Signori, Camila N.
   Pellizari, Vivian H.
   Enrich-Prast, Alex
   Sievert, Stefan M.
TI Spatiotemporal dynamics of marine bacterial and archaeal communities in
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SO DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY
DT Article
AB Seasonal changes in taxonomic and functional diversity of microbial communities in polar regions are commonly observed, requiring strategies of microbes to adapt to the corresponding changes in environmental conditions. These natural fluctuations form the backdrop for changes induced by anthropogenic impacts. The main goal of this study was to assess the seasonal and temporal changes in bacterial and archaeal diversity and community structure off the northern Antarctic Peninsula over several seasons (spring, summer, autumn) from 2013 to 2015. Ten monitoring stations were selected across the Gerlache and Bransfield Straits and nearby Elephant Island, and archaeal and bacterial communities examined by amplicon sequencing of 16S rRNA genes. Alpha-diversity indices were higher in spring and correlated significantly with temperature. Spring was characterized by the presence of SAR11, and microbial communities remaining from winter, including representatives of Thaumarchaeota (Nimosopurnilus), Euryarchaeota, members of Oceanospirillales, SAR324. Summer and autumn were characterized by a high prevalence of Flavobacteria (NS5 marine group and Polaribacter), Alphaproizobacteria (Rhodobacterales and SAR11 Glade) and Gammaproteobacteria (Oceanospirillales/Balneatrix and Celivibrionales), generally known to be associated with organic matter degradation. Relatively higher abundance of phytoplankton groups occurred in spring, mainly characterized by the presence of the haptophyte Phaeocystis and the diatom Corethron, influencing the succession of heterotrophic bacterial communities. Microbial diversity and community structure varied significantly over time, but not over space, i.e., were similar between monitoring stations for the same time. In addition, the observed interannual variability in microbial community structure might be related to an increase in sea surface temperature. Environmental conditions related to seasonal variation, including temperature and most likely phytoplankton derived organic matter, appear to have triggered the observed shifts in microbial communities in the waters off the northern Antarctic Peninsula.
C1 [Signori, Camila N.; Pellizari, Vivian H.] Univ Sao Paulo, Inst Oceanog, Dept Oceanog Biol, Praca Oceanog 191, BR-05508900 Sao Paulo, SP, Brazil.
   [Enrich-Prast, Alex] Linkoping Univ, Dept Themat Studies Environm Change, S-58183 Linkoping, Sweden.
   [Enrich-Prast, Alex] Univ Fed Rio De Janeiro UFRJ, Inst Biol, Dept Bot, Av Carlos Chagas Filho 373, BR-21941902 Rio De Janeiro, Brazil.
   [Sievert, Stefan M.] WHOI, Biol Dept, 266 Woods Hole Rd, Woods Hole, MA 02543 USA.
RP Signori, CN (corresponding author), Univ Sao Paulo, Inst Oceanog, Dept Oceanog Biol, Praca Oceanog 191, BR-05508900 Sao Paulo, SP, Brazil.; Sievert, SM (corresponding author), WHOI, Biol Dept, 266 Woods Hole Rd, Woods Hole, MA 02543 USA.
EM camisignori@hotmail.com; ssievert@whoi.edu
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NR 94
TC 23
Z9 24
PD MAR
PY 2018
VL 149
SI SI
BP 150
EP 160
DI 10.1016/j.dsr2.2017.12.017
UT WOS:000437037100014
DA 2025-07-30
ER

PT J
AU Montes, T
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AF Montes, Tania
   Guerrero-Feijoo, Elisa
   Moreira-Coello, Victor
   Bode, Antonio
   Ruiz-Villarreal, Manuel
   Mourino-Carballido, Beatriz
   Varela, Marta M.
TI Vertical zonation of bacterial assemblages attributed to physical
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SO ESTUARINE COASTAL AND SHELF SCIENCE
DT Article
AB We combined flow cytometry, CARD-FISH, and 16S rRNA gene tag pyrosequencing to investigate bacter-ioplankton dynamics along a transect in shelf waters off A Coruna (Galicia, NW Spain). Over five days (16-20th July 2012) we sampled during the relaxation of a summer upwelling pulse, providing an opportunity to examine the impact of pulses of cold nutrient-rich water into coastal microbial communities. The hydrographic conditions, characterized by intense density stratification of surface waters and the presence of a deep chlorophyll maximum (DCM) at 20-30 m, were relatively maintained over the sampling period. Indeed, bacterial abundance and composition displayed low day to day variation. Alpha diversity analysis suggested that species richness and diversity increased from coastal to shelf stations and from the surface down to the coastal DCM, which could be caused by the mixing of upwelled bacteria with the coastal surface waters. SAR11, SAR86, and Roseobacter were the most abundant bacteria detected in the samples by using CARD-FISH. The assemblages observed by pyrosequencing displayed a strong vertical zonation along the transect. Rhodobacteraceae (under class Alphaproteobacteria) and Bacteriodetes dominated the surface waters and decreased during the upwelling pulse, while SAR 86 (under class Gammaproteobacteria), Actinobacteria and SAR11 Glade increased their relative abundance at the coastal DCM with upwelling relaxation, particularly at the shelf stations. Bacterial assemblages from surface waters were associated with higher temperature and light conditions, while coastal DCM assemblages were rather associated to salinity, inorganic nutrients and a diatom-bloom leading to high chlorophyll-a. Our findings suggest that the vertical variability in environmental conditions induced by the intense density stratification, the exportation of warmer and less saline surface water from the rias to the adjacent shelf, and the fertilizing effect of recently upwelled water at the deeper layer, determined the composition of distinct bacterial assemblages at the subsurface and DCM layers.
C1 [Montes, Tania] Univ A Coruna, Fac Ciencias, Campus Zapateira S-N, La Coruna 15071, Spain.
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RP Varela, MM (corresponding author), Inst Espanol Oceanog, Ctr Oceanog A Coruna, Apdo 130, La Coruna 15080, Spain.
EM marta.varela@ieo.es
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NR 90
TC 5
Z9 5
PD OCT 30
PY 2020
VL 245
AR 106791
DI 10.1016/j.ecss.2020.106791
UT WOS:000582677500001
DA 2025-07-30
ER

PT J
AU Bakenhus, I
   Dlugosch, L
   Billerbeck, S
   Giebel, HA
   Milke, F
   Simon, M
AF Bakenhus, Insa
   Dlugosch, Leon
   Billerbeck, Sara
   Giebel, Helge-Ansgar
   Milke, Felix
   Simon, Meinhard
TI Composition of Total and Cell-Proliferating Bacterioplankton Community
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SO FRONTIERS IN MICROBIOLOGY
DT Article
AB Heterotrophic bacterioplankton communities play an important role in organic matter processing in the oceans worldwide. In order to investigate the significance of distinct phylogenetic bacterial groups it is not only important to assess their quantitative abundance but also their growth dynamics in relation to the entire bacterioplankton. Therefore bacterial abundance, biomass production and the composition of the entire and cell-proliferating bacterioplankton community were assessed in North Sea surface waters between the German Bight and 58 degrees N in early summer by applying catalyzed reporter deposition (CARD-FISH) and bromodeoxyuridine fluorescence in situ hybridization (BrdU-FISH). Bacteroidetes and the Roseobacter group dominated the cell-proliferating fraction with 10-55 and 8-31% of total BrdU-positive cells, respectively. While Bacteroidetes also showed high abundances in the total bacterial fraction, roseobacters constituted only 1-9% of all cells. Despite abundances of up to 55% of total bacterial cells, the SAR11 clade constituted <6% of BrdU-positive cells. Gammaproteobacteria accounted for 2-16% of the total and 2-13% of the cell-proliferating cells. Within the two most active groups, BrdU-positive cells made up 28% of Bacteroidetes as an overall mean and 36% of roseobacters. Estimated mean growth rates of Bacteroidetes and the Roseobacter group were 1.2 and 1.5 day(-1), respectively, and much higher than bulk growth rates of the bacterioplankton whereas those of the SAR11 clade and Gammaproteobacteria were 0.04 and 0.21 day(-1), respectively, and much lower than bulk growth rates. Only numbers of total and cell-proliferating roseobacters but not those of Bacteroidetes and the other groups were significantly correlated to chlorophyll fluorescence and bacterioplankton biomass production. The Roseobacter group, besides Bacteroidetes, appeared to be a major player in processing phytoplankton derived organic matter despite its low partitioning in the total bacterioplankton community.
C1 [Bakenhus, Insa; Dlugosch, Leon; Billerbeck, Sara; Giebel, Helge-Ansgar; Milke, Felix; Simon, Meinhard] Carl von Ossietzky Univ Oldenburg, Inst Chem & Biol Marine Environm, Oldenburg, Germany.
RP Simon, M (corresponding author), Carl von Ossietzky Univ Oldenburg, Inst Chem & Biol Marine Environm, Oldenburg, Germany.
EM m.simon@icbm.de
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NR 48
TC 24
Z9 26
PD SEP 13
PY 2017
VL 8
AR 1771
DI 10.3389/fmicb.2017.01771
UT WOS:000410482000002
DA 2025-07-30
ER

PT J
AU Dadon-Pilosof, A
   Conley, K
   Lombard, F
   Sutherland, KR
   Genin, A
   Richter, M
   Glöckner, FO
   Yahel, G
AF Dadon-Pilosof, Ayelet
   Conley, Keats
   Lombard, Fabien
   Sutherland, Kelly R.
   Genin, Amatzia
   Richter, Michael
   Gloeckner, Frank Oliver
   Yahel, Gitai
TI Differential clearance rates of microbial phylotypes by four
   appendicularian species
SO MARINE ECOLOGY PROGRESS SERIES
DT Article
AB Appendicularians are abundant planktonic filter feeders that play a significant role in the pelagic food web due to their high clearance rates. Their diet and feeding rates have typically been measured as bulk chlorophyll or cell removal, with some attention given to prey size but no differentiation between the microbial phylotypes. Using a combination of in situ and laboratory incubations with flow cytometry and next-generation sequencing, we found species-specific differences in clearance rates and diet compositions of 4 common species: Oikopleura albicans, O. fusiformis, O. longicauda, and O. dioica. While O. albicans most efficiently removed nano-eukaryotic algae, the other smaller species preferentially removed micron-sized pico-eukaryotic algae. Pico- and nano-eukaryotic cells constituted the major food source of the studied appendicularians despite their occurrence in oligotrophic water dominated by prokaryotic cells. Across species, pico- and nano-planktonic microalgae biomass comprised 45 to 75% of the appendicularian diets. Although non-photosynthetic bacteria were removed at lower rates than all other prey groups, their total contribution to the appendicularian diet was not trivial, representing 5 to 19% of the planktonic carbon in the appendicularian diet; pico-cyanobacteria contributed an additional 9 to 18%. Removal rates and efficiencies of pico-eukaryotes were higher than those of prokaryotes of similar size. Strikingly different clearance rates were observed for different prokaryotic phylotypes, indicating that factors other than size are involved in determining the capturability of the cells. Collectively, our findings provide additional evidence for differential retention of microbial prey among mucous-mesh grazers and its substantial effect on the upper-ocean microbial community.
C1 [Dadon-Pilosof, Ayelet; Yahel, Gitai] Ruppin Acad Ctr, Fac Marine Sci, IL-4029700 Mikhmoret, Israel.
   [Dadon-Pilosof, Ayelet; Genin, Amatzia] Hebrew Univ Jerusalem, Dept Ecol Evolut & Behav, IL-9190401 Jerusalem, Israel.
   [Conley, Keats; Sutherland, Kelly R.] Univ Oregon, Oregon Inst Marine Biol, Eugene, OR 97420 USA.
   [Lombard, Fabien] Sorbonne Univ, Inst Mer Villefranche Mer IMEV, Lab Oceanographie Villefranche Mer, F-06230 Villefranche Sur Mer, France.
   [Lombard, Fabien] Inst Univ France, F-75005 Paris, France.
   [Genin, Amatzia] Interuniv Inst Marine Sci Eilat, IL-88103 Elat, Israel.
   [Richter, Michael] Ribocon GmbH, Fahrenheitstr 1, D-28359 Bremen, Germany.
   [Richter, Michael] Alfred Wegener Inst, Helmholtz Ctr Polar & Marine Res, Handelshafen 12, D-27570 Bremerhaven, Germany.
   [Yahel, Gitai] Jacobs Univ, Campus Ring 1, Bremen, Germany.
RP Dadon-Pilosof, A (corresponding author), Ruppin Acad Ctr, Fac Marine Sci, IL-4029700 Mikhmoret, Israel.; Dadon-Pilosof, A (corresponding author), Hebrew Univ Jerusalem, Dept Ecol Evolut & Behav, IL-9190401 Jerusalem, Israel.
EM ayelet@ruppin.ac.il
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NR 77
TC 4
Z9 4
PD FEB 23
PY 2023
VL 706
BP 73
EP 89
DI 10.3354/meps14233
UT WOS:000946221000006
DA 2025-07-30
ER

PT J
AU Ozbayram, EG
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   Albay, M
AF Ozbayram, E. Gozde
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   Oguz, Ayca
   Zengin, Zuhal
   Akcaalan, Reyhan
   Albay, Meric
TI Seasonal dynamics of bacterial communities in a highly polluted coastal
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SO MARINE POLLUTION BULLETIN
DT Article
AB This study aims to evaluate the effects of different environmental gradients and seasonality on the bacterial communities of an impacted coastal lagoon. While the community compositions were homogenous in surface waters with the dominance of Candidatus Pelagibacter, diversity showed high vertical variation due to salinity and dissolved oxygen gradients. Anoxic conditions occurred at deeper parts of the lagoon, particularly at 14 m and 18 m, where nutrient enrichment and high H2S concentration were detected resulting in a shift of bacterial community to anoxic species. Sulfurimonas, Sulfurovum, and Desulfobacula were dominant genera at 14 m and 18 m where the H2S concentration was high. The community composition of the sediment did not change over seasons, dominated by Syntrophus species. The insights gained from this study may contribute to understanding how dissolved oxygen, H2S concentrations and salinity drive bacterial community structure in euxinic ecosystems especially the dominance of anoxic bacteria.
C1 [Ozbayram, E. Gozde; Koker, Latife; Oguz, Ayca; Zengin, Zuhal; Akcaalan, Reyhan; Albay, Meric] Istanbul Univ, Fac Aquat Sci, Dept Marine & Freshwater Resources Management, TR-34134 Istanbul, Turkiye.
RP Ozbayram, EG (corresponding author), Istanbul Univ, Fac Aquat Sci, Dept Marine & Freshwater Resources Management, TR-34134 Istanbul, Turkiye.
EM gozde.ozbayram@istanbul.edu.tr
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NR 48
TC 0
Z9 0
PD DEC
PY 2024
VL 209
AR 117186
DI 10.1016/j.marpolbul.2024.117186
EA NOV 2024
PN A
UT WOS:001350876700001
DA 2025-07-30
ER

PT J
AU Ferrera, I
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AF Ferrera, Isabel
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TI Evaluation of Alternative High-Throughput Sequencing Methodologies for
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SO FRONTIERS IN MARINE SCIENCE
DT Article
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RP Ferrera, I (corresponding author), CSIC, Biol Marina & Oceanog, Inst Ciencies Mar, Barcelona, Spain.
EM iferrera@icm.csic.es
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UT WOS:000457358000144
DA 2025-07-30
ER

PT J
AU Rappé, MS
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AF Rappé, MS
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SO FEMS MICROBIOLOGY ECOLOGY
DT Article
AB In order to extend previous comparisons between coastal marine bacterioplankton communities and their open ocean and freshwater counterparts, here we summarize and provide new data on a clone library of 105 SSU rRNA genes recovered from seawater collected over the western continental shelf of the USA in the Pacific Ocean. Comparisons to previously published data revealed that this coastal bacterioplankton clone library was dominated by SSU rRNA gene phylotypes originally described from surface waters of the open ocean, but also revealed unique SSU rRNA gene lineages of beta Proteobacteria related to those found in clone libraries from freshwater habitats. beta Proteobacteria lineages common to coastal and freshwater samples included members of a clade of obligately methylotrophic bacteria, SSU rRNA genes affiliated with Xylophilus ampelinus, and a clade related to the genus Duganella. Ln addition, SSU rRNA genes were recovered from such previously recognized marine bacterioplankton SSU rRNA gene clone clusters as the SAR86, SAR11, and SAR116 clusters within the class Proteobacteria, the Roseobacter clade of the alpha subclass of the Proteobacteria, the marine group A/SAR406 cluster, and the marine Actinobacteria clade. Overall, these results support and extend previous observations concerning the global distribution of several marine planktonic prokaryote SSU rRNA gene phylotypes, but also show that coastal bacterioplankton communities contain SSU rRNA gene lineages (and presumably bacterioplankton) shown previously to be prevalent in freshwater habitats. (C) 2000 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.
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RP Rappé, MS (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
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NR 52
TC 218
Z9 232
PD SEP
PY 2000
VL 33
IS 3
BP 219
EP 232
DI 10.1016/S0168-6496(00)00064-7
UT WOS:000089847700006
DA 2025-07-30
ER

PT J
AU Howard, EC
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AF Howard, Erinn C.
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   Moran, Mary Ann
TI Bacterial taxa that limit sulfur flux from the ocean
SO SCIENCE
DT Article
AB Flux of dimethylsulfide (DMS) from ocean surface waters is the predominant natural source of sulfur to the atmosphere and influences climate by aerosol formation. Marine bacterioplankton regulate sulfur flux by converting the precursor dimethylsulfoniopropionate (DMSP) either to DMS or to sulfur compounds that are not climatically active. Through the discovery of a glycine cleavage T-family protein with DMSP methyltransferase activity, marine bacterioplankton in the Roseobacter and SAR11 taxa were identified as primary mediators of DMSP demethylation to methylmercaptopropionate. One-third of surface ocean bacteria harbor a DMSP demethylase homolog and thereby route a substantial fraction of global marine primary production away from DMS formation and into the marine microbial food web.
C1 Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
   Univ Georgia, Dept Microbiol, Athens, GA 30602 USA.
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RP Moran, MA (corresponding author), Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
EM mmoran@uga.edu
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TC 275
Z9 332
PD OCT 27
PY 2006
VL 314
IS 5799
BP 649
EP 652
DI 10.1126/science.1130657
UT WOS:000241557800048
DA 2025-07-30
ER

PT J
AU Alonso-Sáez, L
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   Gasol, JM
AF Alonso-Saez, Laura
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   Gasol, Josep M.
TI Bacterial uptake of low molecular weight organics in the subtropical
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SO LIMNOLOGY AND OCEANOGRAPHY
DT Article
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RP Alonso-Sáez, L (corresponding author), Inst Espanol Oceanog, Ctr Oceanog Gijon, Gijon, Spain.
EM laura.alonso@gi.ieo.es
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TC 37
Z9 40
PD MAY
PY 2012
VL 57
IS 3
BP 798
EP 808
DI 10.4319/lo.2012.57.3.0798
UT WOS:000306239300010
DA 2025-07-30
ER

PT J
AU Larkin, AA
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   Fagan, AJ
   Moreno, AR
   Gerace, SD
   Lees, LE
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   Martiny, AC
AF Larkin, Alyse A.
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   Suarez, Stacy A.
   Eloe-Fadrosh, Emiley A.
   Martiny, Adam C.
TI Climate-driven succession in marine microbiome biodiversity and
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SO NATURE COMMUNICATIONS
DT Article
AB Seasonal and El Ni & ntilde;o-Southern Oscillation (ENSO) warming result in similar ocean changes as predicted with climate change. Climate-driven environmental cycles have strong impacts on microbiome diversity, but impacts on microbiome function are poorly understood. Here we quantify changes in microbial genomic diversity and functioning over 11 years covering seasonal and ENSO cycles at a coastal site in the southern California Current. We observe seasonal oscillations between large-genome lineages during cold, nutrient rich conditions in winter and spring versus small-genome lineages, including Prochlorococcus and Pelagibacter, in summer and fall. Parallel interannual changes separate communities depending on ENSO condition. Biodiversity shifts translate into clear oscillations in microbiome functional potential. Ocean warming induced an ecosystem with less iron but more macronutrient stress genes, depressed organic carbon degradation potential and biomass, and elevated carbon-to-nutrient biomass ratios. The consistent microbial response observed across time-scales points towards large climate-driven changes in marine ecosystems and biogeochemical cycles.
C1 [Larkin, Alyse A.; Fagan, Adam J.; Gerace, Skylar D.; Martiny, Adam C.] Univ Calif Irvine, Dept Earth Syst Sci, Irvine, CA 92697 USA.
   [Brock, Melissa L.; Moreno, Allison R.; Lees, Lauren E.; Suarez, Stacy A.; Martiny, Adam C.] Univ Calif Irvine, Dept Ecol & Evolutionary Biol, Irvine, CA 92697 USA.
   [Moreno, Allison R.] Univ Calif Santa Cruz, Ocean Sci Dept, Santa Cruz, CA USA.
   [Eloe-Fadrosh, Emiley A.] US DOE, Joint Genome Inst, Lawrence Berkeley Natl Lab, Berkeley, CA USA.
RP Martiny, AC (corresponding author), Univ Calif Irvine, Dept Earth Syst Sci, Irvine, CA 92697 USA.; Martiny, AC (corresponding author), Univ Calif Irvine, Dept Ecol & Evolutionary Biol, Irvine, CA 92697 USA.
EM amartiny@uci.edu
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NR 89
TC 1
Z9 1
PD APR 25
PY 2025
VL 16
IS 1
AR 3926
DI 10.1038/s41467-025-59382-1
UT WOS:001476786100013
DA 2025-07-30
ER

PT J
AU Pajares, S
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AF Pajares, Silvia
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TI Spatial Distribution Patterns of Bacterioplankton in the Oxygen Minimum
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SO MICROBIAL ECOLOGY
DT Article
AB Microbial communities within oxygen minimum zones (OMZs) are crucial drivers of marine biogeochemical cycles; however, we still lack an understanding of how these communities are distributed across an OMZ. We explored vertical (from 5 to 500 m depth) and horizontal (coast to open ocean) distribution of bacterioplankton and its relationships with the main oceanographic conditions in three transects of the tropical Mexican Pacific OMZ. The distribution of the microbial diversity and the main clades changed along the transition from oxygen-rich surface water to the OMZ core, demonstrating the sensitivity of key bacterial groups to deoxygenation. The euphotic zone was dominated by Synechococcales, followed by Flavobacteriales, Verrucomicrobiales, Rhodobacterales, SAR86, and Cellvibrionales, whereas the OMZ core was dominated by SAR11, followed by SAR406, SAR324, SAR202, UBA10353 marine group, Thiomicrospirales and Nitrospinales. The marked environmental gradients along the water column also supported a high potential for niche partitioning among OMZ microorganisms. Additionally, in the OMZ core, bacterial assemblages from the same water mass were more similar to each other than those from another water mass. There were also important differences between coastal and open-ocean communities: Flavobacteriales, Verrucomicrobiales, Rhodobacterales, SAR86, and Cellvibrionales were more abundant in coastal areas, while Synechococcales, SAR406, SAR324, SAR202, UBA10353 marine group, and Thiomicrospirales were more abundant in the open ocean. Our results suggest a biogeographic structure of the bacterioplankton in this OMZ region, with limited community mixing across water masses, except in upwelling events, and little dispersion of the community by currents in the euphotic zone.
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RP Pajares, S (corresponding author), Univ Nacl Autonoma Mexico, Inst Marine Sci & Limnol, Unidad Acad Ecol & Biodiversidad Acuat, Mexico City, DF, Mexico.
EM spajares@cmarl.unam.mx
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PT J
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DT Article
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C1 [Warwick-Dugdale, Joanna; Michelsen, Michelle L.; Moore, Karen; Farbos, Audrey; Bell, Ashley; Buchholz, Holger H.; Bolanos, Luis M.; Allen, Michael J.; Temperton, Ben] Univ Exeter, Sch Biosci, Exeter EX4 4SB, Devon, England.
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RP Warwick-Dugdale, J; Temperton, B (corresponding author), Univ Exeter, Sch Biosci, Exeter EX4 4SB, Devon, England.; Warwick-Dugdale, J (corresponding author), Plymouth Marine Lab, Plymouth PL1 3DH, Devon, England.
EM jo.warwick@gmail.com; b.temperton@exeter.ac.uk
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NR 118
TC 6
Z9 6
PD MAY 14
PY 2024
VL 15
IS 1
AR 4089
DI 10.1038/s41467-024-48300-6
UT WOS:001222925300036
DA 2025-07-30
ER

PT J
AU Soule, MCK
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   Giovannoni, SJ
   Kujawinski, EB
AF Soule, Melissa C. Kido
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   Giovannoni, Stephen J.
   Kujawinski, Elizabeth B.
TI Impact of instrument and experiment parameters on reproducibility of
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SO ORGANIC GEOCHEMISTRY
DT Article
AB Natural dissolved organic matter (OM) is a complex heterogeneous mixture of compounds that have defied traditional characterization using standard analytical methods. Electrospray ionization mass spectrometry, particularly in ultrahigh resolution mode, provides a new platform for compositional assessment of this important pool of the Earth's reduced carbon. Here, we propose a framework for optimization of instrument and experiment parameters for high quality data acquisition using Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). We report the impact of these parameters on reproducibility of peak detection and repeatability of peak height in replicate injections of Suwannee River fulvic acid (FA), a common terrestrial OM standard. In addition, we examine the variability in peak detection and peak height among different types of experimental replicates of dissolved OM derived from laboratory cultures of Candidatus Pelagibacter ubique, a ubiquitous marine alpha-proteobacterium. (C) 2010 Elsevier Ltd. All rights reserved.
C1 [Soule, Melissa C. Kido; Longnecker, Krista; Kujawinski, Elizabeth B.] Woods Hole Oceanog Inst, Dept Marine Chem & Geochem, Woods Hole, MA 02543 USA.
   [Giovannoni, Stephen J.] Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
RP Kujawinski, EB (corresponding author), Woods Hole Oceanog Inst, Dept Marine Chem & Geochem, Woods Hole, MA 02543 USA.
EM ekujawinski@whoi.edu
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NR 46
TC 81
Z9 88
PD AUG
PY 2010
VL 41
IS 8
BP 725
EP 733
DI 10.1016/j.orggeochem.2010.05.017
UT WOS:000280614600001
DA 2025-07-30
ER

PT J
AU Agogué, H
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   Neal, PR
   Sogin, ML
   Herndl, GJ
AF Agogue, Helene
   Lamy, Dominique
   Neal, Phillip R.
   Sogin, Mitchell L.
   Herndl, Gerhard J.
TI Water mass-specificity of bacterial communities in the North Atlantic
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DT Article
AB Bacterial assemblages from subsurface (100 m depth), meso- (200-1000 m depth) and bathy-pelagic (below 1000 m depth) zones at 10 stations along a North Atlantic Ocean transect from 60 degrees N to 5 degrees S were characterized using massively parallel pyrotag sequencing of the V6 region of the 16S rRNA gene (V6 pyrotags). In a dataset of more than 830 000 pyrotags, we identified 10 780 OTUs of which 52% were singletons. The singletons accounted for less than 2% of the OTU abundance, whereas the 100 and 1000 most abundant OTUs represented 80% and 96% respectively of all recovered OTUs. Non-metric Multi-Dimensional Scaling and Canonical Correspondence Analysis of all the OTUs excluding the singletons revealed a clear clustering of the bacterial communities according to the water masses. More than 80% of the 1000 most abundant OTUs corresponded to Proteobacteria of which 55% were Alphaproteobacteria, mostly composed of the SAR11 cluster. Gammaproteobacteria increased with depth and included a relatively large number of OTUs belonging to Alteromonadales and Oceanospirillales. The bathypelagic zone showed higher taxonomic evenness than the overlying waters, albeit bacterial diversity was remarkably variable. Both abundant and low-abundance OTUs were responsible for the distinct bacterial communities characterizing the major deep-water masses. Taken together, our results reveal that deep-water masses act as bio-oceanographic islands for bacterioplankton leading to water mass-specific bacterial communities in the deep waters of the Atlantic.
C1 [Lamy, Dominique; Herndl, Gerhard J.] Univ Vienna, Dept Marine Biol, A-1090 Vienna, Austria.
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RP Herndl, GJ (corresponding author), Univ Vienna, Dept Marine Biol, Althanstr 14, A-1090 Vienna, Austria.
EM gerhard.herndl@univie.ac.at
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NR 82
TC 198
Z9 217
PD JAN
PY 2011
VL 20
IS 2
BP 258
EP 274
DI 10.1111/j.1365-294X.2010.04932.x
UT WOS:000285970200008
DA 2025-07-30
ER

PT J
AU Hernández, L
   Vicens, A
   Eguiarte, LE
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   De Anda, V
   González, JM
AF Hernandez, Laura
   Vicens, Alberto
   Eguiarte, Luis E.
   Souza, Valeria
   De Anda, Valerie
   Gonzalez, Jose M.
TI Evolutionary history of dimethylsulfoniopropionate (DMSP) demethylation
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SO PEERJ
DT Article
AB Dimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton and bacteria, is primarily degraded by bacteria belonging to the Roseobacter lineage and other marine Alphaproteobacteria via DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common ancestry between DmdA and GcvT gene families and a co-evolution between Roseobacter and the DMSPproducing-phytoplankton around 250 million years ago (Mya). In this work, we analyzed the evolution of DmdA under three possible evolutionary scenarios: (1) a recent common ancestor of DmdA and GcvT, (2) a coevolution between Roseobacter and the DMSP-producing-phytoplankton, and (3) an enzymatic adaptation for utilizing DMSP in marine bacteria prior to Roseobacter origin. Our analyses indicate that DmdA is a new gene family originated from GcvT genes by duplication and functional divergence driven by positive selection before a coevolution between Roseobacter and phytoplankton. Our data suggest that Roseobacter acquired dmdA by horizontal gene transfer prior to an environment with higher DMSP. Here, we propose that the ancestor that carried the DMSP demethylation pathway genes evolved in the Archean, and was exposed to a higher concentration of DMSP in a sulfur-rich atmosphere and anoxic ocean, compared to recent Roseobacter eco-orthologs (orthologs performing the same function under different conditions) which should be adapted to lower concentrations of DMSP.
C1 [Hernandez, Laura; Gonzalez, Jose M.] Univ La Laguna, Dept Microbiol, San Cristobal la Laguna, Spain.
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RP Hernández, L (corresponding author), Univ La Laguna, Dept Microbiol, San Cristobal la Laguna, Spain.
EM lhernanj@ull.edu.es
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NR 88
TC 6
Z9 6
PD SEP 10
PY 2020
VL 8
AR e9861
DI 10.7717/peerj.9861
UT WOS:000567750300002
DA 2025-07-30
ER

PT J
AU Lidbury, I
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AF Lidbury, Ian
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
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RP Chen, Y; Schäfer, H (corresponding author), Univ Warwick, Sch Life Sci, Gibbet Hill Campus, Coventry CV4 7AL, W Midlands, England.
EM Y.chen.25@warwick.ac.uk; H.schaefer@warwick.ac.uk
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NR 72
TC 49
Z9 51
PD AUG
PY 2016
VL 18
IS 8
BP 2754
EP 2766
DI 10.1111/1462-2920.13354
UT WOS:000383388800040
DA 2025-07-30
ER

PT J
AU Reboul, G
   Moreira, D
   Annenkova, NV
   Bertolino, P
   Vershinin, KE
   López-García, P
AF Reboul, Guillaume
   Moreira, David
   Annenkova, Nataliia V.
   Bertolino, Paola
   Vershinin, Konstantin E.
   Lopez-Garcia, Purificacion
TI Marine signature taxa and core microbial community stability along
   latitudinal and vertical gradients in sediments of the deepest
   freshwater lake
SO ISME JOURNAL
DT Article; Early Access
AB Lake Baikal is the deepest (similar to 1.6 km) and most voluminous freshwater reservoir on Earth. Compared to plankton, its benthos remains poorly explored. Here, we ask whether latitude and/or depth determine benthic microbial community structure and how Baikal communities compare to those of other freshwater, brackish and marine sediments. To answer, we collected sediment upper layers (0-1 cm) across a similar to 600 km North-South transect covering the three basins of the lake and from littoral to bathybenthic depths (0.5-1450 m). Analysis of 16S and 18S rRNA gene amplicon sequences revealed communities with high richness and evenness where rare operational taxonomic units (OTUs) collectively dominated. Archaea represented up to 25% or prokaryotic sequences. Baikal sediments harbored typically marine eukaryotic and prokaryotic OTUs recently identified in some lakes (diplonemids, Bolidophyceae, Mamiellales, SAR202, marine-like Synechococcus, Pelagibacterales) but also SAR324, Syndiniales and Radiolaria. We hypothesize that, beyond the salinity barrier, adaptation to oligotrophy explains the presence of these otherwise typically marine lineages. Baikal core benthic communities were relatively stable across sites and seemed not determined by depth or latitude. Comparative analyses with other freshwater, brackish and marine prokaryotic sediment communities confirmed the distinctness of Baikal benthos, which include elements of similarity to marine and hydrothermally influenced systems.
C1 [Reboul, Guillaume; Moreira, David; Bertolino, Paola; Lopez-Garcia, Purificacion] Univ Paris Saclay, AgroParisTech, Ecol Systemat Evolut, Ctr Natl Rech Sci CNRS, Orsay, France.
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RP López-García, P (corresponding author), Univ Paris Saclay, AgroParisTech, Ecol Systemat Evolut, Ctr Natl Rech Sci CNRS, Orsay, France.
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NR 20
TC 0
Z9 0
PD 2021 MAY 19
PY 2021
DI 10.1038/541396-021-01011-y
EA MAY 2021
UT WOS:000652099700002
DA 2025-07-30
ER

PT J
AU Shannon, KC
   St John, G
   Gould, R
   Hartzell, C
   Matthews, H
   Brennan, EJ
   Bolaños, LM
   Lindley, ST
   Field, JC
   Mantua, N
   Johnson, R
   Jeffres, C
   Colwell, FS
   Suffridge, CP
AF Shannon, Kelly C.
   St John, Gillian
   Gould, Robin
   Hartzell, Christopher
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   Brennan, Elizabeth J.
   Bolanos, Luis M.
   Lindley, Steven T.
   Field, John C.
   Mantua, Nate
   Johnson, Rachel
   Jeffres, Carson
   Colwell, Frederick S.
   Suffridge, Christopher P.
TI Springtime upwelling conditions influence microbial communities and
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SO LIMNOLOGY AND OCEANOGRAPHY
DT Article
AB Understanding dissolved concentrations of the essential coenzyme thiamin (vitamin B-1) can provide insights into the biological controls on highly productive upwelling systems such as the California Current Ecosystem. To connect thiamin availability with microbial communities in the California Current Ecosystem, we measured concentrations of dissolved thiamin and its biochemically related moieties (thiamin congeners) and 16S rRNA gene-based microbial communities during the spring. We found that strong upwelling caused a depletion of dissolved thiamin precursor compounds and abiotic degradation products relative to periods of weak upwelling. Specific microbial taxa, including species of SAR11 ecotypes, Candidatus Nitrosopumilus, and SUP05 cluster, were also significantly enriched with strong upwelling. Our data provide evidence that alterations to microbial communities in the mixed layer that occur as a result of upwelling could constrain the availability of dissolved thiamin and its chemical congeners in the California Current Ecosystem.
C1 [Shannon, Kelly C.; St John, Gillian; Matthews, Hailey; Brennan, Elizabeth J.; Colwell, Frederick S.; Suffridge, Christopher P.] Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
   [Gould, Robin; Hartzell, Christopher] Oregon State Univ, Dept Biochem & Biophys, Corvallis, OR USA.
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   [Lindley, Steven T.; Field, John C.; Mantua, Nate; Johnson, Rachel] NOAA Fisheries, Southwest Fisheries Sci Ctr, Santa Cruz, CA USA.
   [Johnson, Rachel; Jeffres, Carson] Univ Calif Davis, Ctr Watershed Sci, Davis, CA USA.
   [Colwell, Frederick S.] Oregon State Univ, Coll Earth Ocean & Atmospher Sci, Corvallis, OR USA.
RP Suffridge, CP (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
EM suffridc@oregonstate.edu
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NR 72
TC 1
Z9 1
PD MAY
PY 2025
VL 70
IS 5
BP 1386
EP 1403
DI 10.1002/lno.70021
EA MAR 2025
UT WOS:001449480000001
DA 2025-07-30
ER

PT J
AU Seymour, JR
   Doblin, MA
   Jeffries, TC
   Brown, MV
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   Ralph, PJ
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AF Seymour, Justin R.
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   Jeffries, Thomas C.
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   Newton, Kelly
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   Baird, Mark
   Mitchell, James G.
TI Contrasting microbial assemblages in adjacent water masses associated
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SO ENVIRONMENTAL MICROBIOLOGY REPORTS
DT Article
AB Different oceanographic provinces host discrete microbial assemblages that are adapted to local physicochemical conditions. We sequenced and compared the metagenomes of two microbial communities inhabiting adjacent water masses in the Tasman Sea, where the recent strengthening of the East Australian Current (EAC) has altered the ecology of coastal environments. Despite the comparable latitude of the samples, significant phylogenetic differences were apparent, including shifts in the relative frequency of matches to Cyanobacteria, Crenarchaeota and Euryarchaeota. Fine-scale variability in the structure of SAR11, Prochlorococcus and Synechococcus populations, with more matches to warm-water ecotypes observed in the EAC, indicates the EAC may drive an intrusion of tropical microbes into temperate regions of the Tasman Sea. Furthermore, significant shifts in the relative importance of 17 metabolic categories indicate that the EAC prokaryotic community has different physiological properties than surrounding waters.
C1 [Seymour, Justin R.; Doblin, Martina A.; Ralph, Peter J.; Baird, Mark] Univ Technol Sydney, Sydney, NSW 2007, Australia.
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RP Seymour, JR (corresponding author), Univ Technol Sydney, POB 123, Sydney, NSW 2007, Australia.
EM justin.seymour@uts.edu.au
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NR 39
TC 23
Z9 26
PD OCT
PY 2012
VL 4
IS 5
BP 548
EP 555
DI 10.1111/j.1758-2229.2012.00362.x
UT WOS:000309445800011
DA 2025-07-30
ER

PT J
AU Halsey, KH
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   Graus, M
   Zhao, YL
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AF Halsey, Kimberly H.
   Giovannoni, Stephen J.
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TI Biological cycling of volatile organic carbon by phytoplankton and
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SO LIMNOLOGY AND OCEANOGRAPHY
DT Article
AB Acetaldehyde, methanol, acetone, and isoprene are important reactive volatile organic compounds (VOCs) in the oceans that partition to the atmosphere in significant amounts. Reports of potentially high rates of VOC turnover in the North Atlantic suggested that both biotic and abiotic processes are involved. The biological basis for VOC cycling by ocean plankton is unknown, but is potentially important because of VOC contributions to carbon cycle budgets and atmospheric chemistry. We designed dynamic stripping chambers that coupled to a proton transfer reaction mass spectrometer to measure VOC production and consumption by cultured phytoplankton and bacterioplankton. The diatom, Thalassiosira pseudonana, produced acetaldehyde in a light-dependent manner. Acetaldehyde was oxidized by the chemoheterotrophic bacterium, Pelagibacter, at rates that suggest that most acetaldehyde is recycled in the ocean before escaping to the atmosphere. These results show that field observations of acetaldehyde turnover reported previously could be explained by biological activity. Rates of production by phytoplankton cultures of methanol, acetone, and isoprene were also measured. These findings support the conclusion that VOCs are a conduit for carbon transfer directly from phytoplankton to bacterioplankton, with the remainder available for escape to the atmosphere.
C1 [Halsey, Kimberly H.; Giovannoni, Stephen J.; Zhao, Yanlin; Landry, Zachary; Thrash, J. Cameron; Vergin, Kevin L.] Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
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   [Zhao, Yanlin] Fujian Agr & Forestry Univ, Coll Life Sci, Fuzhou, Fujian, Peoples R China.
   [Thrash, J. Cameron] Louisiana State Univ, Dept Biol Sci, Baton Rouge, LA 70803 USA.
RP Halsey, KH (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
EM halseyk@science.oregonstate.edu
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NR 62
TC 45
Z9 49
PD NOV
PY 2017
VL 62
IS 6
BP 2650
EP 2661
DI 10.1002/lno.10596
UT WOS:000415930800021
DA 2025-07-30
ER

PT J
AU Nikrad, MP
   Cottrell, MT
   Kirchman, DL
AF Nikrad, Mrinalini P.
   Cottrell, M. T.
   Kirchman, D. L.
TI Abundance and Single-Cell Activity of Heterotrophic Bacterial Groups in
   the Western Arctic Ocean in Summer and Winter
SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Environmental conditions in the western Arctic Ocean range from constant light and nutrient depletion in summer to complete darkness and sea ice cover in winter. This seasonal environmental variation is likely to have an effect on the use of dissolved organic matter (DOM) by heterotrophic bacteria in surface water. However, this effect is not well studied and we know little about the activity of specific bacterial clades in the surface oceans. The use of DOM by three bacterial subgroups in both winter and summer was examined by microautoradiography combined with fluorescence in situ hybridization. We found selective use of substrates by these groups, although the abundances of Ant4D3 (Antarctic Gammaproteobacteria), Polaribacter (Bacteroidetes), and SAR11 (Alphaproteobacteria) were not different between summer and winter in the Beaufort and Chukchi Seas. The number of cells taking up glucose within all three bacterial groups decreased significantly from summer to winter, while the percentage of cells using leucine did not show a clear pattern between seasons. The uptake of the amino acid mix increased substantially from summer to winter by the Ant4D3 group, although such a large increase in uptake was not seen for the other two groups. Use of glucose by bacteria, but not use of leucine or the amino acid mix, related strongly to inorganic nutrients, chlorophyll a, and other environmental factors. Our results suggest a switch in use of dissolved organic substrates from summer to winter and that the three phylogenetic subgroups examined fill different niches in DOM use in the two seasons.
C1 [Nikrad, Mrinalini P.; Cottrell, M. T.; Kirchman, D. L.] Univ Delaware, Sch Marine Sci & Policy, Lewes, DE 19958 USA.
RP Kirchman, DL (corresponding author), Univ Delaware, Sch Marine Sci & Policy, Lewes, DE 19958 USA.
EM kirchman@udel.edu
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NR 45
TC 44
Z9 50
PD APR
PY 2012
VL 78
IS 7
BP 2402
EP 2409
DI 10.1128/AEM.07130-11
UT WOS:000301344300038
DA 2025-07-30
ER

PT J
AU Fuchs, BM
   Woebken, D
   Zubkov, MV
   Burkill, P
   Amann, R
AF Fuchs, BM
   Woebken, D
   Zubkov, MV
   Burkill, P
   Amann, R
TI Molecular identification of picoplankton populations in contrasting
   waters of the Arabian Sea
SO AQUATIC MICROBIAL ECOLOGY
DT Article
AB The composition of picoplankton in the southern oligotrophic, northern mesotrophic waters and deep oxygen minimum zone (OMZ) of the Arabian Sea was determined by 16S ribosomal RNA gene cloning and fluorescence in situ hybridisation (FISH). It was hypothesised that the composition of the heterotrophic picoplankton would be different in these contrasting waters. To reduce the total diversity, cells were sorted by flow cytometry according to their scatter and DNA content before PCR amplification. The 16S rRNA clone libraries resulting from flow-sorted populations were different and often dominated by a small number of clades. Libraries from the Prochlorococcus-dominated southerly waters were dominated by sequences related to uncultured clusters of SAR11, SAR86 and Actinobacteria (HGC 1). From surface waters of the Synechococcus-dominated northern part of the Arabian Sea, mostly sequences related to the uncultured gammaproteobacterial group 'Svalbard' and HGC I were retrieved. The clone libraries from the OMZ were also dominated by sequences falling in the clades SARI 1 and SAR406, but included sequences related to those of sulfate-reducing (Desulfosarcina, Desulfofrigus) and sulfide-oxidising bacteria (endosymbionts of Riftia and Calyptogena). With a recently developed more sensitive FISH protocol approximately 60% of all DAPI stained cells could be identified by general probes as Bacteria, Cren- or Euryarchaeota in both provinces of the Arabian Sea; 40% remained undetected. On this level and on that of the major phylogenetic groups like Alpha- and Gammaproteobacteria only minor differences were detected by FISH. However, the composition of heterotrophic picoplankton clearly differed for the proteobacterial subgroups SAR86, SAR11 and SAR116. These were more abundant in the oligotrophic waters throughout the water column than in the mesotrophic surface waters and the OMZ. This supports our original hypothesis that the contrasting waters in the Arabian Sea harbor different heterotrophic picoplankton communities. In the future, FISH with a larger set of probes for more narrow phylogenetic groups will enable us to quantify these differences in more detail.
C1 Max Planck Inst Marine Microbiol, D-28359 Bremen, Germany.
   Southampton Oceanog Ctr, Southampton SO14 3ZH, Hants, England.
RP Fuchs, BM (corresponding author), Max Planck Inst Marine Microbiol, Celsiusstr 1, D-28359 Bremen, Germany.
EM bfuchs@mpi-bremen.de
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NR 68
TC 123
Z9 131
PD MAY 30
PY 2005
VL 39
IS 2
BP 145
EP 157
DI 10.3354/ame039145
UT WOS:000229867200004
DA 2025-07-30
ER

PT J
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AF Hwang, Jinik
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TI Metagenomic characterization of viral communities in Goseong Bay, Korea
SO OCEAN SCIENCE JOURNAL
DT Article
AB In this study, seawater samples were collected from Goseong Bay, Korea in March 2014 and viral populations were examined by metagenomics assembly. Enrichment of marine viral particles using FeCl3 followed by next-generation sequencing produced numerous sequences. De novo assembly and BLAST search showed that most of the obtained contigs were unknown sequences and only 0.74% of sequences were associated with known viruses. As a result, 138 viruses, including bacteriophages (87%), viruses infecting algae and others (13%) were identified. The identified 138 viruses were divided into 11 orders, 14 families, 34 genera, and 133 species. The dominant viruses were Pelagibacter phage HTVC010P and Roseobacter phage SIO1. The viruses infecting algae, including the Ostreococcus species, accounted for 9.4% of total identified viruses. In addition, we identified pathogenic herpes viruses infecting fishes and giant viruses infecting parasitic acanthamoeba species. This is a comprehensive study to reveal the viral populations in the Goseong Bay using metagenomics. The information associated with the marine viral community in Goseong Bay, Korea will be useful for comparative analysis in other marine viral communities.
C1 [Hwang, Jinik; Park, So Yun; Park, Mirye; Lee, Taek-Kyun] KIOST, South Sea Res Inst, South Sea Environm Res Ctr, Geoje 53201, South Korea.
   [Hwang, Jinik; Park, Mirye; Lee, Taek-Kyun] Korea Univ Sci & Technol, Marine Environm Sci, Daejeon 34113, South Korea.
   [Lee, Sukchan] Sungkyunkwan Univ, Coll Biotechnol & Bioengn, Dept Genet Engn, Suwon 16419, South Korea.
   [Jo, Yeonhwa; Cho, Won Kyong] Seoul Natl Univ, Coll Agr & Life Sci, Dept Agr Biotechnol, Seoul 08826, South Korea.
RP Lee, TK (corresponding author), KIOST, South Sea Res Inst, South Sea Environm Res Ctr, Geoje 53201, South Korea.; Lee, TK (corresponding author), Korea Univ Sci & Technol, Marine Environm Sci, Daejeon 34113, South Korea.
EM tklee@kiost.ac.kr
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NR 39
TC 8
Z9 8
PD DEC
PY 2016
VL 51
IS 4
BP 599
EP 612
DI 10.1007/s12601-016-0051-7
UT WOS:000391426800006
DA 2025-07-30
ER

PT J
AU Sebastián, M
   Gasol, JM
AF Sebastian, Marta
   Gasol, Josep M.
TI Heterogeneity in the nutrient limitation of different bacterioplankton
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SO ISME JOURNAL
DT Article
AB The heterotrophic bacterial community of the Eastern Mediterranean Sea is believed to be limited by phosphorus (P) availability. This observation assumes that all bacterial groups are equally limited, something that has not been hitherto examined. To test this hypothesis, we performed nutrient addition experiments and investigated the response of probe-identified groups using microautoradiography combined with catalyzed reporter deposition fluorescence in situ hybridization. Our results show contrasting responses between the bacterial groups, with Gammaproteobacteria being the group more affected by P availability. The Roseobacter clade was likely colimited by P and nitrogen (N), whereas Bacteroidetes by P, N and organic carbon (C). In contrast, SAR11 cells were active regardless of the nutrient concentration. These results indicate that there is high heterogeneity in the nutrient limitation of the different components of the bacterioplankton community.
C1 [Sebastian, Marta; Gasol, Josep M.] CSIC, Inst Ciencies Mar, Dept Biol Marina & Oceanog, E-08003 Barcelona, Catalunya, Spain.
RP Sebastián, M (corresponding author), CSIC, Inst Ciencies Mar, Dept Biol Marina & Oceanog, Pg Maritim Barceloneta 37-49, E-08003 Barcelona, Catalunya, Spain.
EM msebastian@icm.csic.es
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NR 18
TC 23
Z9 24
PD AUG
PY 2013
VL 7
IS 8
BP 1665
EP 1668
DI 10.1038/ismej.2013.42
UT WOS:000322119600019
DA 2025-07-30
ER

PT J
AU Crump, BC
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AF Crump, BC
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB The Columbia River estuary is a dynamic system in which estuarine turbidity maxims trap and extend the residence time of particles and particle-attached bacteria over those of the water and free-living bacteria. Particle-attached bacteria dominate bacterial activity in the estuary and are an important part of the estuarine food web. PCR-amplified 16S rRNA genes from particle-attached and free-living bacteria in the Columbia River, its estuary, and the adjacent coastal ocean were cloned, and 239 partial sequences were determined. A wide diversity was observed at the species level within at least six different bacterial phyla, including most subphyla of the class Proteobacteria. In the estuary, most particle-attached bacterial clones (75%) were related to members of the genus Cytophaga or of the alpha, gamma, or beta subclass of the class Proteobacteria. These same clones, however, were rare in or absent from either the particle-attached or the free-living bacterial communities of the river and the coastal ocean. In contrast, about half (48%) of the free-living estuarine bacterial clones were similar to clones from the river or the coastal ocean. These free-living bacteria were related to groups of cosmopolitan freshwater bacteria (beta-proteobacteria, gram-positive bacteria, and Verrucomicrobium spp,) and groups of marine organisms (gram-positive bacteria and alpha-proteobacteria [SAR11 and Rhodobacter spp.]). These results suggest that rapidly growing particle-attached bacteria develop into a uniquely adapted estuarine community and that free-living estuarine bacteria are similar to members of the river and the coastal ocean microbial communities. The high degree of diversity in the estuary is the result of the mixing of bacterial communities from the river, estuary, and coastal ocean.
C1 Univ Washington, Sch Oceanog, Seattle, WA 98195 USA.
RP Univ Washington, Sch Oceanog, Seattle, WA 98195 USA.
EM bcrump@u.washington.edu
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NR 48
TC 570
Z9 605
PD JUL
PY 1999
VL 65
IS 7
BP 3192
EP 3204
UT WOS:000081199000054
DA 2025-07-30
ER

PT J
AU Mir, DH
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AF Mir, D. H.
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SO APPLIED BIOCHEMISTRY AND MICROBIOLOGY
DT Article
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C1 [Mir, D. H.; Rather, M. A.] Natl Inst Technol Srinagar, Chem Engn Dept, Srinagar, Jammu And Kashm, India.
RP Mir, DH (corresponding author), Natl Inst Technol Srinagar, Chem Engn Dept, Srinagar, Jammu And Kashm, India.
EM dabeer_03phd19@nitsri.ac.in
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NR 107
TC 1
Z9 1
PD APR
PY 2024
VL 60
IS 2
BP 264
EP 279
DI 10.1134/S000368382402011X
UT WOS:001206575700003
DA 2025-07-30
ER

PT J
AU Hatosy, SM
   Martiny, AC
AF Hatosy, Stephen M.
   Martiny, Adam C.
TI The Ocean as a Global Reservoir of Antibiotic Resistance Genes
SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Recent studies of natural environments have revealed vast genetic reservoirs of antibiotic resistance (AR) genes. Soil bacteria and human pathogens share AR genes, and AR genes have been discovered in a variety of habitats. However, there is little knowledge about the presence and diversity of AR genes in marine environments and which organisms host AR genes. To address this, we identified the diversity of genes conferring resistance to ampicillin, tetracycline, nitrofurantoin, and sulfadimethoxine in diverse marine environments using functional metagenomics (the cloning and screening of random DNA fragments). Marine environments were host to a diversity of AR-conferring genes. Antibiotic-resistant clones were found at all sites, with 28% of the genes identified as known AR genes (encoding beta-lactamases, bicyclomycin resistance pumps, etc.). However, the majority of AR genes were not previously classified as such but had products similar to proteins such as transport pumps, oxidoreductases, and hydrolases. Furthermore, 44% of the genes conferring antibiotic resistance were found in abundant marine taxa (e.g., Pelagibacter, Prochlorococcus, and Vibrio). Therefore, we uncovered a previously unknown diversity of genes that conferred an AR phenotype among marine environments, which makes the ocean a global reservoir of both clinically relevant and potentially novel AR genes.
C1 [Hatosy, Stephen M.; Martiny, Adam C.] Univ Calif Irvine, Dept Ecol & Evolutionary Biol, Irvine, CA 92717 USA.
   [Martiny, Adam C.] Univ Calif Irvine, Dept Earth Syst Sci, Irvine, CA USA.
RP Martiny, AC (corresponding author), Univ Calif Irvine, Dept Ecol & Evolutionary Biol, Irvine, CA 92717 USA.
EM amartiny@uci.edu
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NR 32
TC 170
Z9 197
PD NOV
PY 2015
VL 81
IS 21
BP 7593
EP 7599
DI 10.1128/AEM.00736-15
UT WOS:000363462900025
DA 2025-07-30
ER

PT J
AU Ghuneim, LAJ
   Jones, DL
   Golyshin, PN
   Golyshina, OV
AF Ghuneim, Lydia-Ann J.
   Jones, David L.
   Golyshin, Peter N.
   Golyshina, Olga V.
TI Nano-Sized and Filterable Bacteria and Archaea: Biodiversity and
   Function
SO FRONTIERS IN MICROBIOLOGY
DT Review
AB Nano-sized and filterable microorganisms are thought to represent the smallest living organisms on earth and are characterized by their small size (50-400 nm) and their ability to physically pass through <0.45 mu m pore size filters. They appear to be ubiquitous in the biosphere and are present at high abundance across a diverse range of habitats including oceans, rivers, soils, and subterranean bedrock. Small-sized organisms are detected by culture-independent and culture-dependent approaches, with most remaining uncultured and uncharacterized at both metabolic and taxonomic levels. Consequently, their significance in ecological roles remain largely unknown. Successful isolation, however, has been achieved for some species (e.g., Nanoarchaeum equitans and "Candidatus Pelagibacter ubique"). In many instances, small-sized organisms exhibit a significant genome reduction and loss of essential metabolic pathways required for a free-living lifestyle, making their survival reliant on other microbial community members. In these cases, the nano-sized prokaryotes can only be co-cultured with their 'hosts.' This paper analyses the recent data on small-sized microorganisms in the context of their taxonomic diversity and potential functions in the environment.
C1 [Ghuneim, Lydia-Ann J.; Jones, David L.] Bangor Univ, Sch Environm Nat Resources & Geog, Bangor, Gwynedd, Wales.
   [Golyshin, Peter N.; Golyshina, Olga V.] Bangor Univ, Sch Biol Sci, Bangor, Gwynedd, Wales.
RP Ghuneim, LAJ (corresponding author), Bangor Univ, Sch Environm Nat Resources & Geog, Bangor, Gwynedd, Wales.
EM afp68e@bangor.ac.uk
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NR 107
TC 56
Z9 62
PD AUG 21
PY 2018
VL 9
AR 1971
DI 10.3389/fmicb.2018.01971
UT WOS:000442215400002
DA 2025-07-30
ER

PT J
AU Williams, TJ
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AF Williams, Timothy J.
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   Raftery, Mark J.
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TI A metaproteomic assessment of winter and summer bacterioplankton from
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SO ISME JOURNAL
DT Article
AB A metaproteomic survey of surface coastal waters near Palmer Station on the Antarctic Peninsula, West Antarctica, was performed, revealing marked differences in the functional capacity of summer and winter communities of bacterioplankton. Proteins from Flavobacteria were more abundant in the summer metaproteome, whereas winter was characterized by proteins from ammonia-oxidizing Marine Group I Crenarchaeota. Proteins prevalent in both seasons were from SAR11 and Rhodobacterales clades of Alphaproteobacteria, as well as many lineages of Gammaproteobacteria. The metaproteome data were used to elucidate the main metabolic and energy generation pathways and transport processes occurring at the microbial level in each season. In summer, autotrophic carbon assimilation appears to be driven by oxygenic photoautotrophy, consistent with high light availability and intensity. In contrast, during the dark polar winter, the metaproteome supported the occurrence of chemolithoautotrophy via the 3-hydroxypropionate/4-hydroxybutyrate cycle and the reverse tricarboxylic acid cycle of ammonia-oxidizing archaea and nitrite-oxidizing bacteria, respectively. Proteins involved in nitrification were also detected in the metaproteome. Taurine appears to be an important source of carbon and nitrogen for heterotrophs (especially SAR11), with transporters and enzymes for taurine uptake and degradation abundant in the metaproteome. Divergent heterotrophic strategies for Alphaproteobacteria and Flavobacteria were indicated by the metaproteome data, with Alphaproteobacteria capturing (by high-affinity transport) and processing labile solutes, and Flavobacteria expressing outer membrane receptors for particle adhesion to facilitate the exploitation of non-labile substrates. TonB-dependent receptors from Gammaproteobacteria and Flavobacteria (particularly in summer) were abundant, indicating that scavenging of substrates was likely an important strategy for these clades of Southern Ocean bacteria. This study provides the first insight into differences in functional processes occurring between summer and winter microbial communities in coastal Antarctic waters, and particularly highlights the important role that 'dark' carbon fixation has in winter. The ISME Journal (2012) 6, 1883-1900; doi:10.1038/ismej.2012.28; published online 26 April 2012
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RP Cavicchioli, R (corresponding author), Univ New S Wales, Sch Biotechnol & Biomol Sci, BABS, Sydney, NSW 2052, Australia.
EM alison.murray@dri.edu; r.cavicchioli@unsw.edu.au
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NR 89
TC 160
Z9 175
PD OCT
PY 2012
VL 6
IS 10
BP 1883
EP 1900
DI 10.1038/ismej.2012.28
UT WOS:000309056300008
DA 2025-07-30
ER

PT J
AU Stephens, BM
   Fox, J
   Liu, ST
   Halsey, KH
   Nicholson, DP
   Traylor, S
   Carlson, CA
AF Stephens, Brandon M.
   Fox, James
   Liu, Shuting
   Halsey, Kimberly H.
   Nicholson, David P.
   Traylor, Shawnee
   Carlson, Craig A.
TI Influence of amino acids on bacterioplankton production, biomass and
   community composition at Ocean Station Papa in the subarctic Pacific
SO ELEMENTA-SCIENCE OF THE ANTHROPOCENE
DT Article
AB Bacterioplankton play a central role in carbon cycling, yet their relative contributions to carbon production and removal can be difficult to constrain. As part of the Export Processes in the Ocean from RemoTe Sensing (EXPORTS) program, this study identifies potential influences of bacterioplankton community and dissolved organic matter (DOM) composition on carbon cycling at Ocean Station Papa in August 2018. Surface (5-35 m) bacterioplankton production rates and stocks spanned a 2- to 3-fold range over the 3-week cruise and correlated positively with the DOM degradation state, estimated using the mole proportion of total dissolved amino acids. When the DOM was more degraded, 16S rRNA gene amplicon data revealed a less diverse bacterioplankton community with a significant contribution from members of the Flavobacteriaceae family. Over the course of 7-10 d, as the DOM quality improved (became less degraded) and bacterioplankton productivity increased, the responding bacterioplankton community became more diverse, with increased relative contributions from members of the SAR86, SAR11 and AEGEAN-169 clades. The cruise mean for mixed layer, depth-integrated bacterioplankton carbon demand (gross bacterioplankton production) was 5.2 mmol C m-2 d-1, representing 60% of net primary production, where the difference between net primary production and bacterioplankton carbon demand was less than sinking flux at 50 m. The concentrations of dissolved organic carbon (cruise average of 58.5 mM C) did not exhibit a systematic change over the cruise period. Therefore, we hypothesize that carbon supplied from gross carbon production, values that were 2- to 3-fold greater than net primary production, provided the carbon necessary to account for the sinking flux and bacterioplankton carbon demand that were in excess of net primary production. These findings highlight the central contributions of bacterioplankton to carbon cycling at Ocean Station Papa, a site of high carbon recycling.
C1 [Stephens, Brandon M.; Liu, Shuting; Carlson, Craig A.] Univ Calif Santa Barbara, Marine Sci Inst, Dept Ecol Evolut & Marine Biol, Santa Barbara, CA 93106 USA.
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RP Stephens, BM (corresponding author), Univ Calif Santa Barbara, Marine Sci Inst, Dept Ecol Evolut & Marine Biol, Santa Barbara, CA 93106 USA.
EM bstephens@ucsb.edu
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NR 114
TC 8
Z9 8
PD MAY 2
PY 2023
VL 11
IS 1
AR 00095
DI 10.1525/elementa.2022.00095
UT WOS:000988107400001
DA 2025-07-30
ER

PT J
AU Haro-Moreno, JM
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AF Haro-Moreno, Jose M.
   Lopez-Perez, Mario
   Rodriguez-Valera, Francisco
TI Enhanced Recovery of Microbial Genes and Genomes From a Marine Water
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SO FRONTIERS IN MICROBIOLOGY
DT Article
AB Third-generation sequencing has penetrated little in metagenomics due to the high error rate and dependence for assembly on short-read designed bioinformatics. However, second-generation sequencing metagenomics (mostly Illumina) suffers from limitations, particularly in the assembly of microbes with high microdiversity and retrieval of the flexible (adaptive) fraction of prokaryotic genomes. Here, we have used a third-generation technique to study the metagenome of a well-known marine sample from the mixed epipelagic water column of the winter Mediterranean. We have compared PacBio Sequel II with the classical approach using Illumina Nextseq short reads followed by assembly to study the metagenome. Long reads allow for efficient direct retrieval of complete genes avoiding the bias of the assembly step. Besides, the application of long reads on metagenomic assembly allows for the reconstruction of much more complete metagenome-assembled genomes (MAGs), particularly from microbes with high microdiversity such as Pelagibacterales. The flexible genome of reconstructed MAGs was much more complete containing many adaptive genes (some with biotechnological potential). PacBio Sequel II CCS appears particularly suitable for cellular metagenomics due to its low error rate. For most applications of metagenomics, from community structure analysis to ecosystem functioning, long reads should be applied whenever possible. Specifically, for in silico screening of biotechnologically useful genes, or population genomics, long-read metagenomics appears presently as a very fruitful approach and can be analyzed from raw reads before a computationally demanding (and potentially artifactual) assembly step.
C1 [Haro-Moreno, Jose M.; Lopez-Perez, Mario; Rodriguez-Valera, Francisco] Univ Miguel Hernandez, Div Microbiol, Evolutionary Genom Grp, Alicante, Spain.
   [Rodriguez-Valera, Francisco] Moscow Inst Phys & Technol, Res Ctr Mol Mech Aging & Age Related Dis, Dolgoprudnyi, Russia.
RP Rodriguez-Valera, F (corresponding author), Univ Miguel Hernandez, Div Microbiol, Evolutionary Genom Grp, Alicante, Spain.; Rodriguez-Valera, F (corresponding author), Moscow Inst Phys & Technol, Res Ctr Mol Mech Aging & Age Related Dis, Dolgoprudnyi, Russia.
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NR 128
TC 24
Z9 24
PD AUG 27
PY 2021
VL 12
AR 708782
DI 10.3389/fmicb.2021.708782
UT WOS:000698806400001
DA 2025-07-30
ER

PT J
AU Zhang, ZF
   Chen, F
   Chu, X
   Zhang, H
   Luo, HW
   Qin, F
   Zhai, ZQ
   Yang, MY
   Sun, J
   Zhao, YL
AF Zhang, Zefeng
   Chen, Feng
   Chu, Xiao
   Zhang, Hao
   Luo, Haiwei
   Qin, Fang
   Zhai, Zhiqiang
   Yang, Mingyu
   Sun, Jing
   Zhao, Yanlin
TI Diverse, Abundant, and Novel Viruses Infecting the Marine
   Roseobacter RCA Lineage
SO MSYSTEMS
DT Article
AB Many major marine bacterial lineages such as SAR11, Prochlorococcus, SAR116, and several Roseobacter lineages have members that are abundant, relatively slow-growing, and genome streamlined. The isolation of phages that infect SAR11 and SAR116 have demonstrated the dominance of these phages in the marine virosphere. However, no phages have been isolated from bacteria in the Roseobacter RCA lineage, another abundant group of marine bacteria. In this study, seven RCA phages that infect three different RCA strains were isolated and characterized. All seven RCA phages belong to the Podoviridae family and have genome sizes ranging from 39.6 to 58.1 kb. Interestingly, three RCA phages (CRP-1, CRP-2, and CRP-3) show similar genomic content and architecture as SAR116 phage HMO-2011, which represents one of the most abundant known viral groups in the ocean. The high degree of homology among CRP-1, CRP-2, CRP-3, and HMO-2011 resulted in the contribution of RCA phages to the dominance of the HMO-2011-type group. CRP-4 and CRP-5 are similar to the Cobavirus group roseophages in terms of gene content and organization. The remaining two RCA phages, CRP-6 and CRP-7, show limited genomic similarity with known phages and represent two new phage groups. Metagenomic fragment recruitment analyses reveal that these RCA phage groups are much more abundant in the ocean than most existing marine roseophage groups. The characterization of these RCA phages has greatly expanded our understanding of the genomic diversity and evolution of marine roseophages and suggests the critical need for isolating phages from the abundant but "unculturable" bacteria.
   IMPORTANCE The RCA lineage of the marine Roseobacter group represents one of the slow-growing but dominant components of marine microbial communities. Although dozens of roseophages have been characterized, no phages infecting RCA strains have been reported. In this study, we reported on the first RCA phage genomes and investigated their distribution pattern and relative abundance in comparison with other important marine phage groups. Two of the four RCA phage groups were found closely related to previously reported SAR116 phage HMO-2011 and Cobavirus group roseophages, respectively. The remaining two groups are novel in the genome contents. Our study also revealed that RCA phages are widely distributed and exhibit high abundance in marine viromic data sets. Altogether, our findings have greatly broadened our understanding of RCA phages and emphasize the ecological and evolutionary importance of RCA phages in the marine virosphere.
C1 [Zhang, Zefeng; Qin, Fang; Zhai, Zhiqiang; Yang, Mingyu; Zhao, Yanlin] Fujian Agr & Forestry Univ, Coll Life Sci, Fujian Prov Key Lab Agroecol Proc & Safety Monito, Fuzhou, Fujian, Peoples R China.
   [Chen, Feng] Univ Maryland, Ctr Environm Sci, Inst Marine & Environm Technol, Baltimore, MD 21201 USA.
   [Chu, Xiao; Zhang, Hao; Luo, Haiwei] Chinese Univ Hong Kong, Sch Life Sci, Simon FS Li Marine Sci Lab, Shatin, Hong Kong, Peoples R China.
   [Chu, Xiao; Zhang, Hao; Luo, Haiwei] Chinese Univ Hong Kong, State Key Lab Agrobiotechnol, Shatin, Hong Kong, Peoples R China.
   [Sun, Jing] Chinese Acad Fishery Sci, Yellow Sea Fisheries Res Inst, Qingdao, Shandong, Peoples R China.
RP Zhao, YL (corresponding author), Fujian Agr & Forestry Univ, Coll Life Sci, Fujian Prov Key Lab Agroecol Proc & Safety Monito, Fuzhou, Fujian, Peoples R China.
EM yanlinzhao@fafu.edu.cn
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NR 76
TC 31
Z9 31
PD NOV-DEC
PY 2019
VL 4
IS 6
AR e00494-19
DI 10.1128/mSystems.00494-19
UT WOS:000518852300017
DA 2025-07-30
ER

PT J
AU Rodríguez-Gómez, C
   Durán-Riveroll, LM
   Okolodkov, YB
   Oliart-Ros, RM
   García-Casillas, AM
   Cembella, AD
AF Rodriguez-Gomez, Citlali
   Maria Duran-Riveroll, Lorena
   Okolodkov, Yuri B.
   Oliart-Ros, Rosa Maria
   Garcia-Casillas, Andrea M.
   Cembella, Allan D.
TI Diversity of Bacterioplankton and Bacteriobenthos from the Veracruz Reef
   System, Southwestern Gulf of Mexico
SO MICROORGANISMS
DT Article
AB Bacterial diversity was explored among field samples and cultured isolates from coral reefs within the Veracruz Reef System. Bacterioplankton and bacteriobenthos were characterized by pyrosequencing 16S rRNA genes. Identified sequences belonged to the kingdom Bacteria and classified into 33 phyla. Proteobacteria (likely SAR11 clade) dominated in collective field samples, whereas Firmicutes were the most abundant taxa among cultured isolates. Bioinformatic sorting of sequences to family level revealed 223 bacterial families. Pseudomonadaceae, Exiguobacteraceae and Bacillaceae were dominant among cultured isolates. Vibrionaceae, Alteromonadaceae, and Flavobacteriaceae dominated in reef-associated sediments, whereas Rickettsiaceae and Synechoccaceae were more highly represented in the water column. Bacterial communities from sediments were more diverse than from the water column. This study reveals cryptic bacterial diversity among microenvironmental components of marine microbial reef communities subject to differential influence of anthropogenic stressors. Such investigations are critical for constructing scenarios of environmentally induced shifts in bacterial biodiversity and species composition.
C1 [Rodriguez-Gomez, Citlali; Oliart-Ros, Rosa Maria] Tecnol Nacl Mexico, Inst Tecnol Veracruz, Unidad Invest & Desarrollo Alimentos, Veracruz 91897, Veracruz, Mexico.
   [Maria Duran-Riveroll, Lorena] CONACYT, Dept Biotecnol Marina, Ctr Invest Cient & Educ Super Ensenada, Carretera Tijuana Ensenada 3918, Ensenada 22860, Baja California, Mexico.
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   [Okolodkov, Yuri B.] Univ Veracruzana, Inst Ciencias Marinas & Pesquerias, Mar Mediterraneo 314, Boca Del Rio 94294, Veracruz, Mexico.
   [Garcia-Casillas, Andrea M.] Univ Nacl Autonoma Mexico, Fac Ciencias, Mexico City 0451, DF, Mexico.
RP Durán-Riveroll, LM (corresponding author), CONACYT, Dept Biotecnol Marina, Ctr Invest Cient & Educ Super Ensenada, Carretera Tijuana Ensenada 3918, Ensenada 22860, Baja California, Mexico.; Durán-Riveroll, LM; Cembella, AD (corresponding author), Helmholtz Zentrum Polar & Meeresforsch, Alfred Wegener Inst, D-27570 Bremerhaven, Germany.
EM cileya@yahoo.com; lorena.duran@awi.de; yuriokolodkov@yahoo.com;
   rosa.or@veracruz.tecnm.mx; garciacasillas@ciencias.unam.mx;
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NR 81
TC 3
Z9 3
PD MAR
PY 2021
VL 9
IS 3
AR 619
DI 10.3390/microorganisms9030619
UT WOS:000633901700001
DA 2025-07-30
ER

PT J
AU Moopantakath, J
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   Kumavath, R
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AF Moopantakath, Jamseel
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   Maria Martinez-Espinosa, Rosa
TI Ubiquitousness of Haloferax and Carotenoid Producing Genes in
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SO MARINE DRUGS
DT Article
AB This study presents a comparative analysis of halophiles from the global open sea and coastal biosystems through shotgun metagenomes (n = 209) retrieved from public repositories. The open sea was significantly enriched with Prochlorococcus and Candidatus pelagibacter. Meanwhile, coastal biosystems were dominated by Marinobacter and Alcanivorax. Halophilic archaea Haloarcula and Haloquandratum, predominant in the coastal biosystem, were significantly (p < 0.05) enriched in coastal biosystems compared to the open sea. Analysis of whole genomes (n = 23,540), retrieved from EzBioCloud, detected crtI in 64.66% of genomes, while cruF was observed in 1.69% Bacteria and 40.75% Archaea. We further confirmed the viability and carotenoid pigment production by pure culture isolation (n = 1351) of extreme halophiles from sediments (n = 410 x 3) sampling at the Arabian coastline of India. All red-pigmented isolates were represented exclusively by Haloferax, resistant to saturated NaCl (6 M), and had >60% G + C content. Multidrug resistance to tetracycline, gentamicin, ampicillin, and chloramphenicol were also observed. Our study showed that coastal biosystems could be more suited for bioprospection of halophiles rather than the open sea.
C1 [Moopantakath, Jamseel; Imchen, Madangchanok; Kumavath, Ranjith] Cent Univ Kerala, Sch Biol Sci, Dept Genom Sci, Tejaswini Hills, Periye 671320, Kerala, India.
   [Maria Martinez-Espinosa, Rosa] Univ Alicante, Fac Sci, Agrochem & Biochem Dept, Biochem & Mol Biol Div, Ap 99, E-03080 Alicante, Spain.
   [Maria Martinez-Espinosa, Rosa] Univ Alicante, Multidisciplinary Inst Environm Studies Ramon Mar, Ap 99, E-03080 Alicante, Spain.
RP Kumavath, R (corresponding author), Cent Univ Kerala, Sch Biol Sci, Dept Genom Sci, Tejaswini Hills, Periye 671320, Kerala, India.
EM mailforjamseel@gmail.com; anokimchen@gmail.com;
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NR 129
TC 6
Z9 6
PD AUG
PY 2021
VL 19
IS 8
AR 442
DI 10.3390/md19080442
UT WOS:000689585700001
DA 2025-07-30
ER

PT J
AU Kim, S
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AF Kim, Suhyun
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TI Culturing the ubiquitous freshwater actinobacterial acI lineage by
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SO ISME JOURNAL
DT Article
AB The actinobacterial acI lineage is among the most successful and ubiquitous freshwater bacterioplankton found on all continents, often representing more than half of all microbial cells in the lacustrine environment and constituting multiple ecotypes. However, stably growing pure cultures of the acI lineage have not been established despite various cultivation efforts based on ecological and genomic studies on the lineage, which is in contrast to the ocean from which abundant microorganisms such as Prochlorococcus, Pelagibacter, and Nitrosopumilus have been isolated. Here, we report the first two pure cultures of the acI lineage successfully maintained by supplementing the growth media with catalase. Catalase was critical for stabilizing the growth of acI strains irrespective of the genomic presence of the catalase-peroxidase (katG) gene. The two strains, representing two novel species, displayed differential phenotypes and distinct preferences for reduced sulfurs and carbohydrates, some of which were difficult to predict based on genomic information. Our results suggest that culture of previously uncultured freshwater bacteria can be facilitated by a simple catalase-supplement method and indicate that genome-based metabolic prediction can be complemented by physiological analyses.
C1 [Kim, Suhyun; Kang, Ilnam; Seo, Ji-Hui; Cho, Jang-Cheon] Inha Univ, Dept Biol Sci, Incheon 22212, South Korea.
RP Cho, JC (corresponding author), Inha Univ, Dept Biol Sci, Incheon 22212, South Korea.
EM chojc@inha.ac.kr
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TC 34
Z9 37
PD SEP
PY 2019
VL 13
IS 9
BP 2252
EP 2263
DI 10.1038/s41396-019-0432-x
UT WOS:000482118300010
DA 2025-07-30
ER

PT J
AU Wang, CX
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AF Wang, Chunxia
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DT Article
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C1 Virginia Polytech Inst & State Univ, Virginia Bioinformat Inst, Blacksburg, VA 24061 USA.
RP Williams, KP (corresponding author), Virginia Polytech Inst & State Univ, Virginia Bioinformat Inst, Blacksburg, VA 24061 USA.
EM kellwill@vt.edu
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NR 42
TC 31
Z9 33
PD MAR
PY 2007
VL 189
IS 5
BP 1954
EP 1962
DI 10.1128/JB.01203-06
UT WOS:000244462800051
DA 2025-07-30
ER

PT J
AU Géron, A
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AF Geron, Augustin
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SO FRONTIERS IN MICROBIOLOGY
DT Article
AB Unraveling the complex structure and functioning of microbial communities is essential to accurately predict the impact of perturbations and/or environmental changes. From all molecular tools available today to resolve the dynamics of microbial communities, metaproteomics stands out, allowing the establishment of phenotype-genotype linkages. Despite its rapid development, this technology has faced many technical challenges that still hamper its potential power. How to maximize the number of protein identification, improve quality of protein annotation, and provide reliable ecological interpretation are questions of immediate urgency. In our study, we used a robust metaproteomic workflow combining two protein fractionation approaches (gel-based versus gel-free) and four protein search databases derived from the same metagenome to analyze the same seawater sample. The resulting eight metaproteomes provided different outcomes in terms of (i) total protein numbers, (ii) taxonomic structures, and (iii) protein functions. The characterization and/or representativeness of numerous proteins from ecologically relevant taxa such as Pelagibacterales, Rhodobacterales, and Synechococcales, as well as crucial environmental processes, such as nutrient uptake, nitrogen assimilation, light harvesting, and oxidative stress response, were found to be particularly affected by the methodology. Our results provide clear evidences that the use of different protein search databases significantly alters the biological conclusions in both gel-free and gel-based approaches. Our findings emphasize the importance of diversifying the experimental workflow for a comprehensive metaproteomic study.
C1 [Geron, Augustin; Matallana-Surget, Sabine] Univ Stirling, Fac Nat Sci, Div Biol & Environm Sci, Stirling, Scotland.
   [Geron, Augustin; Wattiez, Ruddy] Univ Mons, Dept Prote & Microbiol, Mons, Belgium.
   [Werner, Johannes] Leibniz Inst Baltic Sea Res, Dept Biol Oceanog, Rostock, Germany.
   [Lebaron, Philippe] UPMC Univ Paris 06, Sorbonne Univ, LBBM, USR 3579,Observ Oceanol, Banyuls Sur Mer, France.
RP Matallana-Surget, S (corresponding author), Univ Stirling, Fac Nat Sci, Div Biol & Environm Sci, Stirling, Scotland.
EM sabine.matallanasurget@stir.ac.uk
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NR 63
TC 15
Z9 16
PD OCT 24
PY 2019
VL 10
AR 2395
DI 10.3389/fmicb.2019.02395
UT WOS:000497430100001
DA 2025-07-30
ER

PT J
AU Sun, Y
   Luo, HW
AF Sun, Ying
   Luo, Haiwei
TI Homologous Recombination in Core Genomes Facilitates Marine Bacterial
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Acquisition of ecologically relevant genes is common among ocean bacteria, but whether it has a major impact on genome evolution in marine environments remains unknown. Here, we analyzed the core genomes of 16 phylogenetically diverse and ecologically relevant bacterioplankton lineages, each consisting of up to five genomes varying at the strain level. Statistical approaches identified from each lineage up to similar to 50 loci showing anomalously high divergence at synonymous sites, which is best explained by recombination with distantly related organisms. The enriched gene categories in these outlier loci match well with the characteristics previously identified as the key phenotypes of these lineages. Examples are antibiotic synthesis and detoxification in Phaeobacter inhibens, exopolysaccharide production in Alteromonas macleodii, hydrocarbon degradation in Marinobacter hydrocarbonoclasticus, and cold adaptation in Pseudo-alteromonas haloplanktis. Intriguingly, the outlier loci feature polysaccharide catabolism in Cellulophaga baltica but not in Cellulophaga lytica, consistent with their primary habitat preferences in macroalgae and beach sands, respectively. Likewise, analysis of Prochlorococcus showed that photosynthesis-related genes listed in the outlier loci are found only in the high-light-adapted ecotype and not in the low-light adapted ecotype. These observations strongly suggest that recombination with distant relatives is a key mechanism driving the ecological diversification among marine bacterial lineages.
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C1 [Luo, Haiwei] Chinese Univ Hong Kong, Simon FS Li Marine Sci Lab, Sch Life Sci, Shatin, Hong Kong, Peoples R China.
   Chinese Univ Hong Kong, Partner State Key Lab Agrobiotechnol, Shatin, Hong Kong, Peoples R China.
RP Luo, HW (corresponding author), Chinese Univ Hong Kong, Simon FS Li Marine Sci Lab, Sch Life Sci, Shatin, Hong Kong, Peoples R China.
EM hluo2006@gmail.com
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NR 86
TC 15
Z9 17
PD JUN
PY 2018
VL 84
IS 11
AR e02545-17
DI 10.1128/AEM.02545-17
UT WOS:000432467000017
DA 2025-07-30
ER

PT J
AU Biller, SJ
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AF Biller, Steven J.
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DT Article
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C1 [Biller, Steven J.; Ryan, M. Gray; Li, Jasmine] Wellesley Coll, Dept Biol Sci, Wellesley, MA 02481 USA.
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RP Biller, SJ (corresponding author), Wellesley Coll, Dept Biol Sci, Wellesley, MA 02481 USA.
EM sbiller@wellesley.edu
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NR 96
TC 1
Z9 1
PD MAR 3
PY 2025
VL 16
IS 1
AR 2126
DI 10.1038/s41467-025-57276-w
UT WOS:001437303700029
DA 2025-07-30
ER

PT J
AU Steinman, M
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   Sponaugle, S
   Sutherland, KR
   Thompson, AW
AF Steinman, Melissa
   Schmid, Moritz S.
   Cowen, Robert K.
   Sponaugle, Su
   Sutherland, Kelly R.
   Thompson, Anne W.
TI The microorganisms associated with doliolids in a productive coastal
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SO LIMNOLOGY AND OCEANOGRAPHY
DT Article
AB Doliolids have a unique ability to impact the marine microbial community through bloom events and filter feeding. Their predation on large eukaryotic microorganisms is established and evidence of predation on smaller prokaryotic microorganisms is beginning to emerge. We studied the association between microorganisms and wild-caught doliolids in the Northern California Current system. Doliolids were collected during bloom events identified at three different shelf locations with variable upwelling intensity. We discovered doliolids were associated with a range of prokaryotic microbial functional groups, which included free-living pelagic Archaea, SAR11, and picocyanobacteria. The results suggest the possibility that doliolids could feed on the smallest members of the microbial community, expanding our understanding of doliolid feeding and microbial mortality. Given the ability of doliolids to clear large portions of seawater by filtration and their high abundance in this system, we suggest that doliolids could be an important player in shaping the microbial community structure of the Northern California Current system.
C1 [Steinman, Melissa; Thompson, Anne W.] Portland State Univ, Dept Biol, Portland, OR 97201 USA.
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RP Thompson, AW (corresponding author), Portland State Univ, Dept Biol, Portland, OR 97201 USA.
EM awt@pdx.edu
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NR 50
TC 2
Z9 2
PD JAN
PY 2025
VL 70
IS 1
BP 244
EP 257
DI 10.1002/lno.12748
EA DEC 2024
UT WOS:001370904200001
DA 2025-07-30
ER

PT J
AU Sun, CC
   Zhao, WJ
   Yue, WZ
   Cheng, H
   Sun, FL
   Wang, YT
   Wu, ML
   Engel, A
   Wang, YS
AF Sun, Cui-Ci
   Zhao, Wen-Jie
   Yue, Wei-Zhong
   Cheng, Hao
   Sun, Fu-Lin
   Wang, Yu-Tu
   Wu, Mei-Lin
   Engel, Anja
   Wang, You-Shao
TI Polymeric carbohydrates utilization separates microbiomes into niches:
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   the inner shelf of the Pearl River Estuary, China
SO FRONTIERS IN MICROBIOLOGY
DT Article
AB Polymeric carbohydrates are abundant and their recycling by microbes is a key process of the ocean carbon cycle. A deeper analysis of carbohydrate-active enzymes (CAZymes) can offer a window into the mechanisms of microbial communities to degrade carbohydrates in the ocean. In this study, metagenomic genes encoding microbial CAZymes and sugar transporter systems were predicted to assess the microbial glycan niches and functional potentials of glycan utilization in the inner shelf of the Pearl River Estuary (PRE). The CAZymes gene compositions were significantly different between in free-living (0.2-3 & mu;m, FL) and particle-associated (>3 & mu;m, PA) bacteria of the water column and between water and surface sediments, reflecting glycan niche separation on size fraction and selective degradation in depth. Proteobacteria and Bacteroidota had the highest abundance and glycan niche width of CAZymes genes, respectively. At the genus level, Alteromonas (Gammaproteobacteria) exhibited the greatest abundance and glycan niche width of CAZymes genes and were marked by a high abundance of periplasmic transporter protein TonB and members of the major facilitator superfamily (MFS). The increasing contribution of genes encoding CAZymes and transporters for Alteromonas in bottom water contrasted to surface water and their metabolism are tightly related with particulate carbohydrates (pectin, alginate, starch, lignin-cellulose, chitin, and peptidoglycan) rather than on the utilization of ambient-water DOC. Candidatus Pelagibacter (Alphaproteobacteria) had a narrow glycan niche and was primarily preferred for nitrogen-containing carbohydrates, while their abundant sugar ABC (ATP binding cassette) transporter supported the scavenging mode for carbohydrate assimilation. Planctomycetota, Verrucomicrobiota, and Bacteroidota had similar potential glycan niches in the consumption of the main component of transparent exopolymer particles (sulfated fucose and rhamnose containing polysaccharide and sulfated-N-glycan), developing considerable niche overlap among these taxa. The most abundant CAZymes and transporter genes as well as the widest glycan niche in the abundant bacterial taxa implied their potential key roles on the organic carbon utilization, and the high degree of glycan niches separation and polysaccharide composition importantly influenced bacterial communities in the coastal waters of PRE. These findings expand the current understanding of the organic carbon biotransformation, underlying the size-fractionated glycan niche separation near the estuarine system.
C1 [Sun, Cui-Ci; Zhao, Wen-Jie; Yue, Wei-Zhong; Cheng, Hao; Sun, Fu-Lin; Wu, Mei-Lin; Wang, You-Shao] Chinese Acad Sci, South China Sea Inst Oceanol, State Key Lab Trop Oceanog, Guangzhou, Peoples R China.
   [Sun, Cui-Ci; Sun, Fu-Lin; Wang, Yu-Tu; Wang, You-Shao] Chinese Acad Sci, Daya Bay Marine Biol Res Stn, Shenzhen, Peoples R China.
   [Zhao, Wen-Jie] Univ Chinese Acad Sci, Beijing, Peoples R China.
   [Engel, Anja] GEOMAR Helmholtz Ctr Ocean Res Kiel, Kiel, Germany.
RP Wang, YS (corresponding author), Chinese Acad Sci, South China Sea Inst Oceanol, State Key Lab Trop Oceanog, Guangzhou, Peoples R China.; Wang, YS (corresponding author), Chinese Acad Sci, Daya Bay Marine Biol Res Stn, Shenzhen, Peoples R China.
EM yswang@scsio.ac.cn
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NR 107
TC 10
Z9 10
PD JUN 21
PY 2023
VL 14
AR 1180321
DI 10.3389/fmicb.2023.1180321
UT WOS:001020002000001
DA 2025-07-30
ER

PT J
AU Ferla, MP
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AF Ferla, Matteo P.
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TI Primordial-like enzymes from bacteria with reduced genomes
SO MOLECULAR MICROBIOLOGY
DT Article
AB The first cells probably possessed rudimentary metabolic networks, built using a handful of multifunctional enzymes. The promiscuous activities of modern enzymes are often assumed to be relics of this primordial era; however, by definition these activities are no longer physiological. There are many fewer examples of enzymes using a single active site to catalyze multiple physiologically-relevant reactions. Previously, we characterized the promiscuous alanine racemase (ALR) activity of Escherichia coli cystathionine -lyase (CBL). Now we have discovered that several bacteria with reduced genomes lack alr, but contain metC (encoding CBL). We characterized the CBL enzymes from three of these: Pelagibacter ubique, the Wolbachia endosymbiont of Drosophila melanogaster (wMel) and Thermotoga maritima. Each is a multifunctional CBL/ALR. However, we also show that CBL activity is no longer required in these bacteria. Instead, the wMel and T. maritima enzymes are physiologically bi-functional alanine/glutamate racemases. They are not highly active, but they are clearly sufficient. Given the abundance of the microorganisms using them, we suggest that much of the planet's biochemistry is carried out by enzymes that are quite different from the highly-active exemplars usually found in textbooks. Instead, primordial-like enzymes may be an essential part of the adaptive strategy associated with streamlining.
C1 [Ferla, Matteo P.; Brewster, Jodi L.; Hall, Kelsi R.; Patrick, Wayne M.] Univ Otago, Dept Biochem, Dunedin, New Zealand.
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RP Patrick, WM (corresponding author), Univ Otago, Dept Biochem, Dunedin, New Zealand.
EM wayne.patrick@otago.ac.nz
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NR 70
TC 31
Z9 38
PD AUG
PY 2017
VL 105
IS 4
BP 508
EP 524
DI 10.1111/mmi.13737
UT WOS:000407427000002
DA 2025-07-30
ER

PT J
AU Liu, JL
   Xue, CX
   Wang, JY
   Crombie, AT
   Carrión, O
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   Zheng, YF
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AF Liu, Jingli
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   Todd, Jonathan D.
TI Oceanospirillales containing the DMSP lyase DddD are key
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SO MICROBIOME
DT Article
AB Background: Ubiquitous and diverse marine microorganisms utilise the abundant organosulfur molecule dimethylsulfoniopropionate (DMSP), the main precursor of the climate-active gas dimethylsulfide (DMS), as a source of carbon, sulfur and/or signalling molecules. However, it is currently difficult to discern which microbes actively catabolise DMSP in the environment, why they do so and the pathways used.
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C1 [Liu, Jingli; Xue, Chun-Xu; Wang, Jinyan; Liu, Ji; Zheng, Yanfen; Zhang, Xiao-Hua] Ocean Univ China, Frontiers Sci Ctr Deep Ocean Multispheres & Earth, Qingdao, Peoples R China.
   [Liu, Jingli; Xue, Chun-Xu; Wang, Jinyan; Liu, Ji; Zheng, Yanfen; Zhang, Xiao-Hua] Ocean Univ China, Coll Marine Life Sci, Qingdao, Peoples R China.
   [Liu, Jingli; Wang, Jinyan; Carrion, Ornella; Johnston, Andrew W. B.; Liu, Ji; Zheng, Yanfen; Todd, Jonathan D.] Univ East Anglia, Sch Biol Sci, Norwich Res Pk, Norwich, Norfolk, England.
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   [Zhang, Xiao-Hua] Qingdao Natl Lab Marine Sci & Technol, Lab Marine Ecol & Environm Sci, Qingdao, Peoples R China.
RP Zhang, XH (corresponding author), Ocean Univ China, Frontiers Sci Ctr Deep Ocean Multispheres & Earth, Qingdao, Peoples R China.; Zhang, XH (corresponding author), Ocean Univ China, Coll Marine Life Sci, Qingdao, Peoples R China.; Todd, JD (corresponding author), Univ East Anglia, Sch Biol Sci, Norwich Res Pk, Norwich, Norfolk, England.; Zhang, XH (corresponding author), Qingdao Natl Lab Marine Sci & Technol, Lab Marine Ecol & Environm Sci, Qingdao, Peoples R China.
EM xhzhang@ouc.edu.cn; jonathan.todd@uea.ac.uk
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NR 102
TC 16
Z9 16
PD JUL 27
PY 2022
VL 10
IS 1
AR 110
DI 10.1186/s40168-022-01304-0
UT WOS:000830722800001
DA 2025-07-30
ER

PT J
AU Murray, AE
   Peng, V
   Tyler, C
   Wagh, P
AF Murray, Alison E.
   Peng, Vivian
   Tyler, Charlotte
   Wagh, Protima
TI Marine bacterioplankton biomass, activity and community structure in the
   vicinity of Antarctic icebergs
SO DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY
DT Article
AB We studied marine bacterioplankton in the Scotia Sea in June 2008 and in the northwest Weddell Sea in March to mid April 2009 in waters proximal to three free-drifting icebergs (SS-1, A-43k, and C-18a), in a region with a high density of smaller icebergs (iceberg alley), and at stations that were upstream of the iceberg trajectories designated as far-field reference sites that were between 16-75 km away. Hydrographic parameters were used to define water masses in which comparisons between bacterioplankton-associated characteristics (abundance, leucine incorporation into protein, aminopeptidase activities and community structure) within and between water masses could be made. Early winter Scotia Sea bacterioplankton had low levels of cells and low heterotrophic production rates in the upper 50 m. Influences of the icebergs on bacterioplankton at this time of year were minimal, if not deleterious, as we found lower levels of heterotrophic production near A-43k in comparison to stations > 16 km away. Additionally, the results point to small but significant differences in cell abundance, heterotrophic production, and community structure between the two icebergs studied. These icebergs differed greatly in size and the findings suggest that the larger iceberg had a greater effect. In the NW Weddell Sea in March-mid April bacterioplankton were twice as abundant and had heterotrophic productions rates that were 8-fold higher than what we determined in the Scotia Sea, though levels were still quite low, which is typical for autumn. We did not detect direct iceberg-related influences on the bacterioplankton characteristics studied here. Clues to understanding bacterioplankton responses may lie in the details of community structure, as there were some significant differences in community structure in the winter water and underlying upper circumpolar deep-water masses between stations occupied close to C-18a and at stations 18 km away (i.e. Polaribacter and Pelagibacter-related 16S rRNA gene fragments were at low levels at the 18 km stations), though higher resolution, high throughput profiling tools will be needed to pinpoint specific organisms and ecological types. Likewise, a better understanding of local to regional scale structure of bacterioplankton communities is necessary. The relationship between bacterioplankton abundance and heterotrophic production suggested bottom up processes were controlling bacterioplankton during March - mid-April in the NW Weddell Sea, and that variation in temperature may play a role in substrate utilization. Trophic linkages seen between phytoplankton and zooplankton were mirrored by tight coupling between primary production and heterotrophic production in the waters immediately surrounding C-18a and in iceberg alley (but not at stations 18 and 75 km away), suggesting that indirect effects on bacterioplankton may also be important. Overall, the results show that bacterioplankton, dominated by Rhodobacteracae Pelagibacter, and uncultivated Gammaproteobacteria groups were minimally influenced by icebergs in the regions and seasons studied here - at least directly - though further work addressing different scales, sizes of icebergs, and seasons is needed to better understand bacterioplankton-associated ecological processes and carbon cycling in regions of high iceberg production. (C) 2010 Elsevier Ltd. All rights reserved.
C1 [Murray, Alison E.; Peng, Vivian; Tyler, Charlotte; Wagh, Protima] Desert Res Inst, Reno, NV 89512 USA.
RP Murray, AE (corresponding author), Desert Res Inst, 2215 Reggio Pkwy, Reno, NV 89512 USA.
EM Alison.Murray@dri.edu
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NR 61
TC 16
Z9 17
PD JUN
PY 2011
VL 58
IS 11-12
BP 1407
EP 1421
DI 10.1016/j.dsr2.2010.11.021
UT WOS:000291079800013
DA 2025-07-30
ER

PT J
AU McCain, JSP
   Allen, AE
   Bertrand, EM
AF McCain, J. Scott P.
   Allen, Andrew E.
   Bertrand, Erin M.
TI Proteomic traits vary across taxa in a coastal Antarctic phytoplankton
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SO ISME JOURNAL
DT Article
AB Production and use of proteins is under strong selection in microbes, but it is unclear how proteome-level traits relate to ecological strategies. We identified and quantified proteomic traits of eukaryotic microbes and bacteria through an Antarctic phytoplankton bloom using in situ metaproteomics. Different taxa, rather than different environmental conditions, formed distinct clusters based on their ribosomal and photosynthetic proteomic proportions, and we propose that these characteristics relate to ecological differences. We defined and used a proteomic proxy for regulatory cost, which showed that SAR11 had the lowest regulatory cost of any taxa we observed at our summertime Southern Ocean study site. Haptophytes had lower regulatory cost than diatoms, which may underpin haptophyte-to-diatom bloom progression in the Ross Sea. We were able to make these proteomic trait inferences by assessing various sources of bias in metaproteomics, providing practical recommendations for researchers in the field. We have quantified several proteomic traits (ribosomal and photosynthetic proteomic proportions, regulatory cost) in eukaryotic and bacterial taxa, which can then be incorporated into trait-based models of microbial communities that reflect resource allocation strategies.
C1 [McCain, J. Scott P.; Bertrand, Erin M.] Dalhousie Univ, Dept Biol, Halifax, NS, Canada.
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RP Bertrand, EM (corresponding author), Dalhousie Univ, Dept Biol, Halifax, NS, Canada.; Bertrand, EM (corresponding author), Dalhousie Univ, Ctr Comparat Genom & Evolutionary Bioinformat, Halifax, NS, Canada.
EM erin.bertrand@dal.ca
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NR 71
TC 9
Z9 9
PD FEB
PY 2022
VL 16
IS 2
BP 569
EP 579
DI 10.1038/s41396-021-01084-9
EA SEP 2021
UT WOS:000693351100001
DA 2025-07-30
ER

PT J
AU Kiefl, E
   Esen, OC
   Miller, SE
   Kroll, KL
   Willis, AD
   Rappé, MS
   Pan, T
   Eren, AM
AF Kiefl, Evan
   Esen, Ozcan C.
   Miller, Samuel E.
   Kroll, Kourtney L.
   Willis, Amy D.
   Rappe, Michael S.
   Pan, Tao
   Eren, A. Murat
TI Structure-informed microbial population genetics elucidate selective
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SO SCIENCE ADVANCES
DT Article
AB Comprehensive sampling of natural genetic diversity with metagenomics enables highly resolved insights into the interplay between ecology and evolution. However, resolving adaptive, neutral, or purifying processes of evolution from intrapopulation genomic variation remains a challenge, partly due to the sole reliance on gene sequences to interpret variants. Here, we describe an approach to analyze genetic variation in the context of predicted protein structures and apply it to a marine microbial population within the SAR11 subclade 1a.3.V, which dominates low-latitude surface oceans. Our analyses reveal a tight association between genetic variation and protein structure. In a central gene in nitrogen metabolism, we observe decreased occurrence of nonsynon- ymous variants from ligand-binding sites as a function of nitrate concentrations, revealing genetic targets of distinct evolutionary pressures maintained by nutrient availability. Our work yields insights into the governing principles of evolution and enables structure-aware investigations of microbial population genetics.
C1 [Kiefl, Evan; Esen, Ozcan C.; Miller, Samuel E.; Eren, A. Murat] Univ Chicago, Dept Med, Chicago, IL 60637 USA.
   [Kiefl, Evan; Kroll, Kourtney L.] Univ Chicago, Grad Program Biophys Sci, Chicago, IL 60637 USA.
   [Miller, Samuel E.; Eren, A. Murat] Marine Biol Lab, Josephine Bay Paul Ctr Comparat Mol Biol & Evolut, Woods Hole, MA 02543 USA.
   [Willis, Amy D.] Univ Washington, Dept Biostat, Seattle, WA 98195 USA.
   [Rappe, Michael S.] Univ Hawaii Manoa, Hawaii Inst Marine Biol, Kaneohe, HI 96822 USA.
   [Pan, Tao] Univ Chicago, Dept Biochem & Mol Biol, Chicago, IL 60637 USA.
   [Eren, A. Murat] Carl von Ossietzky Univ Oldenburg, Inst Chem & Biol Marine Environm, Oldenburg, Germany.
   [Eren, A. Murat] Alfred Wegener Inst Polar & Marine Res, Bremerhaven, Germany.
   [Eren, A. Murat] Helmholtz Inst Funct Marine Biodivers, Oldenburg, Germany.
RP Kiefl, E; Eren, AM (corresponding author), Univ Chicago, Dept Med, Chicago, IL 60637 USA.; Kiefl, E (corresponding author), Univ Chicago, Grad Program Biophys Sci, Chicago, IL 60637 USA.; Eren, AM (corresponding author), Marine Biol Lab, Josephine Bay Paul Ctr Comparat Mol Biol & Evolut, Woods Hole, MA 02543 USA.; Eren, AM (corresponding author), Carl von Ossietzky Univ Oldenburg, Inst Chem & Biol Marine Environm, Oldenburg, Germany.; Eren, AM (corresponding author), Alfred Wegener Inst Polar & Marine Res, Bremerhaven, Germany.; Eren, AM (corresponding author), Helmholtz Inst Funct Marine Biodivers, Oldenburg, Germany.
EM ekiefl@uchicago.edu; meren@hifmb.de
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NR 92
TC 9
Z9 9
PD FEB 24
PY 2023
VL 9
IS 8
AR eabq4632
DI 10.1126/sciadv.abq4632
UT WOS:000948176900021
DA 2025-07-30
ER

PT J
AU Gu, JH
   Wang, XJ
   Ma, XP
   Sun, Y
   Xiao, X
   Luo, HW
AF Gu, Jiahao
   Wang, Xiaojun
   Ma, Xiaopan
   Sun, Ying
   Xiao, Xiang
   Luo, Haiwei
TI Unexpectedly high mutation rate of a deep-sea hyperthermophilic
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DT Article
AB Deep-sea hydrothermal vents resemble the early Earth, and thus the dominant Thermococcaceae inhabitants, which occupy an evolutionarily basal position of the archaeal tree and take an obligate anaerobic hyperthermophilic free-living lifestyle, are likely excellent models to study the evolution of early life. Here, we determined that unbiased mutation rate of a representative species, Thermococcus eurythermalis, exceeded that of all known free-living prokaryotes by 1-2 orders of magnitude, and thus rejected the long-standing hypothesis that low mutation rates were selectively favored in hyperthermophiles. We further sequenced multiple and diverse isolates of this species and calculated that T. eurythermalis has a lower effective population size than other free-living prokaryotes by 1-2 orders of magnitude. These data collectively indicate that the high mutation rate of this species is not selectively favored but instead driven by random genetic drift. The availability of these unusual data also helps explore mechanisms underlying microbial genome size evolution. We showed that genome size is negatively correlated with mutation rate and positively correlated with effective population size across 30 bacterial and archaeal lineages, suggesting that increased mutation rate and random genetic drift are likely two important mechanisms driving microbial genome reduction. Future determinations of the unbiased mutation rate of more representative lineages with highly reduced genomes such as Prochlorococcus and Pelagibacterales that dominate marine microbial communities are essential to test these hypotheses.
C1 [Gu, Jiahao; Ma, Xiaopan; Xiao, Xiang] Shanghai Jiao Tong Univ, State Key Lab Microbial Metab, Shanghai 200240, Peoples R China.
   [Gu, Jiahao; Ma, Xiaopan; Xiao, Xiang] Shanghai Jiao Tong Univ, State Key Lab Ocean Engn, Shanghai 200240, Peoples R China.
   [Wang, Xiaojun; Sun, Ying; Luo, Haiwei] Chinese Univ Hong Kong, Sch Life Sci, Simon FS Li Marine Sci Lab, Shatin, Hong Kong, Peoples R China.
   [Wang, Xiaojun; Sun, Ying; Luo, Haiwei] Chinese Univ Hong Kong, State Key Lab Agrobiotechnol, Shatin, Hong Kong, Peoples R China.
   [Luo, Haiwei] Chinese Univ Hong Kong, Shenzhen Res Inst, Shenzhen 518000, Peoples R China.
   [Luo, Haiwei] Southern Marine Sci & Engn Guangdong Lab Guangzho, Hong Kong Branch, Hong Kong, Peoples R China.
RP Xiao, X (corresponding author), Shanghai Jiao Tong Univ, State Key Lab Microbial Metab, Shanghai 200240, Peoples R China.; Xiao, X (corresponding author), Shanghai Jiao Tong Univ, State Key Lab Ocean Engn, Shanghai 200240, Peoples R China.; Luo, HW (corresponding author), Chinese Univ Hong Kong, Sch Life Sci, Simon FS Li Marine Sci Lab, Shatin, Hong Kong, Peoples R China.; Luo, HW (corresponding author), Chinese Univ Hong Kong, State Key Lab Agrobiotechnol, Shatin, Hong Kong, Peoples R China.; Luo, HW (corresponding author), Chinese Univ Hong Kong, Shenzhen Res Inst, Shenzhen 518000, Peoples R China.; Luo, HW (corresponding author), Southern Marine Sci & Engn Guangdong Lab Guangzho, Hong Kong Branch, Hong Kong, Peoples R China.
EM zjxiao2018@sjtu.edu.cn; hluo2006@gmail.com
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NR 45
TC 9
Z9 10
PD JUN
PY 2021
VL 15
IS 6
BP 1862
EP 1869
DI 10.1038/s41396-020-00888-5
EA JAN 2021
UT WOS:000608003100010
DA 2025-07-30
ER

PT J
AU Zhang, R
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   Liu, Y
   Zhang, HL
   Zhao, ZH
   Zou, LY
AF Zhang, Rui
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DT Article
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C1 [Zhang, Rui] Guangdong Ocean Univ, Shenzhen Inst, Shenzhen 518108, Peoples R China.
   [Zhang, Rui; Zhang, Honglian] Guangdong Ocean Univ, Coll Food Sci & Technol, Modern Biochem Expt Ctr, Zhanjiang 518088, Guangdong, Peoples R China.
   [Liu, Wenchao; Liu, Yu; Zhao, Zhihui] Guangdong Ocean Univ, Coll Agr, Zhanjiang 524088, Guangdong, Peoples R China.
   [Zou, Lingyun] Jinan Univ, Baoan Womens & Childrens Hosp, Shenzhen 518102, Peoples R China.
RP Zhang, R (corresponding author), Guangdong Ocean Univ, Shenzhen Inst, Shenzhen 518108, Peoples R China.
EM zhangrui168@gdou.edu.cn
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UT WOS:000653749800008
DA 2025-07-30
ER

PT J
AU Hopkinson, BM
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AF Hopkinson, Brian M.
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TI Iron transporters in marine prokaryotic genomes and metagenomes
SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB In the pelagic environment, iron is a scarce but essential micronutrient. The iron acquisition capabilities of selected marine bacteria have been investigated, but the recent proliferation of marine prokaryotic genomes and metagenomes offers a more comprehensive picture of microbial iron uptake pathways in the ocean. Searching these data sets, we were able to identify uptake mechanisms for Fe3+, Fe2+ and iron chelates (e.g. siderophore and haem iron complexes). Transport of iron chelates is accomplished by TonB-dependent transporters (TBDTs). After clustering the TBDTs from marine prokaryotic genomes, we identified TBDT clusters for the transport of hydroxamate and catecholate siderophore iron complexes and haem using gene neighbourhood analysis and co-clustering of TBDTs of known function. The genomes also contained two classes of siderophore biosynthesis genes: NRPS (non-ribosomal peptide synthase) genes and NIS (NRPS Independent Siderophore) genes. The most common iron transporters, in both the genomes and metagenomes, were Fe3+ ABC transporters. Iron uptake-related TBDTs and siderophore biosynthesis genes were less common in pelagic marine metagenomes relative to the genomic data set, in part because Pelagibacter ubique and Prochlorococcus species, which almost entirely lacked these Fe uptake systems, dominate the metagenomes. Our results are largely consistent with current knowledge of iron speciation in the ocean, but suggest that in certain niches the ability to acquire siderophores and/or haem iron chelates is beneficial.
C1 [Hopkinson, Brian M.] Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
   [Barbeau, Katherine A.] Univ Calif San Diego, Scripps Inst Oceanog, La Jolla, CA 92093 USA.
RP Hopkinson, BM (corresponding author), Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
EM bmhopkin@uga.edu
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NR 56
TC 88
Z9 97
PD JAN
PY 2012
VL 14
IS 1
SI SI
BP 114
EP 128
DI 10.1111/j.1462-2920.2011.02539.x
UT WOS:000302538900010
DA 2025-07-30
ER

PT J
AU Jensen, S
   Bourne, DG
   Hovland, M
   Murrell, JC
AF Jensen, Sigmund
   Bourne, David G.
   Hovland, Martin
   Murrell, J. Colin
TI High diversity of microplankton surrounds deep-water coral reef in the
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SO FEMS MICROBIOLOGY ECOLOGY
DT Article
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C1 [Jensen, Sigmund] Univ Bergen, Dept Biol, Bergen, Norway.
   [Bourne, David G.] Australian Inst Marine Sci, Townsville, Qld 4810, Australia.
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RP Jensen, S (corresponding author), Univ Bergen, Dept Biol, Bergen, Norway.
EM sigmund.jensen@bio.uib.no
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TC 16
Z9 18
PD OCT
PY 2012
VL 82
IS 1
BP 75
EP 89
DI 10.1111/j.1574-6941.2012.01408.x
UT WOS:000308580900007
DA 2025-07-30
ER

PT J
AU Green, R
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AF Green, Robert
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TI Independent evolutionary origins of functional polyamine biosynthetic
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SO MOLECULAR MICROBIOLOGY
DT Article
AB We have identified gene fusions of polyamine biosynthetic enzymes S-adenosylmethionine decarboxylase (AdoMetDC, speD) and aminopropyltransferase (speE) orthologues in diverse bacterial phyla. Both domains are functionally active and we demonstrate the novel de novo synthesis of the triamine spermidine from the diamine putrescine by fusion enzymes from beta-proteobacterium Delftia acidovorans and delta-proteobacterium Syntrophus aciditrophicus, in a Delta speDE gene deletion strain of Salmonella enterica sv. Typhimurium. Fusion proteins from marine alpha-proteobacterium Candidatus Pelagibacter ubique, actinobacterium Nocardia farcinica, chlorobi species Chloroherpeton thalassium, and beta-proteobacterium D. acidovorans each produce a different profile of non-native polyamines including sym-norspermidine when expressed in Escherichia coli. The different aminopropyltransferase activities together with phylogenetic analysis confirm independent evolutionary origins for some fusions. Comparative genomic analysis strongly indicates that gene fusions arose by merger of adjacent open reading frames. Independent fusion events, and horizontal and vertical gene transfer contributed to the scattered phyletic distribution of the gene fusions. Surprisingly, expression of fusion genes in E. coli and S. Typhimurium revealed novel latent spermidine catabolic activity producing non-native 1,3-diaminopropane in these species. We have also identified fusions of polyamine biosynthetic enzymes agmatine deiminase and N-carbamoylputrescine amidohydrolase in archaea, and of S-adenosylmethionine decarboxylase and ornithine decarboxylase in the single-celled green alga Micromonas.
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NR 49
TC 19
Z9 21
PD AUG
PY 2011
VL 81
IS 4
BP 1109
EP 1124
DI 10.1111/j.1365-2958.2011.07757.x
UT WOS:000293752500020
DA 2025-07-30
ER

PT J
AU Wang, Z
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AF Wang, Zhang
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TI An integrated phylogenomic approach toward pinpointing the origin of
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SO SCIENTIFIC REPORTS
DT Article
AB Overwhelming evidence supports the endosymbiosis theory that mitochondria originated once from the Alphaproteobacteria. However, its exact position in the tree of life remains highly debated. This is because systematic errors, including biased taxonomic sampling, high evolutionary rates and sequence composition bias have long plagued the mitochondrial phylogenetics. In this study, we address this issue by 1) increasing the taxonomic representation of alphaproteobacterial genomes by sequencing 18 phylogenetically novel species. They include 5 Rickettsiales and 4 Rhodospirillales, two orders that have shown close affiliations with mitochondria previously, 2) using a set of 29 slowly evolving mitochondria-derived nuclear genes that are less biased than mitochondria-encoded genes as the alternative "well behaved'' markers for phylogenetic analysis, 3) applying site heterogeneous mixture models that account for the sequence composition bias. With the integrated phylogenomic approach, we are able to for the first time place mitochondria unequivocally within the Rickettsiales order, as a sister clade to the Rickettsiaceae and Anaplasmataceae families, all subtended by the Holosporaceae family. Our results suggest that mitochondria most likely originated from a Rickettsiales endosymbiont already residing in the host, but not from the distantly related free-living Pelagibacter and Rhodospirillales.
C1 [Wang, Zhang; Wu, Martin] Univ Virginia, Dept Biol, Charlottesville, VA 22904 USA.
RP Wu, M (corresponding author), Univ Virginia, Dept Biol, 485 McCormick Rd, Charlottesville, VA 22904 USA.
EM mw4yv@virginia.edu
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NR 76
TC 98
Z9 115
PD JAN 22
PY 2015
VL 5
AR 7949
DI 10.1038/srep07949
UT WOS:000348164600006
DA 2025-07-30
ER

PT J
AU Reboul, G
   Moreira, D
   Annenkova, NV
   Bertolino, P
   Vershinin, KE
   López-García, P
AF Reboul, Guillaume
   Moreira, David
   Annenkova, Nataliia V.
   Bertolino, Paola
   Vershinin, Konstantin E.
   Lopez-Garcia, Purificacion
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   freshwater lake
SO ISME JOURNAL
DT Article
AB Lake Baikal is the deepest (~1.6 km) and most voluminous freshwater reservoir on Earth. Compared to plankton, its benthos remains poorly explored. Here, we ask whether latitude and/or depth determine benthic microbial community structure and how Baikal communities compare to those of other freshwater, brackish and marine sediments. To answer, we collected sediment upper layers (0-1 cm) across a ~600 km North-South transect covering the three basins of the lake and from littoral to bathybenthic depths (0.5-1450 m). Analysis of 16S and 18S rRNA gene amplicon sequences revealed communities with high richness and evenness where rare operational taxonomic units (OTUs) collectively dominated. Archaea represented up to 25% or prokaryotic sequences. Baikal sediments harbored typically marine eukaryotic and prokaryotic OTUs recently identified in some lakes (diplonemids, Bolidophyceae, Mamiellales, SAR202, marine-like Synechococcus, Pelagibacterales) but also SAR324, Syndiniales and Radiolaria. We hypothesize that, beyond the salinity barrier, adaptation to oligotrophy explains the presence of these otherwise typically marine lineages. Baikal core benthic communities were relatively stable across sites and seemed not determined by depth or latitude. Comparative analyses with other freshwater, brackish and marine prokaryotic sediment communities confirmed the distinctness of Baikal benthos, which include elements of similarity to marine and hydrothermally influenced systems.
C1 [Reboul, Guillaume; Moreira, David; Bertolino, Paola; Lopez-Garcia, Purificacion] Univ Paris Saclay, Ctr Natl Rech Sci CNRS, Ecol Systemat Evolut, AgroParisTech, Orsay, France.
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RP López-García, P (corresponding author), Univ Paris Saclay, Ctr Natl Rech Sci CNRS, Ecol Systemat Evolut, AgroParisTech, Orsay, France.
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NR 20
TC 7
Z9 8
PD NOV
PY 2021
VL 15
IS 11
BP 3412
EP 3417
DI 10.1038/s41396-021-01011-y
UT WOS:000709410600022
DA 2025-07-30
ER

PT J
AU Borchardt, T
   Fisher, K
   Ebling, AM
   Westrich, JR
   Xian, P
   Holmes, CD
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   Lipp, EK
   Wetz, MS
   Ottesen, EA
AF Borchardt, Trace
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   Westrich, Jason R.
   Xian, Peng
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SO LIMNOLOGY AND OCEANOGRAPHY
DT Article
AB Deposition of aerosolized desert dust can affect marine microbial community structure and function through pulsed addition of limiting micro- and macronutrients. However, few studies have captured responses to dust deposition in situ following trans-oceanic transport. We conducted a 26-d time series evaluating biogeochemical and microbial community response to Saharan dust deposition in surface waters in the subtropical western Atlantic (Florida Keys National Marine Sanctuary, U.S.A.). Following periods of elevated atmospheric dust concentrations, particulate and dissolved iron concentrations increased in surface waters. Autotrophic picoeukaryote abundance increased rapidly, followed by increases in the abundance of heterotrophic bacteria and Synechococcus. Concomitant to cell count changes, we observed successional shifts in bacterial community composition. The relative abundances of Prochlorococcus and Pelagibacter declined with dust arrival, while relative abundance of heterotrophic bacteria increased, beginning with Vibrionales and followed sequentially by Chrysophyceae, Rhodobacteriaceae, and Flavobacteriaceae. Finally, a peak in Synechococcus cyanobacteria was observed. These results provide new insight into microbial community succession in response to Saharan dust deposition, their association with temporal dynamics in surface water dissolved and particulate iron concentrations, and a potential role for bioprocessing of dust particles in shaping marine microbial responses to deposition events.
C1 [Borchardt, Trace; Ottesen, Elizabeth A.] Univ Georgia, Dept Microbiol, Athens, GA 30602 USA.
   [Fisher, Kelsey, V] Texas A&M Univ Corpus Christi, Dept Life Sci, Corpus Christi, TX USA.
   [Ebling, Alina M.; Holmes, Christopher D.; Landing, William M.] Florida State Univ, Dept Earth Ocean & Atmospher Sci, Tallahassee, FL 32306 USA.
   [Westrich, Jason R.; Lipp, Erin K.] Univ Georgia, Dept Environm Hlth Sci, Athens, GA 30602 USA.
   [Xian, Peng] US Naval Res Lab, Washington, DC USA.
   [Wetz, Michael S.] Texas A&M Univ Corpus Christi, Harte Res Inst Gulf Mexico Studies, Corpus Christi, TX USA.
RP Ottesen, EA (corresponding author), Univ Georgia, Dept Microbiol, Athens, GA 30602 USA.
EM ottesen@uga.edu
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NR 67
TC 11
Z9 13
PD JAN
PY 2020
VL 65
IS 1
BP 191
EP 203
DI 10.1002/lno.11291
EA AUG 2019
UT WOS:000480094800001
DA 2025-07-30
ER

PT J
AU Alonso-Gutiérrez, J
   Lekunberri, I
   Teira, E
   Gasol, JM
   Figueras, A
   Novoa, B
AF Alonso-Gutierrez, Jorge
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   Figueras, Antonio
   Novoa, Beatriz
TI Bacterioplankton composition of the coastal upwelling system of 'Ria de
   Vigo', NW Spain
SO FEMS MICROBIOLOGY ECOLOGY
DT Article
AB Catalysed reported deposition-FISH and clone libraries indicated that Roseobacter, followed by Bacteroidetes, and some gammaproteobacterial groups such as SAR86, dominated the composition of bacterioplankton in Ria de Vigo, NW Spain, in detriment to SARI I (almost absent in this upwelling ecosystem). Since we sampled four times during the year, we observed pronounced changes in the structure of each bacterioplankton component, particularly for the Roseobacter lineage. We suggest that such variations in the coastal upwelling ecosystem of Ria de Vigo were associated with the characteristic phytoplankton communities of the four different hydrographical situations: winter mixing, spring bloom, summer stratification, and autumn upwelling. We retrieved new sequences among the major marine bacterial lineages, particularly among Roseobacter, SAR11, and especially SAR86. The spring community was dominated by two Roseobacter clades that had previously been related to phytoplankton blooms. In the other seasons, communities with higher diversity than the spring one were detected.
C1 [Alonso-Gutierrez, Jorge; Figueras, Antonio; Novoa, Beatriz] CSIC, Inst Invest Marinas, E-36208 Vigo, Spain.
   [Lekunberri, Itziar; Gasol, Josep M.] CSIC, Inst Ciencias Mar, Barcelona, Spain.
   [Teira, Eva] Univ Vigo, Dept Ecol & Biol Anim, Vigo 36310, Spain.
RP Novoa, B (corresponding author), CSIC, Inst Invest Marinas, Eduardo Cabello 6, E-36208 Vigo, Spain.
EM virus@iim.csic.es
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NR 57
TC 38
Z9 42
PD DEC
PY 2009
VL 70
IS 3
BP 493
EP 505
DI 10.1111/j.1574-6941.2009.00766.x
UT WOS:000272348800015
DA 2025-07-30
ER

PT J
AU Zhao, ZH
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   Orellana, MV
   Herndl, GJ
AF Zhao, Zihao
   Amano, Chie
   Reinthaler, Thomas
   Orellana, Monica V.
   Herndl, Gerhard J.
TI Substrate uptake patterns shape niche separation in marine prokaryotic
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DT Article
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C1 [Zhao, Zihao; Amano, Chie; Reinthaler, Thomas; Herndl, Gerhard J.] Univ Vienna, Dept Funct & Evolutionary Ecol, Biooceanog & Marine Biol Unit, Djerassipl 1, A-1030 Vienna, Austria.
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RP Zhao, ZH; Herndl, GJ (corresponding author), Univ Vienna, Dept Funct & Evolutionary Ecol, Biooceanog & Marine Biol Unit, Djerassipl 1, A-1030 Vienna, Austria.; Herndl, GJ (corresponding author), Royal Netherlands Inst Sea Res, NIOZ, Dept Marine Microbiol & Biogeochem, Den Burg, Netherlands.; Herndl, GJ (corresponding author), Univ Vienna, Environm & Climate Res Hub, Althanstr 14, A-1090 Vienna, Austria.
EM zihao.zhao@univie.ac.at; gerhard.herndl@univie.ac.at
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ER

PT J
AU Kujawinski, EB
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AF Kujawinski, Elizabeth B.
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DT Article
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RP Kujawinski, EB (corresponding author), Woods Hole Oceanog Inst, Dept Marine Chem & Geochem, 360 Woods Hole Rd MS 4, Woods Hole, MA 02543 USA.
EM ekujawinski@whoi.edu
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TC 201
Z9 237
PD AUG 1
PY 2009
VL 73
IS 15
BP 4384
EP 4399
DI 10.1016/j.gca.2009.04.033
UT WOS:000267876200006
DA 2025-07-30
ER

PT J
AU Zhou, Y
   Zhu, HH
   Yao, Q
AF Zhou, Yang
   Zhu, Honghui
   Yao, Qing
TI Contrasting P acquisition strategies of the bacterial communities
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SO ENVIRONMENTAL MICROBIOLOGY REPORTS
DT Article
AB Phosphorus (P) cycling is a fundamental process driven by microorganisms, and plants can regulate P cycling directly or via their influence on the soil microbial community. However, the differential P cycling patterns associated with legumes and grass are largely unknown. Therefore, we investigated the microbial community involved in P cycling in subtropical soil grown with stylo (Stylosanthes guianensis, legume) or bahiagrass (Paspalum notatum, grass) using metagenomic sequencing. P fractionation indicated that sparingly soluble inorganic P (Pi) accounted for approximately 75% of P pool. Bacteria involved in sparingly soluble Pi solubilization (pqq, gad, JEN) were more abundant in bahiagrass soil, with Candidatus Pelagibacter, Trichodesmium, Neorickettsia, Nitrobacter, Paraburkholderia, Candidatus Solibacter, Burkholderia as major contributors. In contrast, bacteria involved in organic P (Po) mineralization (php, glpQ, phn) were more abundant in stylo soil, consistent with phosphatase activity and Frankia, Kyrpidia, Thermobispora, Streptomyces, Rhodococcus were major contributors. Bacteria taking up low molecular-weight Po were more abundant in stylo soil than in bahiagrass soil, while those taking up Pi were less abundant. These data suggest that bacterial communities associated with legumes and grass develop contrasting P acquisition strategies, highlighting the possibility of intercropping with legumes and grass for better P cycling.
C1 [Zhou, Yang; Yao, Qing] South China Agr Univ, Guangdong Prov Key Lab Microbial Signals & Dis Co, Guangdong Engn Res Ctr Grass Sci, Coll Hort,Guangdong Engn Ctr Litchi, Guangzhou 510642, Guangdong, Peoples R China.
   [Zhou, Yang; Zhu, Honghui] Guangdong Inst Microbiol, State Key Lab Appl Microbiol Southern China, Guangdong Prov Key Lab Microbial Culture Collect, Guangzhou 510070, Guangdong, Peoples R China.
RP Yao, Q (corresponding author), South China Agr Univ, Guangdong Prov Key Lab Microbial Signals & Dis Co, Guangdong Engn Res Ctr Grass Sci, Coll Hort,Guangdong Engn Ctr Litchi, Guangzhou 510642, Guangdong, Peoples R China.; Zhu, HH (corresponding author), Guangdong Inst Microbiol, State Key Lab Appl Microbiol Southern China, Guangdong Prov Key Lab Microbial Culture Collect, Guangzhou 510070, Guangdong, Peoples R China.
EM zhuhh@gdim.cn; yaoqscau@scau.edu.cn
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TC 21
Z9 23
PD JUN
PY 2018
VL 10
IS 3
BP 310
EP 319
DI 10.1111/1758-2229.12641
UT WOS:000433572100010
DA 2025-07-30
ER

PT J
AU Kim, JG
   Park, SJ
   Quan, ZX
   Jung, MY
   Cha, IT
   Kim, SJ
   Kim, KH
   Yang, EJ
   Kim, YN
   Lee, SH
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AF Kim, Jong-Geol
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DT Article
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C1 [Kim, Jong-Geol; Jung, Man-Young; Cha, In-Tae; Kim, So-Jeong; Rhee, Sung-Keun] Chungbuk Natl Univ, Dept Microbiol, Cheongju 361763, South Korea.
   [Park, Soo-Je] Jeju Natl Univ, Dept Biol, Cheju 690756, South Korea.
   [Quan, Zhe-Xue] Fudan Univ, Sch Life Sci, Dept Microbiol & Microbial Engn, Shanghai 200433, Peoples R China.
   [Kim, Kyoung-Ho] Pukyong Natl Univ, Dept Microbiol, Pusan 608737, South Korea.
   [Yang, Eun-Jin; Kim, Young-Nam; Lee, Sang-Hoon] Korea Polar Res Inst, Div Polar Climate Res, Inchon 406840, South Korea.
   [Kim, Young-Nam] Korea Marine Environm Management Corp KOEM, Marine Ecosyst Management Team, Seoul 135870, South Korea.
RP Rhee, SK (corresponding author), Chungbuk Natl Univ, Dept Microbiol, 12 Gaeshin Dong, Cheongju 361763, South Korea.
EM rhees@chungbuk.ac.kr
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PY 2014
VL 16
IS 6
SI SI
BP 1566
EP 1578
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UT WOS:000337512000011
DA 2025-07-30
ER

PT J
AU Kato, S
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SO FRONTIERS IN MICROBIOLOGY
DT Article
AB To directly access the sub-seafloor microbial communities, seafloor drilling has been done in a deep-sea hydrothermal field of the Suiyo Seamount, Izu-Bonin Arc, Western Pacific. In the present study, crustal fluids were collected from the boreholes, and the bacterial and archaeal communities in the fluids were investigated by culture-independent molecular analysis based on 16S rRNA gene sequences. Bottom seawater, sands, rocks, sulfide mound, and chimneys were also collected around the boreholes and analyzed for comparisons. Comprehensive analysis revealed the characteristics of the microbial community composition in the crustal fluids. Phylotypes closely related to cultured species, e.g., Alteromonas, Halomonas, Marinobacter, were relatively abundant in some crustal fluid samples, whereas the phylotypes related to Pelagibacter and the SUP05-group were relatively abundant in the seawater samples. Phylotypes related to other uncultured environmental clones in Alphaproteobacteria and Gammaproteobacteria were relatively abundant in the sand, rock, sulfide mound, and chimney samples. Furthermore, comparative analysis with previous studies of the Suiyo Seamount crustal fluids indicates the change in the microbial community composition for 3years. Our results provide novel insights into the characteristics of the microbial communities in crustal fluids beneath a deep-sea hydrothermal field.
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RP Yamagishi, A (corresponding author), Tokyo Univ Pharm & Life Sci, Dept Mol Biol, 1432-1 Horinouchi, Hachioji, Tokyo 1920392, Japan.
EM yamagish@toyaku.ac.jp
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NR 35
TC 19
Z9 20
PD APR 17
PY 2013
VL 4
AR 85
DI 10.3389/fmicb.2013.00085
UT WOS:000331051700001
DA 2025-07-30
ER

PT J
AU Espinosa-Asuar, L
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AF Espinosa-Asuar, Laura
   Escalante, Ana E.
   Falcon, Luisa I.
   Bonilla-Rosso, German
   Ramirez-Barahona, Santiago
   Eguiarte, Luis E.
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TI Analysis of three molecular methods to describe sea Yucatan, Mexico
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SO HIDROBIOLOGICA
DT Article
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RP Espinosa-Asuar, L (corresponding author), Univ Nacl Autonoma Mexico, Inst Ecol, Dept Ecol Evolut, AP 70-275, Mexico City 04510, DF, Mexico.
EM souza@unam.mx
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NR 66
TC 0
Z9 1
PD DEC
PY 2014
VL 24
IS 3
BP 257
EP 270
UT WOS:000353094000009
DA 2025-07-30
ER

PT J
AU Bryson, S
   Li, Z
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   Hettich, RL
   Mayali, X
   Pan, C
   Mueller, RS
AF Bryson, Samuel
   Li, Zhou
   Pett-Ridge, Jennifer
   Hettich, Robert L.
   Mayali, Xavier
   Pan, Chongle
   Mueller, Ryan S.
TI Proteomic Stable Isotope Probing Reveals Taxonomically Distinct Patterns
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SO MSYSTEMS
DT Article
AB Heterotrophic marine bacterioplankton are a critical component of the carbon cycle, processing nearly a quarter of annual primary production, yet defining how substrate utilization preferences and resource partitioning structure microbial communities remains a challenge. In this study, proteomic stable isotope probing (proteomic SIP) was used to characterize population-specific assimilation of dissolved free amino acids (DFAAs), a major source of dissolved organic carbon for bacterial secondary production in aquatic environments. Microcosms of seawater collected from Newport, Oregon, and Monterey Bay, California, were incubated with 1 mu M C-13-labeled amino acids for 15 and 32 h. The taxonomic compositions of microcosm metaproteomes were highly similar to those of the sampled natural communities, with Rhodobacteriales, SAR11, and Flavobacteriales representing the dominant taxa. Analysis of C-13 incorporation into protein biomass allowed for quantification of the isotopic enrichment of identified proteins and subsequent determination of differential amino acid assimilation patterns between specific bacterioplankton populations. Proteins associated with Rhodobacterales tended to have a significantly high frequency of C-13-enriched peptides, opposite the trend for Flavobacteriales and SAR11 proteins. Rhodobacterales proteins associated with amino acid transport and metabolism had an increased frequency of C-13-enriched spectra at time point 2. Alteromonadales proteins also had a significantly high frequency of C-13-enriched peptides, particularly within ribosomal proteins, demonstrating their rapid growth during incubations. Overall, proteomic SIP facilitated quantitative comparisons of DFAA assimilation by specific taxa, both between sympatric populations and between protein functional groups within discrete populations, allowing an unprecedented examination of population level metabolic responses to resource acquisition in complex microbial communities.
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C1 [Bryson, Samuel; Mueller, Ryan S.] Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
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RP Mueller, RS (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
EM ryan.mueller@oregonstate.edu
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TC 31
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PD MAR-APR
PY 2016
VL 1
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AR e00027-15
DI 10.1128/mSystems.00027-15
UT WOS:000408191200002
DA 2025-07-30
ER

PT J
AU Alonso-Sáez, L
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AF Alonso-Saez, Laura
   Moran, Xose Anxelu G.
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TI Low activity of lytic pelagiphages in coastal marine waters
SO ISME JOURNAL
DT Article
AB Phages infect marine bacteria impacting their dynamics, diversity and physiology, but little is known about specific phage-host interactions in situ. We analyzed the joint dynamics in the abundance of phage-related transcripts, as an indicator of viral lytic activity, and their potential hosts using a metatranscriptomic dataset obtained over 2 years in coastal temperate waters of the NE Atlantic. Substantial temporal variability was identified in the expression levels of different phages, likely in response to host availability. Indeed, a significant positive relationship between the abundance of transcripts from some of the most abundant phage types (infecting SAR11, SAR116 and cyanobacteria) and their putative hosts was found. Yet, the ratio of increase in phage transcripts per host cell was significantly lower for pelagiphages than for the HMO-2011 phage, which infects SAR116. Despite the high abundance of pelagiphages in the ocean, they may be less active than other phage types in coastal waters.
C1 [Alonso-Saez, Laura] AZTI, Marine Res Div, Sukarrieta, Spain.
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   [Moran, Xose Anxelu G.] KAUST, Red Sea Res Ctr, Biol & Environm Sci & Engn Div, Thuwal, Saudi Arabia.
   [Clokie, Martha R. J.] Univ Leicester, Dept Infect Immun & Inflammat, Leicester, Leics, England.
RP Alonso-Sáez, L (corresponding author), AZTI, Marine Res Div, Sukarrieta, Spain.; Alonso-Sáez, L (corresponding author), Ctr Oceanog Gijon Xixon, IEO, Gijon, Xixon, Spain.
EM laura@azti.es
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PT J
AU Morris, RM
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AF Morris, Robert M.
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DT Review
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RP Morris, RM (corresponding author), Univ Washington, Sch Oceanog, Seattle, WA 98195 USA.
EM morrisrm@uw.edu; rachel.spietz@montana.edu
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NR 81
TC 20
Z9 21
PY 2022
VL 14
BP 261
EP 275
DI 10.1146/annurev-marine-010419-010814
UT WOS:000788648800012
DA 2025-07-30
ER

PT J
AU Lindh, MV
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AF Lindh, Markus V.
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TI Consequences of increased terrestrial dissolved organic matter and
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SO AMBIO
DT Article
AB Predicted increases in runoff of terrestrial dissolved organic matter (DOM) and sea surface temperatures implicate substantial changes in energy fluxes of coastal marine ecosystems. Despite marine bacteria being critical drivers of marine carbon cycling, knowledge of compositional responses within bacterioplankton communities to such disturbances is strongly limited. Using 16S rRNA gene pyrosequencing, we examined bacterioplankton population dynamics in Baltic Sea mesocosms with treatments combining terrestrial DOM enrichment and increased temperature. Among the 200 most abundant taxa, 62 % either increased or decreased in relative abundance under changed environmental conditions. For example, SAR11 and SAR86 populations proliferated in combined increased terrestrial DOM/temperature mesocosms, while the hgcI and CL500-29 clades (Actinobacteria) decreased in the same mesocosms. Bacteroidetes increased in both control mesocosms and in the combined increased terrestrial DOM/temperature mesocosms. These results indicate considerable and differential responses among distinct bacterial populations to combined climate change effects, emphasizing the potential of such effects to induce shifts in ecosystem function and carbon cycling in the future Baltic Sea.
C1 [Lindh, Markus V.; Lundin, Daniel; Pinhassi, Jarone] Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, S-39182 Kalmar, Sweden.
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RP Pinhassi, J (corresponding author), Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, S-39182 Kalmar, Sweden.
EM markusvlindh@gmail.com; robert.lefebure@msc.org;
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NR 48
TC 59
Z9 73
PD JUN
PY 2015
VL 44
SU 3
SI SI
BP S402
EP S412
DI 10.1007/s13280-015-0659-3
UT WOS:000362290800008
DA 2025-07-30
ER

PT J
AU Hwang, J
   Oh, EG
   Jin, Y
AF Hwang, Jinik
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TI Metagenomic Analysis of Seasonal Variations in Viral Dynamics and
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SO JOURNAL OF MARINE SCIENCE AND ENGINEERING
DT Article
AB Jeju, the largest island in Korea, is the most economically important in terms of marine aquaculture. We investigated the marine viral composition adjacent to Jeju Island over four seasons in 2022 and sequenced DNA libraries extracted from samples in March, June, September, and December using Illumina HiSeq 2000. We obtained 212,402, 186,542, 235,441, and 224,513 contigs from the four-season samples, respectively. Among the identified metagenomes, bacteriophages were dominant in all the samples. Bacillus phage G was the dominant species in March and June, whereas Pelagibacter phage HTVC 008M was the dominant species in September and December. Additionally, the number of viruses that infected algal hosts was higher in December than in other seasons. Marine viruses appeared in all seasons and infected marine vertebrates such as fish. Functional analysis using MG-RAST revealed that cell wall- and capsule-related metabolism groups were activated in March and June, whereas virulence-, disease-, and defense-related metabolism groups were activated in September and December. Conclusively, this study revealed seasonal changes in marine viral communities in the sea adjacent to Jeju Island. Our data will be useful in identifying emerging marine viral pathogens and for further community studies on marine organisms.
C1 [Hwang, Jinik; Oh, Eun Gyoung] Natl Inst Fisheries Sci, West Sea Fisheries Inst, Incheon 22383, South Korea.
   [Jin, Youngguk] Natl Inst Fisheries Sci, South Sea Fisheries Res Inst, Yeosu 59780, South Korea.
RP Hwang, J (corresponding author), Natl Inst Fisheries Sci, West Sea Fisheries Inst, Incheon 22383, South Korea.
EM jinike12@korea.kr; ohdagu@korea.kr; jyg4jj@korea.kr
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NR 37
TC 0
Z9 0
PD SEP
PY 2024
VL 12
IS 9
AR 1480
DI 10.3390/jmse12091480
UT WOS:001323372500001
DA 2025-07-30
ER

PT J
AU Matcher, GF
   Dorrington, RA
   Henninger, TO
   Froneman, PW
AF Matcher, G. F.
   Dorrington, R. A.
   Henninger, T. O.
   Froneman, P. W.
TI Insights into the bacterial diversity in a freshwater-deprived
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SO WATER SA
DT Article
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C1 [Matcher, G. F.; Dorrington, R. A.] Rhodes Univ, Dept Biochem Microbiol & Biotechnol, ZA-6140 Grahamstown, South Africa.
   [Henninger, T. O.; Froneman, P. W.] Rhodes Univ, Dept Zool & Entomol, ZA-6140 Grahamstown, South Africa.
RP Matcher, GF (corresponding author), Rhodes Univ, Dept Biochem Microbiol & Biotechnol, POB 94, ZA-6140 Grahamstown, South Africa.
EM g.matcher@ru.ac.za
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NR 61
TC 19
Z9 24
PD JUL
PY 2011
VL 37
IS 3
BP 381
EP 390
UT WOS:000293341500013
DA 2025-07-30
ER

PT J
AU Han, D
   Richter-Heitmann, T
   Kim, IN
   Choy, E
   Park, KT
   Unno, T
   Kim, J
   Nam, SI
AF Han, Dukki
   Richter-Heitmann, Tim
   Kim, Il-Nam
   Choy, Eunjung
   Park, Ki-Tae
   Unno, Tatsuya
   Kim, Jungman
   Nam, Seung-Il
TI Survey of Bacterial Phylogenetic Diversity During the Glacier Melting
   Season in an Arctic Fjord
SO MICROBIAL ECOLOGY
DT Article
AB To understand bacterial biogeography in response to the hydrographic impact of climate change derived from the Arctic glacier melting, we surveyed bacterial diversity and community composition using bacterial 16S rRNA gene metabarcoding in the seawaters of Kongsfjorden, Svalbard, during summer 2016. In the present study, bacterial biogeography in the Kongsfjorden seawaters showed distinct habitat patterns according to water mass classification and habitat transition between Atlantic and fjord surface waters. Moreover, we estimated phylogenetic diversity of bacterial communities using the net relatedness, nearest taxon, and beta nearest taxon indices. We found the influence of freshwater input from glacier melting in shaping bacterial assemblage composition through the stochastic model. We further evaluated bacterial contributions to phytoplankton-derived dimethylsulfoniopropionate (DMSP) using a quantitative PCR (qPCR) measurement with demethylation (dmdA) and cleavage (dddP) genes of two fundamentally different processes. Our qPCR results imply that bacterial DMSP degradation follows the Atlantic inflow during summer in Kongsfjorden. These findings suggest that the Atlantic inflow and glacial melting influence bacterial community composition and assembly processes and thus affect the degradation of phytoplankton-derived organic matter in an Arctic fjord.
C1 [Han, Dukki; Unno, Tatsuya] Jeju Natl Univ, Jeju 63243, Jeju Special Se, South Korea.
   [Han, Dukki; Richter-Heitmann, Tim] Univ Bremen, Fac Biol Chem, Microbial Ecophysiol Grp, Bremen, Germany.
   [Kim, Il-Nam] Incheon Natl Univ, Dept Marine Sci, Incheon 22012, South Korea.
   [Choy, Eunjung; Park, Ki-Tae; Nam, Seung-Il] Korea Polar Res Inst, Incheon 21990, South Korea.
   [Kim, Jungman] Jeju Natl Univ, Res Inst Basic Sci, Jeju 63243, Jeju Special Se, South Korea.
RP Han, D (corresponding author), Jeju Natl Univ, Jeju 63243, Jeju Special Se, South Korea.; Han, D (corresponding author), Univ Bremen, Fac Biol Chem, Microbial Ecophysiol Grp, Bremen, Germany.; Nam, SI (corresponding author), Korea Polar Res Inst, Incheon 21990, South Korea.
EM dukkihan@gmail.com; sinam@kopri.re.kr
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NR 63
TC 11
Z9 12
PD APR
PY 2021
VL 81
IS 3
BP 579
EP 591
DI 10.1007/s00248-020-01616-4
EA OCT 2020
UT WOS:000578439400001
DA 2025-07-30
ER

PT J
AU von Arx, JN
   Kidane, AT
   Philippi, M
   Mohr, W
   Lavik, G
   Schorn, S
   Kuypers, MMM
   Milucka, J
AF von Arx, Jan N.
   Kidane, Abiel T.
   Philippi, Miriam
   Mohr, Wiebke
   Lavik, Gaute
   Schorn, Sina
   Kuypers, Marcel M. M.
   Milucka, Jana
TI Methylphosphonate-driven methane formation and its link to primary
   production in the oligotrophic North Atlantic
SO NATURE COMMUNICATIONS
DT Article
AB Methylphosphonate is an organic phosphorus compound used by microorganisms when phosphate, a key nutrient limiting growth in most marine surface waters, becomes unavailable. Microbial methylphosphonate use can result in the formation of methane, a potent greenhouse gas, in oxic waters where methane production is traditionally unexpected. The extent and controlling factors of such aerobic methane formation remain underexplored. Here, we show high potential net rates of methylphosphonate-driven methane formation (median 0.4 nmol methane L-1 d-1) in the upper water column of the western tropical North Atlantic. The rates are repressed but still quantifiable in the presence of in-situ or added phosphate, suggesting that some methylphosphonate-driven methane formation persists in phosphate-replete waters. The genetic potential for methylphosphonate utilisation is present in and transcribed by key photo- and heterotrophic microbial taxa, such as Pelagibacterales, SAR116, and Trichodesmium. While the large cyanobacterial nitrogen-fixers dominate in the surface layer, phosphonate utilisation by Alphaproteobacteria appears to become more important in deeper depths. We estimate that at our study site, a substantial part (median 11%) of the measured surface carbon fixation can be sustained by phosphorus liberated from phosphonate utilisation, highlighting the ecological importance of phosphonates in the carbon cycle of the oligotrophic ocean.
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C1 [von Arx, Jan N.; Kidane, Abiel T.; Philippi, Miriam; Mohr, Wiebke; Lavik, Gaute; Schorn, Sina; Kuypers, Marcel M. M.; Milucka, Jana] Max Planck Inst Marine Microbiol, Bremen, Germany.
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RP von Arx, JN (corresponding author), Max Planck Inst Marine Microbiol, Bremen, Germany.
EM jarx@mpi-bremen.de
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NR 90
TC 11
Z9 13
PD OCT 16
PY 2023
VL 14
IS 1
AR 6529
DI 10.1038/s41467-023-42304-4
UT WOS:001156991100004
DA 2025-07-30
ER

PT J
AU Lee, HB
   Jeong, DH
   Cho, BC
   Park, JS
AF Lee, Hyeon Been
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TI Comparative analyses of eight primer sets commonly used to target the
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SO FRONTIERS IN MARINE SCIENCE
DT Article
AB Next-generation sequencing (NGS), especially metabarcoding, is commonly used to study the diversity and distribution of microbes in diverse ecosystems. The choice of primer set is critical, given the drawbacks of short amplicons and amplicon sequencing bias inherent to metabarcoding. However, comparative analyses of primer sets have rarely been conducted using field samples. In this study, we compared eight commonly used primer sets, all targeting hypervariable regions in the bacterial 16S rRNA gene: 27F/338R (V1-V2), V2f/V3r (V2-V3), PRK341F/PRK806R (V3-V4), 341F/785R (V3-V4), 515F/806RB (V4), 515F/806R (V4), 515F-Y/926R (V4-V5), and B969F/BA1406R (V6-V8). We conducted NGS in triplicate, with >0.8 billion bases in total using coastal seawater samples. The representation of bacterial community composition varied significantly across the eight primer sets, despite being from the same sample. The 27F/338R primer set showed the highest number of operational taxonomic units (OTUs) and read counts, and accounted for 68% of all the order-level taxa found. Remarkably, a novel complementary combination of two primer sets, 27F/338R and 515F/806RB, covered 89% of all the orders that were present. Compared to other primer sets, this combination detected more OTUs of the orders Pelagibacterales and Rhodobacterales, which are ubiquitous in the oceans. As such, use of this combination in future studies may help to reduce diversity bias in ocean-derived samples, in particular temperate coastal samples.
C1 [Lee, Hyeon Been; Jeong, Dong Hyuk; Park, Jong Soo] Kyungpook Natl Univ, Dept Oceanog, Daegu, South Korea.
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RP Park, JS (corresponding author), Kyungpook Natl Univ, Dept Oceanog, Daegu, South Korea.
EM jongsoopark@knu.ac.kr
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NR 80
TC 9
Z9 11
PD OCT 9
PY 2023
VL 10
AR 1199116
DI 10.3389/fmars.2023.1199116
UT WOS:001089262300001
DA 2025-07-30
ER

PT J
AU Arikawa, S
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AF Arikawa, Sui
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TI Solid-state NMR for the characterization of retinal chromophore and
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SO BIOPHYSICS AND PHYSICOBIOLOGY
DT Article
AB TAT rhodopsin extracted from the marine bacterium SAR11 HIMB114 has a characteristic Thr- Ala-Thr motif and contains both protonated and deprotonated states of Schiff base at physiological pH conditions due to the low pKa. Here, using solid-state NMR spectroscopy, we investigated the 13C and 15N NMR signals of retinal in only the protonated state of TAT in the 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine/1-palmitoyl- 2-oleoyl-snglycero-3- phospho (1'-rac-glycerol) (POPE/POPG) membrane at weakly acidic conditions. In the 13C NMR spectrum of 13C retinal-labeled TAT rhodopsin, the isolated 14- 13C signals of 13-trans/15-anti and 13-cis/15-syn isomers were observed at a ratio of 7:3. 15N retinal protonated Schiff base (RPSB) had a significantly higher magnetic field resonance at 160 ppm. In 15N RPSB/.max analysis, the plot of TAT largely deviated from the trend based on the retinylidene-halide model compounds and microbial rhodopsins. Our findings indicate that the RPSB of TAT forms a very weak interaction with the counterion.
C1 [Arikawa, Sui; Kawamura, Izuru] Yokohama Natl Univ, Grad Sch Engn Sci, Yokohama, Kanagawa 2408501, Japan.
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RP Kawamura, I (corresponding author), Yokohama Natl Univ, Tokiwadai 79-5,Hodogaya Ku, Yokohama, Kanagawa 2408501, Japan.
EM izuruk@ynu.ac.jp
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NR 34
TC 6
Z9 6
PY 2023
VL 20
SU S
SI SI
DI 10.2142/biophysico.bppb-v20.s017
UT WOS:000994201700017
DA 2025-07-30
ER

PT J
AU Xie, ZX
   Yan, KQ
   Kong, LF
   Gai, YB
   Jin, T
   He, YB
   Wang, YY
   Chen, F
   Lin, L
   Lin, ZL
   Xu, HK
   Shao, ZZ
   Liu, SQ
   Wang, DZ
AF Xie, Zhang-Xian
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   Kong, Ling-Fen
   Gai, Ying-Bao
   Jin, Tao
   He, Yan-Bin
   Wang, Ya-Yu
   Chen, Feng
   Lin, Lin
   Lin, Zhi-Long
   Xu, Hong-Kai
   Shao, Zong-Ze
   Liu, Si-Qi
   Wang, Da-Zhi
TI Metabolic tuning of a stable microbial community in the surface
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SO MARINE LIFE SCIENCE & TECHNOLOGY
DT Article
AB Understanding the mechanisms, structuring microbial communities in oligotrophic ocean surface waters remains a major ecological endeavor. Functional redundancy and metabolic tuning are two mechanisms that have been proposed to shape microbial response to environmental forcing. However, little is known about their roles in the oligotrophic surface ocean due to less integrative characterization of community taxonomy and function. Here, we applied an integrated meta-omics-based approach, from genes to proteins, to investigate the microbial community of the oligotrophic northern Indian Ocean. Insignificant spatial variabilities of both genomic and proteomic compositions indicated a stable microbial community that was dominated by Prochlorococcus, Synechococcus, and SAR11. However, fine tuning of some metabolic functions that are mainly driven by salinity and temperature was observed. Intriguingly, a tuning divergence occurred between metabolic potential and activity in response to different environmental perturbations. Our results indicate that metabolic tuning is an important mechanism for sustaining the stability of microbial communities in oligotrophic oceans. In addition, integrated meta-omics provides a powerful tool to comprehensively understand microbial behavior and function in the ocean.
C1 [Xie, Zhang-Xian; Kong, Ling-Fen; Lin, Lin; Wang, Da-Zhi] Xiamen Univ, State Key Lab Marine Environm Sci, Coll Environm & Ecol, Xiamen 361005, Peoples R China.
   [Xie, Zhang-Xian] Xiamen Univ, Coll Ocean & Earth Sci, Xiamen 361005, Peoples R China.
   [Xie, Zhang-Xian; Lin, Lin; Wang, Da-Zhi] Sun Yat Sen Univ, Southern Marine Sci & Engn Guangdong Lab Zhuhai, Zhuhai 519082, Peoples R China.
   [Yan, Ke-Qiang; Jin, Tao; He, Yan-Bin; Wang, Ya-Yu; Lin, Zhi-Long; Xu, Hong-Kai; Liu, Si-Qi] BGI Shenzhen, Beishan Ind Zone 11th Bldg, Shenzhen 518083, Peoples R China.
   [Yan, Ke-Qiang; Xu, Hong-Kai] Univ Chinese Acad Sci, BGI Educ Ctr, Shenzhen 518083, Peoples R China.
   [Gai, Ying-Bao; Shao, Zong-Ze] Minist Nat Resources China, Key Lab Marine Genet Resources, Inst Oceanog 3, Xiamen 361005, Peoples R China.
   [Gai, Ying-Bao; Shao, Zong-Ze] Fujian Key Lab Marine Genet Resources, State Key Lab Breeding Base Marine Genet Resource, Xiamen 361005, Peoples R China.
   [Chen, Feng] Univ Maryland, Inst Marine & Environm Technol, Ctr Environm Sci, Baltimore, MD 21202 USA.
RP Wang, YY; Liu, SQ (corresponding author), BGI Shenzhen, Beishan Ind Zone 11th Bldg, Shenzhen 518083, Peoples R China.
EM dzwang@xmu.edu.cn; siqiliu@genomics.cn
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NR 57
TC 8
Z9 9
PD MAY
PY 2022
VL 4
IS 2
BP 277
EP 290
DI 10.1007/s42995-021-00119-6
EA JAN 2022
UT WOS:000736935600002
DA 2025-07-30
ER

PT J
AU Chénard, C
   Wijaya, W
   Vaulot, D
   dos Santos, AL
   Martin, P
   Kaur, A
   Lauro, FM
AF Chenard, Caroline
   Wijaya, Winona
   Vaulot, Daniel
   Lopes dos Santos, Adriana
   Martin, Patrick
   Kaur, Avneet
   Lauro, Federico M.
TI Temporal and spatial dynamics of Bacteria, Archaea and protists in
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SO SCIENTIFIC REPORTS
DT Article
AB Singapore, an equatorial island in South East Asia, is influenced by a bi-annual reversal of wind directions which defines two monsoon seasons. We characterized the dynamics of the microbial communities of Singapore coastal waters by collecting monthly samples between February 2017 and July 2018 at four sites located across two straits with different trophic status, and sequencing the V6-V8 region of the small sub-unit ribosomal RNA gene (rRNA gene) of Bacteria, Archaea, and Eukaryota. Johor Strait, which is subjected to wider environmental fluctuations from anthropogenic activities, presented a higher abundance of copiotrophic microbes, including Cellvibrionales and Rhodobacterales. The mesotrophic Singapore Strait, where the seasonal variability is caused by changes in the oceanographic conditions, harboured a higher proportion of typically marine microbe groups such as Synechococcales, Nitrosupumilales, SAR11, SAR86, Marine Group II Archaea and Radiolaria. In addition, we observed seasonal variability of the microbial communities in the Singapore Strait, which was possibly influenced by the alternating monsoon regime, while no seasonal pattern was detected in the Johor Strait.
C1 [Chenard, Caroline; Wijaya, Winona; Vaulot, Daniel; Lopes dos Santos, Adriana; Martin, Patrick; Kaur, Avneet; Lauro, Federico M.] Nanyang Technol Univ, Asian Sch Environm, 50 Nanyang Ave, Singapore 639798, Singapore.
   [Vaulot, Daniel] Sorbonne Univ, Ecol Marine Plankton Team, Stn Biol Roscoff, CNRS,UMR7144, F-29680 Roscoff, France.
   [Lopes dos Santos, Adriana] Univ Mayor, GEMA Ctr Genom Ecol & Environm, Camino Piramide, Santiago 5750, Chile.
   [Lauro, Federico M.] Nanyang Technol Univ, SCELSE, 60 Nanyang Dr, Singapore 637551, Singapore.
RP Lauro, FM (corresponding author), Nanyang Technol Univ, Asian Sch Environm, 50 Nanyang Ave, Singapore 639798, Singapore.; Lauro, FM (corresponding author), Nanyang Technol Univ, SCELSE, 60 Nanyang Dr, Singapore 637551, Singapore.
EM flauro@ntu.edu.sg
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NR 80
TC 37
Z9 39
PD NOV 8
PY 2019
VL 9
AR 16390
DI 10.1038/s41598-019-52648-x
UT WOS:000495373400008
DA 2025-07-30
ER

PT J
AU Coleman, ML
   Chisholm, SW
AF Coleman, Maureen L.
   Chisholm, Sallie W.
TI Ecosystem-specific selection pressures revealed through comparative
   population genomics
SO PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
   AMERICA
DT Article
AB Bacterial populations harbor vast genetic diversity that is continually shaped by abiotic and biotic selective pressures, as well as by neutral processes. Individuals coexisting in the same geographically defined population often have significantly different gene content, but whether this variation is largely adaptive or neutral remains poorly understood. Here we quantify heterogeneity in gene content for two model marine microbes, Prochlorococcus and Pelagibacter, within and between populations in the Atlantic and Pacific Oceans, to begin to understand the selective pressures that are shaping these "population genomes." We discovered a large fraction of genes that are rare in each population, reflecting continual gene transfer and loss. Despite this high variation within each population, only a few genes significantly differ in abundance between the two biogeochemically distinct environments; nearly all of these are related to phosphorus acquisition and are enriched in the Atlantic relative to the Pacific. Moreover, P-related genes from the two sites form phylogenetically distinct clusters, whereas housekeeping genes do not, consistent with a recent spread of adaptive P-related genes in the Atlantic populations. These findings implicate phosphorus availability as the dominant selective force driving divergence between these populations, and demonstrate the promise of this approach for revealing selective agents in more complex microbial systems.
C1 [Coleman, Maureen L.; Chisholm, Sallie W.] MIT, Dept Civil & Environm Engn, Cambridge, MA 02139 USA.
   [Chisholm, Sallie W.] MIT, Dept Biol, Cambridge, MA 02139 USA.
RP Chisholm, SW (corresponding author), MIT, Dept Civil & Environm Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA.
EM chisholm@mit.edu
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NR 50
TC 196
Z9 221
PD OCT 26
PY 2010
VL 107
IS 43
BP 18634
EP 18639
DI 10.1073/pnas.1009480107
UT WOS:000283677400074
DA 2025-07-30
ER

PT C
AU Chen, C
   Zhang, ZC
   Ding, AZ
   Wu, JY
   Xiao, JF
   Sun, YJ
AF Chen Cheng
   Zhang Zaichao
   Ding Aizhong
   Wu Jiayan
   Xiao Jingfa
   Sun Yujiao
BE Zhu, R
TI Bar-Coded Pyrosequencing Reveals the Bacterial Community during
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SO SECOND SREE CONFERENCE ON CHEMICAL ENGINEERING (CCE 2011)
SE Procedia Engineering
DT Proceedings Paper
CT 2nd SREE Conference on Chemical Engineering (CCE)
CY DEC 17-18, 2011
CL Macao, PEOPLES R CHINA
AB An understanding of bacterial community composition is a fundamental goal of identifying ecological efficiency caused by Microcystis bloom in aquatic system. In this study, we employed bar-coded 454 pyrosequencing approach to investigate the bacterial community variation during a Microcystis water bloom in Guanting Reservoir, Beijing. More than 140,000 sequences were generated and assigned to 7133 operational taxonomic units (OTUs) which belong to 18 phyla through Ribosomal Database Pyrosequencing (RDP) database. Microcystis was detected at low abundance in July then broke out and became the exclusive dominant genus in September. Meanwhile, bacteria composition changed dramatically after the Microcystis water bloom reflected by the decrease of bacteria abundance, diversity and evenness indices. The classify results indicated that dominant species in July were Pelagibacter, Haliscomenobacter, Rhodobacter and Fluviicola. In September, Methylotenera, Flavobacterium and Methylophilus were the dominant genera. It is worth noticing that all the dominant genera in July was more or less related to nitrogen and phosphorus cycling while in September, dominant genera Flavobacterium was reported as Microcystis lysing bacterium and may be a symptom of the coming postbloom phase of Microcystis water bloom in Guanting Reservoir. (C) 2010 Published by Elsevier Ltd. Selection and/or peer-review under responsibility of Society for Resources, Environment and Engineering
C1 [Chen Cheng; Ding Aizhong; Sun Yujiao] Beijing Normal Univ, Coll Water Sci, 19 Xinjiekouwai St, Beijing 100875, Peoples R China.
   [Zhang Zaichao; Wu Jiayan; Xiao Jingfa] Chinese Acad Sci, Beijing Inst Genom, Key Lab Genome Sci & Informat, CAS, Beijing 100029, Peoples R China.
RP Chen, C (corresponding author), Beijing Normal Univ, Coll Water Sci, 19 Xinjiekouwai St, Beijing 100875, Peoples R China.
EM sunyujiao@bnu.edu.cn
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DA 2025-07-30
ER

PT J
AU Thiele, S
   Vader, A
   Thomson, S
   Saubrekka, K
   Petelenz, E
   Müller, O
   Bratbak, G
   Ovreås, L
AF Thiele, Stefan
   Vader, Anna
   Thomson, Stuart
   Saubrekka, Karoline
   Petelenz, Elzbieta
   Mueller, Oliver
   Bratbak, Gunnar
   ovreas, Lise
TI Seasonality of the bacterial and archaeal community composition of the
   Northern Barents Sea
SO FRONTIERS IN MICROBIOLOGY
DT Article
AB The Barents Sea is a transition zone between the Atlantic and the Arctic Ocean. The ecosystem in this region is highly variable, and a seasonal baseline of biological factors is needed to monitor the effects of global warming. In this study, we report the results from the investigations of the bacterial and archaeal community in late winter, spring, summer, and early winter along a transect through the northern Barents Sea into the Arctic Ocean east of Svalbard using 16S rRNA metabarcoding. Winter samples were dominated by members of the SAR11 clade and a community of nitrifiers, namely Cand. Nitrosopumilus and LS-NOB (Nitrospinia), suggest a prevalence of chemoautotrophic metabolisms. During spring and summer, members of the Gammaproteobacteria (mainly members of the SAR92 and OM60(NOR5) clades, Nitrincolaceae) and Bacteroidia (mainly Polaribacter, Formosa, and members of the NS9 marine group), which followed a succession based on their utilization of different phytoplankton-derived carbon sources, prevailed. Our results indicate that Arctic marine bacterial and archaeal communities switch from carbon cycling in spring and summer to nitrogen cycling in winter and provide a seasonal baseline to study the changes in these processes in response to the effects of climate change.
C1 [Thiele, Stefan; Petelenz, Elzbieta; Mueller, Oliver; Bratbak, Gunnar; ovreas, Lise] Univ Bergen, Dept Biol Sci, Bergen, Norway.
   [Thiele, Stefan] Bjerknes Ctr Climate Res, Bergen, Norway.
   [Vader, Anna; Thomson, Stuart; ovreas, Lise] Univ Ctr Svalbard UNIS, Longyearbyen, Norway.
   [Saubrekka, Karoline] Univ Oslo, Dept Biosci, Oslo, Norway.
RP Thiele, S (corresponding author), Univ Bergen, Dept Biol Sci, Bergen, Norway.; Thiele, S (corresponding author), Bjerknes Ctr Climate Res, Bergen, Norway.
EM stefan.thiele@uib.no
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AR 1213718
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UT WOS:001033178800001
DA 2025-07-30
ER

PT J
AU Gronniger, JL
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AF Gronniger, Jessica L.
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TI Rapid changes in coastal ocean microbiomes uncoupled with shifts in
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Disturbances, here defined as events that directly alter microbial community composition, are commonly studied in host-associated and engineered systems. In spite of global change both altering environmental averages and increasing extreme events, there has been relatively little research into the causes, persistence and population-level impacts of disturbance in the dynamic coastal ocean. Here, we utilize 3 years of observations from a coastal time series to identify disturbances based on the largest week-over-week changes in the microbiome (i.e. identifying disturbance as events that alter the community composition). In general, these microbiome disturbances were not clearly linked to specific environmental factors and responsive taxa largely differed, aside from SAR11, which generally declined. However, several disturbance metagenomes identified increased phage-associated genes, suggesting that unexplained community shifts might be caused by increased mortality. Furthermore, a category 1 hurricane, the only event that would likely be classified a priori as an environmental disturbance, was not an outlier in microbiome composition, but did enhance a bloom in seasonally abundant phytoplankton. Thus, as extreme environmental changes intensify, assumptions of what constitutes a disturbance should be re-examined in the context of ecological history and microbiome responses.
C1 [Gronniger, Jessica L.; Wang, Zhao; Ward, Christopher S.; Mu, Han; Gu, Junyao; Johnson, Zackary I.; Hunt, Dana E.] Duke Univ, Marine Lab, Beaufort, NC 28516 USA.
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   [Johnson, Zackary I.; Hunt, Dana E.] Duke Univ, Biol & Civil & Environm Engn, Durham, NC 27708 USA.
RP Hunt, DE (corresponding author), Duke Univ, Marine Lab, Beaufort, NC 28516 USA.; Hunt, DE (corresponding author), Duke Univ, Biol & Civil & Environm Engn, Durham, NC 27708 USA.
EM dana.hunt@duke.edu
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NR 51
TC 3
Z9 5
PD SEP
PY 2022
VL 24
IS 9
BP 4167
EP 4177
DI 10.1111/1462-2920.16086
EA JUN 2022
UT WOS:000812435800001
DA 2025-07-30
ER

PT J
AU Ruiz-González, C
   Lefort, T
   Galí, M
   Sala, MM
   Sommaruga, R
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   Gasol, JM
AF Ruiz-Gonzalez, Clara
   Lefort, Thomas
   Gali, Marti
   Sala, Maria Montserrat
   Sommaruga, Ruben
   Simo, Rafel
   Gasol, Josep M.
TI Seasonal patterns in the sunlight sensitivity of bacterioplankton from
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SO FEMS MICROBIOLOGY ECOLOGY
DT Article
AB The sensitivity of coastal marine bacterioplankton to natural photosynthetically active radiation (PAR, 400700 nm) and ultraviolet radiation (UVR, 280400 nm) was evaluated in five experiments over a seasonal cycle in the Blanes Bay, NW Mediterranean Sea. Exposure to natural solar radiation generally inhibited bulk bacterial activities or damaged membrane integrity when irradiances were high (i.e. spring and summer experiments) and, in general, UVB (280320 nm) accounted for most of the inhibition. When assessing activity (3H-leucine uptake) at the single-cell level by microautoradiography and rRNA gene probing, seasonally varying responses and sensitivities were found among bacterial groups. While autumn and winter irradiances seemed too low to cause changes in activity, variable effects were found in spring and summer. SAR11 was consistently inhibited by UVR and PAR exposure, whereas Gammaproteobacteria and Bacteroidetes showed higher resistance. Roseobacter, Synechococcus and the NOR5 clade were occasionally photostimulated in their activity, mainly because of PAR. Our results indicate that a component of seasonality exists in the bacterial responses to solar radiation, which vary not only depending on the irradiance and the spectral characteristics, but also on the previous light history and the taxonomic composition of the community.
C1 [Ruiz-Gonzalez, Clara; Lefort, Thomas; Gali, Marti; Sala, Maria Montserrat; Simo, Rafel; Gasol, Josep M.] Inst Ciencies Mar CSIC, Pg Maritim Barceloneta 37-49, Barcelona 08003, Catalunya, Spain.
   [Sommaruga, Ruben] Univ Innsbruck, Lab Aquat Photobiol & Plankton Ecol, Inst Ecol, A-6020 Innsbruck, Austria.
RP Ruiz-González, C (corresponding author), Inst Ciencies Mar CSIC, Pg Maritim Barceloneta 37-49, Barcelona 08003, Catalunya, Spain.
EM clararg@icm.csic.es
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NR 67
TC 39
Z9 40
PD MAR
PY 2012
VL 79
IS 3
BP 661
EP 674
DI 10.1111/j.1574-6941.2011.01247.x
UT WOS:000299257300009
DA 2025-07-30
ER

PT J
AU Lambert, S
   Tragin, M
   Lozano, JC
   Ghiglione, JF
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   Bouget, FY
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AF Lambert, Stefan
   Tragin, Margot
   Lozano, Jean-Claude
   Ghiglione, Jean-Francois
   Vaulot, Daniel
   Bouget, Francois-Yves
   Galand, Pierre E.
TI Rhythmicity of coastal marine picoeukaryotes, bacteria and archaea
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SO ISME JOURNAL
DT Article
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C1 [Lambert, Stefan; Lozano, Jean-Claude; Ghiglione, Jean-Francois; Bouget, Francois-Yves] Sorbonne Univ, CNRS, Lab Oceanog Microbienne LOMIC, Observ Oceanol Banyuls, Paris, France.
   [Tragin, Margot; Vaulot, Daniel] Sorbonne Univ, CNRS, Stn Biol Roscoff, UMR7144, Paris, France.
   [Galand, Pierre E.] Sorbonne Univ, CNRS, Lab Ecogeochim Environm Benth LECOB, Observ Oceanol Banyuls, Paris, France.
RP Bouget, FY (corresponding author), Sorbonne Univ, CNRS, Lab Oceanog Microbienne LOMIC, Observ Oceanol Banyuls, Paris, France.; Galand, PE (corresponding author), Sorbonne Univ, CNRS, Lab Ecogeochim Environm Benth LECOB, Observ Oceanol Banyuls, Paris, France.
EM francois-yves.bouget@obs-banyuls.fr; pierre.galand@obs-banyuls.fr
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NR 61
TC 84
Z9 88
PD FEB
PY 2019
VL 13
IS 2
BP 388
EP 401
DI 10.1038/s41396-018-0281-z
UT WOS:000455747900012
DA 2025-07-30
ER

PT J
AU Hopkinson, BM
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AF Hopkinson, Brian M.
   Roe, Kelly L.
   Barbeau, Katherine A.
TI Heme uptake by Microscilla marina and evidence for heme uptake
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
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RP Hopkinson, BM (corresponding author), Princeton Univ, Dept Geosci, Princeton, NJ 08544 USA.
EM bhopkins@princeton.edu
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NR 53
TC 44
Z9 54
PD OCT
PY 2008
VL 74
IS 20
BP 6263
EP 6270
DI 10.1128/AEM.00964-08
UT WOS:000259985300012
DA 2025-07-30
ER

PT J
AU Martinez-Hernandez, F
   Fornas, O
   Martinez-Garcia, M
AF Martinez-Hernandez, Francisco
   Fornas, Oscar
   Martinez-Garcia, Manuel
TI Into the Dark: Exploring the Deep Ocean with Single-Virus Genomics
SO VIRUSES-BASEL
DT Article
AB Single-virus genomics (SVGs) has been successfully applied to ocean surface samples allowing the discovery of widespread dominant viruses overlooked for years by metagenomics, such as the uncultured virus vSAG 37-F6 infecting the ubiquitous Pelagibacter spp. In SVGs, one uncultured virus at a time is sorted from the environmental sample, whole-genome amplified, and sequenced. Here, we have applied SVGs to deep-ocean samples (200-4000 m depth) from global Malaspina and MEDIMAX expeditions, demonstrating the feasibility of this method in deep-ocean samples. A total of 1328 virus-like particles were sorted from the North Atlantic Ocean, the deep Mediterranean Sea, and the Pacific Ocean oxygen minimum zone (OMZ). For this proof of concept, sixty single viruses were selected at random for sequencing. Genome annotation identified 27 of these genomes as bona fide viruses, and detected three auxiliary metabolic genes involved in nucleotide biosynthesis and sugar metabolism. Massive protein profile analysis confirmed that these viruses represented novel viral groups not present in databases. Although they were not previously assembled by viromics, global fragment recruitment analysis showed a conserved profile of relative abundance of these viruses in all analyzed samples spanning different oceans. Altogether, these results reveal the feasibility in using SVGs in this vast environment to unveil the genomes of relevant viruses.
C1 [Martinez-Hernandez, Francisco; Martinez-Garcia, Manuel] Univ Alicante, Dept Physiol Genet & Microbiol, Alicante 03690, Spain.
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RP Martinez-Garcia, M (corresponding author), Univ Alicante, Dept Physiol Genet & Microbiol, Alicante 03690, Spain.
EM franmh@ua.es; oscar.fornas@upf.edu; m.martinez@ua.es
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NR 37
TC 6
Z9 6
PD JUL
PY 2022
VL 14
IS 7
AR 1589
DI 10.3390/v14071589
UT WOS:000833826100001
DA 2025-07-30
ER

PT J
AU Sosa, OA
   Repeta, DJ
   DeLong, EF
   Ashkezari, MD
   Karl, DM
AF Sosa, Oscar A.
   Repeta, Daniel J.
   DeLong, Edward F.
   Ashkezari, Mohammad D.
   Karl, David M.
TI Phosphate-limited ocean regions select for bacterial populations
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB In tropical and subtropical oceanic surface waters phosphate scarcity can limit microbial productivity. However, these environments also have bioavailable forms of phosphorus incorporated into dissolved organic matter (DOM) that microbes with the necessary transport and hydrolysis metabolic pathways can access to supplement their phosphorus requirements. In this study we evaluated how the environment shapes the abundance and taxonomic distribution of the bacterial carbon-phosphorus (C-P) lyase pathway, an enzyme complex evolved to extract phosphate from phosphonates. Phosphonates are organophosphorus compounds characterized by a highly stable C-P bond and are enriched in marine DOM. Similar to other known bacterial adaptions to low phosphate environments, C-P lyase was found to become more prevalent as phosphate concentrations decreased. C-P lyase was particularly enriched in the Mediterranean Sea and North Atlantic Ocean, two regions that feature sustained periods of phosphate depletion. In these regions, C-P lyase was prevalent in several lineages of Alphaproteobacteria (Pelagibacter, SAR116, Roseobacter and Rhodospirillales), Gammaproteobacteria, and Actinobacteria. The global scope of this analysis supports previous studies that infer phosphonate catabolism via C-P lyase is an important adaptive strategy implemented by bacteria to alleviate phosphate limitation and expands the known geographic extent and taxonomic affiliation of this metabolic pathway in the ocean.
C1 [Sosa, Oscar A.; DeLong, Edward F.; Karl, David M.] Univ Hawaii Manoa, Daniel K Inouye Ctr Microbial Oceanog, Res & Educ, Honolulu, HI 96822 USA.
   [Repeta, Daniel J.] Woods Hole Oceanog Inst, Dept Marine Chem & Geochem, Woods Hole, MA 02540 USA.
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   [Sosa, Oscar A.] Univ Puget Sound, Dept Biol, Tacoma, WA 98416 USA.
RP Sosa, OA (corresponding author), Univ Hawaii Manoa, Daniel K Inouye Ctr Microbial Oceanog, Res & Educ, Honolulu, HI 96822 USA.; Sosa, OA (corresponding author), Univ Puget Sound, Dept Biol, Tacoma, WA 98416 USA.
EM ososa@hawaii.edu
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NR 73
TC 86
Z9 99
PD JUL
PY 2019
VL 21
IS 7
BP 2402
EP 2414
DI 10.1111/1462-2920.14628
UT WOS:000474294900015
DA 2025-07-30
ER

PT J
AU Mena, C
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AF Mena, Catalina
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   Martin, Melissa
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   Sintes, Eva
TI Seasonal Niche Partitioning of Surface Temperate Open Ocean Prokaryotic
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SO FRONTIERS IN MICROBIOLOGY
DT Article
AB Surface microbial communities are exposed to seasonally changing environmental conditions, resulting in recurring patterns of community composition. However, knowledge on temporal dynamics of open ocean microbial communities remains scarce. Seasonal patterns and associations of taxa and oligotypes from surface and chlorophyll maximum layers in the western Mediterranean Sea were studied over a 2-year period. Summer stratification versus winter mixing governed not only the prokaryotic community composition and diversity but also the temporal dynamics and co-occurrence association networks of oligotypes. Flavobacteriales, Rhodobacterales, SAR11, SAR86, and Synechococcales oligotypes exhibited contrasting seasonal dynamics, and consequently, specific microbial assemblages and potential inter-oligotype connections characterized the different seasons. In addition, oligotypes composition and dynamics differed between surface and deep chlorophyll maximum (DCM) prokaryotic communities, indicating depth-related environmental gradients as a major factor affecting association networks between closely related taxa. Taken together, the seasonal and depth specialization of oligotypes suggest temporal dynamics of community composition and metabolism, influencing ecosystem function and global biogeochemical cycles. Moreover, our results indicate highly specific associations between microbes, pointing to keystone ecotypes and fine-tuning of the microbes realized niche.
C1 [Mena, Catalina; Reglero, Patricia; Balbin, Rosa; Martin, Melissa; Santiago, Rocio; Sintes, Eva] Inst Espanol Oceanog, Ctr Oceanog Balears, Ecosyst Oceanog Grp GRECO, Palma De Mallorca, Spain.
RP Mena, C (corresponding author), Inst Espanol Oceanog, Ctr Oceanog Balears, Ecosyst Oceanog Grp GRECO, Palma De Mallorca, Spain.
EM c.mena.oliver@gmail.com
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NR 99
TC 15
Z9 16
PD JUL 28
PY 2020
VL 11
AR 1749
DI 10.3389/fmicb.2020.01749
UT WOS:000561210800001
DA 2025-07-30
ER

PT J
AU Lami, R
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   Lebaron, P
AF Lami, Raphael
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TI Annual patterns of presence and activity of marine bacteria monitored by
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SO AQUATIC MICROBIAL ECOLOGY
DT Article
AB The annual dynamics of the bacterial community structure and its activity remain poorly studied in marine environments. Our goal was to gain new insights into the year-long bacterial dynamics and activity in correlation with environmental changes in the NW Mediterranean Sea. To accomplish this goal, we combined 16S rDNA versus 16S rRNA fingerprints and environmental variables using multivariate analyses. A clone library was constructed to determine to which bacterial taxa the major ribotypes were related. Our results revealed similar environmental controls of bacterial community structure at both the DNA and RNA levels. The 16S rRNA signal of several ribotypes differed relative to their 16S rDNA counterpart, suggesting that the members of the community have either a higher or lower activity than their relative abundance would suggest. Such differences included the dominant ribotypes observed in the fingerprints, such as Roseobacter, Synechococcus, SAR11 and SAR116, All these results give support to the 16S rDNA and 16S rRNA fingerprinting approach to monitor bacterial community structure and activity in marine environments.
C1 [Lami, Raphael; Ghiglione, Jean-Francois; Desdevises, Yves; West, Nyree J.; Lebaron, Philippe] Univ Paris 06, Lab Arago, F-66650 Banyuls Sur Mer, France.
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RP Lami, R (corresponding author), Univ Delaware, Coll Marine & Earth Studies, Lewes, DE 19958 USA.
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NR 48
TC 33
Z9 34
PY 2009
VL 54
IS 2
BP 199
EP 210
DI 10.3354/ame01264
UT WOS:000265158200008
DA 2025-07-30
ER

PT J
AU Lee, JW
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AF Lee, Jin-Woo
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DT Article
AB Succession of bacterial communities during the first 36 h of biofilm formation in coastal water was investigated at 3 similar to 15 h intervals. Three kinds of surfaces (i.e., acryl, glass, and steel substratum) were submerged in situ at Sacheon harbor, Korea. Biofilms were harvested by scraping the surfaces, and the compositions of bacterial communities were analyzed by terminal restriction fragment length polymorphism (T-RFLP), and cloning and sequencing of 16S rRNA genes. While community structure based on T-RFLP analysis showed slight differences by substratum, dramatic changes were commonly observed for all substrata between 9 and 24 h. Identification of major populations by 16S rRNA gene sequences indicated that gamma-Proteobacteria (Pseudomonas, Acinetobacter, Alteromonas, and uncultured gamma-Proteobacteria) were predominant in the community during 0-9 h, while the ratio of alpha-Proteobacteria (Loktanella, Methylobacterium, Pelagibacter, and uncultured alpha-Proteobacteria) increased 2.6 similar to 4.8 folds during 24 similar to 36 h of the biofilm formation, emerging as the most predominant group. Previously, alpha-Proteobacteria were recognized as the pioneering organisms in marine biofilm formation. However, results of this study, which revealed the bacterial succession with finer temporal resolution, indicated some species of gamma-Proteobacteria were more important as the pioneering population. Measures to control pioneering activities of these species can be useful in prevention of marine biofilm formation.
C1 [Lee, Jin-Woo; Nam, Ji-Hyun; Kim, Yang-Hoon; Lee, Dong-Hun] Chungbuk Natl Univ, Dept Microbiol, Chungbuk 361763, South Korea.
   [Lee, Kyu-Ho] Hankuk Univ Foreign Studies, Dept Environm Sci, Kyonggi Do 449791, South Korea.
RP Lee, DH (corresponding author), Chungbuk Natl Univ, Dept Microbiol, Chungbuk 361763, South Korea.
EM donghun@chungbuk.ac.kr
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NR 26
TC 192
Z9 229
PD APR
PY 2008
VL 46
IS 2
BP 174
EP 182
DI 10.1007/s12275-008-0032-3
UT WOS:000255438700008
DA 2025-07-30
ER

PT J
AU López-García, P
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AF López-García, P
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DT Article
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NR 35
TC 113
Z9 126
PD JUL
PY 2001
VL 36
IS 2-3
BP 193
EP 202
DI 10.1016/S0168-6496(01)00133-7
UT WOS:000170051100013
DA 2025-07-30
ER

PT J
AU Sun, FL
   Wang, YS
   Wu, ML
   Sun, CC
   Jiang, ZY
   Cheng, H
   Fei, J
AF Sun, Fu-Lin
   Wang, You-Shao
   Wu, Mei-Lin
   Sun, Cui-Ci
   Jiang, Zhao-Yu
   Cheng, Hao
   Fei, Jiao
TI Bacterial community variations in the South China Sea driven by
   different chemical conditions
SO ECOTOXICOLOGY
DT Article
AB In this study, Illumina MiSeq sequencing of the 16 S rRNA gene was used to describe the bacterial communities in the South China Sea (SCS) during the southwest monsoon period. We targeted different regions in the SCS and showed that bacterial community was driven by the effects of the river, upwelling, and mesoscale eddy through changing the environmental factors (salinity, temperature, and nutrients). Distinct bacterial communities were observed among different chemical conditions, especially between the estuary and the open sea. The abundance of Burkholderiales, Frankiales, Flavobacteriales, and Rhodobacterales dominated the estuary and its adjacent waters. Bacteria in cyclonic eddy were dominated by Methylophilales and Pseudomonadales, whereas Prochlorococcus, SAR11 clade, and Oceanospirillales had relatively high abundance in the anticyclonic eddy. Overall, the abundance of specific phylotypes significantly varied among samples with different chemical conditions. Chemical conditions probably act as a driver that shapes and controls the diversity of bacteria in the SCS. This study suggests that the interaction between microbial and environmental conditions needs to be further considered to fully understand the diversity and function of marine microbes.
C1 [Sun, Fu-Lin; Wang, You-Shao; Wu, Mei-Lin; Sun, Cui-Ci; Jiang, Zhao-Yu; Cheng, Hao; Fei, Jiao] Chinese Acad Sci, South China Sea Inst Oceanol, State Key Lab Trop Oceanog, Guangzhou 510301, Peoples R China.
   [Sun, Fu-Lin; Wang, You-Shao; Sun, Cui-Ci] Chinese Acad Sci, South China Sea Inst Oceanol, Daya Bay Marine Biol Res Stn, Shenzhen 518121, Peoples R China.
   [Sun, Fu-Lin; Wang, You-Shao; Wu, Mei-Lin; Sun, Cui-Ci; Jiang, Zhao-Yu; Cheng, Hao; Fei, Jiao] Southern Marine Sci & Engn Guangdong Lab Guangzho, Guangzhou 511458, Peoples R China.
   [Sun, Fu-Lin; Wang, You-Shao; Wu, Mei-Lin; Sun, Cui-Ci; Jiang, Zhao-Yu; Cheng, Hao; Fei, Jiao] Chinese Acad Sci, Innovat Acad South China Sea Ecol & Environm Engn, Guangzhou 510301, Peoples R China.
RP Wang, YS (corresponding author), Chinese Acad Sci, South China Sea Inst Oceanol, State Key Lab Trop Oceanog, Guangzhou 510301, Peoples R China.; Wang, YS (corresponding author), Chinese Acad Sci, South China Sea Inst Oceanol, Daya Bay Marine Biol Res Stn, Shenzhen 518121, Peoples R China.; Wang, YS (corresponding author), Southern Marine Sci & Engn Guangdong Lab Guangzho, Guangzhou 511458, Peoples R China.; Wang, YS (corresponding author), Chinese Acad Sci, Innovat Acad South China Sea Ecol & Environm Engn, Guangzhou 510301, Peoples R China.
EM yswang@scsio.ac.cn
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NR 37
TC 6
Z9 6
PD NOV
PY 2021
VL 30
IS 9
BP 1808
EP 1815
DI 10.1007/s10646-021-02455-w
EA JUL 2021
UT WOS:000674083500001
DA 2025-07-30
ER

PT J
AU Atamna-Ismaeel, N
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   Sharon, I
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AF Atamna-Ismaeel, Nof
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   Witzel, Karl-Paul
   Labrenz, Matthias
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   Barkay, Tamar
   Stomp, Maayke
   Huisman, Jef
   Beja, Oded
TI Widespread distribution of proteorhodopsins in freshwater and brackish
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SO ISME JOURNAL
DT Article
AB Proteorhodopsins (PRs) are light-driven proton pumps that have been found in a variety of marine environments. The goal of this study was to search for PR presence in different freshwater and brackish environments and to explore the diversity of non-marine PR protein. Here, we show that PRs exist in distinctly different aquatic environments, ranging from clear water lakes to peat lakes and in the Baltic Sea. Some of the PRs observed in this study formed unique clades that were not previously observed in marine environments, whereas others were similar to PRs found in non-marine samples of the Global Ocean Sampling (GOS) expedition. Furthermore, the similarity of several PRs isolated from lakes in different parts of the world suggests that these genes are dispersed globally and that they may encode unique functional capabilities enabling successful competition in a wide range of freshwater environments. Phylogenomic analysis of genes found on these GOS scaffolds suggests that some of the freshwater PRs are found in freshwater Flavobacteria and freshwater SAR11-like bacteria.
C1 [Atamna-Ismaeel, Nof; Sabehi, Gazalah; Sharon, Itai; Beja, Oded] Technion Israel Inst Technol, Fac Biol, IL-32000 Haifa, Israel.
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   [Labrenz, Matthias; Juergens, Klaus] Leibniz Inst Balt Sea Res, Dept Biol Oceanog, Rostock, Germany.
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RP Beja, O (corresponding author), Technion Israel Inst Technol, Fac Biol, IL-32000 Haifa, Israel.
EM beja@tx.technion.ac.il
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NR 31
TC 89
Z9 102
PD JUN
PY 2008
VL 2
IS 6
BP 656
EP 662
DI 10.1038/ismej.2008.27
UT WOS:000256753700008
DA 2025-07-30
ER

PT J
AU Reintjes, G
   Arnosti, C
   Fuchs, B
   Amann, R
AF Reintjes, Greta
   Arnosti, Carol
   Fuchs, B.
   Amann, Rudolf
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SO ISME JOURNAL
DT Article
AB Identifying the roles played by individual heterotrophic bacteria in the degradation of high molecular weight (HMW) substrates is critical to understanding the constraints on carbon cycling in the ocean. At five sites in the Atlantic Ocean, we investigated the processing of organic matter by tracking changes in microbial community composition as HMW polysaccharides were enzymatically hydrolysed over time. During this investigation, we discovered that a considerable fraction of heterotrophic bacteria uses a newly-identified 'selfish' mode of substrate processing. We therefore additionally examined the balance of individual substrate utilisation mechanisms at different locations by linking individual microorganisms to distinct substrate utilisation mechanisms. Through FISH and uptake of fluorescently-labelled polysaccharides, 'selfish' organisms were identified as belonging to the Bacteroidetes, Planctomycetes and Gammaproteobacteria. 'Sharing' (extracellular enzyme producing) and 'scavenging' (non-enzyme producing) organisms predominantly belonged to the Alteromonadaceae and SAR11 clades, respectively. The extent to which individual mechanisms prevail depended on the initial population structure of the bacterial community at a given location and time, as well as the growth rate of specific bacteria. Furthermore, the same substrate was processed in different ways by different members of a pelagic microbial community, pointing to significant follow-on effects for carbon cycling.
C1 [Reintjes, Greta; Fuchs, B.; Amann, Rudolf] Max Planck Inst Marine Microbiol, Dept Mol Ecol, Bremen, Germany.
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RP Amann, R (corresponding author), Max Planck Inst Marine Microbiol, Dept Mol Ecol, Bremen, Germany.; Arnosti, C (corresponding author), Univ N Carolina, Dept Marine Sci, Chapel Hill, NC 27515 USA.
EM arnosti@email.unc.edu; ramann@mpi-bremen.de
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NR 83
TC 107
Z9 114
PD MAY
PY 2019
VL 13
IS 5
BP 1119
EP 1132
DI 10.1038/s41396-018-0326-3
UT WOS:000464960400001
DA 2025-07-30
ER

PT J
AU Savio, D
   Sinclair, L
   Ijaz, UZ
   Parajka, J
   Reischer, GH
   Stadler, P
   Blaschke, AP
   Blöschl, G
   Mach, RL
   Kirschner, AKT
   Farnleitner, AH
   Eiler, A
AF Savio, Domenico
   Sinclair, Lucas
   Ijaz, Umer Z.
   Parajka, Juraj
   Reischer, Georg H.
   Stadler, Philipp
   Blaschke, Alfred P.
   Bloeschl, Guenter
   Mach, Robert L.
   Kirschner, Alexander K. T.
   Farnleitner, Andreas H.
   Eiler, Alexander
TI Bacterial diversity along a 2600 km river continuum
SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB The bacterioplankton diversity in large rivers has thus far been under-sampled despite the importance of streams and rivers as components of continental landscapes. Here, we present a comprehensive dataset detailing the bacterioplankton diversity along the midstream of the Danube River and its tributaries. Using 16S rRNA-gene amplicon sequencing, our analysis revealed that bacterial richness and evenness gradually declined downriver in both the free-living and particle-associated bacterial communities. These shifts were also supported by beta diversity analysis, where the effects of tributaries were negligible in regards to the overall variation. In addition, the river was largely dominated by bacteria that are commonly observed in freshwaters. Dominated by the acI lineage, the freshwater SAR11 (LD12) and the Polynucleobacter group, typical freshwater taxa increased in proportion downriver and were accompanied by a decrease in soil and groundwater-affiliated bacteria. Based on views of the meta-community and River Continuum Concept, we interpret the observed taxonomic patterns and accompanying changes in alpha and beta diversity with the intention of laying the foundation for a unified concept for river bacterioplankton diversity.
C1 [Sinclair, Lucas; Eiler, Alexander] Uppsala Univ, Dept Ecol & Genet, Limnol Sci Life Lab, Uppsala, Sweden.
   [Savio, Domenico; Parajka, Juraj; Stadler, Philipp; Blaschke, Alfred P.; Bloeschl, Guenter; Farnleitner, Andreas H.] Vienna Univ Technol, CWRS, A-1040 Vienna, Austria.
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   [Ijaz, Umer Z.] Univ Glasgow, Sch Engn, Glasgow, Lanark, Scotland.
   [Reischer, Georg H.; Kirschner, Alexander K. T.; Farnleitner, Andreas H.] Interuniv Cooperat Ctr Water & Hlth, London, England.
   [Kirschner, Alexander K. T.] Med Univ Vienna, Inst Hyg & Appl Immunol Water Hyg, Vienna, Austria.
RP Eiler, A (corresponding author), Uppsala Univ, Dept Ecol & Genet, Limnol Sci Life Lab, Uppsala, Sweden.
EM alexander.eiler@ebc.uu.se
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NR 67
TC 259
Z9 288
PD DEC
PY 2015
VL 17
IS 12
BP 4994
EP 5007
DI 10.1111/1462-2920.12886
UT WOS:000368457800015
DA 2025-07-30
ER

PT J
AU Mary, I
   Cummings, DG
   Biegala, IC
   Burkill, PH
   Archer, SD
   Zubkov, MV
AF Mary, I
   Cummings, DG
   Biegala, IC
   Burkill, PH
   Archer, SD
   Zubkov, MV
TI Seasonal dynamics of bacterioplankton community structure at a coastal
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SO AQUATIC MICROBIAL ECOLOGY
DT Article
AB An annual study of the bacterioplankton community structure was carried out at Stn L4 (50 degrees 15'N, 04 degrees 13'W) in the western English Channel between August 2003 and July 2004. Bacterioplankton abundance and community structure were assessed using flow cytometry and fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes, respectively. The Eubacteria domain dominated over the Archaea domain (< 15 %) at the highest phylogenetic level. The Sphingo-bacteria-Flavobacteria group of the Bacteroidetes phylum (SFB) numerically dominated in spring and early summer. The alpha-Proteobacteria dominated from late summer to winter. The SAR11 clade represented similar to 13% of the microbial community throughout the year and accounted for up to 69% of a-Proteobacteria in late spring. Annually, gamma-Proteobacteria were 2 or 3 times less abundant than the other groups and showed no obvious seasonal trend. The SAR86 cluster accounted for up to half of gamma-Proteobacteria when it peaked in summer. Consequently, we found that community structure at higher taxonomic level did not change dramatically with season but lower level phylogenetic groups showed pronounced seasonal peaks.
C1 Natl Oceanog Ctr, Southampton SO14 3ZH, Hants, England.
   PlymouthMarine Lab, Plymouth PL1 DH, Devon, England.
   Ctr Oceanol Marseille, Inst Rech Dev, F-13007 Marseille, France.
RP Mary, I (corresponding author), Natl Oceanog Ctr, Waterfront Campus,European Way, Southampton SO14 3ZH, Hants, England.
EM imary@noc.soton.ac.uk
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NR 66
TC 48
Z9 50
PD FEB 28
PY 2006
VL 42
IS 2
BP 119
EP 126
DI 10.3354/ame042119
UT WOS:000237261900002
DA 2025-07-30
ER

PT J
AU Noell, SE
   Brennan, E
   Washburn, Q
   Davis, EW 
   Hellweger, FL
   Giovannoni, SJ
AF Noell, Stephen E.
   Brennan, Elizabeth
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   Davis, Edward W., II
   Hellweger, Ferdi L.
   Giovannoni, Stephen J.
TI Differences in the regulatory strategies of marine oligotrophs and
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Aquatic bacteria frequently are divided into lifestyle categories oligotroph or copiotroph. Oligotrophs have proportionately fewer transcriptional regulatory genes than copiotrophs and are generally non-motile/chemotactic. We hypothesized that the absence of chemotaxis/motility in oligotrophs prevents them from occupying nutrient patches long enough to benefit from transcriptional regulation. We first confirmed that marine oligotrophs are generally reduced in genes for transcriptional regulation and motility/chemotaxis. Next, using a non-motile oligotroph (Ca. Pelagibacter st. HTCC7211), a motile copiotroph (Alteromonas macleodii st. HOT1A3), and [C-14](L)-ala-nine, we confirmed that (L)-alanine catabolism is not transcriptionally regulated in HTCC7211 but is in HOT1A3. We then found that HOT1A3 took 2.5-4 min to initiate (L)-alanine oxidation at patch (L)-alanine concentrations, compared to < 30 s for HTCC7211. By modelling cell trajectories, we predicted that, in most scenarios, non-motile cells spend < 2 min in patches, compared to > 4 min for chemotactic/motile cells. Thus, the time necessary for transcriptional regulation to initiate prevents transcriptional regulation from being beneficial for non-motile oligotrophs. This is supported by a mechanistic model we developed, which predicted that HTCC7211 cells with transcriptional regulation of (L)-alanine metabolism would produce 12% of their standing ATP stock upon encountering an (L)-alanine patch, com-pared to 880% in HTCC7211 cells without transcriptional regulation.
C1 [Noell, Stephen E.; Brennan, Elizabeth; Washburn, Quinn; Giovannoni, Stephen J.] Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
   [Davis, Edward W., II] Oregon State Univ, Ctr Quantitat Life Sci, Corvallis, OR USA.
   [Hellweger, Ferdi L.] Water Qual Engn, Berlin, Germany.
   [Noell, Stephen E.] Univ Waikato, Sch Sci, Hamilton, New Zealand.
RP Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
EM steve.giovannoni@oregonstate.edu
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NR 94
TC 8
Z9 8
PD JUL
PY 2023
VL 25
IS 7
BP 1265
EP 1280
DI 10.1111/1462-2920.16357
EA MAR 2023
UT WOS:000943248900001
DA 2025-07-30
ER

PT J
AU Bakenhus, I
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   Wietz, M
AF Bakenhus, Insa
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   Simon, Meinhard
   Wietz, Matthias
TI Distinct biogeographic patterns of bacterioplankton composition and
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DT Article
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C1 [Bakenhus, Insa; Dlugosch, Leon; Giebel, Helge-Ansgar; Beardsley, Christine; Simon, Meinhard; Wietz, Matthias] Inst Chem & Biol Marine Environm, Oldenburg, Germany.
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RP Wietz, M (corresponding author), Inst Chem & Biol Marine Environm, Oldenburg, Germany.
EM matthias.wietz@uni-oldenburg.de
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NR 58
TC 6
Z9 6
PD AUG
PY 2018
VL 20
IS 8
SI SI
BP 3100
EP 3108
DI 10.1111/1462-2920.14383
UT WOS:000445184600030
DA 2025-07-30
ER

PT J
AU Mou, XZ
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   Sun, SL
   Zhao, WD
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   Moran, MA
AF Mou, Xiaozhen
   Vila-Costa, Maria
   Sun, Shulei
   Zhao, Weidong
   Sharma, Shalabh
   Moran, Mary Ann
TI Metatranscriptomic signature of exogenous polyamine utilization by
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SO ENVIRONMENTAL MICROBIOLOGY REPORTS
DT Article
AB The polyamines putrescine (PUT) and spermidine (SPD) are ubiquitous in seawater, but mechanisms that drive the degradation of these important nitrogen sources by marine bacteria remain unclear. We employed a comparative metatranscriptomics approach to compare gene transcription patterns between coastal bacterioplankton communities with and without amendments of PUT or SPD, in an effort to understand how bacterial communities and their genes shape polyamine biogeochemistry in the ocean. Statistically different transcript categories in the PUT (25 COG groups) and SPD (23 COG groups) samples, relative to controls that received no amendment (CTRL), indicated that genes encoding the cellular translation machinery and the metabolism of organic nitrogen and carbon became enriched in the community transcriptome when polyamine availability increased. Of the three known pathways for bacterial polyamine degradation, only genes in the transamination pathway were enriched in the PUT and SPD libraries, suggesting that this route dominated polyamine degradation. Taxonomic affiliation of significantly enriched diagnostic genes in the PUT and SPD libraries pointed to roseobacter- and SAR11-affiliated bacteria as the predominant taxa driving transformation in this coastal ocean, although other diverse marine bacterioplankton groups (Gammaproteobacteria, Betaproteobacteria, Actinobacteria and Bacteroidetes) also contributed to polyamine-related gene transcription.
C1 [Mou, Xiaozhen] Kent State Univ, Dept Biol Sci, Kent, OH 44242 USA.
   [Vila-Costa, Maria; Sun, Shulei; Sharma, Shalabh; Moran, Mary Ann] Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
   [Zhao, Weidong] Northeastern Ohio Univ Coll Med & Pharm, Coll Med, Rootstown, OH 44272 USA.
   [Zhao, Weidong] Northeastern Ohio Univ Coll Med & Pharm, Coll Pharm, Rootstown, OH 44272 USA.
RP Mou, XZ (corresponding author), Kent State Univ, Dept Biol Sci, Kent, OH 44242 USA.
EM xmou@kent.edu
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AU Bayer, B
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   Bittner, MJ
   Noriega-Ortega, BE
   Niggemann, J
   Dittmar, T
   Herndl, GJ
AF Bayer, Barbara
   Hansman, Roberta L.
   Bittner, Meriel J.
   Noriega-Ortega, Beatriz E.
   Niggemann, Jutta
   Dittmar, Thorsten
   Herndl, Gerhard J.
TI Ammonia-oxidizing archaea release a suite of organic compounds
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Ammonia-oxidizing archaea (AOA) constitute a considerable fraction of microbial biomass in the global ocean, comprising 20%-40% of the ocean's prokaryotic plankton. However, it remains enigmatic to what extent these chemolithoautotrophic archaea release dissolved organic carbon (DOC). A combination of targeted and untargeted metabolomics was used to characterize the exometabolomes of three model AOA strains of the Nitrosopumilus genus. Our results indicate that marine AOA exude a suite of organic compounds with potentially varying reactivities, dominated by nitrogen-containing compounds. A significant fraction of the released dissolved organic matter (DOM) consists of labile compounds, which typically limit prokaryotic heterotrophic activity in open ocean waters, including amino acids, thymidine and B vitamins. Amino acid release rates corresponded with ammonia oxidation activity and the three Nitrosopumilus strains predominantly released hydrophobic amino acids, potentially as a result of passive diffusion. Despite the low contribution of DOC released by AOA (similar to 0.08%-1.05%) to the heterotrophic prokaryotic carbon demand, the release of physiologically relevant metabolites could be crucial for microbes that are auxotrophic for some of these compounds, including members of the globally abundant and ubiquitous SAR11 clade.
C1 [Bayer, Barbara; Hansman, Roberta L.; Bittner, Meriel J.; Herndl, Gerhard J.] Univ Vienna, Ctr Funct Ecol, Dept Limnol & Biooceanog, Div Biooceanog, A-1090 Vienna, Austria.
   [Hansman, Roberta L.] Intemat Atom Energy Agcy, Radioecol Lab, Environm Labs, MC-98000 Monaco, Monaco.
   [Noriega-Ortega, Beatriz E.; Niggemann, Jutta; Dittmar, Thorsten] Carl von Ossietzky Univ Oldenburg, ICBM MPI Bridging Grp Marine Geochem, D-26129 Oldenburg, Germany.
   [Herndl, Gerhard J.] NIOZ Royal Netherlands Inst Sea Res, Dept Marine Microbiol & Biogeochem, NL-1790 AB Den Burg, Texel, Netherlands.
   [Herndl, Gerhard J.] Univ Utrecht, NL-1790 AB Den Burg, Texel, Netherlands.
RP Bayer, B (corresponding author), Univ Vienna, Ctr Funct Ecol, Dept Limnol & Biooceanog, Div Biooceanog, A-1090 Vienna, Austria.
EM barbara.bayer@outlook.com
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NR 96
TC 70
Z9 77
PD NOV
PY 2019
VL 21
IS 11
BP 4062
EP 4075
DI 10.1111/1462-2920.14755
EA AUG 2019
UT WOS:000480009600001
DA 2025-07-30
ER

PT J
AU Silvano, E
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AF Silvano, Eleonora
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TI Lipidomic Analysis of Roseobacters of the Pelagic RCA Cluster and Their
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SO FRONTIERS IN MICROBIOLOGY
DT Article
AB The marine roseobacter-clade affiliated cluster (RCA) represents one of the most abundant groups of bacterioplankton in the global oceans, particularly in temperate and sub-polar regions. They play a key role in the biogeochemical cycling of various elements and are important players in oceanic climate-active trace gas metabolism. In contrast to copiotrophic roseobacter counterparts such as Ruegeria pomeroyi DSS-3 and Phaeobacter sp. MED193, RCA bacteria are truly pelagic and have smaller genomes. We have previously shown that RCA bacteria do not appear to encode the PlcP-mediated lipid remodeling pathway, whereby marine heterotrophic bacteria remodel their membrane lipid composition in response to phosphorus (P) stress by substituting membrane glycerophospholipids with alternative glycolipids or betaine lipids. In this study, we report lipidomic analysis of six RCA isolates. In addition to the commonly found glycerophospholipids such as phosphatidylglycerol (PG) and phosphatidylethanolamine (PE), RCA bacteria synthesize a relatively uncommon phospholipid, acylphosphatidylglycerol, which is not found in copiotrophic roseobacters. Instead, like the abundant SAR11 clade, RCA bacteria upregulate ornithine lipid biosynthesis in response to P stress, suggesting a key role of this aminolipid in the adaptation of marine heterotrophs to oceanic nutrient limitation.
C1 [Silvano, Eleonora; Scanlan, David J.; Chen, Yin] Univ Warwick, Sch Life Sci, Coventry, W Midlands, England.
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RP Chen, Y (corresponding author), Univ Warwick, Sch Life Sci, Coventry, W Midlands, England.
EM Y.chen.25@warwick.ac.uk
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TC 9
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PD DEC 21
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VL 11
AR 552135
DI 10.3389/fmicb.2020.552135
UT WOS:000604300800001
DA 2025-07-30
ER

PT J
AU De Corte, D
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   Tiroch, J
   Mena, C
   Herndl, GJ
   Sintes, E
AF De Corte, Daniele
   Muck, Simone
   Tiroch, Johanna
   Mena, Catalina
   Herndl, Gerhard J.
   Sintes, Eva
TI Microbes mediating the sulfur cycle in the Atlantic Ocean and their link
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Only about 10%-30% of the organic matter produced in the epipelagic layers reaches the dark ocean. Under these limiting conditions, reduced inorganic substrates might be used as an energy source to fuel prokaryotic chemoautotrophic and/or mixotrophic activity. The aprA gene encodes the alpha subunit of the adenosine-5 '-phosphosulfate (APS) reductase, present in sulfate-reducing (SRP) and sulfur-oxidizing prokaryotes (SOP). The sulfur-oxidizing pathway can be coupled to inorganic carbon fixation via the Calvin-Benson-Bassham cycle. The abundances of aprA and cbbM, encoding RuBisCO form II (the key CO2 fixing enzyme), were determined over the entire water column along a latitudinal transect in the Atlantic from 64 degrees N to 50 degrees S covering six oceanic provinces. The abundance of aprA and cbbM genes significantly increased with depth reaching the highest abundances in meso- and upper bathypelagic layers. The contribution of cells containing these genes also increased from mesotrophic towards oligotrophic provinces, suggesting that under nutrient limiting conditions alternative energy sources are advantageous. However, the aprA/cbbM ratios indicated that only a fraction of the SOP is associated with inorganic carbon fixation. The aprA harbouring prokaryotic community was dominated by Pelagibacterales in surface and mesopelagic waters, while Candidatus Thioglobus, Chromatiales and the Deltaproteobacterium_SCGC dominated the bathypelagic realm. Noticeably, the contribution of the SRP to the prokaryotic community harbouring aprA gene was low, suggesting a major utilization of inorganic sulfur compounds either as an energy source (occasionally coupled with inorganic carbon fixation) or in biosynthesis pathways.
C1 [De Corte, Daniele] Carl von Ossietzky Univ Oldenburg, Inst Chem & Biol Marine Environm, Oldenburg, Germany.
   [Muck, Simone; Tiroch, Johanna; Herndl, Gerhard J.; Sintes, Eva] Univ Vienna, Dept Funct & Evolutionary Ecol, Vienna, Austria.
   [Mena, Catalina; Sintes, Eva] Inst Espanol Oceanog, Ctr Oceanog Baleares, Palma De Mallorca, Spain.
   [Herndl, Gerhard J.] Univ Utrecht, Royal Netherlands Inst Sea Res, Dept Marine Microbiol & Biogeochem, NIOZ, Den Burg, Netherlands.
RP De Corte, D (corresponding author), Carl von Ossietzky Univ Oldenburg, Inst Chem & Biol Marine Environm, Oldenburg, Germany.
EM daniele.de.corte@uni-oldenburg.de
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NR 72
TC 7
Z9 7
PD NOV
PY 2021
VL 23
IS 11
BP 7152
EP 7167
DI 10.1111/1462-2920.15759
EA SEP 2021
UT WOS:000697383000001
DA 2025-07-30
ER

PT J
AU LeCleir, GR
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   Boyd, PW
   Wilhelm, SW
AF LeCleir, Gary R.
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   Maas, Elizabeth W.
   Boyd, Philip W.
   Wilhelm, Steven W.
TI Temporal changes in particle-associated microbial communities after
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SO FEMS MICROBIOLOGY ECOLOGY
DT Article
AB Using marine sediment traps (named RESPIRE for REspiration of Sinking Particles In the subsuRface ocEan) designed to collect sinking particles and associated microbial communities in situ, we collected and incubated marine aggregates/particles in the southern Pacific Ocean from separate phytoplankton bloom events in situ. We determined the phylogenetic affiliation for the microorganisms growing on aggregates by pyrosequencing partial 16S rRNA gene amplicons. Water column samples were also collected and sequenced for comparison between sinking-particle-associated and planktonic bacterial communities. Statistically significant differences were found between the water column and sediment trap bacteria. Relative abundances of Pelagibacter sp. and multiple members of the Flavobacteria, Actinobacteria, and -Proteobacteria were elevated in water column samples, while trap samples contained members of the Roseobacter clade of -Proteobacteria in high relative abundances. Our findings indicated that rapid changes - within 24h of collection - occurred to the microbial community associated with aggregates from either bloom type. There was a little change in the bacterial assemblage after the initial 24-h incubation period. The most abundant early colonizer was a Sulfitobacter sp. This study provides further evidence that Roseobacters are rapid colonizers of marine aggregates and that colonization can occur on short timescales. This study further demonstrates that particle origin may be insignificant regarding the heterotrophic bacterial population that degrades them.
C1 [LeCleir, Gary R.; Wilhelm, Steven W.] Univ Tennessee, Dept Microbiol, Knoxville, TN 37996 USA.
   [DeBruyn, Jennifer M.] Univ Tennessee, Knoxville, TN 37996 USA.
   [Maas, Elizabeth W.] Natl Inst Water & Atmospher Res, Wellington, New Zealand.
   [Boyd, Philip W.] Univ Otago, Dept Chem, NIWA Ctr Chem & Phys Oceanog, Dunedin, New Zealand.
   [Boyd, Philip W.] Univ Tasmania, Inst Marine & Antarctic Studies, Hobart, Tas, Australia.
RP Wilhelm, SW (corresponding author), Univ Tennessee, Dept Microbiol, Knoxville, TN 37996 USA.
EM wilhelm@utk.edu
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NR 56
TC 35
Z9 38
PD JAN
PY 2014
VL 87
IS 1
BP 153
EP 163
DI 10.1111/1574-6941.12213
UT WOS:000329170100015
DA 2025-07-30
ER

PT J
AU Du, S
   Wu, Y
   Ying, HQ
   Wu, ZQ
   Yang, MY
   Chen, F
   Shao, JB
   Liu, H
   Zhang, ZF
   Zhao, YL
AF Du, Sen
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   Ying, Hanqi
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   Shao, Jiabing
   Liu, He
   Zhang, Zefeng
   Zhao, Yanlin
TI Genome sequences of the first Autographiviridae phages infecting marine
   Roseobacter
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DT Article
AB The ubiquitous and abundant marine phages play critical roles in shaping the composition and function of bacterial communities, impacting biogeochemical cycling in marine ecosystems. Autographiviridae is among the most abundant and ubiquitous phage families in the ocean. However, studies on the diversity and ecology of Autographiviridae phages in marine environments are restricted to isolates that infect SAR11 bacteria and cyanobacteria. In this study, ten new roseophages that infect marine Roseobacter strains were isolated from coastal waters. These new roseophages have a genome size ranging from 38 917 to 42 634 bp and G+C content of 44.6-50 %. Comparative genomics showed that they are similar to known Autographiviridae phages regarding gene content and architecture, thus representing the first Autographiviridae roseophages. Phylogenomic analysis based on concatenated conserved genes showed that the ten roseophages form three distinct subgroups within the Autographiviridae, and sequence analysis revealed that they belong to eight new genera. Finally, viromic read- mapping showed that these new Autographiviridae phages are widely distributed in global oceans, mostly inhabiting polar and estuarine locations. This study has expanded the current understanding of the genomic diversity, evolution and ecology of Autographiviridae phages and roseophages. We suggest that Autographiviridae phages play important roles in the mortality and community structure of roseobacters, and have broad ecological applications.
C1 [Du, Sen; Wu, Ying; Ying, Hanqi; Wu, Zuqing; Yang, Mingyu; Shao, Jiabing; Liu, He; Zhang, Zefeng; Zhao, Yanlin] Fujian Agr & Forestry Univ, Coll Juncao Sci & Ecol, Fuzhou, Peoples R China.
   [Chen, Feng] Univ Maryland, Ctr Environm Sci, Inst Marine & Environm Technol, Baltimore, MD 21201 USA.
   [Zhao, Yanlin] Fujian Agr & Forestry Univ, Inst Oceanol, Key Lab Marine Biotechnol Fujian Prov, Fuzhou, Peoples R China.
RP Zhang, ZF; Zhao, YL (corresponding author), Fujian Agr & Forestry Univ, Coll Juncao Sci & Ecol, Fuzhou, Peoples R China.; Zhao, YL (corresponding author), Fujian Agr & Forestry Univ, Inst Oceanol, Key Lab Marine Biotechnol Fujian Prov, Fuzhou, Peoples R China.
EM zfengbio@126.com; yanlinzhao@fafu.edu.cn
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UT WOS:001263742000006
DA 2025-07-30
ER

PT J
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TI Ultramicrobacteria from Nitrate- and Radionuclide-Contaminated
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SO SUSTAINABILITY
DT Article
AB The goal of the present work was to investigate the physicochemical and radiochemical conditions and the microbial diversity in groundwater collected near the Lake Karachai (Russia), which was formerly used for the disposal of liquid radioactive waste, to isolate the dominant bacteria, and to determine their taxonomy and the physiological characteristics responsible for their adaptation to this environment. Groundwater samples contained high concentrations of acetate, oxalate, nitrate, and sulfate, as well as radionuclides. High-throughput sequencing and analysis of the clone libraries revealed lower microbial diversity in the most strongly contaminated groundwater and a predominance of bacteria of the genera Polynucleobacter, Pusillimonas, Candidatus Pelagibacter, and of the candidate phylum Parcubacteria; these groups include species with an ultra small cell size. Archaeal sequences in the libraries belonged to ammonium oxidizers of the phylum Thaumarchaeota and methanogens of the phylum Euryarchaeota. Pure cultures of obligate and facultative ultramicrobacteria belonging to the genera Chryseobacterium, Microbacterium, Salinibacterium, Pusillimonas, Roseomonas, and Janibacter were isolated from water samples. In genomes of Pusillimonas and Roseomonas strains the genes associated with nitrate reduction, resistance to heavy metals and metalloids were revealed. Several isolates are able to participate in the geochemical process of nitrate conversion to N-2 using acetate; this results in decreasing redox potential, which in turn may stimulate radionuclide reduction and decrease radionuclide migration in groundwater.
C1 [Nazina, Tamara; Babich, Tamara; Kostryukova, Nadezhda; Sokolova, Diyana; Abdullin, Ruslan; Tourova, Tatyana] Russian Acad Sci, Res Ctr Biotechnol, Winogradsky Inst Microbiol, Moscow 119071, Russia.
   [Nazina, Tamara; Novikov, Alexander] Russian Acad Sci, VI Vernadsky Inst Geochem & Analyt Chem, Moscow 119071, Russia.
   [Kadnikov, Vitaly; Mardanov, Andrey; Ravin, Nikolai; Grouzdev, Denis] Russian Acad Sci, Inst Bioengn, Res Ctr Biotechnol, Moscow 119071, Russia.
   [Poltaraus, Andrey] Russian Acad Sci, Engelhardt Inst Mol Biol, Moscow 119071, Russia.
   [Kalmykov, Stepan] Lomonosov Moscow State Univ, Chem Fac, Moscow 119991, Russia.
   [Safonov, Alexey; Zakharova, Elena] Russian Acad Sci, Frumkin Inst Phys Chem & Electrochem, Moscow 119071, Russia.
   [Kato, Kenji] Shizuoka Univ, Fac Sci, Dept Geosci, Shizuoka 4228529, Japan.
RP Nazina, T (corresponding author), Russian Acad Sci, Res Ctr Biotechnol, Winogradsky Inst Microbiol, Moscow 119071, Russia.; Nazina, T (corresponding author), Russian Acad Sci, VI Vernadsky Inst Geochem & Analyt Chem, Moscow 119071, Russia.
EM nazina@inmi.ru; microb101@yandex.ru; npavlova@mail.ru;
   sokolovadiyana@gmail.com; rusfbm@gmail.com; tptour@rambler.ru;
   vkadnikov@bk.ru; andrey.mardanov@gmail.com; nravin@mail.ru;
   denisgrouzdev@gmail.com; abpolt@gmail.com; stepan@radio.chem.msu.ru;
   alexeysafonof@gmail.com; zakharova@ipc.rssi.ru; novikov@geokhi.ru;
   kato.kenji@shizuoka.ac.jp
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NR 66
TC 10
Z9 11
PD FEB
PY 2020
VL 12
IS 3
AR 1239
DI 10.3390/su12031239
UT WOS:000524899604020
DA 2025-07-30
ER

PT J
AU Xie, ZX
   He, YB
   Zhang, SF
   Lin, L
   Wang, MH
   Wang, DZ
AF Xie, Zhang-Xian
   He, Yan-Bin
   Zhang, Shu-Feng
   Lin, Lin
   Wang, Ming-Hua
   Wang, Da-Zhi
TI Metaexoproteomics Reveals Microbial Behavior in the Ocean's Interior
SO FRONTIERS IN MICROBIOLOGY
DT Article
AB The proteins present in the extracellular environment of cells, named the "exoproteome," are critical for microbial survival, growth, and interaction with their surroundings. However, little is known about microbial exoproteomes in natural marine environments. Here, we used a metaproteomic approach to characterize the exoprotein profiles (10 kDa-0.2 mu m) throughout a water column in the South China Sea. Viruses, together with Alpha- and Gammaproteobacteria were the predominant contributors. However, the exoprotein-producing microbial communities varied with depth: SAR11 in the shallow waters, Pseudomonadales and Nitrososphaeria in the mesopelagic layer, and Alteromonadales, Rhizobiales, and Betaproteobacteria in the bathypelagic layer. Besides viral and unknown proteins, diverse transporters contributed substantially to the exoproteomes and varied vertically in their microbial origins, but presented similar patterns in their predicted substrate identities throughout the water column. Other microbial metabolic processes subject to vertical zonation included proteolysis, the oxidation of ammonia, nitrite and carbon monoxide, C1 metabolism, and the degradation of sulfur-containing dissolved organic matter (DOM). Our metaexoproteomic study provides insights into the depth-variable trends in the in situ ecological traits of the marine microbial community hidden in the non-cellular world, including nutrient cycling, niche partitioning and DOM remineralization.
C1 [Xie, Zhang-Xian; Zhang, Shu-Feng; Lin, Lin; Wang, Ming-Hua; Wang, Da-Zhi] Xiamen Univ, Coll Environm & Ecol, State Key Lab Marine Environm Sci, Xiamen, Peoples R China.
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   [He, Yan-Bin] BGI Shenzhen, Shenzhen, Peoples R China.
RP Wang, DZ (corresponding author), Xiamen Univ, Coll Environm & Ecol, State Key Lab Marine Environm Sci, Xiamen, Peoples R China.; Wang, DZ (corresponding author), Sun Yat Sen Univ, Southern Marine Sci & Engn Guangdong Lab Zhuhai, Zhuhai, Peoples R China.
EM dzwang@xmu.edu.cn
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NR 64
TC 2
Z9 2
PD FEB 16
PY 2022
VL 13
AR 749874
DI 10.3389/fmicb.2022.749874
UT WOS:000764162700001
DA 2025-07-30
ER

PT J
AU Shai, Y
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AF Shai, Yael
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TI Response of oligotrophic coastal microbial populations in the SE
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SO ESTUARINE COASTAL AND SHELF SCIENCE
DT Article
AB Anthropogenically-induced oil spills release large amounts of organic pollutants into the marine environment. To date, little is known about the response of microbial populations (biomass, activity and diversity) to crude oil pollution in Low Nutrients Low Chlorophyll and warm systems. Here, we investigated the daily dynamics of phytoplankton and heterotrophic bacteria in response to an oil spill (500 um thick layer) in the coastal waters of the SE Mediterranean Sea (SEMS), using mesocosms during winter and summer. Crude oil addition caused a marked decrease in phytoplankton biomass (40-76%) and production rates (22-96%), whereas heterotmphic bacterial abundance and production increased (4-68% and 17-165%, respectively). Concurrently, amplicon sequencing of the 16S rRNA gene revealed that oil-degrading bacteria became abundant 48-96 h post-oil addition, while the cosmopolitan Synechococcus and SAR11 lineages were significantly reduced (by 78-98% and 59-98%, respectively). Fertilization with inorganic nutrients (NO3 and PO4) reduced the deleterious effects of the oil, resulting in a less distinct reduction in phytoplankton biomass/abundance. Our results highlight the potential of intrinsic microbial communities to degrade oil-derived pollutants in oligotrophic coastal waters.
C1 [Shai, Yael; Angel, Dror L.] Univ Haifa, Charney Sch Marine Sci, Dept Maritime Civilizat, Haifa, Israel.
   [Shai, Yael; Zurel, Dror] Minist Environm Protect, Marine Environm Protect Div, Jerusalem, Israel.
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RP Angel, DL (corresponding author), Univ Haifa, Charney Sch Marine Sci, Dept Maritime Civilizat, Haifa, Israel.; Rahav, E (corresponding author), Israel Oceanog & Limnol Res, Natl Inst Oceanog, Haifa, Israel.
EM dangel@univ.haifa.ac.il; eyal.rahav@ocean.org.il
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NR 79
TC 13
Z9 16
PD FEB 5
PY 2021
VL 249
AR 107102
DI 10.1016/j.ecss.2020.107102
EA JAN 2021
UT WOS:000609304600006
DA 2025-07-30
ER

PT J
AU Carrión, O
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   Peng, M
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AF Carrion, Ornella
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   Todd, Jonathan D.
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TI DMSOP-cleaving enzymes are diverse and widely distributed in marine
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SO NATURE MICROBIOLOGY
DT Article
AB Dimethylsulfoxonium propionate (DMSOP) is a recently identified and abundant marine organosulfur compound with roles in oxidative stress protection, global carbon and sulfur cycling and, as shown here, potentially in osmotolerance. Microbial DMSOP cleavage yields dimethyl sulfoxide, a ubiquitous marine metabolite, and acrylate, but the enzymes responsible, and their environmental importance, were unknown. Here we report DMSOP cleavage mechanisms in diverse heterotrophic bacteria, fungi and phototrophic algae not previously known to have this activity, and highlight the unappreciated importance of this process in marine sediment environments. These diverse organisms, including Roseobacter, SAR11 bacteria and Emiliania huxleyi, utilized their dimethylsulfoniopropionate lyase 'Ddd' or 'Alma' enzymes to cleave DMSOP via similar catalytic mechanisms to those for dimethylsulfoniopropionate. Given the annual teragram predictions for DMSOP production and its prevalence in marine sediments, our results highlight that DMSOP cleavage is likely a globally significant process influencing carbon and sulfur fluxes and ecological interactions.
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C1 [Carrion, Ornella; Li, Chun-Yang; Peng, Ming; Wang, Jinyan; Zhang, Xiao-Hua; Wang, Peng; Todd, Jonathan D.; Zhang, Yu-Zhong] Ocean Univ China, MOE Key Lab Evolut & Marine Biodivers, Frontiers Sci Ctr Deep Ocean Multispheres & Earth, Qingdao, Peoples R China.
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   [Zhang, Yu-Zhong] Shandong Univ, Joint Res Ctr Marine Microbial Sci & Technol, Qingdao, Peoples R China.
   [Zhang, Yu-Zhong] Ocean Univ China, Qingdao, Peoples R China.
RP Carrión, O; Li, CY; Todd, JD; Zhang, YZ (corresponding author), Ocean Univ China, MOE Key Lab Evolut & Marine Biodivers, Frontiers Sci Ctr Deep Ocean Multispheres & Earth, Qingdao, Peoples R China.; Carrión, O; Li, CY; Todd, JD; Zhang, YZ (corresponding author), Ocean Univ China, Coll Marine Life Sci, Qingdao, Peoples R China.; Carrión, O; Todd, JD (corresponding author), Univ East Anglia, Sch Biol Sci, Norwich, England.; Zhang, YZ (corresponding author), Shandong Univ, Marine Biotechnol Res Ctr, State Key Lab Microbial Technol, Qingdao, Peoples R China.; Zhang, YZ (corresponding author), Frontiers Sci Ctr Deep Ocean Multispheres & Earth, Qingdao, Peoples R China.; Zhang, YZ (corresponding author), Shandong Univ, Joint Res Ctr Marine Microbial Sci & Technol, Qingdao, Peoples R China.; Zhang, YZ (corresponding author), Ocean Univ China, Qingdao, Peoples R China.
EM O.Carrion-Fonseca@uea.ac.uk; Lcy@ouc.edu.cn; jonathan.todd@uea.ac.uk;
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TC 17
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PD DEC
PY 2023
VL 8
IS 12
BP 2326
EP 2337
DI 10.1038/s41564-023-01526-4
UT WOS:001111125400012
DA 2025-07-30
ER

PT J
AU Wang, Y
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AF Wang, Yong
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SO DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS
DT Article
AB The deepest point of the oceans is over 10 km depth and is characterized with extremely high hydrostatic pressure. Water sampling from the hadal zone for microbiological studies is therefore difficult. In this study, we demonstrate the application of an in situ microbial filtration and fixation (ISMIFF) apparatus in sampling work from the Challenger Deep. A total of 2300 L hadal waters were filtered by the ISMIFF equipped on a hadal lander during seven deployments. The microbial communities in the hadal samples ( > 6000 m) collected by the ISMIFF were composed of more heterotrophic Marinimicrobia and less photoautotrophic Prochlorococcus and SAR11 bacteria, compared with those by Niskin bottles. Such a difference in the community structure was not observed in the samples collected by the two methods from 5000-m depth, indicating an effect of greater depths on sample quality. Our results indicate that the ISMIFF or similar filtration apparatuses are indispensable for hadal water sampling since using Niskin bottles is probably difficult to obtain pristine samples from the hadal zone. Application of the ISMIFF will pave the way to meta-omics studies on the hadal microbes.
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RP Wang, Y (corresponding author), Chinese Acad Sci, Inst Deep Sea Sci & Engn, 28 Luhuitou Rd, Sanya, Hainan, Peoples R China.
EM wangy@idsse.ac.cn
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NR 30
TC 26
Z9 29
PD FEB
PY 2019
VL 144
BP 132
EP 137
DI 10.1016/j.dsr.2019.01.009
UT WOS:000460831000011
DA 2025-07-30
ER

PT J
AU Sargeant, SL
   Murrell, JC
   Nightingale, PD
   Dixon, JL
AF Sargeant, S. L.
   Murrell, J. C.
   Nightingale, P. D.
   Dixon, J. L.
TI Seasonal variability in microbial methanol utilisation in coastal waters
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SO MARINE ECOLOGY PROGRESS SERIES
DT Article
AB Methanol is ubiquitous in seawater and is the most abundant oxygenated volatile organic compound (OVOC) in the atmosphere, where it influences oxidising capacity and ozone formation. Marine methylotrophic bacteria utilise methanol in seawater as an energy and/or growth substrate. This work represents the first fully resolved seasonal study of marine microbial methanol uptake dynamics. Rates of microbial methanol dissimilation in coastal surface waters of the UK varied between 0.7 and 11.2 nmol l(-1) h(-1) and reached a maximum in February. Rates of microbial methanol assimilation varied between 0.04 and 2.64 x 10(-2) nmol l(-1) h(-1) and reached a maximum in August. Temporal variability in microbial methanol uptake rates shows that methanol assimilation and dissimilation display opposing seasonal cycles, although overall, <1% of methanol was assimilated. Correlative approaches with 16S rRNA pyrosequencing data suggested that bacteria of the SAR11 clade and Rhodobacterales could be significantly influencing rates of methanol dissimilation and assimilation, respectively, at Station L4 in the western English Channel.
C1 [Sargeant, S. L.; Nightingale, P. D.; Dixon, J. L.] Plymouth Marine Lab, Prospect Pl, Plymouth PL1 3DH, Devon, England.
   [Murrell, J. C.] Univ East Anglia, Sch Environm Sci, Norwich Res Pk, Norwich NR4 7TJ, Norfolk, England.
   [Sargeant, S. L.] Univ West England, Dept Biol Biomed & Analyt Sci, Frenchay Campus,Coldharbour Lane, Bristol BS16 1QY, Avon, England.
RP Sargeant, SL (corresponding author), Plymouth Marine Lab, Prospect Pl, Plymouth PL1 3DH, Devon, England.; Sargeant, SL (corresponding author), Univ West England, Dept Biol Biomed & Analyt Sci, Frenchay Campus,Coldharbour Lane, Bristol BS16 1QY, Avon, England.
EM stephanie.sargeant@uwe.ac.uk
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NR 56
TC 12
Z9 14
PD MAY 25
PY 2016
VL 550
BP 53
EP 64
DI 10.3354/meps11705
UT WOS:000379811700004
DA 2025-07-30
ER

PT J
AU Moitinho-Silva, L
   Seridi, L
   Ryu, T
   Voolstra, CR
   Ravasi, T
   Hentschel, U
AF Moitinho-Silva, Lucas
   Seridi, Loqmane
   Ryu, Taewoo
   Voolstra, Christian R.
   Ravasi, Timothy
   Hentschel, Ute
TI Revealing microbial functional activities in the Red Sea sponge
   Stylissa carteri by metatranscriptomics
SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Sponges are important components of marine benthic environments and are associated with microbial symbionts that carry out ecologically relevant functions. Stylissa carteri is an abundant, low-microbial abundance species in the Red Sea. We aimed to achieve the functional and taxonomic characterization of the most actively expressed prokaryotic genes in S.carteri. Prokaryotic mRNA was enriched from sponge total RNA, sequenced using Illumina HiSeq technology and annotated using the metagenomics Rapid Annotation using Subsystem Technology (MG-RAST) pipeline. We detected high expression of archaeal ammonia oxidation and photosynthetic carbon fixation by members of the genus Synechococcus. Functions related to stress response and membrane transporters were among the most highly expressed by S.carteri symbionts. Unexpectedly, gene functions related to methylotrophy were highly expressed by gammaproteobacterial symbionts. The presence of seawater-derived microbes is indicated by the phylogenetic proximity of organic carbon transporters to orthologues of members from the SAR11 clade. In summary, we revealed the most expressed functions of the S.carteri-associated microbial community and linked them to the dominant taxonomic members of the microbiome. This work demonstrates the applicability of metatranscriptomics to explore poorly characterized symbiotic consortia and expands our knowledge of the ecologically relevant functions carried out by coral reef sponge symbionts.
C1 [Moitinho-Silva, Lucas; Hentschel, Ute] Univ Wurzburg, Julius von Sachs Inst Biol Sci, Dept Bot 2, D-97082 Wurzburg, Germany.
   [Seridi, Loqmane; Ryu, Taewoo; Ravasi, Timothy] King Abdullah Univ Sci & Technol, Div Biol & Environm Sci & Engn, Thuwal, Saudi Arabia.
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RP Hentschel, U (corresponding author), Univ Wurzburg, Julius von Sachs Inst Biol Sci, Dept Bot 2, Julius von Sachs Pl 3, D-97082 Wurzburg, Germany.
EM ute.hentschel@uni-wuerzburg.de
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NR 91
TC 54
Z9 60
PD DEC
PY 2014
VL 16
IS 12
SI SI
BP 3683
EP 3698
DI 10.1111/1462-2920.12533
UT WOS:000348463100007
DA 2025-07-30
ER

PT J
AU West, NJ
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AF West, Nyree J.
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SO MICROBIOLOGYOPEN
DT Article
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C1 [West, Nyree J.] Sorbonne Univ, CNRS, Observ Oceanol Banyuls OOB, FR3724, Banyuls Sur Mer, France.
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RP West, NJ (corresponding author), Observ Oceanol Banyuls Sur Mer, F-66650 Banyuls Sur Mer, France.
EM nyree.west@obs-banyuls.fr
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NR 101
TC 2
Z9 2
PD AUG
PY 2024
VL 13
IS 4
AR e1428
DI 10.1002/mbo3.1428
UT WOS:001287508700001
DA 2025-07-30
ER

PT J
AU Liu, YY
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   Feng, JR
   Yang, FM
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   Hu, Z
   Wang, H
AF Liu, Yanyang
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   Feng, Jiarong
   Yang, Fumin
   Du, Hong
   Hu, Zhong
   Wang, Hui
TI Differences in metabolic potential between particle -associated and
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SO SCIENCE OF THE TOTAL ENVIRONMENT
DT Article
AB Particulate organic matter (POM) in aquatic ecosystem is critical for biogeochemical cycling and host distinct communities of microbes, compared to its surrounding water. In this study, the structures and functional potentials of microbial communities associated with particles or free-living in water samples from the Pearl River Estuary were investigated using 16S rRNA gene sequencing and GeoChip 5.0 analysis. Significant differences in the community structure and genetic functional potentials between particle-associated bacteria and free-living bacteria were observed across all eight sampling sites. In particle-associated bacteria communities, Rhodobacteraceae and Flavobacteriaceae were more abundant, while SAR11 clade and SAR86 clade were the most abundant in free-living bacteria communities. The richness and abundance of functional genes involved in nutrient cycling and stress response, including carbon degradation, nitrogen fixation, DMSP degradation, and polyphosphate degradation, were much higher in particle-associated bacteria compared with free-living bacteria. Thus, the particle-associated bacteria seem to play a much more important role in the biogeochemical cycles than free-living bacteria. In conclusion, the results from this study highlight the central role played by particle-associated bacteria in structuring microbial assemblages, and their importance for mediating biogeochemical cycling in the estuarine ecosystem.
C1 [Liu, Yanyang; Lin, Qun; Feng, Jiarong; Yang, Fumin; Du, Hong; Hu, Zhong; Wang, Hui] Shantou Univ, Coll Sci, Biol Dept, Shantou 515063, Peoples R China.
   [Liu, Yanyang; Lin, Qun; Feng, Jiarong; Yang, Fumin; Du, Hong; Hu, Zhong; Wang, Hui] Shantou Univ, Inst Marine Sci, Shantou 515063, Peoples R China.
   [Liu, Yanyang; Lin, Qun; Feng, Jiarong; Yang, Fumin; Du, Hong; Hu, Zhong; Wang, Hui] Shantou Univ, Guangdong Prov Key Lab Marine Biotechnol, Shantou 515063, Peoples R China.
RP Wang, H (corresponding author), Shantou Univ, Coll Sci, Biol Dept, Shantou 515063, Peoples R China.
EM wanghui@stu.edu.cn
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NR 50
TC 48
Z9 51
PD AUG 1
PY 2020
VL 728
AR 138856
DI 10.1016/j.scitotenv.2020.138856
UT WOS:000541009200012
DA 2025-07-30
ER

PT J
AU Huanca-Valenzuela, P
   Fuchsman, CA
   Tully, BJ
   Sylvan, JB
   Cram, JA
AF Huanca-Valenzuela, Paulina
   Fuchsman, Clara A.
   Tully, Benjamin J.
   Sylvan, Jason B.
   Cram, Jacob A.
TI Quantitative microbial taxonomy across particle size, depth, and oxygen
   concentration
SO FRONTIERS IN MICROBIOLOGY
DT Article
AB Introduction Marine particles form in the ocean surface sink through the water column into the deep ocean, sequestering carbon. Microorganisms inhabit and consume carbon in these particles. The East Pacific Rise (EPR) harbors both an Oxygen Deficient Zone (ODZ) and a non-buoyant plume region formed from hydrothermal vents located on the ocean floor, allowing us to explore relationships between microbial community and particle size between a range of environments. Methods In this study, we quantified microbial diversity using a fractionation method that separated particles into seven fine scale fractions (0.2-1.2, 1.2-5, 5-20, 20-53, 53-180,180-500, >500 mu m), and included a spike-in standard for sequencing the 16S rRNA gene. Size fractionated organic carbon into the same fractions enabled the calculation of bacterial 16S rRNA copies per mu g C and per liter. Results There was a large increase in the bacterial 16S rRNA copies/ug C and copies/L on particles >180 mu m between the upper water column and the deep water column. Though the total concentration of organic C in particles decreased in the deep water column, the density of bacteria on large particles increased at depth. The microbial community varied statistically significantly as a function of particle size and depth. Quantitative abundance estimates found that ostensibly obligate free-living microbes, such as SAR11 and Thaumarcheota, were more abundant in the free-living fraction but also common and abundant in the particulate size fractions. Conversely, ostensibly obligate particle attached bacteria such as members of Bacteroidetes and Planctomycetes, while most abundant on particles, were also present in the free living fraction. Total bacterial abundance, and the abundance of many taxonomic groups, increased in the ODZ region, particularly in the free-living fraction. Contrastingly, in the non-buoyant plume, there were highly abundant bacteria in the 5-20 and 20-53 mu m fractions but reduced bacteria present in the 53-180 and 180-500 mu m fractions. Conclusion Quantitative examination of microbial communities highlights the distribution of microbial taxa unburdened by compositional effects. These data are congruent with existing models which suggest high levels of exchange between particle-attached and free-living communities.
C1 [Huanca-Valenzuela, Paulina; Fuchsman, Clara A.; Cram, Jacob A.] Univ Maryland, Ctr Environm Sci, Horn Point Lab, Cambridge, MD 21613 USA.
   [Tully, Benjamin J.] Univ Southern Calif, Ctr Dark Energy Biosphere Invest, Los Angeles, CA USA.
   [Tully, Benjamin J.] Branchpoint Sci, Los Angeles, CA USA.
   [Sylvan, Jason B.] Texas A&M Univ, Dept Oceanog, College Stn, TX USA.
RP Cram, JA (corresponding author), Univ Maryland, Ctr Environm Sci, Horn Point Lab, Cambridge, MD 21613 USA.
EM jcram@umces.edu
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TC 1
Z9 1
PD MAY 23
PY 2025
VL 16
AR 1552305
DI 10.3389/fmicb.2025.1552305
UT WOS:001504482600001
DA 2025-07-30
ER

PT J
AU McMullen, A
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AF McMullen, Africa
   Martinez-Hernandez, Francisco
   Martinez-Garcia, Manuel
TI Absolute quantification of infecting viral particles by chip-based
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SO ENVIRONMENTAL MICROBIOLOGY REPORTS
DT Article
AB In silico and empirical quantification of viruses is paramount for obtaining information on viral populations that have a major impact on biogeochemical cycles. The uncultured Pelagibacter virus vSAG 37-F6 discovered via single-virus genomics is one of the most abundant and cosmopolitan marine viruses; however, little is understood about its temporal variation. Here, we estimated the absolute number of infecting 37-F6 viruses in coastal bacterioplankton from the Mediterranean Sea by using a novel, feasible SYBR Green I chip-based digital PCR (SYBR dPCR) technique, not implemented before for enumerating (uncultured) microbes. Quantitative SYBR dPCR estimated 450-3480 genome copies of virus 37-F6 in cells/mL (i.e. infecting viruses) and a total of approximate to 10-400 putative infected cells/mL with a potential C release of 0.12-4.9 pg/ml in the analysed samples. Considering that virus 37-F6 is ubiquitous and abundant in all Tara samples, an enormous amount of C could be transformed by this virus through the 'viral shunt'. Thus, this SYBR dPCR technique has enabled the absolute quantification of an ecologically relevant uncultured virus in nature and the estimation of its potential contribution on biogeochemical cycles. Overall, our study also shows that this approach has a broad applicability for quantifying any other target loci in Microbiology and Virology.
C1 [McMullen, Africa; Martinez-Hernandez, Francisco; Martinez-Garcia, Manuel] Univ Alicante, Dept Physiol Genet & Microbiol, Alicante, Spain.
RP Martinez-Garcia, M (corresponding author), Univ Alicante, Dept Physiol Genet & Microbiol, Alicante, Spain.
EM m.martinez@ua.es
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NR 25
TC 7
Z9 7
PD DEC
PY 2019
VL 11
IS 6
BP 855
EP 860
DI 10.1111/1758-2229.12804
EA NOV 2019
UT WOS:000495561100001
DA 2025-07-30
ER

PT J
AU Park, JS
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AF Park, Joon Sang
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   Lee, Taek-Kyun
   Jung, Seung Won
TI Characterization of bacterial community structure in two alcyonacean
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SO CORAL REEFS
DT Article
AB Microbes in the coral holobiont play important roles in nitrogen fixation, carbon supply, antibiotic production, mucus recycling, and food supply to maintain homeostasis in corals. However, microbes can also induce coral diseases in response to environmental changes under non-optimal conditions. Therefore, studies of microbial communities are needed to understand the health statuses of corals in response to environmental changes. In this study, we performed 16S rDNA metabarcoding to investigate the bacterial communities in two healthy alcyonacean soft coral species (Sinularia sp. and Litophyton sp.) inhabiting the coast of Weno Island (Chuuk, Micronesia) and in ambient seawater. We identified 18 bacterial phyla, 24 classes, 54 orders, 109 families, and 222 genera associated with the two corals and seawater. The bacterial communities differed in the corals and seawater. The bacterial community in Sinularia sp. was dominated by the genus Spirochaeta in Spirochaetaceae (63.9% relative abundance), followed by Endozoicomonas (10%). In Litophyton sp., the bacterial community also contained Spirochaeta (19.5%) and Endozoicomonas (4.7%), although Cellvibrionaceae (23.7%) was dominant and other groups such as Rhizobiales (11.5%) and Rhodospirillales (8.7%) were evenly distributed. In ambient seawater, the predominant bacteria were Pelagibacter (29.2%), Rhodobacteraceae (15.5%), Prochlorococcus (11.3%), and Vibrio (5.8%), which are distinct from the species in the two coral species. The microbial communities between the two alcyonacean soft corals and seawater were different, and the microbial community differences were coral species-specific.
C1 [Park, Joon Sang; Kim, Hyun-Jung; Jung, Seung Won] Korea Inst Ocean Sci & Technol, Lib Marine Samples, Geoje 53201, South Korea.
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   [Suh, Sung-Suk] Mokpo Natl Univ, Dept Biosci, Muan Gun 58554, South Korea.
   [Lee, Taek-Kyun] Korea Inst Ocean Sci & Technol, Risk Assessment Res Ctr, Geoje 53201, South Korea.
   [Lee, Taek-Kyun; Jung, Seung Won] Univ Sci & Technol, Dept Ocean Sci, Daejeon 34113, South Korea.
RP Jung, SW (corresponding author), Korea Inst Ocean Sci & Technol, Lib Marine Samples, Geoje 53201, South Korea.; Lee, TK (corresponding author), Korea Inst Ocean Sci & Technol, Risk Assessment Res Ctr, Geoje 53201, South Korea.; Lee, TK; Jung, SW (corresponding author), Univ Sci & Technol, Dept Ocean Sci, Daejeon 34113, South Korea.
EM tklee@kiost.ac.kr; diatoms@kiost.ac.kr
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NR 88
TC 5
Z9 6
PD JUN
PY 2022
VL 41
IS 3
SI SI
BP 563
EP 574
DI 10.1007/s00338-021-02176-w
EA SEP 2021
UT WOS:000695781300001
DA 2025-07-30
ER

PT J
AU Schuller, DJ
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   Lanzilotta, WN
AF Schuller, David J.
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   Lanzilotta, William N.
TI Structures of dimethylsulfoniopropionate-dependent demethylase from the
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SO PROTEIN SCIENCE
DT Article
AB Dimethylsulfoniopropionate (DMSP) is a ubiquitous algal metabolite and common carbon and sulfur source for marine bacteria. DMSP is a precursor for the climatically active gas dimethylsulfide that is readily oxidized to sulfate, sulfur dioxide, methanesulfonic acid, and other products that act as cloud condensation nuclei. Although the environmental importance of DMSP metabolism has been known for some time, the enzyme responsible for DMSP demethylation by marine bacterioplankton, dimethylsufoniopropionate-dependent demethylase A (DmdA, EC 2.1.1.B5), has only recently been identified and biochemically characterized. In this work, we report the structure for the apoenzyme DmdA from Pelagibacter ubique (2.1 angstrom), as well as for DmdA co-crystals soaked with substrate DMSP (1.6 angstrom) or the cofactor tetrahydrofolate (THF) (1.6 angstrom). Surprisingly, the overall fold of the DmdA is not similar to other enzymes that typically utilize the reduced form of THF and in fact is a triple domain structure similar to what has been observed for the glycine cleavage T protein or sarcosine oxidase. Specifically, while the THF binding fold appears conserved, previous biochemical studies have shown that all enzymes with a similar fold produce 5,10-methylene-THF, while DmdA catalyzes a redox-neutral methyl transfer reaction to produce 5-methyl-THF. On the basis of the findings presented herein and the available biochemical data, we outline a mechanism for a redox-neutral methyl transfer reaction that is novel to this conserved THF binding domain.
C1 [Schuller, David J.] Cornell Univ, Cornell High Energy Synchrotron Source, Ithaca, NY 14853 USA.
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   [Lanzilotta, William N.] Univ Georgia, Dept Biochem & Mol Biol, Athens, GA 30602 USA.
RP Lanzilotta, WN (corresponding author), Green St,A220B Life Sci Bldg, Athens, GA 30605 USA.
EM wlanzilo@bmb.uga.edu
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NR 35
TC 24
Z9 27
PD FEB
PY 2012
VL 21
IS 2
BP 289
EP 298
DI 10.1002/pro.2015
UT WOS:000299209500014
DA 2025-07-30
ER

PT J
AU Hashihama, F
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AF Hashihama, Fuminori
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   Saito, Hiroaki
   Ogura, Yoshitoshi
   Hayashi, Tetsuya
   Mori, Hiroshi
   Kurokawa, Ken
   Suzuki, Shotaro
   Hamasaki, Koji
TI Arsenate and microbial dynamics in different phosphorus regimes of the
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SO PROGRESS IN OCEANOGRAPHY
DT Article
AB Biologically toxic arsenate is physicochemically similar to biologically essential phosphate. Because arsenate and phosphate are indiscriminately incorporated by microbes, their ambient concentration ratios can be an important factor controlling microbial growth and metabolism. This study investigated the spatial distributions of arsenate and phosphate and the associated biogeochemical dynamics in the subtropical North and South Pacific Ocean. Vertical arsenate and phosphate profiles (<= 150 m) in most of the study areas showed a nutrient-type distribution where the concentrations increased below the euphotic zone. The arsenate and phosphate concentrations in the surface waters ranged from the detection limits (5 nM and 4 nM, respectively) to approximately 40 nM and 400 nM, respectively. The surface arsenate:phosphate ratios were typically lower than 1, but those in the western subtropical North Pacific (WSNP) were frequently higher than 1 due to phosphate depletion. In the WSNP surface waters, Prochlorococcus and Pelagibacter arsenic detoxification and phosphorus acquisition genes were abundant. Results of the onboard bioassays involving the addition of arsenate or phosphate to the surface water indicated that microbes throughout the study areas possessed arsenate resistance and those in the WSNP during summer were under serious phosphate limitation. Although phosphate limitation likely accelerates the relative cellular accumulation of toxic arsenate, the lowest particulate As:P ratios were observed in the summer WSNP, concurrent with the lowest dissolved organic P (DOP) concentrations and the highest alkaline phosphatase activities. These results imply that active As excretion and/or DOP utilization could alleviate As accumulation while maintaining the cellular P quota.
C1 [Hashihama, Fuminori; Suwa, Shuhei; Kanda, Jota; Ehama, Makoto; Sakuraba, Ryousuke; Kinouchi, Shinko] Tokyo Univ Marine Sci & Technol, Dept Ocean Sci, Tokyo 1088477, Japan.
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RP Hashihama, F (corresponding author), Tokyo Univ Marine Sci & Technol, Dept Ocean Sci, Tokyo 1088477, Japan.
EM f-hashi@kaiyodai.ac.jp
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NR 51
TC 12
Z9 13
PD SEP
PY 2019
VL 176
AR 102115
DI 10.1016/j.pocean.2019.05.007
UT WOS:000483411800005
DA 2025-07-30
ER

PT J
AU Choi, DH
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AF Choi, Dong Han
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TI Daily variation in the prokaryotic community during a spring bloom in
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DT Article
AB To understand prokaryotic responses during a spring bloom in offshore shelf waters, prokaryotic parameters were measured daily at a station located in the middle of the East China Sea over a six-week period from March 25 to May 19. The site experienced a phytoplankton bloom in late April, triggering changes in prokaryotic abundance and production after a lag of approximately one week. Before the bloom, changes in prokaryotic composition were small. Both during the bloom and in the post-bloom period, successive changes among bacterial groups were apparent. A SAR11 group became more dominant during the bloom period, and diverse groups belonging to the Flavobacteriia occurred dominantly during both the bloom and post-bloom periods. However, bacterial community changes at the species level during the bloom and post-bloom periods occurred rapidly in a time scale of a few days. Especially, NS5, NS4 and Formosa bacteria belonging to Flavobacteriia and bacteria belonging to Halieaceae and Arenicellaceae families of Gammaproteobacteria showed a successive pattern with large short-term variation during the period. The changes in prokaryotic composition were found to be related to phytoplankton biomass and composition, as well as seawater temperature and variations in nutrients.
C1 [Choi, Dong Han; An, Sung Min; Yang, Eun Chan; Lee, Howon; Noh, Jae Hoon] Korea Inst Ocean Sci & Technol, Marine Ecosyst & Biol Res Ctr, Busan 49111, South Korea.
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RP Noh, JH (corresponding author), Korea Inst Ocean Sci & Technol, Marine Ecosyst & Biol Res Ctr, Busan 49111, South Korea.
EM jhnoh@kiost.ac.kr
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NR 52
TC 15
Z9 15
PD SEP
PY 2018
VL 94
IS 9
AR fiy134
DI 10.1093/femsec/fiy134
UT WOS:000442373800015
DA 2025-07-30
ER

PT J
AU Wilkins, D
   Lauro, FM
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   Brown, MV
   Hoffman, JM
   Andrews-Pfannkoch, C
   Mcquaid, JB
   Riddle, MJ
   Rintoul, SR
   Cavicchioli, R
AF Wilkins, David
   Lauro, Federico M.
   Williams, Timothy J.
   Demaere, Matthew Z.
   Brown, Mark V.
   Hoffman, Jeffrey M.
   Andrews-Pfannkoch, Cynthia
   Mcquaid, Jeffrey B.
   Riddle, Martin J.
   Rintoul, Stephen R.
   Cavicchioli, Ricardo
TI Biogeographic partitioning of Southern Ocean microorganisms revealed by
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB We performed a metagenomic survey (6.6Gbp of 454 sequence data) of Southern Ocean (SO) microorganisms during the austral summer of 20072008, examining the genomic signatures of communities across a latitudinal transect from Hobart (44 degrees S) to the Mertz Glacier, Antarctica (67 degrees S). Operational taxonomic units (OTUs) of the SAR11 and SAR116 clades and the cyanobacterial genera Prochlorococcus and Synechococcus were strongly overrepresented north of the Polar Front (PF). Conversely, OTUs of the Gammaproteobacterial Sulfur Oxidizer-EOSA-1 (GSO-EOSA-1) complex, the phyla Bacteroidetes and Verrucomicrobia and order Rhodobacterales were characteristic of waters south of the PF. Functions enriched south of the PF included a range of transporters, sulfur reduction and histidine degradation to glutamate, while branched-chain amino acid transport, nucleic acid biosynthesis and methionine salvage were overrepresented north of the PF. The taxonomic and functional characteristics suggested a shift of primary production from cyanobacteria in the north to eukaryotic phytoplankton in the south, and reflected the different trophic statuses of the two regions. The study provides a new level of understanding about SO microbial communities, describing the contrasting taxonomic and functional characteristics of microbial assemblages either side of the PF.
C1 [Wilkins, David; Lauro, Federico M.; Williams, Timothy J.; Demaere, Matthew Z.; Brown, Mark V.; Cavicchioli, Ricardo] Univ New S Wales, Sch Biotechnol & Biomol Sci, Sydney, NSW 2052, Australia.
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   [Rintoul, Stephen R.] CSIRO Wealth Oceans Natl Res Flagship, Hobart, Tas 7001, Australia.
   [Rintoul, Stephen R.] Antarctic Climate & Ecosyst Cooperat Res Ctr, Hobart, Tas 7001, Australia.
RP Cavicchioli, R (corresponding author), Univ New S Wales, Sch Biotechnol & Biomol Sci, Sydney, NSW 2052, Australia.
EM r.cavicchioli@unsw.edu.au
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NR 99
TC 64
Z9 70
PD MAY
PY 2013
VL 15
IS 5
SI SI
BP 1318
EP 1333
DI 10.1111/1462-2920.12035
UT WOS:000318041800007
DA 2025-07-30
ER

PT J
AU Cerro-Gálvez, E
   Casal, P
   Lundin, D
   Piña, B
   Pinhassi, J
   Dachs, J
   Vila-Costa, M
AF Cerro-Galvez, Elena
   Casal, Paulo
   Lundin, Daniel
   Pina, Benjamin
   Pinhassi, Jarone
   Dachs, Jordi
   Vila-Costa, Maria
TI Microbial responses to anthropogenic dissolved organic carbon in the
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Thousands of semi-volatile hydrophobic organic pollutants (OPs) reach open oceans through atmospheric deposition, causing a chronic and ubiquitous pollution by anthropogenic dissolved organic carbon (ADOC). Hydrophobic ADOC accumulates in cellular lipids, inducing harmful effects on marine biota, and can be partially prone to microbial degradation. Unfortunately, their possible effects on microorganisms, key drivers of global biogeochemical cycles, remain unknown. We challenged coastal microbial communities from Ny-angstrom lesund (Arctic) and Livingston Island (Antarctica) with ADOC concentrations within the range of oceanic concentrations in 24 h. ADOC addition elicited clear transcriptional responses in multiple microbial heterotrophic metabolisms in ubiquitous groups such as Flavobacteriia, Gammaproteobacteria and SAR11. Importantly, a suite of cellular adaptations and detoxifying mechanisms, including remodelling of membrane lipids and transporters, was detected. ADOC exposure also changed the composition of microbial communities, through stimulation of rare biosphere taxa. Many of these taxa belong to recognized OPs degraders. This work shows that ADOC at environmentally relevant concentrations substantially influences marine microbial communities. Given that emissions of organic pollutants are growing during the Anthropocene, the results shown here suggest an increasing influence of ADOC on the structure of microbial communities and the biogeochemical cycles regulated by marine microbes.
C1 [Cerro-Galvez, Elena; Casal, Paulo; Pina, Benjamin; Dachs, Jordi; Vila-Costa, Maria] CSIC, IDAEA, Dept Environm Chem, Jordi Girona 18-26, ES-08034 Barcelona, Catalunya, Spain.
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RP Vila-Costa, M (corresponding author), CSIC, IDAEA, Dept Environm Chem, Jordi Girona 18-26, ES-08034 Barcelona, Catalunya, Spain.
EM maria.vila@idaea.csic.es
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PD APR
PY 2019
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BP 1466
EP 1481
DI 10.1111/1462-2920.14580
UT WOS:000464373000022
DA 2025-07-30
ER

PT J
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NR 98
TC 14
Z9 15
PD FEB
PY 2022
VL 201
AR 102736
DI 10.1016/j.pocean.2021.102736
EA JAN 2022
UT WOS:000780412700001
DA 2025-07-30
ER

PT J
AU Ghai, R
   Rodríguez-Valera, F
   McMahon, KD
   Toyama, D
   Rinke, R
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   Garcia, JW
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AF Ghai, Rohit
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   Garcia, Jose Wagner
   de Miranda, Fernando Pellon
   Henrique-Silva, Flavio
TI Metagenomics of the Water Column in the Pristine Upper Course of the
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SO PLOS ONE
DT Article
AB River water is a small percentage of the total freshwater on Earth but represents an essential resource for mankind. Microbes in rivers perform essential ecosystem roles including the mineralization of significant quantities of organic matter originating from terrestrial habitats. The Amazon river in particular is famous for its size and importance in the mobilization of both water and carbon out of its enormous basin. Here we present the first metagenomic study on the microbiota of this river. It presents many features in common with the other freshwater metagenome available (Lake Gatun in Panama) and much less similarity with marine samples. Among the microbial taxa found, the cosmopolitan freshwater acI lineage of the actinobacteria was clearly dominant. Group I Crenarchaea and the freshwater sister group of the marine SAR11 clade, LD12, were found alongside more exclusive and well known freshwater taxa such as Polynucleobacter. A metabolism-centric analysis revealed a disproportionate representation of pathways involved in heterotrophic carbon processing, as compared to those found in marine samples. In particular, these river microbes appear to be specialized in taking up and mineralizing allochthonous carbon derived from plant material.
C1 [Ghai, Rohit; Rodriguez-Valera, Francisco; McMahon, Katherine D.] Univ Miguel Hernandez, Evolutionary Genom Grp, Dept Prod Vegetal & Microbiol, Alicante, Spain.
   [Toyama, Danyelle; Rinke, Raquel; Henrique-Silva, Flavio] Univ Fed Sao Carlos, Mol Biol Lab, Dept Genet & Evolucao, BR-13560 Sao Carlos, SP, Brazil.
   [Souza de Oliveira, Tereza Cristina] Univ Fed Amazonas, Manaus, AM, Brazil.
   [Garcia, Jose Wagner] Noosfera Projetos Especiais Ltda, Sao Paulo, Brazil.
   [de Miranda, Fernando Pellon] Petr Brasileiro SA Petrobras, Ctr Pesquisas & Desenvolvimento Leopoldo Amer Mig, Rio De Janeiro, Brazil.
RP Ghai, R (corresponding author), Univ Miguel Hernandez, Evolutionary Genom Grp, Dept Prod Vegetal & Microbiol, Alicante, Spain.
EM frvalera@umh.es; dfhs@ufscar.br
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NR 66
TC 155
Z9 168
PD AUG 19
PY 2011
VL 6
IS 8
AR e23785
DI 10.1371/journal.pone.0023785
UT WOS:000294128100031
DA 2025-07-30
ER

PT J
AU García, CSY
   Porcel, S
   Schiaffino, MR
   Lancelotti, J
   Marinone, MC
   Metz, S
   Roesler, I
   Izaguirre, I
AF Sabio y Garcia, Carmen
   Porcel, Sol
   Schiaffino, M. Romina
   Lancelotti, Julio
   Marinone, Maria Cristina
   Metz, Sebastian
   Roesler, Ignacio
   Izaguirre, Irina
TI Differences in bacterial community composition between fish-stocked and
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SO HYDROBIOLOGIA
DT Article
AB Bacterial community composition (BCC) can be modulated by different indirect and direct factors. The Strobel Lake Plateau (Patagonia, Argentina) holds natural fishless lakes. Fish introduction in some of these lakes has affected the structure of their zooplankton, phytoplankton and autotrophic picoplankton communities, whereas its effects on bacterioplankton are unknown. Hence, we analyzed BCC to assess the potential effect of fish introduction on this community in lakes of this region. We sampled fishless and fish-stocked lakes during three summer campaigns and analyzed the BCC. Our results revealed a contrasting arrangement in the main limnological variables and significant differences in the BCC between fishless and stocked lakes. In fish-stocked lakes, Alphaproteobacteria class had a higher proportion and SAR11_cladeIII was the most abundant amplicon sequence variant (ASV); these lakes also showed a marginally higher mean richness but less exclusive ASVs. Environmental and biotic factors contributed to explain BCC variations. The lower percentage of exclusive ASVs and the closer BCC ordination in a non-metric multidimensional scaling suggest a homogenizing effect in fish-stocked lakes. This study contributes to understand the consequences of fish introduction on the plankton communities in lakes of this invaluable region for biodiversity conservation.
C1 [Sabio y Garcia, Carmen; Porcel, Sol; Roesler, Ignacio; Izaguirre, Irina] Univ Buenos Aires, Dept Ecol Genet & Evoluc, Lab Limnol, Inst Ecol Genet & Evoluc Buenos Aires,CONICET, Buenos Aires, Argentina.
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   [Lancelotti, Julio] Consejo Nacl Invest Cient & Tecn, Inst Patagon Estudio Ecosistemas Continentales CEN, Puerto Madryn, Chubut, Argentina.
   [Marinone, Maria Cristina] Univ Buenos Aires, Fac Ciencias Exactas & Nat, Dept Biodivers & Biol Expt, Buenos Aires, Argentina.
   [Metz, Sebastian] IIB INTECH, Lab Ecol Acuat, Chascomus, Buenos Aires, Argentina.
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RP García, CSY (corresponding author), Univ Buenos Aires, Dept Ecol Genet & Evoluc, Lab Limnol, Inst Ecol Genet & Evoluc Buenos Aires,CONICET, Buenos Aires, Argentina.
EM carmeniica@gmail.com
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BP 4709
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DI 10.1007/s10750-024-05622-2
EA JUL 2024
UT WOS:001260374700002
DA 2025-07-30
ER

PT J
AU Lidbury, I
   Mausz, MA
   Scanlan, DJ
   Chen, Y
AF Lidbury, Ian
   Mausz, Michaela A.
   Scanlan, David J.
   Chen, Yin
TI Identification of dimethylamine monooxygenase in marine bacteria reveals
   a metabolic bottleneck in the methylated amine degradation pathway
SO ISME JOURNAL
DT Article
AB Methylated amines (MAs) are ubiquitous in the marine environment and their subsequent flux into the atmosphere can result in the formation of aerosols and ultimately cloud condensation nuclei. Therefore, these compounds have a potentially important role in climate regulation. Using Ruegeria pomeroyi as a model, we identified the genes encoding dimethylamine (DMA) monooxygenase (dmmABC) and demonstrate that this enzyme degrades DMA to monomethylamine (MMA). Although only dmmABC are required for enzyme activity in recombinant Escherichia coli, we found that an additional gene, dmmD, was required for the growth of R. pomeroyi on MAs. The dmmDABC genes are absent from the genomes of multiple marine bacteria, including all representatives of the cosmopolitan SAR11 clade. Consequently, the abundance of dmmDABC in marine metagenomes was substantially lower than the genes required for other metabolic steps of the MA degradation pathway. Thus, there is a genetic and potential metabolic bottleneck in the marine MA degradation pathway. Our data provide an explanation for the observation that DMA-derived secondary organic aerosols (SOAs) are among the most abundant SOAs detected in fine marine particles over the North and Tropical Atlantic Ocean.
C1 [Lidbury, Ian; Mausz, Michaela A.; Scanlan, David J.; Chen, Yin] Univ Warwick, Sch Life Sci, Gibbet Hill Campus,Gibbet Hill Rd, Coventry CV4 7AL, W Midlands, England.
RP Chen, Y (corresponding author), Univ Warwick, Sch Life Sci, Gibbet Hill Campus,Gibbet Hill Rd, Coventry CV4 7AL, W Midlands, England.
EM Y.chen.25@warwick.ac.uk
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NR 46
TC 31
Z9 33
PD JUL
PY 2017
VL 11
IS 7
BP 1592
EP 1601
DI 10.1038/ismej.2017.31
UT WOS:000403675200008
DA 2025-07-30
ER

PT J
AU Tinta, T
   Vojvoda, J
   Mozetic, P
   Talaber, I
   Vodopivec, M
   Malfatti, F
   Turk, V
AF Tinta, T.
   Vojvoda, J.
   Mozetic, P.
   Talaber, I.
   Vodopivec, M.
   Malfatti, F.
   Turk, V.
TI Bacterial community shift is induced by dynamic environmental parameters
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB The potential link between the microbial dynamics and the environmental parameters was investigated in a semi-enclosed and highly dynamic coastal system (Gulf of Trieste, northern Adriatic Sea, NE Mediterranean Sea). Our comprehensive 2-year time-series study showed that despite the shallowness of this area, there was a significant difference between the surface and the bottom bacterial community structure. The bottom bacterial community was more diverse than the surface one and influenced by sediment re-suspension. The surface seawater temperature had a profound effect on bacterial productivity, while the bacterial community structure was more affected by freshwater-borne nutrients and phytoplankton blooms. Phytoplankton blooms caused an increase of Gammaproteobacteria (Alteromonadaceae, SAR86 and Vibrionaceae) and shift in dominance from SAR11 to Rhodobacteraceae taxon at the surface. Our results propose the importance of the water mass movements as drivers of freshwater-borne nutrients and of allochthonous microbial taxa. This study emphasizes the prediction power based on association networks analyses that are fed with long-term measurements of microbial and environmental parameters. These interaction maps offer valuable insights into the response of marine ecosystem to climate- and anthropogenic-driven stressors.
C1 [Tinta, T.; Vojvoda, J.; Mozetic, P.; Talaber, I.; Vodopivec, M.; Turk, V.] Natl Inst Biol, Marine Biol Stn, Piran, Slovenia.
   [Malfatti, F.] Univ Calif San Diego, Scripps Inst Oceanog, La Jolla, CA 92093 USA.
   [Malfatti, F.] OGS Natl Inst Oceanog & Expt Geophys, Trieste, Italy.
RP Tinta, T (corresponding author), Natl Inst Biol, Marine Biol Stn, Piran, Slovenia.
EM tinta@mbss.org
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NR 82
TC 66
Z9 73
PD OCT
PY 2015
VL 17
IS 10
SI SI
BP 3581
EP 3596
DI 10.1111/1462-2920.12519
UT WOS:000363448500013
DA 2025-07-30
ER

PT J
AU Collins, RE
   Rocap, G
   Deming, JW
AF Collins, R. Eric
   Rocap, Gabrielle
   Deming, Jody W.
TI Persistence of bacterial and archaeal communities in sea ice through an
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB The structure of bacterial communities in first-year spring and summer sea ice differs from that in source seawaters, suggesting selection during ice formation in autumn or taxon-specific mortality in the ice during winter. We tested these hypotheses by weekly sampling (January March 2004) of first-year winter sea ice (Franklin Bay, Western Arctic) that experienced temperatures from -9 degrees C to -26 degrees C, generating community fingerprints and clone libraries for Bacteria and Archaea. Despite severe conditions and significant decreases in microbial abundance, no significant changes in richness or community structure were detected in the ice. Communities of Bacteria and Archaea in the ice, as in under-ice seawater, were dominated by SAR11 clade Alphaproteobacteria and Marine Group I Crenarchaeota, neither of which is known from later season sea ice. The bacterial ice library contained clones of Gammaproteobacteria from oligotrophic seawater clades (e.g. OM60, OM182) but no clones from gammaproteobacterial genera commonly detected in later season sea ice by similar methods (e.g. Colwellia, Psychrobacter). The only common sea ice bacterial genus detected in winter ice was Polaribacter. Overall, selection during ice formation and mortality during winter appear to play minor roles in the process of microbial succession that leads to distinctive spring and summer sea ice communities.
C1 [Collins, R. Eric; Rocap, Gabrielle; Deming, Jody W.] Univ Washington, Sch Oceanog, Seattle, WA 98195 USA.
RP Collins, RE (corresponding author), Univ Washington, Sch Oceanog, Box 357940,1503 NE Boat St, Seattle, WA 98195 USA.
EM rec3141@ocean.washington.edu
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BP 1828
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UT WOS:000280101200004
DA 2025-07-30
ER

PT J
AU Liu, Y
   Blain, S
   Crispi, O
   Rembauville, M
   Obernosterer, I
AF Liu, Yan
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   Crispi, Olivier
   Rembauville, Mathieu
   Obernosterer, Ingrid
TI Seasonal dynamics of prokaryotes and their associations with diatoms in
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB The Southern Ocean remains one of the least explored marine environments. The investigation of temporal microbial dynamics has thus far been hampered by the limited access to this remote ocean. We present here high-resolution seasonal observations of the prokaryotic community composition during phytoplankton blooms induced by natural iron fertilization. A total of 18 seawater samples were collected by a moored remote autonomous sampler over 4 months at 5-11 day intervals in offshore surface waters (central Kerguelen Plateau). Illumina sequencing of the 16S rRNA gene revealed that among the most abundant amplicon sequence variants, SAR92 andAurantivirgawere the first bloom responders,Pseudomonadaceae,NitrincolaceaeandPolaribacterhad successive peaks during the spring bloom decline, andAmylibacterincreased in relative abundance later in the season. SAR11 and SUP05 were abundant prior to and after the blooms. Using network analysis, we identified two groups of diatoms representative of the spring and summer bloom that had opposite correlation patterns with prokaryotic taxa. Our study provides the first seasonal picture of microbial community dynamics in the open Southern Ocean and thereby offers biological insights to the cycling of carbon and iron, and to an important puzzling issue that is the modest nitrate decrease associated to iron fertilization.
C1 [Liu, Yan; Blain, Stephane; Crispi, Olivier; Rembauville, Mathieu; Obernosterer, Ingrid] Sorbonne Univ, CNRS, Lab Oceanog Microbienne LOMIC, Banyuls Sur Mer, France.
   [Liu, Yan] Ocean Univ China, Coll Marine Life Sci, Qingdao, Peoples R China.
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RP Obernosterer, I (corresponding author), Sorbonne Univ, CNRS, Lab Oceanog Microbienne LOMIC, Banyuls Sur Mer, France.
EM ingrid.obernosterer@obs-banyuls.fr
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PY 2020
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BP 3968
EP 3984
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EA SEP 2020
UT WOS:000565331500001
DA 2025-07-30
ER

PT J
AU Schütte, UME
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AF Schutte, Ursel M. E.
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SO FRONTIERS IN MICROBIOLOGY
DT Article
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C1 [Schutte, Ursel M. E.; White, Jeffrey R.] Indiana Univ, Integrated Program Environm, Bloomington, IN 47405 USA.
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RP Schütte, UME (corresponding author), Indiana Univ, Integrated Program Environm, Bloomington, IN 47405 USA.; Schütte, UME (corresponding author), Univ Alaska Fairbanks, Inst Arctic Biol, Fairbanks, AK 99775 USA.
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NR 101
TC 20
Z9 23
PD JUL 5
PY 2016
VL 7
AR 1035
DI 10.3389/fmicb.2016.01035
UT WOS:000443464600001
DA 2025-07-30
ER

PT J
AU Straza, TRA
   Cottrell, MT
   Ducklow, HW
   Kirchman, DL
AF Straza, Tiffany R. A.
   Cottrell, Matthew T.
   Ducklow, Hugh W.
   Kirchman, David L.
TI Geographic and Phylogenetic Variation in Bacterial Biovolume as Revealed
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Biovolume is an important characteristic of cells that shapes the contribution of microbes to total biomass and biogeochemical cycling. Most studies of bacterial cell volumes use DAPI (4',6'-diamidino-2-phenylindole), which stains nucleic acids and therefore only a portion of the cell. We used SYPRO Ruby protein stain combined with fluorescence in situ hybridization to examine biovolumes of bacteria in the total community, as well in phylogenetic subgroups. Protein-based volumes varied more and were consistently larger than DNA-based volumes by 3.3-fold on average. Bacterial cells were ca. 30% larger in the Arctic Ocean and Antarctic coastal waters than in temperate regimes. We hypothesized that geographic differences in the abundance of specific bacterial groups drove the observed patterns in biovolume. In support of this hypothesis, we found that Gammaproteobacteria and members of the Sphingobacteria-Flavobacteria group were larger in higher-latitude waters and that the mean volumes of both groups were larger than the mean bacterial volume in all environments tested. The mean cell size of SAR11 bacteria was larger than the mean cell size of the total bacterial community on average, although this varied. Protein staining increases the accuracy of biovolume measurements and gives insights into how the biomass of marine microbial communities varies over time and space.
C1 [Straza, Tiffany R. A.; Cottrell, Matthew T.; Kirchman, David L.] Univ Delaware, Coll Marine & Earth Studies, Lewes, DE 19958 USA.
   [Ducklow, Hugh W.] Marine Biol Lab, Ctr Ecosyst, Woods Hole, MA 02543 USA.
RP Kirchman, DL (corresponding author), Univ Delaware, Coll Marine & Earth Studies, 700 Pilottown Rd, Lewes, DE 19958 USA.
EM kirchman@udel.edu
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NR 48
TC 33
Z9 38
PD JUN 15
PY 2009
VL 75
IS 12
BP 4028
EP 4034
DI 10.1128/AEM.00183-09
UT WOS:000266782300024
DA 2025-07-30
ER

PT J
AU Ohkusa, T
   Kato, K
   Sekizuka, T
   Sugiyama, T
   Sato, N
   Kuroda, M
AF Ohkusa, Toshifumi
   Kato, Kimitoshi
   Sekizuka, Tsuyoshi
   Sugiyama, Toshiro
   Sato, Nobuhiro
   Kuroda, Makoto
TI Comparison of the Gut Microbiota of Patients Who Improve with Antibiotic
   Combination Therapy for Ulcerative Colitis and Those Who Do Not:
   Investigation by Fecal Metagenomic Analyses
SO NUTRIENTS
DT Article
AB Background/Objectives: The cause of ulcerative colitis (UC) may be related to commensal bacteria in genetically susceptible patients. We previously demonstrated that triple antibiotic combination therapy induces remission in patients with active UC in randomized controlled trials (RCTs). Now, we investigate changes in the gut microbiota of patients who responded to the antibiotic combination therapy. Methods: Thirty-one patients with UC given ATM/AFM (amoxicillin, metronidazole, and tetracycline or fosfomycin) therapy for two weeks were enrolled in this study. The clinical conditions of these UC patients were evaluated by the partial Mayo score. The gut microbiota was compared via the metagenomic shot gun analysis of fecal samples. Results: Of the 31 patients, 16 and 8 experienced complete and partial remission, respectively, over three months in response to ATM/AFM therapy, whereas ATM/AFM showed no efficacy in 7 patients. The dysbiosis before treatment in the active stage could be associated with increased populations of Bacteroides, Parabacteroides, Rickenella, Clostridium, Flavonifractor, Pelagibacter, Bordetella, Massilia, and Piscrickettsia species. Metagenomic analysis revealed dramatic changes in the gut microbiota at an early stage, that is, just two weeks after starting ATM/AFM therapy. After treatment in the responder group, the populations of bifidobacterium and lactobacilli species were significantly increased, while the population of bacteroides decreased. Conclusions: These results suggest that metagenomic analysis demonstrated a marked change in the gut microbiota after antibiotic combination treatment. In the triple antibiotic combination therapy, remission was associated with an increase in bifidobacterium and lactobacilli species.
C1 [Ohkusa, Toshifumi; Sato, Nobuhiro] Juntendo Univ, Dept Microbiota Res, Grad Sch Med, Tokyo 1130033, Japan.
   [Ohkusa, Toshifumi] Jikei Univ, Sch Med, Div Gastroenterol & Hepatol, Dept Internal Med, Kashiwa, Chiba 2778567, Japan.
   [Kato, Kimitoshi] Nihon Univ, Sch Med, Div Res Planning & Dev, Tokyo 1738610, Japan.
   [Sekizuka, Tsuyoshi; Kuroda, Makoto] Natl Inst Infect Dis, Pathogen Genom Ctr, Tokyo 1628640, Japan.
   [Sugiyama, Toshiro] Hokkaido Univ Hosp, Adv Gastrointestinal Canc Mol Targeted Therapy &, Sapporo 0608648, Japan.
RP Ohkusa, T (corresponding author), Juntendo Univ, Dept Microbiota Res, Grad Sch Med, Tokyo 1130033, Japan.; Ohkusa, T (corresponding author), Jikei Univ, Sch Med, Div Gastroenterol & Hepatol, Dept Internal Med, Kashiwa, Chiba 2778567, Japan.
EM ohkusa@juntendo.ac.jp; vyk01273@nifty.com; sekizuka@nih.go.jp;
   toshisugi5397@ac.cyberhome.ne.jp; nsato@juntendo.ac.jp;
   makokuro@nih.go.jp
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NR 31
TC 2
Z9 2
PD OCT
PY 2024
VL 16
IS 20
AR 3500
DI 10.3390/nu16203500
UT WOS:001341599200001
DA 2025-07-30
ER

PT J
AU Roda-Garcia, JJ
   Haro-Moreno, JM
   Rodriguez-Valera, F
   Almagro-Moreno, S
   López-Pérez, M
AF Roda-Garcia, Juan J.
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   Almagro-Moreno, Salvador
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TI Single-amplified genomes reveal most streamlined free-living marine
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Evolutionary adaptations of prokaryotes to the environment sometimes result in genome reduction. Our knowledge of this phenomenon among free-living bacteria remains scarce. We address the dynamics and limits of genome reduction by examining one of the most abundant bacteria in the ocean, the SAR86 clade. Despite its abundance, comparative genomics has been limited by the absence of pure cultures and the poor representation in metagenome-assembled genomes. We co-assembled multiple previously available single-amplified genomes to obtain the first complete genomes from members of the four families. All families showed a convergent evolutionary trajectory with characteristic features of streamlined genomes, most pronounced in the TMED112 family. This family has a genome size of ca. 1 Mb and only 1 bp as median intergenic distance, exceeding values found in other abundant microbes such as SAR11, OM43 and Prochlorococcus. This genomic simplification led to a reduction in the biosynthesis of essential molecules, DNA repair-related genes, and the ability to sense and respond to environmental factors, which could suggest an evolutionary dependence on other co-occurring microbes for survival (Black Queen hypothesis). Therefore, these reconstructed genomes within the SAR86 clade provide new insights into the limits of genome reduction in free-living marine bacteria.
C1 [Roda-Garcia, Juan J.; Haro-Moreno, Jose M.; Rodriguez-Valera, Francisco; Lopez-Perez, Mario] Univ Miguel Hernandez, Dept Prod Vegetal & Microbiol, Evolutionary Genom Grp, Alicante, Spain.
   [Almagro-Moreno, Salvador] Univ Cent Florida, Burnett Sch Biomed Sci, Orlando, FL USA.
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RP López-Pérez, M (corresponding author), Univ Miguel Hernandez, Dept Prod Vegetal & Microbiol, Evolutionary Genom Grp, Apartado 18, Alicante 03550, Spain.
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NR 121
TC 9
Z9 9
PD JUN
PY 2023
VL 25
IS 6
BP 1136
EP 1154
DI 10.1111/1462-2920.16348
EA FEB 2023
UT WOS:000933627100001
DA 2025-07-30
ER

PT J
AU Boysen, AK
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   Kumler, W
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   Heal, KR
   Carlson, LT
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AF Boysen, Angela K.
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   Key, Rebecca S.
   Heal, Katherine R.
   Carlson, Laura T.
   Groussman, Ryan D.
   Armbrust, E. Virginia
   Ingalls, Anitra E.
TI Glycine betaine uptake and metabolism in marine microbial communities
SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Glycine betaine (GBT) is a compatible solute in high concentrations in marine microorganisms. As a component of labile organic matter, GBT has complex biochemical potential as a substrate for microbial use that is unconstrained in the environment. Here we determine the uptake kinetics and metabolic fate of GBT in two natural microbial communities in the North Pacific characterized by different nitrate concentrations. Dissolved GBT had maximum uptake rates of 0.36 and 0.56 nM h(-1) with half-saturation constants of 79 and 11 nM in the high nitrate and low nitrate stations respectively. During multiday incubations, most GBT taken into cells was retained as a compatible solute. Stable isotopes derived from the added GBT were also observed in other metabolites, including choline, carnitine and sarcosine, suggesting that GBT was used for biosynthesis and for catabolism to pyruvate and ammonium. Where nitrate was scarce, GBT was primarily metabolized via demethylation to glycine. Gene transcript data were consistent with SAR11 using GBT as a source of methyl groups to fuel the methionine cycle. Where nitrate concentrations were higher, more GBT was partitioned for lipid biosynthesis by both bacteria and eukaryotic phytoplankton. Our data highlight unexpected metabolic pathways and potential routes of microbial metabolite exchange.
C1 [Boysen, Angela K.; Kumler, William; Heal, Katherine R.; Carlson, Laura T.; Groussman, Ryan D.; Armbrust, E. Virginia; Ingalls, Anitra E.] Univ Washington, Sch Oceanog, Seattle, WA 98195 USA.
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RP Ingalls, AE (corresponding author), Univ Washington, Sch Oceanog, Seattle, WA 98195 USA.
EM aingalls@uw.edu
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NR 108
TC 29
Z9 32
PD MAY
PY 2022
VL 24
IS 5
SI SI
BP 2380
EP 2403
DI 10.1111/1462-2920.16020
EA MAY 2022
UT WOS:000791546400001
DA 2025-07-30
ER

PT J
AU Zeng, YX
   Yu, Y
   Li, HR
   He, JF
   Lee, SH
   Sun, K
AF Zeng Yinxin
   Yu Yong
   Li Huirong
   He Jianfeng
   Lee, Sang H.
   Sun Kun
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   region in summer
SO ACTA OCEANOLOGICA SINICA
DT Article
AB Planktonic bacteria are abundant in the Chukchi Borderland region. However, little is known about their diversity and the roles of various bacteria in the ocean. Seawater samples were collected from two stations K2S and K4S where sea ice was melting obviously. The analysis of water samples with fluorescence in situ hybridization (FISH) showed that DMSP-degrading bacteria accounted for 13% of the total bacteria at the station K2S. No aerobic anoxygenic phototrophic (AAP) bacteria were detected in both samples. The bacterial communities were characterized by two 16S rRNA gene clone libraries. Sequences fell into four major lineages of the domain Bacteria, including Proteobacteria (Alpha, Beta and Gamma subclasses), Bacteroidetes, Actinobacteria and Firmicutes. No significant difference was found between the two clone libraries. SAR11 and Rhodobacteraceae clades of Alphaproteobacteria and Pseudoalteromonas of Gammaproteobacteria constituted three dominant fractions in the clone libraries. A total of 191 heterotrophic bacterial strains were isolated and 76% showed extracellular proteolytic activity. Phylogenetic analysis reveals that the isolates fell into Gammaproteobacteria, Bacteroidetes, Actinobacteria and Firmicutes. The most common genus in both the bacterial isolates and protease-producing bacteria was Pseudoalteromonas. UniFrac data showed suggestive differences in bacterial communities between the Chukchi Borderland and the northern Bering Sea.
C1 [Zeng Yinxin; Yu Yong; Li Huirong; He Jianfeng; Sun Kun] Polar Res Inst China, State Ocean Adm, Key Lab Polar Sci, Shanghai 200136, Peoples R China.
   [Zeng Yinxin] Jimei Univ, Coll Biol Engn, Xiamen 361021, Peoples R China.
   [Lee, Sang H.] Pusan Natl Univ, Dept Oceanog, Pusan 609735, South Korea.
RP Zeng, YX (corresponding author), Polar Res Inst China, State Ocean Adm, Key Lab Polar Sci, Shanghai 200136, Peoples R China.
EM yxzeng@yahoo.com
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NR 61
TC 12
Z9 12
PD JUN
PY 2013
VL 32
IS 6
BP 66
EP 74
DI 10.1007/s13131-013-0271-y
UT WOS:000320094400009
DA 2025-07-30
ER

PT J
AU Simu, K
   Hagström, Å
AF Simu, K
   Hagström, Å
TI Oligotrophic bacterioplankton with a novel single-cell life strategy
SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB A large fraction of the marine bacterioplankton community is unable to form colonies on agar surfaces, which so far no experimental evidence can explain. Here we describe a previously undescribed growth behavior of three non-colony-forming oligotrophic bacterioplankton, including a SAR11 cluster representative, the world's most abundant organism. We found that these bacteria exhibit a behavior that promotes growth and dispersal instead of colony formation. Although these bacteria do not form colonies on agar, it was possible to monitor growth on the surface of seawater agar slides containing a fluorescent stain, 4',6'-diamidino-2-phenylindole (DAPI). Agar slides were prepared by pouring a solution containing 0.7% agar and 0.5 mug of DAPI per ml in seawater onto glass slides. Prompt dispersal of newly divided cells explained the inability to form colonies since immobilized cells (cells immersed in agar) formed microcolonies. The behavior observed suggests a life strategy intended to optimize access of individual cells to substrates. Thus, the inability to form colonies or biofilms appears to be part of a K-selected population strategy in which oligotrophic bacteria explore dissolved organic matter in seawater as single cells.
C1 Univ Kalmar, SE-39182 Kalmar, Sweden.
RP Univ Kalmar, SE-39182 Kalmar, Sweden.
EM ake.hagstrom@hik.se
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NR 29
TC 66
Z9 94
PD APR
PY 2004
VL 70
IS 4
BP 2445
EP 2451
DI 10.1128/AEM.70.4.2445-2451.2004
UT WOS:000220792200067
DA 2025-07-30
ER

PT J
AU Acker, M
   Hogle, SL
   Berube, PM
   Hackl, T
   Coe, A
   Stepanauskas, R
   Chisholm, SW
   Repeta, DJ
AF Acker, Marianne
   Hogle, Shane L.
   Berube, Paul M.
   Hackl, Thomas
   Coe, Allison
   Stepanauskas, Ramunas
   Chisholm, Sallie W.
   Repeta, Daniel J.
TI Phosphonate production by marine microbes: Exploring new sources and
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SO PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
   AMERICA
DT Article
AB Phosphonates are organophosphorus metabolites with a characteristic C-P bond. They are ubiquitous in the marine environment, their degradation broadly supports ecosystem productivity, and they are key components of the marine phosphorus (P) cycle. However, the microbial producers that sustain the large oceanic inventory of phosphonates as well as the physiological and ecological roles of phosphonates are enigmatic. Here, we show that phosphonate synthesis genes are rare but widely distributed among diverse bacteria and archaea, including Prochlorococcus and SAR11, the two major groups of bacteria in the ocean. In addition, we show that Prochlorococcus can allocate over 40% of its total cellular P-quota toward phosphonate production. However, we find no evidence that Prochlorococcus uses phosphonates for surplus P storage, and nearly all producer genomes lack the genes necessary to degrade and assimilate phosphonates. Instead, we postulate that phosphonates are associated with cell-surface glycoproteins, suggesting that phosphonates mediate ecological interactions between the cell and its surrounding environment. Our findings indicate that the oligotrophic surface ocean phosphonate pool is sustained by a relatively small fraction of the bacterioplankton cells allocating a significant portion of their P quotas toward secondary metabolism and away from growth and reproduction.
C1 [Acker, Marianne] Woods Hole Oceanog Inst, MIT Woods Hole Oceanog Inst Joint Program Oceanog, Woods Hole, MA 02543 USA.
   [Acker, Marianne; Repeta, Daniel J.] Woods Hole Oceanog Inst, Dept Chem & Geochem, Woods Hole, MA 02543 USA.
   [Hogle, Shane L.; Berube, Paul M.; Hackl, Thomas; Coe, Allison; Chisholm, Sallie W.] MIT, Dept Civil & Environm Engn, Cambridge, MA 02139 USA.
   [Hogle, Shane L.] Univ Turku, Dept Biol, SF-20500 Turku, Finland.
   [Stepanauskas, Ramunas] Single Cell Genom Ctr, Bigelow Lab Ocean Sci, East Boothbay, ME 04544 USA.
   [Chisholm, Sallie W.] MIT, Dept Biol, Cambridge, MA 02139 USA.
RP Repeta, DJ (corresponding author), Woods Hole Oceanog Inst, Dept Chem & Geochem, Woods Hole, MA 02543 USA.
EM drepeta@whoi.edu
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NR 129
TC 41
Z9 45
PD MAR 15
PY 2022
VL 119
IS 11
AR e2113386119
DI 10.1073/pnas.2113386119
UT WOS:000772224400011
DA 2025-07-30
ER

PT J
AU Camarena-Gómez, MT
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TI Bacterioplankton dynamics driven by interannual and spatial variation in
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SO LIMNOLOGY AND OCEANOGRAPHY
DT Article
AB In parts of the Baltic Sea, the phytoplankton spring bloom communities, commonly dominated by diatoms, are shifting toward the co-occurrence of diatoms and dinoflagellates. Although phytoplankton are known to shape the composition and function of associated bacterioplankton communities, the potential bacterial responses to such a decrease of diatoms are unknown. Here we explored the changes in bacterial communities and heterotrophic production during the spring bloom in four consecutive spring blooms across several sub-basins of the Baltic Sea and related them to changes in environmental variables and in phytoplankton community structure. The taxonomic structure of bacterioplankton assemblages was partially explained by salinity and temperature but also linked to the phytoplankton community. Higher carbon biomass of the diatomsAchnanthes taeniata,Skeletonema marinoi,Thalassiosira levanderi, andChaetocerosspp. was associated with more diverse bacterial communities dominated by copiotrophic bacteria (Flavobacteriia, Gammaproteobacteria, and Betaproteobacteria) and higher bacterial production. During dinoflagellate dominance, bacterial production was low and bacterial communities were dominated by Alphaproteobacteria, mainly SAR11. Our results suggest that increases in dinoflagellate abundance during the spring bloom will largely affect the structuring and functioning of the associated bacterial communities. This could decrease pelagic remineralization of organic matter and possibly affect the bacterial grazers communities.
C1 [Camarena-Gomez, Maria Teresa; Piiparinen, Jonna; Lipsewers, Tobias; Spilling, Kristian] Finnish Environm Inst, Marine Res Ctr, Helsinki, Finland.
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RP Camarena-Gómez, MT (corresponding author), Finnish Environm Inst, Marine Res Ctr, Helsinki, Finland.; Camarena-Gómez, MT (corresponding author), Univ Helsinki, Tvarminne Zool Stn, Hango, Finland.
EM m.t.camarena@gmail.com
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TC 18
Z9 20
PD JAN
PY 2021
VL 66
IS 1
BP 255
EP 271
DI 10.1002/lno.11601
EA OCT 2020
UT WOS:000574018300001
DA 2025-07-30
ER

PT J
AU Morris, RM
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AF Morris, R. M.
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DT Article
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RP Morris, RM (corresponding author), Cornell Univ, Dept Microbiol, Ithaca, NY 14853 USA.
EM rm352@cornell.edu
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NR 42
TC 150
Z9 165
PD AUG
PY 2006
VL 8
IS 8
BP 1361
EP 1370
DI 10.1111/j.1462-2920.2006.01029.x
UT WOS:000238885300006
DA 2025-07-30
ER

PT J
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AF Hou, Shengwei
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DT Article
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C1 [Hou, Shengwei; Pfreundt, Ulrike; Hess, Wolfgang R.] Univ Freiburg, Fac Biol, Genet & Expt Bioinformat, Schanzlestr 1, D-79104 Freiburg, Germany.
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RP Hess, WR (corresponding author), Univ Freiburg, Fac Biol, Genet & Expt Bioinformat, Schanzlestr 1, D-79104 Freiburg, Germany.
EM wolfgang.hess@biologie.uni-freiburg.de
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NR 85
TC 12
Z9 12
PD OCT 19
PY 2016
VL 6
AR 35470
DI 10.1038/srep35470
UT WOS:000385953000001
DA 2025-07-30
ER

PT J
AU Alonso-Sáez, L
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AF Alonso-Saez, Laura
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   Pedros-Alio, Carlos
TI Winter-to-summer changes in the composition and single-cell activity of
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
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C1 [Alonso-Saez, Laura; Gasol, Josep M.; Balague, Vanessa; Pedros-Alio, Carlos] CSIC, Inst Ciencias Mar, Dept Biol Marina & Oceanog, E-08003 Barcelona, Catalunya, Spain.
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RP Alonso-Sáez, L (corresponding author), CSIC, Inst Ciencias Mar, Dept Biol Marina & Oceanog, E-08003 Barcelona, Catalunya, Spain.
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NR 58
TC 128
Z9 142
PD SEP
PY 2008
VL 10
IS 9
BP 2444
EP 2454
DI 10.1111/j.1462-2920.2008.01674.x
UT WOS:000258203500023
DA 2025-07-30
ER

PT J
AU Brinkhoff, T
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   Simon, M
AF Brinkhoff, Thorsten
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   Simon, Meinhard
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DT Review
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C1 [Brinkhoff, Thorsten; Giebel, Helge-Ansgar; Simon, Meinhard] Carl von Ossietzky Univ Oldenburg, ICMBM, D-26111 Oldenburg, Germany.
RP Brinkhoff, T (corresponding author), Carl von Ossietzky Univ Oldenburg, ICMBM, POB 2503, D-26111 Oldenburg, Germany.
EM Thorsten.Brinkhoff@icbm.de
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NR 49
TC 323
Z9 357
PD JUN
PY 2008
VL 189
IS 6
BP 531
EP 539
DI 10.1007/s00203-008-0353-y
UT WOS:000255741700001
DA 2025-07-30
ER

PT J
AU MULLINS, TD
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   KREST, RL
   GIOVANNONI, SJ
AF MULLINS, TD
   BRITSCHGI, TB
   KREST, RL
   GIOVANNONI, SJ
TI GENETIC COMPARISONS REVEAL THE SAME UNKNOWN BACTERIAL LINEAGES IN
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SO LIMNOLOGY AND OCEANOGRAPHY
DT Article
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TC 351
Z9 385
PD JAN
PY 1995
VL 40
IS 1
BP 148
EP 158
DI 10.4319/lo.1995.40.1.0148
UT WOS:A1995QT29200014
DA 2025-07-30
ER

PT J
AU Fahlgren, C
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AF Fahlgren, Camilla
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   Zabori, Julia
   Lindh, Markus V.
   Krejci, Radovan
   Martensson, E. Monica
   Nilsson, Douglas
   Pinhassi, Jarone
TI Seawater mesocosm experiments in the Arctic uncover differential
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SO ENVIRONMENTAL MICROBIOLOGY REPORTS
DT Article
AB Biogenic aerosols critically control atmospheric processes. However, although bacteria constitute major portions of living matter in seawater, bacterial aerosolization from oceanic surface layers remains poorly understood. We analysed bacterial diversity in seawater and experimentally generated aerosols from three Kongsfjorden sites, Svalbard. Construction of 16S rRNA gene clone libraries from paired seawater and aerosol samples resulted in 1294 sequences clustering into 149 bacterial and 34 phytoplankton operational taxonomic units (OTUs). Bacterial communities in aerosols differed greatly from corresponding seawater communities in three out of four experiments. Dominant populations of both seawater and aerosols were Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria. Across the entire dataset, most OTUs from seawater could also be found in aerosols; in each experiment, however, several OTUs were either selectively enriched in aerosols or little aerosolized. Notably, a SAR11 clade OTU was consistently abundant in the seawater, but was recorded in significantly lower proportions in aerosols. A strikingly high proportion of colony-forming bacteria were pigmented in aerosols compared with seawater, suggesting that selection during aerosolization contributes to explaining elevated proportions of pigmented bacteria frequently observed in atmospheric samples. Our findings imply that atmospheric processes could be considerably influenced by spatiotemporal variations in the aerosolization efficiency of different marine bacteria.
C1 [Fahlgren, Camilla; Gomez-Consarnau, Laura; Lindh, Markus V.; Pinhassi, Jarone] Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, SE-39182 Kalmar, Sweden.
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RP Pinhassi, J (corresponding author), Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, Barlastgatan 11, SE-39182 Kalmar, Sweden.
EM jarone.pinhassi@lnu.se
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NR 51
TC 29
Z9 32
PD JUN
PY 2015
VL 7
IS 3
BP 460
EP 470
DI 10.1111/1758-2229.12273
UT WOS:000354375100011
DA 2025-07-30
ER

PT J
AU Denux, M
   Armenteros, M
   Weber, L
   Miller, CA
   Sántha, K
   Apprill, A
AF Denux, Manon
   Armenteros, Maickel
   Weber, Laura
   Miller, Carolyn A.
   Santha, Kinga
   Apprill, Amy
TI Coral Reef Water Microbial Communities of Jardines de la Reina, Cuba
SO MICROORGANISMS
DT Article
AB Globally, coral reef ecosystems are undergoing significant change related to climate change and anthropogenic activities. Yet, the Cuban archipelago of Jardines de la Reina (JR) has experienced fewer stressors due to its geographical remoteness and high level of conservation. This study examines the surface and benthic reef water microbial communities associated with 32 reef sites along the JR archipelago and explores the relationship between the community composition of reef microorganisms examined using bacterial and archaeal small subunit ribosomal RNA gene (16S rRNA gene) sequencing compared to geographic, conservation/protection level, environmental, physicochemical, and reef benthic and pelagic community features. Reef nutrient concentrations were low and microbial communities dominated by picocyanobacteria and SAR11 and SAR86 clade bacteria, characteristic of an oligotrophic system. Reef water microbial community alpha and beta diversity both varied throughout the archipelago and were strongly related to geography. Three sites in the western archipelago showed unique microbial communities, which may be related to the hydrogeography and influences of the channels linking the Ana Maria gulf with the Caribbean Sea. Overall, this work provides the first extensive description of the reef microbial ecology of the Caribbean's 'Crown Jewel' reef system and a framework to evaluate the influence of ongoing stressors on the reef microorganisms.
C1 [Denux, Manon; Weber, Laura; Miller, Carolyn A.; Santha, Kinga; Apprill, Amy] Woods Hole Oceanog Inst, 266 Woods Hole Rd, Woods Hole, MA 02543 USA.
   [Armenteros, Maickel] Univ Nacl Autonoma Mexico, Unidad Acad Mazatlan, Inst Ciencias Mar & Limnol, Mazatlan 82040, Mexico.
   [Santha, Kinga] Univ Lausanne, Fac Geosci & Environm, CH-1015 Lausanne, Switzerland.
RP Apprill, A (corresponding author), Woods Hole Oceanog Inst, 266 Woods Hole Rd, Woods Hole, MA 02543 USA.
EM denuxmanon@gmail.com; maickel_armenteros@ola.icmyl.unam.mx;
   aapprill@whoi.edu
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NR 49
TC 0
Z9 0
PD SEP
PY 2024
VL 12
IS 9
AR 1822
DI 10.3390/microorganisms12091822
UT WOS:001323242900001
DA 2025-07-30
ER

PT J
AU Teng, ZJ
   Qin, QL
   Zhang, WP
   Li, J
   Fu, HH
   Wang, P
   Lan, MS
   Lu, GF
   He, JF
   McMinn, A
   Wang, M
   Chen, XL
   Zhang, YZ
   Chen, Y
   Li, CY
AF Teng, Zhao-Jie
   Qin, Qi-Long
   Zhang, Weipeng
   Li, Jian
   Fu, Hui-Hui
   Wang, Peng
   Lan, Musheng
   Lu, Guangfu
   He, Jianfeng
   McMinn, Andrew
   Wang, Min
   Chen, Xiu-Lan
   Zhang, Yu-Zhong
   Chen, Yin
   Li, Chun-Yang
TI Biogeographic traits of dimethyl sulfide and dimethylsulfoniopropionate
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SO MICROBIOME
DT Article
AB Background: Dimethyl sulfide (DMS) is the dominant volatile organic sulfur in global oceans. The predominant source of oceanic DMS is the cleavage of dimethylsulfoniopropionate (DMSP), which can be produced by marine bacteria and phytoplankton. Polar oceans, which represent about one fifth of Earth's surface, contribute significantly to the global oceanic DMS sea-air flux. However, a global overview of DMS and DMSP cycling in polar oceans is still lacking and the key genes and the microbial assemblages involved in DMSP/DMS transformation remain to be fully unveiled.
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C1 [Teng, Zhao-Jie; Qin, Qi-Long; Li, Jian; Zhang, Yu-Zhong] Shandong Univ, State Key Lab Microbial Technol, Marine Biotechnol Res Ctr, Qingdao 266237, Peoples R China.
   [Zhang, Weipeng; Fu, Hui-Hui; Wang, Peng; Wang, Min; Chen, Xiu-Lan; Zhang, Yu-Zhong; Chen, Yin; Li, Chun-Yang] Ocean Univ China, Coll Marine Life Sci, Inst Adv Ocean Study, Qingdao 266003, Peoples R China.
   [Fu, Hui-Hui; Wang, Peng; Chen, Xiu-Lan; Zhang, Yu-Zhong; Li, Chun-Yang] Pilot Natl Lab Marine Sci & Technol Qingdao, Lab Marine Biol & Biotechnol, Qingdao 266373, Peoples R China.
   [Lan, Musheng; Lu, Guangfu; He, Jianfeng] Polar Res Inst China, Key Lab Polar Sci MNR, Shanghai 200136, Peoples R China.
   [McMinn, Andrew] Univ Tasmania, Inst Marine & Antarctic Studies, Hobart, Tas, Australia.
   [Chen, Yin] Univ Warwick, Sch Life Sci, Coventry, W Midlands, England.
RP Chen, Y; Li, CY (corresponding author), Ocean Univ China, Coll Marine Life Sci, Inst Adv Ocean Study, Qingdao 266003, Peoples R China.; Li, CY (corresponding author), Pilot Natl Lab Marine Sci & Technol Qingdao, Lab Marine Biol & Biotechnol, Qingdao 266373, Peoples R China.; Chen, Y (corresponding author), Univ Warwick, Sch Life Sci, Coventry, W Midlands, England.
EM Y.Chen.25@warwick.ac.uk; lcy@ouc.edu.cn
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NR 107
TC 29
Z9 31
PD OCT 16
PY 2021
VL 9
IS 1
AR 207
DI 10.1186/s40168-021-01153-3
UT WOS:000707635100001
DA 2025-07-30
ER

PT J
AU Bittner, MJ
   Bannon, CC
   Rowland, E
   Sundh, J
   Bertrand, EM
   Andersson, AF
   Paerl, RW
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AF Bittner, Meriel J.
   Bannon, Catherine C.
   Rowland, Elden
   Sundh, John
   Bertrand, Erin M.
   Andersson, Anders F.
   Paerl, Ryan W.
   Riemann, Lasse
TI New chemical and microbial perspectives on vitamin B1 and vitamer
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SO ISME COMMUNICATIONS
DT Article
AB Vitamin B1 (thiamin, B1) is an essential micronutrient for cells, yet intriguingly in aquatic systems most bacterioplankton are unable to synthesize it de novo (auxotrophy), requiring an exogenous source. Cycling of this valuable metabolite in aquatic systems has not been fully investigated and vitamers (B1-related compounds) have only begun to be measured and incorporated into the B1 cycle. Here, we identify potential key producers and consumers of B1 and gain new insights into the dynamics of B1 cycling through measurements of B1 and vitamers (HMP: 4-amino-5-hydroxymethyl-2-methylpyrimidine, HET: 4-methyl-5-thiazoleethanol, FAMP: N-formyl-4-amino- 5-aminomethyl-2-methylpyrimidine) in the particulate and dissolved pool in a temperate coastal system. Dissolved B1 was not the primary limiting nutrient for bacterial production and was relatively stable across seasons with concentrations ranging from 74-117 pM, indicating a balance of supply and demand. However, vitamer concentration changed markedly with season as did transcripts related to vitamer salvage and transport suggesting use of vitamers by certain bacterioplankton, e.g. Pelagibacterales. Genomic and transcriptomic analyses showed that up to 78% of the bacterioplankton taxa were B1 auxotrophs. Notably, de novo B1 production was restricted to a few abundant bacterioplankton (e.g. Vulcanococcus, BACL14 ( Burkholderiales ), Verrucomicrobiales) across seasons. In summer, abundant picocyanobacteria were important putative B1 sources, based on transcriptional activity, leading to an increase in the B1 pool. Our results provide a new dynamic view of the players and processes involved in B1 cycling over time in coastal waters, and identify specific priority populations and processes for future study.
C1 [Bittner, Meriel J.; Riemann, Lasse] Univ Copenhagen, Dept Biol, Marine Biol Sect, Strandpromenaden 5, DK-3000 Helsingor, Denmark.
   [Bannon, Catherine C.; Rowland, Elden; Bertrand, Erin M.] Dalhousie Univ, Dept Biol, Halifax, NS B3H 4R2, Canada.
   [Sundh, John] Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Natl Bioinformat Infrastruct Sweden, Box 1031, S-17121 Solna, Sweden.
   [Andersson, Anders F.] KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Dept Gene Technol, Sci Life Lab, S-17165 Stockholm, Sweden.
   [Paerl, Ryan W.] North Carolina State Univ, Dept Marine Earth & Atmospher Sci, Raleigh, NC USA.
   [Paerl, Ryan W.] NC State Univ, Dept Marine Earth & Atmospher Sci, 4135 Jordan Hall,2800 Faucette Dr, Raleigh, NC 27695 USA.
RP Bittner, MJ; Riemann, L (corresponding author), Univ Copenhagen, Dept Biol, Marine Biol Sect, Strandpromenaden 5, DK-3000 Helsingor, Denmark.; Paerl, RW (corresponding author), NC State Univ, Dept Marine Earth & Atmospher Sci, 4135 Jordan Hall,2800 Faucette Dr, Raleigh, NC 27695 USA.
EM meriel.bittner@bio.ku.dk; rpaerl@ncsu.edu; lriemann@bio.ku.dk
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NR 104
TC 5
Z9 5
PD JAN 10
PY 2024
VL 4
IS 1
AR ycad016
DI 10.1093/ismeco/ycad016
UT WOS:001346731500002
DA 2025-07-30
ER

PT J
AU Liu, L
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   Zheng, Q
AF Liu, Lu
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   Jiao, Nianzhi
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Microbial growth and mortality are fundamental to community assembly and drive the elemental biogeochemical cycles in the ocean. Virus-induced host lysis contributes, on average, half of prokaryotic mortality and has a substantial effect on composition and diversity of marine microbes. Nevertheless, virus-mediated taxon-specific cell lysis is few studied to date. In the present study, we investigated the taxon-specific cell lysis and estimated its contribution to the variations of community composition in rare and abundant microbial taxa. The dominant taxa Prochlorococcus, Synechococcus, SAR11, and Rhodobacteraceae displayed lower cell lysis index (CLI, the rate of extracellular to intracellular rRNA) in surface seawater. Meanwhile, Alteromonas, Pseudomonas, and Halomonas had high CLI values in the bottom seawater. Cell lysis contributed a larger percentage of variation in rare taxa (5.0%-9.4%) than in abundant taxa (0.1%-1.7%). Furthermore, linear regression analysis indicated that rare taxa were more likely to experience higher viral lysis pressure relative to abundant taxa. Our findings provide insight into the impact of virus-mediated cell lysis on prokaryotic community structure and diversity and further improve our understanding of the various abiotic and biotic factors contributing to community assembly in the ocean.IMPORTANCEVirus-induced host lysis contributes up to 40% of total prokaryotic mortality and plays crucial roles in shaping microbial composition and diversity in the ocean. Nonetheless, what taxon-specific cell lysis is caused by viruses remains to be studied. The present study, therefore, examined the taxon-specific cell lysis and estimated its contribution to the variations in the rare and abundant microbial taxa. The results demonstrate that taxon-specific mortality differed in surface and bottom of the coastal environment. In addition, active rare taxa are more susceptible to heightened lytic pressure and suggested the importance of viral lysis in regulating the microbial community composition. These results improve our understanding of bottom-up (abiotic environmental variables) and top-down (viral lysis) controls contributing to microbial community assembly in the ocean.
   Virus-induced host lysis contributes up to 40% of total prokaryotic mortality and plays crucial roles in shaping microbial composition and diversity in the ocean. Nonetheless, what taxon-specific cell lysis is caused by viruses remains to be studied. The present study, therefore, examined the taxon-specific cell lysis and estimated its contribution to the variations in the rare and abundant microbial taxa. The results demonstrate that taxon-specific mortality differed in surface and bottom of the coastal environment. In addition, active rare taxa are more susceptible to heightened lytic pressure and suggested the importance of viral lysis in regulating the microbial community composition. These results improve our understanding of bottom-up (abiotic environmental variables) and top-down (viral lysis) controls contributing to microbial community assembly in the ocean.
C1 [Liu, Lu; Chen, Qi; Wang, Yu; Zhang, Ting; Jiao, Nianzhi; Zheng, Qiang] Xiamen Univ, Inst Marine Microbes & Ecospheres, Coll Ocean & Earth Sci, State Key Lab Marine Environm Sci, Xiamen, Peoples R China.
   [Liu, Lu; Chen, Qi; Wang, Yu; Zhang, Ting; Jiao, Nianzhi; Zheng, Qiang] Xiamen Univ, Fujian Key Lab Marine Carbon Sequestrat, Xiamen, Peoples R China.
   [Zhong, Kevin Xu] Univ British Columbia, Dept Earth Ocean & Atmospher Sci, Vancouver, BC, Canada.
RP Zheng, Q (corresponding author), Xiamen Univ, Inst Marine Microbes & Ecospheres, Coll Ocean & Earth Sci, State Key Lab Marine Environm Sci, Xiamen, Peoples R China.; Zheng, Q (corresponding author), Xiamen Univ, Fujian Key Lab Marine Carbon Sequestrat, Xiamen, Peoples R China.
EM zhengqiang@xmu.edu.cn
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NR 85
TC 1
Z9 1
PD DEC
PY 2023
VL 89
IS 12
DI 10.1128/aem.01393-23
EA NOV 2023
UT WOS:001124421000001
DA 2025-07-30
ER

PT J
AU Thiele, S
   Vader, A
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AF Thiele, Stefan
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   Bratbak, Gunnar
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TI The summer bacterial and archaeal community composition of the northern
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SO PROGRESS IN OCEANOGRAPHY
DT Review
AB Climate change related alterations in the Arctic have influences on the marine ecosystems, in particular on phytoplankton bloom dynamics. Since phytoplankton blooms are the main provider of carbon sources to the microbial loop, the bacterial and archaeal community are affected by the changes as well. Warmer water and less sea ice can lead to an earlier onset of phytoplankton blooms and consequently also to changes in the bacterial and archaeal community dynamics throughout Arctic summers. Here, we compared the bacterial and archaeal community composition during three summers (2018, 2019, and 2021) along a transect from the Barents Sea to the Arctic Ocean north of Svalbard. We used 16S rRNA gene sequencing to investigate changes in the communities in time and space. The main results showed that, Gammaproteobacteria (Nitrincolaceae), Bacteroidia (Polaribacter), and Alphaproteobacteria (SAR11 clade 1a members) dominated the bacterial and archaeal community in the surface waters but varied in abundance patterns between the years. The variations are potentially a result of different phytoplankton bloom stages and consequently differences in the availability of carbon sources. The distinctly different deep water communities were dominated by Candidatos Nitrosopumilus, Marinimicrobia, and members of the SAR324 clade in all years. The results indicate that changes in phytoplankton bloom dynamics can influence bacterial and archaeal community and thereby marine carbon cycling in surface waters, although direct links to the effects of global warming remain uncertain.
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RP Thiele, S (corresponding author), Univ Bergen, Dept Biol Sci, Thorm Ohlensgate 53 A-B, N-5020 Bergen, Norway.
EM Stefan.thiele@uib.no
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NR 69
TC 11
Z9 11
PD JUL
PY 2023
VL 215
AR 103054
DI 10.1016/j.pocean.2023.103054
EA MAY 2023
UT WOS:001015146400001
DA 2025-07-30
ER

PT J
AU Parab, AS
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AF Parab, Ashutosh Shankar
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TI Insights into the seasonal changes in the taxonomic and functional
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SO MARINE ENVIRONMENTAL RESEARCH
DT Article
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RP Manohar, CS (corresponding author), CSIR Natl Inst Oceanog, Biol Oceanog Div, Panaji 403004, Goa, India.
EM cathrine@nio.org
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NR 111
TC 5
Z9 5
PD JUL
PY 2024
VL 199
AR 106616
DI 10.1016/j.marenvres.2024.106616
EA JUN 2024
UT WOS:001261981600001
DA 2025-07-30
ER

PT J
AU Sebastián, M
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   Fredricks, HF
   Van Mooy, B
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   Mestre, M
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   Pitta, P
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   Chen, Y
AF Sebastian, Marta
   Smith, Alastair F.
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   Fredricks, Helen F.
   Van Mooy, Benjamin
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   Brandsma, Joost
   Koster, Grielof
   Mestre, Mireia
   Mostajir, Behzad
   Pitta, Paraskevi
   Postle, Anthony D.
   Sanchez, Pablo
   Gasol, Josep M.
   Scanlan, David J.
   Chen, Yin
TI Lipid remodelling is a widespread strategy in marine heterotrophic
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SO ISME JOURNAL
DT Article
AB Upon phosphorus (P) deficiency, marine phytoplankton reduce their requirements for P by replacing membrane phospholipids with alternative non-phosphorus lipids. It was very recently demonstrated that a SAR11 isolate also shares this capability when phosphate starved in culture. Yet, the extent to which this process occurs in other marine heterotrophic bacteria and in the natural environment is unknown. Here, we demonstrate that the substitution of membrane phospholipids for a variety of non-phosphorus lipids is a conserved response to P deficiency among phylogenetically diverse marine heterotrophic bacteria, including members of the Alphaproteobacteria and Flavobacteria. By deletion mutagenesis and complementation in the model marine bacterium Phaeobacter sp. MED193 and heterologous expression in recombinant Escherichia coli, we confirm the roles of a phospholipase C (PlcP) and a glycosyltransferase in lipid remodelling. Analyses of the Global Ocean Sampling and Tara Oceans metagenome data sets demonstrate that PlcP is particularly abundant in areas characterized by low phosphate concentrations. Furthermore, we show that lipid remodelling occurs seasonally and responds to changing nutrient conditions in natural microbial communities from the Mediterranean Sea. Together, our results point to the key role of lipid substitution as an adaptive strategy enabling heterotrophic bacteria to thrive in the vast P-depleted areas of the ocean.
C1 [Sebastian, Marta; Mestre, Mireia; Sanchez, Pablo; Gasol, Josep M.] CSIC, Inst Ciencies Mar, Dept Biol Marina & Oceanog, Barcelona, Spain.
   [Smith, Alastair F.; Scanlan, David J.; Chen, Yin] Univ Warwick, Sch Life Sci, Coventry CV4 7AL, W Midlands, England.
   [Gonzalez, Jose M.] Univ La Laguna, Dept Microbiol, E-38207 San Cristobal la Laguna, Spain.
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   [Mostajir, Behzad] Univ Montpellier, CNRS, UMR 9190, Ctr Marine Biodivers Exploitat & Conservat,IRD,IF, Pl Eugene Bataillon,Case 93, F-34059 Montpellier, France.
   [Pitta, Paraskevi] Oceanog Inst, Hellen Ctr Marine Res, Iraklion, Greece.
RP Sebastián, M (corresponding author), CSIC, Inst Ciencies Mar CMIMA, Dept Biol Marina & Oceanog, Pg Maritim Barceloneta 37-49, E-08003 Barcelona, Spain.
EM msebastian@icm.csic.es
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NR 56
TC 91
Z9 95
PD APR
PY 2016
VL 10
IS 4
BP 968
EP 978
DI 10.1038/ismej.2015.172
UT WOS:000372364000016
DA 2025-07-30
ER

PT J
AU Durham, BP
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   Groussman, RD
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   Cain, KR
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AF Durham, Bryndan P.
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   Armbrust, E. Virginia
TI Sulfonate-based networks between eukaryotic phytoplankton and
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SO NATURE MICROBIOLOGY
DT Article
AB In the surface ocean, phytoplankton transform inorganic substrates into organic matter that fuels the activity of heterotrophic microorganisms, creating intricate metabolic networks that determine the extent of carbon recycling and storage in the ocean. Yet, the diversity of organic molecules and interacting organisms has hindered detection of specific relationships that mediate this large flux of energy and matter. Here, we show that a tightly coupled microbial network based on organic sulfur compounds (sulfonates) exists among key lineages of eukaryotic phytoplankton producers and heterotrophic bacterial consumers in the North Pacific Subtropical Gyre. We find that cultured eukaryotic phytoplankton taxa produce sulfonates, often at millimolar internal concentrations. These same phytoplankton-derived sulfonates support growth requirements of an open-ocean isolate of the SAR11 Glade, the most abundant group of marine heterotrophic bacteria. Expression of putative sulfonate biosynthesis genes and sulfonate abundances in natural plankton communities over the diel cycle link sulfonate production to light availability. Contemporaneous expression of sulfonate catabolism genes in heterotrophic bacteria highlights active cycling of sulfonates in situ. Our study provides evidence that sulfonates serve as an ecologically important currency for nutrient and energy exchange between microbial autotrophs and heterotrophs, highlighting the importance of organic sulfur compounds in regulating ecosystem function.
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RP Durham, BP (corresponding author), Univ Washington, Sch Oceanog, Seattle, WA 98195 USA.
EM bpdurham@uw.eu
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NR 70
TC 106
Z9 122
PD OCT
PY 2019
VL 4
IS 10
BP 1706
EP 1715
DI 10.1038/s41564-019-0507-5
UT WOS:000487286800016
DA 2025-07-30
ER

PT J
AU Jensen, S
   Lynch, MDJ
   Ray, JL
   Neufeld, JD
   Hovland, M
AF Jensen, Sigmund
   Lynch, Michael D. J.
   Ray, Jessica L.
   Neufeld, Josh D.
   Hovland, Martin
TI Norwegian deep-water coral reefs: cultivation and molecular analysis of
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Deep-sea coral reefs do not receive sunlight and depend on plankton. Little is known about the plankton composition at such reefs, even though they constitute habitats for many invertebrates and fish. We investigated plankton communities from three reefs at 260-350m depth at hydrocarbon fields off the mid-Norwegian coast using a combination of cultivation and small subunit (SSU) rRNA gene and transcript sequencing. Eight months incubations of a reef water sample with minimal medium, supplemented with carbon dioxide and gaseous alkanes at in situ-like conditions, enabled isolation of mostly Alphaproteobacteria (Sulfitobacter, Loktanella),Gammaproteobacteria (Colwellia) and Flavobacteria (Polaribacter). The relative abundance of isolates in the original sample ranged from approximate to 0.01% to 0.80%. Comparisons of bacterial SSU sequences from filtered plankton of reef and non-reef control samples indicated high abundance and metabolic activity of primarily Alphaproteobacteria (SAR11 Ia), Gammaproteobacteria (ARCTIC96BD-19), but also of Deltaproteobacteria (Nitrospina, SAR324). Eukaryote SSU sequences indicated metabolically active microalgae and animals, including codfish, at the reef sites. The plankton community composition varied between reefs and differed between DNA and RNA assessments. Over 5000 operational taxonomic units were detected, some indicators of reef sites (e.g. Flavobacteria, Cercozoa, Demospongiae) and some more active at reef sites (e.g. Gammaproteobacteria, Ciliophora, Copepoda).
C1 [Jensen, Sigmund] Univ Bergen, Dept Biol, Bergen, Norway.
   [Hovland, Martin] Univ Bergen, Ctr Geobiol, Bergen, Norway.
   [Jensen, Sigmund] Inst Marine Res, N-5024 Bergen, Norway.
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RP Jensen, S (corresponding author), Univ Bergen, Dept Biol, Bergen, Norway.
EM sigmund.jensen@bio.uib.no
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NR 74
TC 9
Z9 9
PD OCT
PY 2015
VL 17
IS 10
SI SI
BP 3597
EP 3609
DI 10.1111/1462-2920.12531
UT WOS:000363448500014
DA 2025-07-30
ER

PT J
AU Dong, HP
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AF Dong, Hong-Po
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   Lu, Songhui
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TI Metaproteomics reveals the major microbial players and their
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SO ENVIRONMENTAL MICROBIOLOGY REPORTS
DT Article
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C1 [Dong, Hong-Po; Lu, Songhui] Jinan Univ, Res Ctr Harmful Algae & Marine Biol, Key Lab Eutrophicat & Red Tide Prevent, Guangdong Higher Educ Inst, Guangzhou 510632, Guangdong, Peoples R China.
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RP Dong, HP (corresponding author), Jinan Univ, Res Ctr Harmful Algae & Marine Biol, Key Lab Eutrophicat & Red Tide Prevent, Guangdong Higher Educ Inst, Guangzhou 510632, Guangdong, Peoples R China.
EM lusonghui1963@163.com
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NR 47
TC 25
Z9 30
PD DEC
PY 2014
VL 6
IS 6
BP 683
EP 695
DI 10.1111/1758-2229.12188
UT WOS:000345702700017
DA 2025-07-30
ER

PT J
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
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C1 [Preston, Christina M.; Marin, Roman, III; Jensen, Scott D.; Feldman, Jason; Birch, James M.; Massion, Eugene I.; Wheeler, Kevin; Scholin, Christopher A.] Monterey Bay Aquarium Res Inst, Moss Landing, CA 95039 USA.
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   [DeLong, Edward F.] MIT, Dept Civil & Environm Engn, Cambridge, MA 02139 USA.
   [DeLong, Edward F.] MIT, Div Biol Engn, Cambridge, MA 02139 USA.
   [Suzuki, Marcelino] Univ Maryland, Chesapeake Biol Lab, Solomons, MD 20668 USA.
   [Wheeler, Kevin] NASA, Ames Res Ctr, Moffett Field, CA 94035 USA.
RP Preston, CM (corresponding author), Monterey Bay Aquarium Res Inst, Moss Landing, CA 95039 USA.
EM preston@mbari.org
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NR 50
TC 51
Z9 56
PD MAY
PY 2009
VL 11
IS 5
BP 1168
EP 1180
DI 10.1111/j.1462-2920.2009.01848.x
UT WOS:000265481600012
DA 2025-07-30
ER

PT J
AU Tsiola, A
   Krasakopoulou, E
   Daffonchio, D
   Frangoulis, C
   Tsagaraki, TM
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   Pitta, P
AF Tsiola, Anastasia
   Krasakopoulou, Evangelia
   Daffonchio, Daniele
   Frangoulis, Constantin
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   Fodelianakis, Stilianos
   Pitta, Paraskevi
TI Responses of Free-Living Planktonic Bacterial Communities to
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SO MICROORGANISMS
DT Article
AB Climate change driven by human activities encompasses the increase in atmospheric CO2 concentration and sea-surface temperature. Little is known regarding the synergistic effects of these phenomena on bacterial communities in oligotrophic marine ecosystems that are expected to be particularly vulnerable. Here, we studied bacterial community composition changes based on 16S rRNA sequencing at two fractions (0.1-0.2 and >0.2 mu m) during a 10- day fully factorial mesocosm experiment in the eastern Mediterranean where the pH decreased by similar to 0.3 units and temperature increased by similar to 3 degrees C to project possible future changes in surface waters. The bacterial community experienced significant taxonomic differences driven by the combined effect of time and treatment; a community shift one day after the manipulations was noticed, followed by a similar state between all mesocosms at the third day, and mild shifts later on, which were remarkable mainly under sole acidification. The abundance of Synechococcus increased in response to warming, while the SAR11 clade immediately benefited from the combined acidification and warming. The effect of the acidification itself had a more persistent impact on community composition. This study highlights the importance of studying climate change consequences on ecosystem functioning both separately and simultaneously, considering the ambient environmental parameters.
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RP Tsiola, A (corresponding author), Hellen Ctr Marine Res, Inst Oceanog, Iraklion 71003, Crete, Greece.
EM atsiola@hcmr.gr
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NR 68
TC 3
Z9 3
PD FEB
PY 2023
VL 11
IS 2
AR 273
DI 10.3390/microorganisms11020273
UT WOS:000939937300001
DA 2025-07-30
ER

PT J
AU Zwart, G
   van Hannen, EJ
   Kamst-van Agterveld, MP
   Van der Gucht, K
   Lindström, ES
   Van Wichelen, J
   Lauridsen, T
   Crump, BC
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AF Zwart, G
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   Crump, BC
   Han, SK
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TI Rapid screening for freshwater bacterial groups by using reverse line
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB The identification of phylogenetic clusters of bacteria that are common in freshwater has provided a basis for probe design to target important freshwater groups. We present a set of 16S ribosomal RNA gene-based oligonucleotide probes specific for 15 of these freshwater clusters. The probes were applied in reverse line blot hybridization, a simple method that enables the rapid screening of PCR products from many samples against an array of probes. The optimized assay was made stringent to discriminate at approximately the single-mismatch level. This made 10 of the probes highly specific, with at least two mismatches to the closest noncluster member in the global database. Screening of PCR products from bacterioplankton of 81 diverse lakes from Belgium, The Netherlands, Denmark, Sweden, and Norway showed that the respective probes were reactive against 5 to 100% of the lake samples. Positive reactivity of six highly specific probes showed that bacteria from actinobacterial clusters ACK-M1 and Sta2-30 and from verrucomicrobial cluster CLO-14 occurred in at least 90% of the investigated lakes. Furthermore, bacteria from alpha-proteobacterial cluster LD12 (closely related to the marine SAR11 cluster), beta-proteobacterial cluster LD28 and cyanobacterial cluster Synechococcus 6b occurred in more than 70% of the lakes. Reverse line blot hybridization is a new tool in microbial ecology that will facilitate research on distribution and habitat specificity of target species at relatively low costs.
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   Catholic Univ Louvain, Aquat Ecol Lab, B-3000 Louvain, Belgium.
   Uppsala Univ, Dept Limnol, Evolut Biol Ctr, SE-75236 Uppsala, Sweden.
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   Univ Calif Riverside, Dept Environm Sci, Riverside, CA 92521 USA.
RP Ctr Limnol, NIOO KNAW, Rijksstraatweg 6, NL-3631 AC Nieuwersluis, Netherlands.
EM g.zwart@nioo.knaw.nl
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NR 40
TC 88
Z9 120
PD OCT
PY 2003
VL 69
IS 10
BP 5875
EP 5883
DI 10.1128/AEM.69.10.5875-5883.2003
UT WOS:000185881300019
DA 2025-07-30
ER

PT J
AU Fortin, SG
   Song, B
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AF Fortin, Samantha G.
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TI Blooms of the harmful algae Margalefidinium polykrikoides and
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SO HARMFUL ALGAE
DT Article
AB Harmful algal blooms (HABs) cause damage to fisheries, aquaculture, and human health around the globe. However, the impact of HABs on water column microbiomes and biogeochemistry is poorly understood. This study examined the impacts of consecutive blooms of the ichthyotoxic dinoflagellates Margalefidinium polykrikoides and Alexandrium monilatum on the water microbiome in the York River Estuary, Chesapeake Bay, USA. The samples dominated by single dinoflagellate species and by a mix of the two dinoflagellates had different microbiome compositions than the ones with low levels of both species. The M. polykrikoides bloom was co dominated by Winogradskyella and had increased concentrations of dissolved organic carbon. The A. monilatum bloom had little impact on the prokaryotic portion of the whole community but was associated with a specific group of prokaryotes in the particle-attached (>3 mu m) fraction including Candidatus Nitrosopumilus, Candidatus Actinomarina, SAR11 Clade Ia, Candidatus Bealeia, and Rhodobacteraceae HIMB11. Thus, blooms of these two algal species impacted the estuarine microbiome in different ways, likely leading to shifts in estuarine carbon and nutrient cycling, with M. polykrikoides potentially having a greater impact on carbon cycling in the estuarine ecosystem than A. monilatum.
C1 [Fortin, Samantha G.; Song, Bongkeun; Anderson, Iris C.; Reece, Kimberly S.] Virginia Inst Marine Sci, Gloucester Point, VA 23062 USA.
RP Fortin, SG; Song, B (corresponding author), Virginia Inst Marine Sci, Gloucester Point, VA 23062 USA.
EM sgfortin@vims.edu; songb@vims.edu
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NR 51
TC 15
Z9 18
PD MAY
PY 2022
VL 114
AR 102216
DI 10.1016/j.hal.2022.102216
EA MAR 2022
UT WOS:000784337500003
DA 2025-07-30
ER

PT J
AU Li, DX
   Zhang, H
   Chen, XH
   Xie, ZX
   Zhang, Y
   Zhang, SF
   Lin, L
   Chen, F
   Wang, DZ
AF Li, Dong-Xu
   Zhang, Hao
   Chen, Xiao-Huang
   Xie, Zhang-Xian
   Zhang, Yong
   Zhang, Shu-Feng
   Lin, Lin
   Chen, Feng
   Wang, Da-Zhi
TI Metaproteomics reveals major microbial players and their metabolic
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Interactions between bacteria and phytoplankton during bloom events are essential for both partners, which impacts their physiology, alters ambient chemistry and shapes ecosystem diversity. Here, we investigated the community structure and metabolic activities of free-living bacterioplankton in different blooming phases of a dinoflagellate Prorocentrum donghaiense using a metaproteomic approach. The Fibrobacteres-Chlorobi-Bacteroidetes group, Rhodobacteraceae, SAR11 and SAR86 clades contributed largely to the bacterial community in the middle-blooming phase while the Pseudoalteromonadaceae exclusively dominated in the late-blooming phase. Transporters and membrane proteins, especially TonB-dependent receptors were highly abundant in both blooming phases. Proteins involved in carbon metabolism, energy metabolism and stress response were frequently detected in the middle-blooming phase while proteins participating in proteolysis andcentral carbon metabolism were abundant in the late-blooming phase. Beta-glucosidase with putative algicidal capability was identified from the Pseudoalteromonadaceae only in the late-blooming phase, suggesting an active role of this group in lysing P. donghaiense cells. Our results indicated that diverse substrate utilization strategies and different capabilities for environmental adaptation among bacteria shaped their distinct niches in different bloom phases, and certain bacterial species from the Pseudoalteromonadaceae might be crucial for the termination of a dinoflagellate bloom.
C1 [Li, Dong-Xu; Zhang, Hao; Chen, Xiao-Huang; Xie, Zhang-Xian; Zhang, Yong; Zhang, Shu-Feng; Lin, Lin; Wang, Da-Zhi] Xiamen Univ, State Key Lab Marine Environm Sci, Coll Environm & Ecol, Xiamen, Peoples R China.
   [Chen, Feng] Univ Maryland, Ctr Environm Sci, Inst Marine & Environm Technol, Baltimore, MD 21201 USA.
RP Wang, DZ (corresponding author), Xiamen Univ, State Key Lab Marine Environm Sci, Coll Environm & Ecol, Xiamen, Peoples R China.
EM dzwang@xmu.edu.cn
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NR 82
TC 36
Z9 47
PD FEB
PY 2018
VL 20
IS 2
BP 632
EP 644
DI 10.1111/1462-2920.13986
UT WOS:000425019400016
DA 2025-07-30
ER

PT J
AU Deng, YQ
   Cheng, CH
   Feng, J
   Liu, SL
   Ma, HL
   Chen, XL
   Chen, HX
   Guo, ZX
AF Deng, Yiqin
   Cheng, Changhong
   Feng, Juan
   Liu, Songlin
   Ma, Hongling
   Chen, Xiaolong
   Chen, HaoXiang
   Guo, Zhixun
TI Rapid environmental change shapes pond water microbial community
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SO APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
DT Article
AB The aquatic microbial community is sensitive to environmental change; however, the impacts of those changes combined with disease outbreaks affecting S. paramamosain are unknown. Thus, from March to October, we explored the interaction between aquacultural environmental conditions and microbial composition and function in open-air aquaculture ponds containing S. paramamosain in Southern China. The microbial community structure was significantly positively correlated with microbial community function. The environment variables such as temperature and salinity during May and June changed more quickly compared with other periods, resulting changes in the structure and function of the microbial community affected S. paramamosain survivability, with higher crab mortality observed from May to June compared with other periods. These included changes in the relative abundance of Microtrichales, Synechococcales, Rhodobacterales, Chitinophagales, and SAR11_clade, and corresponding functions associated with glycolysis and/or gluconeogenesis, porphyrin and chlorophyll metabolism, photosynthetic proteins, and transcription factors. These changes could impact S. paramamosain mortality and be used to evaluate the health status of the ponds. Though the environment variables during July~October changed slowly comparing to May and June, the ponds microflora changed which benefit S. paramamosain survivability with correspondingly low S. paramamosain mortality. Therefore, rapid environmental change alters the structure and function of the aquatic microflora, increasing S. paramamosain mortality.
C1 [Deng, Yiqin; Cheng, Changhong; Feng, Juan; Ma, Hongling; Chen, Xiaolong; Chen, HaoXiang; Guo, Zhixun] Chinese Acad Fishery Sci, South China Sea Fisheries Res Inst, Minist Agr & Rural Affairs, Key Lab South China Sea Fishery Resources Exploit, Guangzhou 510300, Peoples R China.
   [Deng, Yiqin; Feng, Juan] Chinese Acad Fisheries Sci, South China Sea Fisheries Res Inst, Guangdong Prov Key Lab Fishery Ecol & Environm, Guangzhou 510300, Peoples R China.
   [Deng, Yiqin; Feng, Juan] Chinese Acad Fishery Sci, Trop Aquaculture Res & Dev Ctr, South China Sea Fisheries Res Inst, Sanya 572426, Hainan, Peoples R China.
   [Liu, Songlin] Chinese Acad Sci, South China Sea Inst Oceanol, Key Lab Trop Marine Bioresources & Ecol, Guangzhou 510301, Peoples R China.
RP Guo, ZX (corresponding author), Chinese Acad Fishery Sci, South China Sea Fisheries Res Inst, Minist Agr & Rural Affairs, Key Lab South China Sea Fishery Resources Exploit, Guangzhou 510300, Peoples R China.
EM guozhixun1@163.com
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NR 48
TC 15
Z9 17
PD MAR
PY 2020
VL 104
IS 5
BP 2229
EP 2241
DI 10.1007/s00253-019-10328-w
UT WOS:000529946400032
DA 2025-07-30
ER

PT J
AU Luo, HW
   Huang, YJ
   Stepanauskas, R
   Tang, JJ
AF Luo, Haiwei
   Huang, Yongjie
   Stepanauskas, Ramunas
   Tang, Jijun
TI Excess of non-conservative amino acid changes in marine bacterioplankton
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SO NATURE MICROBIOLOGY
DT Article
AB Surface ocean waters are dominated by planktonic bacterial lineages with highly reduced genomes. The best examples are the cyanobacterial genus Prochlorococcus, the alphaproteobacterial clade SAR11 and the gammaproteobacterial clade SAR86, which together represent over 50% of the cells in surface oceans. Several studies have identified signatures of selection on these lineages in today's ocean and have postulated selection as the primary force throughout their evolutionary history. However, massive loss of genomic DNA in these lineages often occurred in the distant past, and the selective pressures underlying these ancient events have not been assessed. Here, we probe ancient selective pressures by computing % GC-corrected rates of conservative and radical nonsynonymous nucleotide substitutions. Surprisingly, we found an excess of radical changes in several of these lineages in comparison to their relatives with larger genomes. Furthermore, analyses of allelic genome sequences of several populations within these lineages consistently supported that radical replacements are more likely to be deleterious than conservative changes. Our results suggest coincidence of massive genomic DNA losses and increased power of genetic drift, but we also suggest that additional evidence independent of the nucleotide substitution analyses is needed to support a primary role of genetic drift driving ancient genome reduction of marine bacterioplankton lineages.
C1 [Luo, Haiwei; Huang, Yongjie] Chinese Univ Hong Kong, Sch Life Sci, Simon FS Li Marine Sci Lab, Hong Kong, Hong Kong, Peoples R China.
   [Luo, Haiwei] Chinese Univ Hong Kong, Ctr Soybean Res, Partner State Key Lab Agrobiotechnol, Hong Kong, Hong Kong, Peoples R China.
   [Luo, Haiwei] Chinese Univ Hong Kong, Inst Environm Energy & Sustainabil, Hong Kong, Hong Kong, Peoples R China.
   [Luo, Haiwei; Huang, Yongjie] Chinese Univ Hong Kong, Shenzhen Res Inst, Shenzhen 518000, Peoples R China.
   [Stepanauskas, Ramunas] Bigelow Lab Ocean Sci, East Boothbay, ME 04544 USA.
   [Tang, Jijun] Tianjin Univ, Minist Educ, Key Lab Syst Bioengn, Tianjin 300072, Peoples R China.
   [Tang, Jijun] Univ South Carolina, Dept Comp Sci & Engn, Columbia, SC 29208 USA.
RP Luo, HW (corresponding author), Chinese Univ Hong Kong, Sch Life Sci, Simon FS Li Marine Sci Lab, Hong Kong, Hong Kong, Peoples R China.; Luo, HW (corresponding author), Chinese Univ Hong Kong, Ctr Soybean Res, Partner State Key Lab Agrobiotechnol, Hong Kong, Hong Kong, Peoples R China.; Luo, HW (corresponding author), Chinese Univ Hong Kong, Inst Environm Energy & Sustainabil, Hong Kong, Hong Kong, Peoples R China.; Luo, HW (corresponding author), Chinese Univ Hong Kong, Shenzhen Res Inst, Shenzhen 518000, Peoples R China.
EM hluo2006@gmail.com
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NR 53
TC 31
Z9 34
PD AUG
PY 2017
VL 2
IS 8
AR 17091
DI 10.1038/nmicrobiol.2017.91
UT WOS:000410619800010
DA 2025-07-30
ER

PT J
AU Hagström, Å
   Azam, F
   Berg, C
   Zweifel, UL
AF Hagstrom, Ake
   Azam, Farooq
   Berg, Carlo
   Zweifel, Ulla Li
TI Isolates as models to study bacterial ecophysiology and biogeochemistry
SO AQUATIC MICROBIAL ECOLOGY
DT Article
AB Here, we examine the use of bacterial isolates growing in artificial media or seawater as a means to investigate bacterial activity in the upper ocean. The discovery of a major role of bacteria in the ocean's carbon cycle owes greatly to the development of culture-independent assemblage-level approaches; however, this should not detract from the recognition of model isolates as representing the environmental microbiome. A long-established tool for culturing bacteria, in medicine and general microbiology, has been agar plates. In addition, a great variety of liquid substrates including seawater have been used to successfully identify and cultivate important bacteria such as Pelagibacter ubique. Yet, the discrepancy between microscopic counts and plate counts, the great plate count anomaly, has led to a biased perception of the limited relevance of isolated bacteria. Linking isolates to whole-genome sequencing, phylogenetic analysis and computational modeling will result in culturable model bacteria from different habitats. Our main message is that bacterial ecophysiology, particularly growth rates in seawater, and functionalities inferred through the identity, abundance and expression of specific genes could be mechanistically linked if more work is done to isolate, culture and study bacteria in pure cultures. When we rally behind a strategy aimed at culturing targeted phenotypes, we are not saying that culture independent studies of bacteria in the sea are not informative. We are suggesting that culturebased studies can help integrate the ecological and genomic views.
C1 [Hagstrom, Ake; Berg, Carlo] Linnaeus Univ, Dept Biol & Environm Sci, S-39182 Kalmar, Sweden.
   [Azam, Farooq] Univ Calif San Diego, Scripps Inst Oceanog, Marine Biol Res Div, San Diego, CA 92093 USA.
   [Zweifel, Ulla Li] Gothenburg Univ, Swedish Inst Marine Environm, Box 260, S-40530 Gothenburg, Sweden.
RP Hagström, Å (corresponding author), Linnaeus Univ, Dept Biol & Environm Sci, S-39182 Kalmar, Sweden.
EM ake.hagstrom@lnu.se
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NR 75
TC 12
Z9 12
PY 2018
VL 80
IS 1
BP 15
EP 27
DI 10.3354/ame01838
UT WOS:000414556400002
DA 2025-07-30
ER

PT J
AU O'Brien, J
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AF O'Brien, James
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TI Biogeographical and seasonal dynamics of the marine Roseobacter
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SO ISME COMMUNICATIONS
DT Article
AB Ecological interactions between marine bacteria and phytoplankton play a pivotal role in governing the ocean's major biogeochemical cycles. Among these, members of the marine Roseobacter Group (MRG) can establish mutualistic relationships with phytoplankton that are, in part, maintained by exchanges of the organosulfur compound, dimethylsulfoniopropionate (DMSP). Yet most of what is known about these interactions has been derived from culture-based laboratory studies. To investigate temporal and spatial co-occurrence patterns between members of the MRG and DMSP-producing phytoplankton we analysed 16S and 18S rRNA gene amplicon sequence variants (ASVs) derived from 5 years of monthly samples from seven environmentally distinct Australian oceanographic time-series. The MRG and DMSP-producer communities often displayed contemporaneous seasonality, which was greater in subtropical and temperate environments compared to tropical environments. The relative abundance of both groups varied latitudinally, displaying a poleward increase, peaking (MRG at 33% of total bacteria, DMSP producers at 42% of eukaryotic phototrophs) during recurrent spring-summer phytoplankton blooms in the most temperate site (Maria Island, Tasmania). Network analysis identified 20,140 significant positive correlations between MRG ASVs and DMSP producers and revealed that MRGs exhibit significantly stronger correlations to high DMSP producers relative to other DMSP-degrading bacteria (Pelagibacter, SAR86 and Actinobacteria). By utilising the power of a continental network of oceanographic time-series, this study provides in situ confirmation of interactions found in laboratory studies and demonstrates that the ecological dynamics of an important group of marine bacteria are shaped by the production of an abundant and biogeochemically significant organosulfur compound.
C1 [O'Brien, James; Bramucci, Anna R.; Siboni, Nachshon; Ostrowski, Martin; Kahlke, Tim; Messer, Lauren F.; Seymour, Justin R.] Univ Technol Sydney, Climate Change Cluster, Broadway, NSW, Australia.
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   [Mcparland, Erin L.] Woods Hole Oceanog Inst, Dept Marine Chem & Geochem, Woods Hole, MA USA.
   [Levine, Naomi M.] Univ Southern Calif, Dept Biol Sci, Los Angeles, CA USA.
   [Brown, Mark V.] Univ Newcastle, Sch Environm & Life Sci, Callaghan, NSW, Australia.
   [van de Kamp, Jodie; Bodrossy, Levente] CSIRO Oceans & Atmosphere, Hobart, Tas, Australia.
   [Messer, Lauren F.] Queensland Univ Technol QUT, Ctr Microbiome Res, Sch Biomed Sci, Brisbane, Qld, Australia.
RP O'Brien, J; Seymour, JR (corresponding author), Univ Technol Sydney, Climate Change Cluster, Broadway, NSW, Australia.; O'Brien, J (corresponding author), Univ Technol Sydney, Sch Life Sci, Broadway, NSW, Australia.
EM james.obrien@student.uts.edu.au; justin.seymour@uts.edu.au
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NR 95
TC 12
Z9 12
PD FEB 14
PY 2022
VL 2
IS 1
AR 16
DI 10.1038/s43705-022-00099-3
UT WOS:001105612400001
DA 2025-07-30
ER

PT J
AU Farnelid, H
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AF Farnelid, Hanna
   Turk-Kubo, Kendra
   Zehr, Jonathan P.
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
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C1 [Farnelid, Hanna; Turk-Kubo, Kendra; Zehr, Jonathan P.] Univ Calif Santa Cruz, Ocean Sci Dept, Santa Cruz, CA 95064 USA.
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RP Farnelid, H (corresponding author), Univ Calif Santa Cruz, Ocean Sci Dept, Santa Cruz, CA 95064 USA.; Farnelid, H (corresponding author), Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, Kalmar, Sweden.
EM hanna.farnelid@lnu.se
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NR 60
TC 6
Z9 6
PD MAR
PY 2021
VL 23
IS 3
BP 1469
EP 1480
DI 10.1111/1462-2920.15351
EA DEC 2020
UT WOS:000600024200001
DA 2025-07-30
ER

PT J
AU Molina, V
   Fernández, C
AF Molina, Veronica
   Fernandez, Camila
TI Bacterioplankton response to nitrogen and dissolved organic matter
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SO MICROBIOLOGYOPEN
DT Article
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C1 [Molina, Veronica] Univ Playa Ancha, Fac Ciencias Nat Exactas, Dept Biol, Programa Biodiversidad & Observ Eco Microbiana, Valparaiso, Chile.
   [Molina, Veronica] Univ Playa Ancha, HUB Ambiental UPLA, Valparaiso, Chile.
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RP Fernández, C (corresponding author), Univ Concepcion, Ctr Interdisciplinario Acuicultura Sustentable IN, Concepcion, Chile.
EM fernandez@obs-banyuls.fr
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NR 40
TC 11
Z9 12
PD DEC
PY 2020
VL 9
IS 12
AR e1132
DI 10.1002/mbo3.1132
EA NOV 2020
UT WOS:000591778900001
DA 2025-07-30
ER

PT J
AU Clifford, EL
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AF Clifford, Elisabeth L.
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   De Corte, Daniele
   Bode, Antonio
   Ortiz, Victor
   Herndl, Gerhard J.
   Sintes, Eva
TI Taurine Is a Major Carbon and Energy Source for Marine Prokaryotes in
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SO MICROBIAL ECOLOGY
DT Article
AB Taurine, an amino acid-like compound, acts as an osmostress protectant in many marine metazoans and algae and is released via various processes into the oceanic dissolved organic matter pool. Taurine transporters are widespread among members of the marine prokaryotic community, tentatively indicating that taurine might be an important substrate for prokaryotes in the ocean. In this study, we determined prokaryotic taurine assimilation and respiration throughout the water column along two transects in the North Atlantic off the Iberian Peninsula. Taurine assimilation efficiency decreased from the epipelagic waters from 55 +/- 14% to 27 +/- 20% in the bathypelagic layers (means of both transects). Members of the ubiquitous alphaproteobacterial SAR11 clade accounted for a large fraction of cells taking up taurine, especially in surface waters. Archaea (Thaumarchaeota + Euryarchaeota) were also able to take up taurine in the upper water column, but to a lower extent than Bacteria. The contribution of taurine assimilation to the heterotrophic prokaryotic carbon biomass production ranged from 21% in the epipelagic layer to 16% in the bathypelagic layer. Hence, we conclude that dissolved free taurine is a significant carbon and energy source for prokaryotes throughout the oceanic water column being utilized with similar efficiencies as dissolved free amino acids.
C1 [Clifford, Elisabeth L.; Ortiz, Victor; Herndl, Gerhard J.; Sintes, Eva] Univ Vienna, Ctr Funct Ecol, Dept Limnol & Biooceanog, Althanstr 14, A-1090 Vienna, Austria.
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EM eva.sintes@univie.ac.at
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NR 82
TC 44
Z9 47
PD AUG
PY 2019
VL 78
IS 2
BP 299
EP 312
DI 10.1007/s00248-019-01320-y
UT WOS:000475700200003
DA 2025-07-30
ER

PT J
AU dos Reis, MC
   Romac, S
   Le Gall, F
   Marie, D
   Frada, MJ
   Koplovitz, G
   Cariou, T
   Henry, N
   de Vargas, C
   Jeanthon, C
AF dos Reis, Mariana Camara
   Romac, Sarah
   Le Gall, Florence
   Marie, Dominique
   Frada, Miguel J.
   Koplovitz, Gil
   Cariou, Thierry
   Henry, Nicolas
   de Vargas, Colomban
   Jeanthon, Christian
TI Exploring the phycosphere of Emiliania huxleyi: From bloom
   dynamics to microbiome assembly experiments
SO MOLECULAR ECOLOGY
DT Article
AB Coccolithophores have global ecological and biogeochemical significance as the most important calcifying marine phytoplankton group. The structure and selection of prokaryotic communities associated with the most abundant coccolithophore and bloom-forming species, Emiliania huxleyi, are still poorly known. In this study, we assessed the diversity of bacterial communities associated with an E. huxleyi bloom in the Celtic Sea (Eastern North Atlantic), exposed axenic E. huxleyi cultures to prokaryotic communities derived from bloom and non-bloom conditions, and followed the dynamics of their microbiome composition over one year. Bloom-associated prokaryotic communities were dominated by SAR11, Marine group II Euryarchaeota and Rhodobacterales and contained substantial proportions of known indicators of phytoplankton bloom demises such as Flavobacteriaceae and Pseudoalteromonadaceae. The taxonomic richness of bacteria derived from natural communities associated with axenic E. huxleyi rapidly shifted and then stabilized over time. The succession of microorganisms recruited from the environment was consistently dependent on the composition of the initial bacterioplankton community. Phycosphere-associated communities derived from the E. huxleyi bloom were highly similar to one another, suggesting deterministic processes, whereas cultures from non-bloom conditions show an effect of stochasticity. Overall, this work sheds new light on the importance of the initial inoculum composition in microbiome recruitment and elucidates the temporal dynamics of its composition and long-term stability.
C1 [dos Reis, Mariana Camara; Romac, Sarah; Le Gall, Florence; Marie, Dominique; Henry, Nicolas; de Vargas, Colomban; Jeanthon, Christian] Sorbonne Univ, Ctr Natl Rech Sci, Stn Biol Roscoff, UMR7144,Adaptat & Diversit Milieu Marin, Roscoff, France.
   [dos Reis, Mariana Camara; Henry, Nicolas; de Vargas, Colomban; Jeanthon, Christian] Res Federat study Global Ocean Syst Ecol & Evolut, Tara GOSEE, FR2022, Paris, France.
   [Frada, Miguel J.; Koplovitz, Gil] Interuniv Inst Marine Sci Eilat, Elat, Israel.
   [Frada, Miguel J.] Hebrew Univ Jerusalem, Silberman Inst Life Sci, Dept Ecol Evolut & Behav, Jerusalem, Israel.
   [Cariou, Thierry] Sorbonne Univ, Ctr Natl Rech Sci, Stn Biol Roscoff, FR2424, Roscoff, France.
   [dos Reis, Mariana Camara] BIOCITECH, Biomillenia Design Pharmaceut, Romainville, France.
   [Cariou, Thierry] IRD, US191, Instrumentat Moyens Analyt Observ Geophys & Ocean, Plouzane, France.
   [Henry, Nicolas] Sorbonne Univ, Ctr Natl Rech Sci, FR2424, ABIMS Bioinformat Platform,Stat Biol Roscoff, Roscoff, France.
RP dos Reis, MC; Jeanthon, C (corresponding author), Sorbonne Univ, Ctr Natl Rech Sci, Stn Biol Roscoff, UMR7144,Adaptat & Diversit Milieu Marin, Roscoff, France.
EM maricamarareis@gmail.com; jeanthon@sb-roscoff.fr
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NR 114
TC 11
Z9 11
PD DEC
PY 2023
VL 32
IS 23
SI SI
BP 6507
EP 6522
DI 10.1111/mec.16829
EA JAN 2023
UT WOS:000916084400001
DA 2025-07-30
ER

PT J
AU Widner, B
   Fuchsman, CA
   Chang, BX
   Rocap, G
   Mulholland, MR
AF Widner, Brittany
   Fuchsman, Clara A.
   Chang, Bonnie X.
   Rocap, Gabrielle
   Mulholland, Margaret R.
TI Utilization of urea and cyanate in waters overlying and within the
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SO FEMS MICROBIOLOGY ECOLOGY
DT Article
AB In marine oxygen deficient zones (ODZs), which contribute up to half of marine N loss, microbes use nitrogen (N) for assimilatory and dissimilatory processes. Here, we examine N utilization above and within the ODZ of the Eastern Tropical North Pacific Ocean, focusing on distribution, uptake and genes for the utilization of two simple organic N compounds, urea and cyanate. Ammonium, urea and cyanate concentrations generally peaked in the oxycline while uptake rates were highest in the surface. Within the ODZ, concentrations were lower, but urea N and C and cyanate C were taken up. All identified autotrophs had an N assimilation pathway that did not require external ammonium: ODZ Prochlorococcus possessed genes to assimilate nitrate, nitrite and urea; nitrite oxidizers (Nitrospina) possessed genes to assimilate nitrite, urea and cyanate; anammox bacteria (Scalindua) possessed genes to utilize cyanate; and ammonia-oxidizing Thaumarchaeota possessed genes to utilize urea. Urease genes were present in 20% of microbes, including SAR11, suggesting the urea utilization capacity was widespread. In the ODZ core, cyanate genes were largely (similar to 95%) associated with Scalindua, suggesting that, within this ODZ, cyanate N is primarily used for N loss via anammox (cyanammox), and that anammox does not require ammonium for N loss.
C1 [Widner, Brittany; Mulholland, Margaret R.] Old Dominion Univ, Dept Ocean Earth & Atmospher Sci, Norfolk, VA USA.
   [Fuchsman, Clara A.; Rocap, Gabrielle] Univ Washington, Sch Oceanog, Seattle, WA 98195 USA.
   [Fuchsman, Clara A.] Univ Maryland, Horn Point Lab, Ctr Environm Sci, Cambridge, MD USA.
   [Chang, Bonnie X.] Univ Washington, Joint Inst Study Atmosphere & Ocean, Seattle, WA 98195 USA.
   [Chang, Bonnie X.] Natl Ocean & Atmospher Adm, Pacific Marine Environm Lab, Seattle, WA USA.
RP Widner, B (corresponding author), Woods Hole Oceanog Inst, Dept Marine Chem & Geochem, MS 4, Woods Hole, MA 02543 USA.
EM bwidner@whoi.edu
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NR 86
TC 33
Z9 36
PD OCT
PY 2018
VL 94
IS 10
AR fiy138
DI 10.1093/femsec/fiy138
UT WOS:000448167900002
DA 2025-07-30
ER

PT J
AU Alonso-Sáez, L
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DT Article
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RP Alonso-Sáez, L (corresponding author), CSIC, Inst Ciencies Mar, Dept Biol Marina & Oceanog, Pg Maritim Barcelona 37-49, Barcelona 08003, Catalunya, Spain.
EM lalonso@icm.csic.es
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NR 69
TC 66
Z9 69
PD JAN 19
PY 2007
VL 46
IS 1
BP 43
EP 53
DI 10.3354/ame046043
UT WOS:000244194200004
DA 2025-07-30
ER

PT J
AU Xie, ZX
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AF Xie, Zhang-Xian
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TI Metaproteomics of marine viral concentrates reveals key viral
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
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C1 [Xie, Zhang-Xian; Zhang, Shu-Feng; Wang, Ming-Hua; Zhang, Hao; Kong, Ling-Fen; Dai, Min-Han; Hong, Hua-Sheng; Lin, Lin; Wang, Da-Zhi] Xiamen Univ, Coll Environm & Ecol, State Key Lab Marine Environm Sci, Xiamen 361005, Peoples R China.
   [Chen, Feng] Univ Maryland, Ctr Environm Sci, Inst Marine & Environm Technol, Baltimore, MD 21201 USA.
RP Wang, DZ (corresponding author), Xiamen Univ, Coll Environm & Ecol, State Key Lab Marine Environm Sci, Xiamen 361005, Peoples R China.
EM dzwang@xmu.edu.cn
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NR 76
TC 6
Z9 6
PD FEB
PY 2018
VL 20
IS 2
BP 477
EP 491
DI 10.1111/1462-2920.13937
UT WOS:000425019400005
DA 2025-07-30
ER

PT J
AU Rivers, AR
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AF Rivers, Adam R.
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TI Transcriptional response of bathypelagic marine bacterioplankton to the
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SO ISME JOURNAL
DT Article
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C1 [Rivers, Adam R.; Sharma, Shalabh; Joye, Samantha B.; Moran, Mary Ann] Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
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RP Moran, MA (corresponding author), Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
EM mmoran@uga.edu
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NR 57
TC 124
Z9 135
PD DEC
PY 2013
VL 7
IS 12
BP 2315
EP 2329
DI 10.1038/ismej.2013.129
UT WOS:000327451800007
DA 2025-07-30
ER

PT J
AU Yeung, CW
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AF Yeung, C. William
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DT Article
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C1 [Yeung, C. William; Greer, Charles W.] Natl Res Council Canada, Biotechnol Res Inst, Montreal, PQ H4P 2R2, Canada.
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RP Greer, CW (corresponding author), Natl Res Council Canada, Biotechnol Res Inst, 6100 Royalmount Ave, Montreal, PQ H4P 2R2, Canada.
EM charles.greer@nrc-cnrc.gc.ca
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NR 44
TC 6
Z9 7
PD MAY
PY 2010
VL 56
IS 5
BP 421
EP 431
DI 10.1139/W10-028
UT WOS:000279243400008
DA 2025-07-30
ER

PT J
AU Lozada, M
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AF Lozada, Mariana
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DT Article
AB Alginate lyases and oligoalginate lyases catalyze the cleavage of the glycosidic bonds of alginate, an acidic polysaccharide synthesized by brown algae and other organisms. These enzymes are highly diverse, currently classified into 15 families of the Carbohydrate-Active Enzyme (CAZy) database. We explored the structural and taxonomic diversity, the biogeographic distribution of the genes and transcripts, and the potential environmental drivers of putative alginate-degrading enzymes from picoplanktonic communities of the upper layers of the global ocean. The identified sequences were first analyzed using sequence similarity networks to assess their relationship with CAZy members. Sequences related to the PL5, PL6, PL7, PL17, and PL38 families had higher gene and transcript abundances, with temperature being a key driver of the structuring of the community members carrying putative alginate lyase genes. PL5 homologs included variants in a key residue of the active site, and sequences assigned to 'Candidatus Pelagibacter' showed high gene and transcript abundances that negatively correlated with inorganic phosphorus concentrations. Sequences assigned to Flavobacteriia and/or Gammaproteobacteria classes dominated the PL6, PL7, and PL17 families, in particular those closely related to sequences from uncultured Polaribacter and Alteromonas australica. In the PL38 family, while sequences assigned to taxa from the Planctomycetota, Verrucomicrobiota, and Bacteroidota phyla showed the highest relative gene abundance at most regions and depths, high expression levels were observed at high latitudes in sequences assigned to Eukaryota (e.g., Phaeocystis antarctica). Overall, the putative enzymes uncovered in this study could be involved in various physiological processes, including alginate assimilation and biosynthesis.
C1 [Lozada, Mariana] Consejo Nacl Invest Cient & Tecn, Inst Biol Organismos Marinos IBIOMAR, U9120ACD, Blvd Brown 2915, Puerto Madryn, Chubut, Argentina.
   [Dionisi, Hebe M.] Consejo Nacl Invest Cient & Tecn, Ctr Estudio Sistemas Marinos CESIMAR, U9120ACD, Blvd Brown 2915, Puerto Madryn, Chubut, Argentina.
RP Dionisi, HM (corresponding author), Consejo Nacl Invest Cient & Tecn, Ctr Estudio Sistemas Marinos CESIMAR, U9120ACD, Blvd Brown 2915, Puerto Madryn, Chubut, Argentina.
EM hdionisi@cenpat-conicet.gob.ar
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NR 122
TC 0
Z9 0
PD MAR 8
PY 2025
VL 15
IS 1
AR 8111
DI 10.1038/s41598-025-92960-3
UT WOS:001439898100016
DA 2025-07-30
ER

PT J
AU Mohit, V
   Archambault, P
   Toupoint, N
   Lovejoy, C
AF Mohit, Vani
   Archambault, Philippe
   Toupoint, Nicolas
   Lovejoy, Connie
TI Phylogenetic Differences in Attached and Free-Living Bacterial
   Communities in a Temperate Coastal Lagoon during Summer, Revealed via
   High-Throughput 16S rRNA Gene Sequencing
SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Most of what is known about coastal free-living and attached bacterial diversity is based on open coasts, with high particulate and nutrient riverine supply, terrestrial runoffs, and anthropogenic activities. The Magdalen Islands in the Gulf of St. Lawrence (Canada) are dominated by shallow lagoons with small, relatively pristine catchments and no freshwater input apart from rain. Such conditions provided an opportunity to investigate coastal free-living and attached marine bacterial diversity in the absence of confounding effects of steep freshwater gradients. We found significant differences between the two communities and marked temporal patterns in both. Taxonomic richness and diversity were greater in the attached than in the free-living community, increasing over summer, especially within the least abundant bacterial phyla. The highest number of reads fell within the SAR 11 clade (Pelagibacter, Alphaproteobacteria), which dominated free-living communities. The attached communities had deeper phylum-level diversity than the free-living fraction. Distance-based redundancy analysis indicated that the particulate organic matter (POM) concentration was the main variable separating early and late summer samples with salinity and temperature changes also significantly correlated to bacterial community structure. Our approach using high-throughput sequencing detected differences in free-living versus attached bacteria in the absence of riverine input, in keeping with the concept that marine attached communities are distinct from cooccurring free-living taxa. This diversity likely reflects the diverse microhabitats of available particles, implying that the total bacterial diversity in coastal systems is linked to particle supply and variability, with implications for understanding microbial biodiversity in marine systems.
C1 [Mohit, Vani; Lovejoy, Connie] Univ Laval, Dept Biol, Quebec Ocean, Quebec City, PQ G1K 7P4, Canada.
   [Mohit, Vani; Lovejoy, Connie] Univ Laval, Inst Biol Integrat & Syst, Quebec City, PQ, Canada.
   [Archambault, Philippe; Toupoint, Nicolas] UQAR, Inst Sci Mer ISMER, Rimouski, PQ, Canada.
RP Lovejoy, C (corresponding author), Univ Laval, Dept Biol, Quebec Ocean, Quebec City, PQ G1K 7P4, Canada.
EM connie.lovejoy@bio.ulaval.ca
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NR 116
TC 92
Z9 100
PD APR
PY 2014
VL 80
IS 7
BP 2071
EP 2083
DI 10.1128/AEM.02916-13
UT WOS:000332840700004
DA 2025-07-30
ER

PT J
AU Hwang, J
   Park, SY
   Park, M
   Lee, S
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AF Hwang, Jinik
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TI Seasonal Dynamics and Metagenomic Characterization of Marine Viruses in
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SO PLOS ONE
DT Article
AB Viruses are the most abundant biological entities in the oceans, and account for a significant amount of the genetic diversity of marine ecosystems. However, there is little detailed information about the biodiversity of viruses in marine environments. Rapid advances in metagenomics have enabled the identification of previously unknown marine viruses. We performed metagenomic profiling of seawater samples collected at 6 sites in Goseong Bay (South Sea, Korea) during the spring, summer, autumn, and winter of 2014. The results in-dicated the presence of highly diverse virus communities. The DNA libraries from samples collected during four seasons were sequenced using Illumina HiSeq 2000. The number of viral reads was 136,850 during March, 70,651 during June, 66,165 during September, and 111,778 during December. Species identification indicated that Pelagibacter phage HTVC010P, Ostreococcus lucimarinus OIV5 and OIV1, and Roseobacter phage SIO1 were the most common species in all samples. For viruses with at least 10 reads, there were 204 species during March, 189 during June, 170 during September, and 173 during December. Analysis of virus families indicated that the Myoviridae was the most common during all four seasons, and viruses in the Polyomaviridae were only present during March. Viruses in the Iridoviridae were only present during three seasons. Additionally, viruses in the Iridoviridae, Herpesviridae, and Poxviridae, which may affect fish and marine animals, appeared during different seasons. These results suggest that seasonal changes in temperature contribute to the dynamic structure of the viral community in the study area. The information presented here will be useful for comparative analyses with other marine viral communities.
C1 [Hwang, Jinik; Park, So Yun; Park, Mirye; Lee, Taek-Kyun] Korea Inst Ocean Sci & Technol, South Sea Environm Res Dept, Geoje, South Korea.
   [Hwang, Jinik; Park, Mirye; Lee, Taek-Kyun] Korea Univ Sci & Technol, Marine Environm Sci, Daejeon, South Korea.
   [Lee, Sukchan] Sungkyunkwan Univ, Dept Genet Engn, Suwon, South Korea.
RP Lee, TK (corresponding author), Korea Inst Ocean Sci & Technol, South Sea Environm Res Dept, Geoje, South Korea.
EM tklee@kiost.ac.kr
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NR 50
TC 25
Z9 27
PD JAN 25
PY 2017
VL 12
IS 1
AR e0169841
DI 10.1371/journal.pone.0169841
UT WOS:000396167300064
DA 2025-07-30
ER

PT J
AU Sun, FL
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   Sun, CC
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AF Sun, Fulin
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TI Anticyclonic Eddy Driving Significant Changes in Prokaryotic and
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SO FRONTIERS IN MARINE SCIENCE
DT Article
AB Mesoscale eddies play an important role in ocean energy and material transport. However, the effect of eddies on bacterial and eukaryotic community and their ecological effects remains unclear, regarding anticyclonic eddies (ACE). In this study, bacterial and eukaryotic community composition was examined across an ACE in the South China Sea, using high-throughput sequencing of the 16S rRNA and 18S rRNA gene. Environmental variables reflected the hydrographic characteristics of the ACE, which enhanced bacterial diversity and eukaryotic diversity in most water layers, relative to adjacent regions. Principal component analysis (PCoA) showed that bacterial and eukaryotic communities had certain different compositions between inside and outside the eddy above 75 m water. An obvious effect of the ACE was the increase in abundance and depth distribution of small photosynthetic and heterotrophic bacteria, such as SAR11, Prochlorococcus, Rhodospirillales and Oceanospirillales. While ACE decreased the relative abundance of nutrient-rich phytoplankton (Bacillariophyta and Mamiellophyceae), resulted in more growth space for other eukaryotes that prefer oligotrophic environment (especially Fungi, Dictyochophyceae, and Synurophyceae). Canonical correlation analysis (CCA) showed temperature, salinity, nitrate, phosphate and nitrite had significantly affected on microbial community. The special environment of ACE (especially temperature) shaped the composition of its specific microbe. This study shed important light on the effect of ACEs on environmental conditions to impact marine ecosystem structure.
C1 [Sun, Fulin; Wang, Youshao; Sun, Cuici; Cheng, Hao; Wang, Yutu; Fei, Jiao; Wu, Meilin] Chinese Acad Sci, South China Sea Inst Oceanol, State Key Lab Trop Oceanog, Guangzhou, Peoples R China.
   [Sun, Fulin; Wang, Youshao; Sun, Cuici; Wang, Yutu] Chinese Acad Sci, South China Sea Inst Oceanol, Daya Bay Marine Biol Res Stn, Shenzhen, Peoples R China.
   [Sun, Fulin; Xia, Xiaomin; Wang, Youshao; Sun, Cuici; Cheng, Hao; Wang, Yutu; Fei, Jiao; Wu, Meilin] Southern Marine Sci & Engn Guangdong Lab Guangzho, Guangzhou, Peoples R China.
   [Sun, Fulin; Xia, Xiaomin; Wang, Youshao; Sun, Cuici; Cheng, Hao; Wang, Yutu; Fei, Jiao; Wu, Meilin] South China Sea Inst Oceanol, Sanya Inst Oceanol, Sanya, Peoples R China.
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   [Simon, Meinhard] Carl von Ossietzky Univ Oldenburg, Inst Chem & Biol Marine Environm, Oldenburg, Germany.
   [Zhao, Hui] Guangdong Ocean Univ, Coll Chem & Environm Sci, Zhanjiang, Peoples R China.
   [Hu, Shuibo] Shenzhen Univ, MNR Key Lab Geoenvironm Monitoring Great Bay Area, Shenzhen, Peoples R China.
   [Hu, Shuibo] Shenzhen Univ, Guangdong Key Lab Urban Informat, Shenzhen, Peoples R China.
   [Hu, Shuibo] Shenzhen Univ, Shenzhen Key Lab Spatial Smart Sensing & Serv, Shenzhen, Peoples R China.
RP Wu, ML (corresponding author), Chinese Acad Sci, South China Sea Inst Oceanol, State Key Lab Trop Oceanog, Guangzhou, Peoples R China.; Wu, ML (corresponding author), Southern Marine Sci & Engn Guangdong Lab Guangzho, Guangzhou, Peoples R China.; Wu, ML (corresponding author), South China Sea Inst Oceanol, Sanya Inst Oceanol, Sanya, Peoples R China.
EM mlwu@scsio.ac.cn
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NR 60
TC 12
Z9 13
PD FEB 24
PY 2022
VL 9
AR 773548
DI 10.3389/fmars.2022.773548
UT WOS:000770802000001
DA 2025-07-30
ER

PT J
AU Wang, MM
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AF Wang, Mengmeng
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TI Diversity of Pelagic and Benthic Bacterial Assemblages in the Western
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SO FRONTIERS IN MICROBIOLOGY
DT Article
AB Despite numerous studies on marine prokaryotes, the vertical distribution patterns of bacterial community, either on the taxonomic composition or the functional structure, remains relatively unexplored. Using HiSeq-derived 16S rRNA data, the depth-related distribution patterns of taxonomic diversity and functional structure predicted from diversity data in the water column and sediments of the Western Pacific Ocean were explored. The OTU richness declined along the water column after peaking between 100 to 200 m deep. Relative abundance of Cyanobacteria and SAR11 decreased significantly with depth, while Actinobacteria and Gammaproteobacteria increased. This clearly mirrors the vertical distribution pattern of the predicted functional composition with the shift between phototrophic to chemoheterotrophic groups from the surface to the deeper layers. In terms of community composition and functional structure, the epipelagic zone differed from other deeper ones (i.e., meso-, bathy-, and abyssopelagic zones) where no obvious differences were detected. For the epipelagic zone, temperature, dissolved oxygen, and salinity were recognized as the crucial factors shaping both community composition and the functional structure of bacteria. Compared with water samples, benthic sediment samples harbored unexpectedly higher read abundance of Proteobacteria, presenting distinguishable taxonomic and functional compositions. This study provides novel knowledge on the vertical distribution of bacterial taxonomic and functional compositions in the western Pacific.
C1 [Wang, Mengmeng; Ma, Yiyuan; Li, Wei] Ocean Univ China, Coll Marine Life Sci, Qingdao, Peoples R China.
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RP Li, W (corresponding author), Ocean Univ China, Coll Marine Life Sci, Qingdao, Peoples R China.
EM liwei01@ouc.edu.cn
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NR 66
TC 18
Z9 20
PD SEP 10
PY 2020
VL 11
AR 1730
DI 10.3389/fmicb.2020.01730
UT WOS:000575378200001
DA 2025-07-30
ER

PT J
AU Lindh, MV
   Sjöstedt, J
   Ekstam, B
   Casini, M
   Lundin, D
   Hugerth, LW
   Hu, YOO
   Andersson, AF
   Andersson, A
   Legrand, C
   Pinhassi, J
AF Lindh, Markus V.
   Sjostedt, Johanna
   Ekstam, Borje
   Casini, Michele
   Lundin, Daniel
   Hugerth, Luisa W.
   Hu, Yue O. O.
   Andersson, Anders F.
   Andersson, Agneta
   Legrand, Catherine
   Pinhassi, Jarone
TI Metapopulation theory identifies biogeographical patterns among core and
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Metapopulation theory developed in terrestrial ecology provides applicable frameworks for interpreting the role of local and regional processes in shaping species distribution patterns. Yet, empirical testing of metapopulation models on microbial communities is essentially lacking. We determined regional bacterioplankton dynamics from monthly transect sampling in the Baltic Sea Proper using 16S rRNA gene sequencing. A strong positive trend was found between local relative abundance and occupancy of populations. Notably, the occupancy-frequency distributions were significantly bimodal with a satellite mode of rare endemic populations and a core mode of abundant cosmopolitan populations (e.g. Synechococcus, SAR11 and SAR86 clade members). Temporal changes in population distributions supported several theoretical frameworks. Still, bimodality was found among bacterioplankton communities across the entire Baltic Sea, and was also frequent in globally distributed datasets. Datasets spanning waters with widely different physicochemical characteristics or environmental gradients typically lacked significant bimodal patterns. When such datasets were divided into subsets with coherent environmental conditions, bimodal patterns emerged, highlighting the importance of positive feedbacks between local abundance and occupancy within specific biomes. Thus, metapopulation theory applied to microbial biogeography can provide novel insights into the mechanisms governing shifts in biodiversity resulting from natural or anthropogenically induced changes in the environment.
C1 [Lindh, Markus V.; Sjostedt, Johanna; Lundin, Daniel; Legrand, Catherine; Pinhassi, Jarone] Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, SE-39182 Kalmar, Sweden.
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RP Pinhassi, J (corresponding author), Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, SE-39182 Kalmar, Sweden.
EM jarone.pinhassi@lnu.se
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NR 74
TC 28
Z9 30
PD MAR
PY 2017
VL 19
IS 3
BP 1222
EP 1236
DI 10.1111/1462-2920.13650
UT WOS:000397525100031
DA 2025-07-30
ER

PT J
AU Parsons, RJ
   Nelson, CE
   Carlson, CA
   Denman, CC
   Andersson, AJ
   Kledzik, AL
   Vergin, KL
   McNally, SP
   Treusch, AH
   Giovannoni, SJ
AF Parsons, Rachel J.
   Nelson, Craig E.
   Carlson, Craig A.
   Denman, Carmen C.
   Andersson, Andreas J.
   Kledzik, Andrew L.
   Vergin, Kevin L.
   McNally, Sean P.
   Treusch, Alexander H.
   Giovannoni, Stephen J.
TI Marine bacterioplankton community turnover within seasonally hypoxic
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Understanding bacterioplankton community dynamics in coastal hypoxic environments is relevant to global biogeochemistry because coastal hypoxia is increasing worldwide. The temporal dynamics of bacterioplankton communities were analysed throughout the illuminated water column of Devil's Hole, Bermuda during the 6-week annual transition from a strongly stratified water column with suboxic and high-pCO(2) bottom waters to a fully mixed and ventilated state during 2008. A suite of culture-independent methods provided a quantitative spatiotemporal characterization of bacterioplankton community changes, including both direct counts and rRNA gene sequencing. During stratification, the surface waters were dominated by the SAR11 clade of Alphaproteobacteria and the cyanobacterium Synechococcus. In the suboxic bottom waters, cells from the order Chlorobiales prevailed, with gene sequences indicating members of the genera Chlorobium and Prosthecochloris - anoxygenic photoautotrophs that utilize sulfide as a source of electrons for photosynthesis. Transitional zones of hypoxia also exhibited elevated levels of methane- and sulfur-oxidizing bacteria relative to the overlying waters. The abundance of both Thaumarcheota and Euryarcheota were elevated in the suboxic bottom waters (>10(9) cells l(-1)). Following convective mixing, the entire water column returned to a community typical of oxygenated waters, with Euryarcheota only averaging 5% of cells, and Chlorobiales and Thaumarcheota absent.
C1 [Parsons, Rachel J.; Carlson, Craig A.; Andersson, Andreas J.; McNally, Sean P.] BIOS, St Georges, Bermuda.
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RP Parsons, RJ (corresponding author), BIOS, GE 01, St Georges, Bermuda.
EM rachel.parsons@bios.edu
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NR 97
TC 20
Z9 26
PD OCT
PY 2015
VL 17
IS 10
SI SI
BP 3481
EP 3499
DI 10.1111/1462-2920.12445
UT WOS:000363448500006
DA 2025-07-30
ER

PT J
AU Haas, S
   Desai, DK
   LaRoche, J
   Pawlowicz, R
   Wallace, DWR
AF Haas, Sebastian
   Desai, Dhwani K.
   LaRoche, Julie
   Pawlowicz, Rich
   Wallace, Douglas W. R.
TI Geomicrobiology of the carbon, nitrogen and sulphur cycles in Powell
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB We present the first geomicrobiological characterization of the meromictic water column of Powell Lake (British Columbia, Canada), a former fjord, which has been stably stratified since the last glacial period. Its deepest layers (300-350 m) retain isolated, relict seawater from that period. Fine-scale vertical profiling of the water chemistry and microbial communities allowed subdivision of the water column into distinct geomicrobiological zones. These zones were further characterized by phylogenetic and functional marker genes from amplicon and shotgun metagenome sequencing. Binning of metagenomic reads allowed the linkage of function to specific taxonomic groups. Statistical analyses (analysis of similarities, Bray-Curtis similarity) confirmed that the microbial community structure followed closely the geochemical zonation. Yet, our characterization of the genetic potential relevant to carbon, nitrogen and sulphur cycling of each zone revealed unexpected features, including potential for facultative anaerobic methylotrophy, nitrogen fixation despite high ammonium concentrations and potential micro-aerobic nitrifiers within the chemocline. At the oxic-suboxic interface, facultative anaerobic potential was found in the widespread freshwater lineage acI (Actinobacteria), suggesting intriguing ecophysiological similarities to the marine SAR11. Evolutionary divergent lineages among diverse phyla were identified in the ancient seawater zone and may indicate novel adaptations to this unusual environment.
C1 [Haas, Sebastian; Wallace, Douglas W. R.] Dalhousie Univ, Dept Oceanog, 1355 Oxford St, Halifax, NS, Canada.
   [Desai, Dhwani K.; LaRoche, Julie] Dalhousie Univ, Dept Biol, 1355 Oxford St, Halifax, NS, Canada.
   [Pawlowicz, Rich] Univ British Columbia, Dept Earth & Ocean Sci, 6339 Stores Rd, Vancouver, BC, Canada.
RP Haas, S (corresponding author), Dalhousie Univ, Dept Oceanog, 1355 Oxford St, Halifax, NS, Canada.
EM s.haas@dal.ca
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NR 158
TC 11
Z9 12
PD OCT
PY 2019
VL 21
IS 10
BP 3927
EP 3952
DI 10.1111/1462-2920.14743
EA AUG 2019
UT WOS:000478983600001
DA 2025-07-30
ER

PT J
AU Zinser, ER
AF Zinser, Erik R.
TI Cross-protection from hydrogen peroxide by helper microbes: the impacts
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SO ENVIRONMENTAL MICROBIOLOGY REPORTS
DT Review
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C1 [Zinser, Erik R.] Univ Tennessee, Dept Microbiol, Knoxville, TN 37996 USA.
RP Zinser, ER (corresponding author), Univ Tennessee, Dept Microbiol, Knoxville, TN 37996 USA.
EM ezinser@utk.edu
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NR 110
TC 26
Z9 29
PD AUG
PY 2018
VL 10
IS 4
BP 399
EP 411
DI 10.1111/1758-2229.12625
UT WOS:000442577600001
DA 2025-07-30
ER

PT J
AU Wietz, M
   Wemheuer, B
   Simon, H
   Giebel, HA
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   Brinkhoff, T
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AF Wietz, Matthias
   Wemheuer, Bernd
   Simon, Heike
   Giebel, Helge-Ansgar
   Seibt, Maren A.
   Daniel, Rolf
   Brinkhoff, Thorsten
   Simon, Meinhard
TI Bacterial community dynamics during polysaccharide degradation at
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB The bacterial degradation of polysaccharides is central to marine carbon cycling, but little is known about the bacterial taxa that degrade specific marine polysaccharides. Here, bacterial growth and community dynamics were studied during the degradation of the polysaccharides chitin, alginate and agarose in microcosm experiments at four contrasting locations in the Southern and Atlantic Oceans. At the Southern polar front, chitin-supplemented microcosms were characterized by higher fractions of actively growing cells and a community shift from Alphaproteobacteria to Gammaproteobacteria and Bacteroidetes. At the Antarctic ice shelf, chitin degradation was associated with growth of Bacteroidetes, with 24% higher cell numbers compared with the control. At the Patagonian continental shelf, alginate and agarose degradation covaried with growth of different Alteromonadaceae populations, each with specific temporal growth patterns. At the Mauritanian upwelling, only the alginate hydrolysis product guluronate was consumed, coincident with increasing abundances of Alteromonadaceae and possibly cross-feeding SAR11. 16S rRNA gene amplicon libraries indicated that growth of the Bacteroidetes-affiliated genus Reichenbachiella was stimulated by chitin at all cold and temperate water stations, suggesting comparable ecological roles over wide geographical scales. Overall, the predominance of location-specific patterns showed that bacterial communities from contrasting oceanic biomes have members with different potentials to hydrolyse polysaccharides.
C1 [Wietz, Matthias; Simon, Heike; Giebel, Helge-Ansgar; Brinkhoff, Thorsten; Simon, Meinhard] Carl von Ossietzky Univ Oldenburg, Inst Chem & Biol Marine Environm, D-26129 Oldenburg, Germany.
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RP Wietz, M (corresponding author), Carl von Ossietzky Univ Oldenburg, Inst Chem & Biol Marine Environm, D-26129 Oldenburg, Germany.
EM matthias.wietz@uni-oldenburg.de
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NR 74
TC 79
Z9 82
PD OCT
PY 2015
VL 17
IS 10
SI SI
BP 3822
EP 3831
DI 10.1111/1462-2920.12842
UT WOS:000363448500029
DA 2025-07-30
ER

PT J
AU Wear, EK
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   Nelson, CE
   Carlson, CA
AF Wear, Emma K.
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
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C1 [Wear, Emma K.; Wilbanks, Elizabeth G.; Carlson, Craig A.] Univ Calif Santa Barbara, Dept Ecol Evolut & Marine Biol, Santa Barbara, CA 93106 USA.
   [Wear, Emma K.; Wilbanks, Elizabeth G.; Carlson, Craig A.] Univ Calif Santa Barbara, Marine Sci Inst, Santa Barbara, CA 93106 USA.
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   [Nelson, Craig E.] Univ Hawaii Manoa, Sea Grant Coll Program, Honolulu, HI 96822 USA.
   [Wear, Emma K.] Univ Montana, Flathead Lake Biol Stn, Polson, MT 59860 USA.
RP Wear, EK (corresponding author), Univ Calif Santa Barbara, Dept Ecol Evolut & Marine Biol, Santa Barbara, CA 93106 USA.; Wear, EK (corresponding author), Univ Calif Santa Barbara, Marine Sci Inst, Santa Barbara, CA 93106 USA.; Wear, EK (corresponding author), Univ Montana, Flathead Lake Biol Stn, Polson, MT 59860 USA.
EM emma.wear@flbs.umt.edu
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NR 43
TC 108
Z9 119
PD AUG
PY 2018
VL 20
IS 8
SI SI
BP 2709
EP 2726
DI 10.1111/1462-2920.14091
UT WOS:000445184600003
DA 2025-07-30
ER

PT J
AU Sun, FL
   Wang, YS
   Wu, ML
   Jiang, ZY
   Sun, CC
   Cheng, H
AF Sun, Fu-Lin
   Wang, You-Shao
   Wu, Mei-Lin
   Jiang, Zhao-Yu
   Sun, Cui-Ci
   Cheng, Hao
TI Genetic Diversity of Bacterial Communities and Gene Transfer Agents in
   Northern South China Sea
SO PLOS ONE
DT Article
AB Pyrosequencing of the 16S ribosomal RNA gene (rDNA) amplicons was performed to investigate the unique distribution of bacterial communities in northern South China Sea (nSCS) and evaluate community structure and spatial differences of bacterial diversity. Cyanobacteria, Proteobacteria, Actinobacteria, and Bacteroidetes constitute the majority of bacteria. The taxonomic description of bacterial communities revealed that more Chroococcales, SAR11 clade, Acidimicrobiales, Rhodobacterales, and Flavobacteriales are present in the nSCS waters than other bacterial groups. Rhodobacterales were less abundant in tropical water (nSCS) than in temperate and cold waters. Furthermore, the diversity of Rhodobacterales based on the gene transfer agent (GTA) major capsid gene (g5) was investigated. Four g5 gene clone libraries were constructed from samples representing different regions and yielded diverse sequences. Fourteen g5 clusters could be identified among 197 nSCS clones. These clusters were also related to known g5 sequences derived from genome-sequenced Rhodobacterales. The composition of g5 sequences in surface water varied with the g5 sequences in the sampling sites; this result indicated that the Rhodobacterales population could be highly diverse in nSCS. Phylogenetic tree analysis result indicated distinguishable diversity patterns among tropical (nSCS), temperate, and cold waters, thereby supporting the niche adaptation of specific Rhodobacterales members in unique environments.
C1 [Sun, Fu-Lin; Wang, You-Shao; Wu, Mei-Lin; Jiang, Zhao-Yu; Sun, Cui-Ci; Cheng, Hao] Chinese Acad Sci, State Key Lab Trop Oceanog, South China Sea Inst Oceanol, Guangzhou, Guangdong, Peoples R China.
   [Sun, Fu-Lin; Wang, You-Shao; Sun, Cui-Ci] Chinese Acad Sci, South China Sea Inst Oceanol, Daya Bay Marine Biol Res Stn, Shenzhen, Peoples R China.
RP Wang, YS (corresponding author), Chinese Acad Sci, State Key Lab Trop Oceanog, South China Sea Inst Oceanol, Guangzhou, Guangdong, Peoples R China.
EM yswang@scsio.ac.cn
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NR 36
TC 9
Z9 13
PD NOV 3
PY 2014
VL 9
IS 11
AR e111892
DI 10.1371/journal.pone.0111892
UT WOS:000345558100134
DA 2025-07-30
ER

PT J
AU Brown, MV
   Schwalbach, MS
   Hewson, I
   Fuhrman, JA
AF Brown, MV
   Schwalbach, MS
   Hewson, I
   Fuhrman, JA
TI Coupling 16S-ITS rDNA clone libraries and automated ribosomal intergenic
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB We outline an approach to simultaneously assess multilevel microbial diversity patterns utilizing 16S-ITS rDNA clone libraries coupled with automated ribosomal intergenic spacer analysis (ARISA). Sequence data from 512 clones allowed estimation of ARISA fragment lengths associated with bacteria in a coastal marine environment. We matched 92% of ARISA peaks (each comprising > 1% total amplified product) with corresponding lengths from clone libraries. These peaks with putative identification accounted for an average of 83% of total amplified community DNA. At 16S rDNA similarities < 98%, most taxa displayed differences in ARISA fragment lengths > 10 bp, readily detectable and suggesting ARISA resolution is near the 'species' level. Prochlorococcus abundance profiles from ARISA were strongly correlated (r (2) = 0.86) to Prochlorococcus cell counts, indicating ARISA data are roughly proportional to actual cell abundance within a defined taxon. Analysis of ARISA profiles for 42 months elucidated patterns of microbial presence and abundance providing insights into community shifts and ecological niches for specific organisms, including a coupling of ecological patterns for taxa within the Prochlorococcus, the Gamma Proteobacteria and Actinobacteria. Clade-specific ARISA protocols were developed for the SAR11 and marine cyanobacteria to resolve ambiguous identifications and to perform focused studies. 16S-ITS data allowed high-resolution identification of organisms by ITS sequence analysis, and examination of microdiversity.
C1 Univ So Calif, Dept Biol Sci, Los Angeles, CA 90089 USA.
   Univ So Calif, Wrigley Inst Marine Studies, Los Angeles, CA 90089 USA.
RP Univ So Calif, Dept Biol Sci, 3616 Trousdale Pkwy,AHF B4, Los Angeles, CA 90089 USA.
EM mbrown@ifa.hawaii.edu
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NR 39
TC 214
Z9 250
PD SEP
PY 2005
VL 7
IS 9
BP 1466
EP 1479
DI 10.1111/j.1462-2920.2005.00835.x
UT WOS:000231024000019
DA 2025-07-30
ER

PT J
AU Schauer, M
   Balagué, V
   Pedrós-Alió, C
   Massana, R
AF Schauer, M
   Balagué, V
   Pedrós-Alió, C
   Massana, R
TI Seasonal changes in the taxonomic composition of bacterioplankton in a
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SO AQUATIC MICROBIAL ECOLOGY
DT Article
AB The succession of taxa within the bacterioplankton assemblage was followed over a whole seasonal cycle in Blanes Bay, an oligotrophic coastal system (average chl a: 0.5 mug l(-1)) in the NW Mediterranean Sea. Phylogenetic composition of the bacterioplankton was studied by means of DGGE (denaturing gradient gel electrophoresis) and sequencing of predominant bands. Analysis of DGGE fingerprints showed gradual changes in the dominant bacterial members over the sampling period. The time scale during which a single population appeared in significant amounts in the system ranged between weeks and months. Most of the DGGE bands sequenced showed high similarities to sequences of uncultured marine bacteria. The bacterial assemblage appeared to be dominated by members of alpha-Proteobacteria (mostly from the Roseobacter clade), Cytophaga-Flavobacteria-Bacteroides (CFB) and cyanobacteria throughout the year. Two bands related to prasinophyte chloroplasts were detected, whereas no bands related to SAR11 (alpha-Proteobacteria) or SAR86 (gamma-Proteobacteria) clusters were found. Contrasting with the relative stability of broad phylogenetic groups, examination of bands belonging to alpha-Proteobacteria, CFB and cyanobacteria revealed a substitution of closely related phylotypes during the seasonal cycle within each one of these 3 groups. Overall, the taxonomic composition of the bacterioplankton in this coastal marine system appeared to be rather stable in time, showing gradual changes throughout the year.
C1 CSIC, Inst Ciencies Mar, CMIMA, E-08003 Barcelona, Catalonia, Spain.
RP Massana, R (corresponding author), CSIC, Inst Ciencies Mar, CMIMA, Passeig Maritim Barceloneta 37-49, E-08003 Barcelona, Catalonia, Spain.
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NR 48
TC 164
Z9 172
PD MAR 13
PY 2003
VL 31
IS 2
BP 163
EP 174
DI 10.3354/ame031163
UT WOS:000181870100005
DA 2025-07-30
ER

PT J
AU Thompson, MA
   Valentine, DL
   Peng, XF
AF Thompson, Madeleine A.
   Valentine, David L.
   Peng, Xuefeng
TI Size fractionation informs microbial community composition and
   interactions in the eastern tropical North Pacific Ocean
SO FEMS MICROBES
DT Article
AB Marine microorganisms are drivers of biogeochemical cycles in the world's oceans, including oxygen minimum zones (OMZs). Using a metabarcoding survey of the 16S rRNA gene, we investigated prokaryotic communities, as well as their potential interactions with fungi, at the coastal, offshore, and peripheral OMZ of the eastern tropical North Pacific. Water samples were collected along a vertical oxygen gradient, and large volumes were filtered through three size fractions, 0.22, 2, and 22 mu m. The changes in community composition along the oxygen gradient were driven by Planctomycetota, Bacteroidota, Verrucomicrobiota, and Gammaproteobacteria; most are known degraders of marine polysaccharides and usually associated with the large particle-associated (LPA) community. The relative abundance of Nitrososphaerota, Alphaproteobacteria, Actinomycetota, and Nitrospinota was high in free-living and small particle-associated (SPA) communities. Network analyses identified putative interactions between fungi and prokaryotes in the particle-associated fractions, which have been largely overlooked in the ocean. In the SPAnetwork analysis, fungal amplicon sequence variants (ASVs) had exclusively negative connections with SAR11 nodes. In the LPA network analysis, fungal ASVs displayed both negative and positive connections with Pseudomonadota, SAR324, and Thermoplasmatota. Our findings demonstrate the utility of three-stage size-fractioned filtration in providing novel insights into marine microbial ecology.
   Large-volume size-fractioned filtration informs prokaryotic community composition and interactions between prokaryotes and marine fungi in the eastern tropical North Pacific Ocean oxygen minimum zone.
C1 [Thompson, Madeleine A.; Peng, Xuefeng] Univ South Carolina, Sch Earth Ocean & Environm, 701 Sumter St,EWS 617, Columbia, SC 29201 USA.
   [Valentine, David L.; Peng, Xuefeng] Univ Calif Santa Barbara, Marine Sci Inst, Santa Barbara, CA 93106 USA.
   [Valentine, David L.] Univ Calif Santa Barbara, Dept Earth Sci, Santa Barbara, CA 93106 USA.
RP Peng, XF (corresponding author), Univ South Carolina, Sch Earth Ocean & Environm, 701 Sumter St,EWS 617, Columbia, SC 29201 USA.
EM xpeng@seoe.sc.edu
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NR 123
TC 1
Z9 1
PD SEP 26
PY 2024
VL 5
AR xtae028
DI 10.1093/femsmc/xtae028
UT WOS:001319731300001
DA 2025-07-30
ER

PT J
AU Yamahara, KM
   Preston, CM
   Birch, J
   Walz, K
   Marin, R 
   Jensen, S
   Pargett, D
   Roman, B
   Ussler, W 
   Zhang, YW
   Ryan, J
   Hobson, B
   Kieft, B
   Raanan, B
   Goodwin, KD
   Chavez, FP
   Scholin, C
AF Yamahara, Kevan M.
   Preston, Christina M.
   Birch, James
   Walz, Kristine
   Marin, Roman, III
   Jensen, Scott
   Pargett, Douglas
   Roman, Brent
   Ussler, William, III
   Zhang, Yanwu
   Ryan, John
   Hobson, Brett
   Kieft, Brian
   Raanan, Ben
   Goodwin, Kelly D.
   Chavez, Francisco P.
   Scholin, Christopher
TI In situ Autonomous Acquisition and Preservation of Marine
   Environmental DNA Using an Autonomous Underwater Vehicle
SO FRONTIERS IN MARINE SCIENCE
DT Article
AB Environmental DNA (eDNA) can be used to identify macroorganisms and describe biodiversity, and thus has promise to supplement biological monitoring in marine ecosystems. Despite this promise, scaling sample acquisition to the spatial and temporal scales needed for effective monitoring would require prohibitively large investments in time and human resources. To address this challenge, we evaluated the efficacy of an autonomous eDNA sampling system and compare results obtained to traditional eDNA sampling methods. The autonomous sampling instrument consisted of the Environmental Sample Processor (ESP) coupled to an autonomous underwater vehicle (AUV). We tested equivalency between the ESP and traditional eDNA sampling techniques by comparing the quantification of eDNA across a broad range of taxa, from microbes (SAR11), phytoplankton (Pseudo-nitzschia spp.), and invertebrates (krill: Euphausia pacifica) to vertebrates (anchovy: Engraulis mordax). No significant differences in eDNA densities were observed between the two sample collection and filtration methods. eDNA filters collected by the ESP were preserved and stable for 21 days, the typical deployment length of the instrumentation. Finally, we demonstrated the unique capabilities of an autonomous, mobile ESP during a deployment near Monterey Bay, CA, by remotely and repeatedly sampling a water mass over 12 h. The development of a mobile ESP demonstrates the promise of utilizing eDNA measurements to observe complex biological processes in the ocean absent a human presence.
C1 [Yamahara, Kevan M.; Preston, Christina M.; Birch, James; Walz, Kristine; Marin, Roman, III; Jensen, Scott; Pargett, Douglas; Roman, Brent; Ussler, William, III; Zhang, Yanwu; Ryan, John; Hobson, Brett; Kieft, Brian; Raanan, Ben; Chavez, Francisco P.; Scholin, Christopher] Monterey Bay Aquarium Res Inst, Moss Landing, CA 95039 USA.
   [Goodwin, Kelly D.] NOAA, Ocean Chem & Ecosyst Div, Atlantic Oceanog & Meteorol Lab, NMFS,SWFSC, Miami, FL USA.
RP Yamahara, KM (corresponding author), Monterey Bay Aquarium Res Inst, Moss Landing, CA 95039 USA.
EM kyamahara@mbari.org
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PY 2019
VL 6
AR 373
DI 10.3389/fmars.2019.00373
UT WOS:000475989000001
DA 2025-07-30
ER

PT J
AU Zhang, SH
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AF Zhang, Sihai
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TI Assessing the shaping factors for archaeal and bacterial communities in
   tidal wetland soils contaminated with polycyclic aromatic hydrocarbons
SO ENVIRONMENTAL TECHNOLOGY & INNOVATION
DT Article
AB The environment and biome of coastal ecosystems are challenged by diverse human disturbances including soil pollution. Both archaea and bacteria are the main players in the biogeochemical cycling of coastal ecosystems, but their interactions with soil factors are far from being elucidated. In the tidal flats of Hangzhou Bay China, 16 soil physiochemical properties were discerned, including the major organic pollutants of polycyclic aromatic hydrocarbons (PAHs). Soil salinity, dissolved organic carbon, and PAHs varied between tidal soils and exhibited differential impacts on microbial commu-nities. Particularly, soil salinity interacted with the beta diversity of both bacterial and archaeal communities. In comparison, soil dissolved organic carbon exhibited immense impacts on bacterial alpha diversity, beta diversity, and individual taxa but not on archaeal ones. Moreover, soil PAHs exhibited an average concentration of 463.21 mu g/kg in the tidal soils and were significantly correlated with bacterial alpha diversity and two bacterial genera of Algoriphagus and Candidatus Pelagibacter Additionally, archaeal and bacterial communities exhibited a strong correlation, suggesting a role of inter-kingdom interactions in shaping the microbiomes in tidal soils. Overall, our results indicated the differential impacts of soil factors on archaeal and bacterial communities. In the context of increasing human disturbance in coastal ecosystems, our findings are valuable for comprehending the determinants that influence microbial community assembly. (c) 2023 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
C1 [Zhang, Sihai] Lishui Univ, Sch Ecol, Lishui 323000, Zhejiang, Peoples R China.
   [Zhang, Sihai; Xu, Linya; Tan, Xiangfeng] Zhejiang Univ, Inst Soil & Water Resources & Environm Sci, Coll Environm & Resource Sci, Hangzhou 310058, Zhejiang, Peoples R China.
   [Kong, Dedong; Tan, Xiangfeng] Zhejiang Acad Agr Sci, Inst Digital Agr, Hangzhou 310021, Peoples R China.
RP Tan, XF (corresponding author), Zhejiang Univ, Inst Soil & Water Resources & Environm Sci, Coll Environm & Resource Sci, Hangzhou 310058, Zhejiang, Peoples R China.
EM zhangsihai2352@163.com; blueeestar@foxmail.com; ntzx@zju.edu.cn;
   tan_xiangfeng@yeah.net
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NR 67
TC 3
Z9 3
PD AUG
PY 2023
VL 31
AR 103191
DI 10.1016/j.eti.2023.103191
EA MAY 2023
UT WOS:001000910900001
DA 2025-07-30
ER

PT J
AU Jessen, GL
   Chen, LX
   Mori, JF
   Nelson, TEC
   Slater, GF
   Lindsay, MBJ
   Banfield, JF
   Warren, LA
AF Jessen, Gerdhard L.
   Chen, Lin-Xing
   Mori, Jiro F.
   Nelson, Tara E. Colenbrander
   Slater, Gregory F.
   Lindsay, Matthew B. J.
   Banfield, Jillian F.
   Warren, Lesley A.
TI Alum Addition Triggers Hypoxia in an Engineered Pit Lake
SO MICROORGANISMS
DT Article
AB Here, we examine the geobiological response to a whole-lake alum (aluminum sulfate) treatment (2016) of Base Mine Lake (BML), the first pilot-scale pit lake established in the Alberta oil sands region. The rationale for trialing this management amendment was based on its successful use to reduce internal phosphorus loading to eutrophying lakes. Modest increases in water cap epilimnetic oxygen concentrations, associated with increased Secchi depths and chlorophyll-a concentrations, were co-incident with anoxic waters immediately above the fluid fine tailings (FFT) layer post alum. Decreased water cap nitrate and detectable sulfide concentrations, as well as increased hypolimnetic phospholipid fatty acid abundances, signaled greater anaerobic heterotrophic activity. Shifts in microbial community to groups associated with greater organic carbon degradation (i.e., SAR11-LD12 subclade) and the SRB group Desulfuromonodales emerged post alum and the loss of specialist groups associated with carbon-limited, ammonia-rich restricted niches (i.e., MBAE14) also occurred. Alum treatment resulted in additional oxygen consumption associated with increased autochthonous carbon production, watercap anoxia and sulfide generation, which further exacerbate oxygen consumption associated with on-going FFT mobilized reductants. The results illustrate the importance of understanding the broader biogeochemical implications of adaptive management interventions to avoid unanticipated outcomes that pose greater risks and improve tailings reclamation for oil sands operations and, more broadly, the global mining sector.
C1 [Jessen, Gerdhard L.] Univ Austral Chile, Inst Ciencias Marinas & Limnol, Valdivia 5090000, Chile.
   [Jessen, Gerdhard L.; Mori, Jiro F.; Nelson, Tara E. Colenbrander; Warren, Lesley A.] Univ Toronto, Dept Civil & Mineral Engn, Toronto, ON M5S 1A4, Canada.
   [Chen, Lin-Xing; Banfield, Jillian F.] Univ Calif Berkeley, Dept Earth & Planetary Sci, Berkeley, CA 94706 USA.
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   [Lindsay, Matthew B. J.] Univ Saskatchewan, Dept Geol Sci, Saskatoon, SK S7N 5E2, Canada.
RP Jessen, GL (corresponding author), Univ Austral Chile, Inst Ciencias Marinas & Limnol, Valdivia 5090000, Chile.; Jessen, GL; Warren, LA (corresponding author), Univ Toronto, Dept Civil & Mineral Engn, Toronto, ON M5S 1A4, Canada.; Warren, LA (corresponding author), McMaster Univ, Sch Earth Environm & Soc, Hamilton, ON L8S 4L8, Canada.
EM gerdhard.jessen@uach.cl; linxingchen@berkeley.edu;
   morij@yokohama-cu.ac.jp; tara.nelson@utoronto.ca; gslater@mcmaster.ca;
   matt.lindsay@usask.ca; jbanfield@berkeley.edu; lesley.warren@utoronto.ca
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NR 55
TC 5
Z9 5
PD MAR
PY 2022
VL 10
IS 3
AR 510
DI 10.3390/microorganisms10030510
UT WOS:000774133700001
DA 2025-07-30
ER

PT J
AU Mestre, M
   Höfer, J
   Sala, MM
   Gasol, JM
AF Mestre, Mireia
   Hoefer, Juan
   Montserrat Sala, M.
   Gasol, Josep M.
TI Seasonal Variation of Bacterial Diversity Along the Marine Particulate
   Matter Continuum
SO FRONTIERS IN MICROBIOLOGY
DT Article
AB Seasonal dynamics of ocean prokaryotic communities in the free-living fraction have been widely described, but less is known about the seasonality of prokaryotes inhabiting marine particles. We describe the seasonality of bacterial communities in the particulate matter continuum by sampling monthly over two years in a temperate oligotrophic coastal ecosystem and using a serial filtration (including six size-fractions spanning from 0.2 to 200 mu m). We observed that bacterial communities in the particulate matter continuum had annual changes following harmonic seasonal oscillations, where alpha, beta, and gamma diversity increased during the warm period and decreased during the cold period. Communities in each size-fraction changed gradually over time, being the communities in larger size-fractions the ones with stronger annual changes. Annual community changes were driven mainly by day length and sea surface temperature, and each size-fraction was additionally affected by other variables (e.g., smaller size-fractions by dissolved PO(4)and larger size-fractions by turbidity). While some taxonomic groups mantained their preference for a given size fraction during most of the year, others varied their distribution into different size fractions over time, as e.g., SAR11, which increased its presence in particles during the cold period. Our results indicate that the size-fractionation scheme provides novel seasonal patterns that are not possible to unveil by analyzing only free-living bacteria, and that help to better understand the temporal dynamics of prokaryotes.
C1 [Mestre, Mireia; Montserrat Sala, M.; Gasol, Josep M.] Inst Ciencies Mar ICM CSIC, Dept Marine Biol & Oceanog, Barcelona, Spain.
   [Mestre, Mireia] Univ Concepcion, Ctr Invest Oceanog COPAS Sur Austral, Dept Oceanog, Concepcion, Chile.
   [Mestre, Mireia] Univ Austral Chile, Ctr FONDAP Invest Dinam Ecosistemas Marinos Altas, Valdivia, Chile.
   [Hoefer, Juan] Pontificia Univ Catolica Valparaiso, Escuela Ciencias Mar, Valparaiso, Chile.
   [Gasol, Josep M.] Edith Cowan Univ, Ctr Marine Ecosyst Res, Sch Sci, Joondalup, WA, Australia.
RP Mestre, M; Gasol, JM (corresponding author), Inst Ciencies Mar ICM CSIC, Dept Marine Biol & Oceanog, Barcelona, Spain.; Mestre, M (corresponding author), Univ Concepcion, Ctr Invest Oceanog COPAS Sur Austral, Dept Oceanog, Concepcion, Chile.; Mestre, M (corresponding author), Univ Austral Chile, Ctr FONDAP Invest Dinam Ecosistemas Marinos Altas, Valdivia, Chile.; Gasol, JM (corresponding author), Edith Cowan Univ, Ctr Marine Ecosyst Res, Sch Sci, Joondalup, WA, Australia.
EM mireia@icm.csic.es; pepgasol@icm.csic.es
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NR 94
TC 48
Z9 50
PD JUL 21
PY 2020
VL 11
AR 1590
DI 10.3389/fmicb.2020.01590
UT WOS:000558900100001
DA 2025-07-30
ER

PT J
AU Suzuki, MT
   Preston, CM
   Chavez, FP
   DeLong, EF
AF Suzuki, MT
   Preston, CM
   Chavez, FP
   DeLong, EF
TI Quantitative mapping of bacterioplankton populations in seawater: field
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SO AQUATIC MICROBIAL ECOLOGY
DT Article
AB Few methods are available for quantifying specific prokaryotic taxa in marine plankton samples. In this study, we report a novel sampling and analysis strategy that circumvents some of the difficulties associated with current methods. This new approach allows for increased spatial, temporal and phylogenetic resolution over what has been achievable in routine bacterioplankton surveys. Picoplankton from small volume samples (30 mi) were collected on polysulfone filters and DNA was extracted with a commercially available DNA purification kit. The contribution of different bacterioplankton members at the group and subgroup levels was quantified by 5' nuclease assays. Percentages of small subunit (SSU) rDNAs from SAR11, SAR86, Roseobacter, Cytophaga and Synechococcus clades in DNA extracted from small samples were compared with SSU rDNA in DNA samples extracted from 6 to 91 seawater. Only small differences were observed between the methods. The approach was also tested by estimating gene copy numbers in a seawater sample spiked with varying numbers of cells from a cultivated marine Roseobacter strain. Finally we measured SSU rDNAs from the same groups of marine bacterioplankton in samples from a rapid survey of an upwelling plume in Monterey Bay, California, USA. A strong negative correlation between the percentage of Cytophagales and recently upwelled water, and an overlap between higher SAR86 percentages and a chlorophyll a concentration peak was found. The results confirm that rapid mapping of specific bacterioplankton groups is achievable using small samples and 5' nuclease assays.
C1 Monterey Bay Aquarium Res Inst, Moss Landing, CA 95039 USA.
RP DeLong, EF (corresponding author), Monterey Bay Aquarium Res Inst, 7700 Sandholdt Rd,POB 628, Moss Landing, CA 95039 USA.
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NR 36
TC 101
Z9 111
PD MAY 30
PY 2001
VL 24
IS 2
BP 117
EP 127
DI 10.3354/ame024117
UT WOS:000169446700002
DA 2025-07-30
ER

PT J
AU Ottesen, EA
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AF Ottesen, Elizabeth A.
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TI Pattern and synchrony of gene expression among sympatric marine
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SO PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
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DT Article
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C1 [Ottesen, Elizabeth A.; Young, Curtis R.; Eppley, John M.; DeLong, Edward F.] MIT, Dept Civil & Environm Engn, Cambridge, MA 02139 USA.
   [DeLong, Edward F.] MIT, Dept Biol Engn, Cambridge, MA 02139 USA.
   [Ryan, John P.; Chavez, Francisco P.; Scholin, Christopher A.] Monterey Bay Aquarium Res Inst, Moss Landing, CA 95039 USA.
RP DeLong, EF (corresponding author), MIT, Dept Civil & Environm Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA.
EM delong@mit.edu
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NR 35
TC 141
Z9 165
PD FEB 5
PY 2013
VL 110
IS 6
BP E488
EP E497
DI 10.1073/pnas.1222099110
UT WOS:000315209800007
DA 2025-07-30
ER

PT J
AU Sjöstedt, J
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AF Sjostedt, Johanna
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DT Article
AB To explore the potential linkage between distribution of marine bacterioplankton groups, environmental conditions, and water mass, we investigated the factors determining the abundance of bacterial taxa across the hydrographically complex Subtropical Convergence Zone in the Sargasso Sea. Based on information from 16S rRNA gene clone libraries from various locations and two depths, abundances of the predominant taxa (eubacteria, Archaea, Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and the Roseobacter, SAR11, and SAR86 clades) were quantified by real-time PCR. In addition, the abundances of Synechococcus, Prochlorococcus, and picoalgae were determined by flow cytometry. Linear multiple-regression models determining the relative effects of eight environmental variables and of water mass explained 35 to 86% of the variation in abundance of the quantified taxa, even though only one to three variables were significantly related to any particular taxon's abundance. Most of the variation in abundance was explained by depth and chlorophyll a. The predominant phototrophs, Prochlorococcus and picoalgae, were negatively correlated with phosphate, whereas eubacteria, heterotrophic bacteria, and SAR86 were negatively correlated with nitrite. Water mass showed limited importance for explaining the abundance of the taxonomical groups (significant only for Roseobacter, explaining 14% of the variation). The results suggest the potential for predicting the abundance of broad bacterioplankton groups throughout the Sargasso Sea using only a few environmental parameters.
C1 [Sjostedt, Johanna] Linnaeus Univ, Dept Nat Sci, Kalmar, Sweden.
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   [Munk, Peter] Tech Univ Denmark, Natl Inst Aquat Resources, Charlottenlund, Denmark.
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RP Riemann, L (corresponding author), Univ Copenhagen, Marine Biol Sect, Helsingor, Denmark.
EM LRiemann@bio.ku.dk
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NR 85
TC 18
Z9 22
PD MAY
PY 2014
VL 80
IS 9
BP 2786
EP 2795
DI 10.1128/AEM.00099-14
UT WOS:000334583300017
DA 2025-07-30
ER

PT J
AU Nelson, CE
   Carlson, CA
AF Nelson, Craig E.
   Carlson, Craig A.
TI Tracking differential incorporation of dissolved organic carbon types
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
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C1 [Nelson, Craig E.] Univ Calif Santa Barbara, Inst Marine Sci, Santa Barbara, CA 93106 USA.
   Univ Calif Santa Barbara, Dept Ecol Evolut & Marine Biol, Santa Barbara, CA 93106 USA.
RP Nelson, CE (corresponding author), Univ Calif Santa Barbara, Inst Marine Sci, Santa Barbara, CA 93106 USA.
EM craig.nelson@lifesci.ucsb.edu
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NR 72
TC 132
Z9 147
PD JUN
PY 2012
VL 14
IS 6
BP 1500
EP 1516
DI 10.1111/j.1462-2920.2012.02738.x
UT WOS:000304866600013
DA 2025-07-30
ER

PT J
AU Quaiser, A
   Zivanovic, Y
   Moreira, D
   López-García, P
AF Quaiser, Achim
   Zivanovic, Yvan
   Moreira, David
   Lopez-Garcia, Purificacion
TI Comparative metagenomics of bathypelagic plankton and bottom sediment
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SO ISME JOURNAL
DT Article
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C1 [Quaiser, Achim; Moreira, David; Lopez-Garcia, Purificacion] Univ Paris 11, CNRS, UMR8079, Unite Ecol Systemat & Evolut, F-91405 Orsay, France.
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   [Zivanovic, Yvan] Univ Paris 11, UMR C8621, Inst Genet & Microbiol, F-91405 Orsay, France.
RP López-García, P (corresponding author), Univ Paris 11, CNRS, UMR8079, Unite Ecol Systemat & Evolut, Batiment 360, F-91405 Orsay, France.
EM puri.lopez@u-psud.fr
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DA 2025-07-30
ER

PT J
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   Giovannoni, SJ
AF Wolf, Sarah
   Jayawickrama, Clare
   Carlson, Craig A.
   Deutsch, Curtis
   Davis II, Edward W.
   Daniels, Benjamin N.
   Chan, Francis
   Giovannoni, Stephen J.
TI Microbial carbon oxidation in seawater below the hypoxic threshold
SO SCIENTIFIC REPORTS
DT Article
AB Global oxygen minimum zones (OMZs) often reach hypoxia but seldom reach anoxia. Recently it was reported that Michaelis Menten constants (Km) of oxidative enzymes are orders of magnitude higher than respiratory Km values, and in the Hypoxic Barrier Hypothesis it was proposed that, in ecosystems experiencing falling oxygen, oxygenase enzyme activities become oxygen-limited long before respiration. We conducted a mesocosm experiment with a phytoplankton bloom as an organic carbon source and controlled dissolved oxygen (DO) concentrations in the dark to determine whether hypoxia slows carbon oxidation and oxygen decline. Total oxygen utilization (TOU) in hypoxic treatment (ca. 7.1 mu M O2) was 21.7% lower than the oxic treatment (ca. 245.1 mu M O2) over the first 43 days of the experiment. In addition, following the restoration of fully oxic conditions to the hypoxic treatment, TOU accelerated, demonstrating that oxidative processes are sensitive to DO concentrations found in large volumes of the ocean. Microbial amplicon-based community composition diverged between oxic treatments, indicating a specialized microbiome that included Thioglobaceae (SUP05 Gammaproteobacteria), OM190 (Planctomycetota), ABY1 (Patescibacteria), and SAR86 subclade D2472, thrived in the hypoxic treatment, while the genus Candidatus Actinomarina and SAR11 alphaproteobacteria were sharply inhibited. Our findings support the hypothesis that oxygenase kinetics might slow the progression of ocean deoxygenation in oxygen-poor regions and be a factor in the evolution of microbial taxa adapted to hypoxic environments.
C1 [Wolf, Sarah; Jayawickrama, Clare; Daniels, Benjamin N.; Giovannoni, Stephen J.] Oregon State Univ, Dept Microbiol, 220 Nash Hall, Corvallis, OR 97330 USA.
   [Carlson, Craig A.] UC Santa Barbara, Inst Marine Sci, Santa Barbara, CA USA.
   [Carlson, Craig A.] Dept Ecol Evolut & Marine Biol, Santa Barbara, CA USA.
   [Deutsch, Curtis] Princeton Univ, Dept Geosci, Princeton, NJ USA.
   [Davis II, Edward W.] Oregon State Univ, Ctr Quantitat Life Sci, Corvallis, OR USA.
   [Chan, Francis] Oregon State Univ, Dept Integrat Biol, Corvallis, OR 97330 USA.
RP Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, 220 Nash Hall, Corvallis, OR 97330 USA.; Chan, FC (corresponding author), Oregon State Univ, Dept Integrat Biol, Corvallis, OR 97330 USA.
EM francis.chan@oregonstate.edu; steve.giovannoni@oregonstate.edu
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NR 109
TC 1
Z9 1
PD JAN 22
PY 2025
VL 15
IS 1
AR 2838
DI 10.1038/s41598-024-82438-z
UT WOS:001404844700035
DA 2025-07-30
ER

PT J
AU Tada, Y
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AF Tada, Yuya
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TI Differing Growth Responses of Major Phylogenetic Groups of Marine
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Growth and productivity of phytoplankton substantially change organic matter characteristics, which affect bacterial abundance, productivity, and community structure in aquatic ecosystems. We analyzed bacterial community structures and measured activities inside and outside phytoplankton blooms in the western North Pacific Ocean by using bromodeoxyuridine immunocytochemistry and fluorescence in situ hybridization (BIC-FISH). Roseobacter/Rhodobacter, SAR11, Betaproteobacteria, Alteromonas, SAR86, and Bacteroidetes responded differently to changes in organic matter supply. Roseobacter/Rhodobacter bacteria remained widespread, active, and proliferating despite large fluctuations in organic matter and chlorophyll a (Chl-a) concentrations. The relative contribution of Bacteroidetes to total bacterial production was consistently high. Furthermore, we documented the unexpectedly large contribution of Alteromonas to total bacterial production in the bloom. Bacterial abundance, productivity, and growth potential (the proportion of growing cells in a population) were significantly correlated with Chl-a and particulate organic carbon concentrations. Canonical correspondence analysis showed that organic matter supply was critical for determining bacterial community structures. The growth potential of each bacterial group as a function of Chl-a concentration showed a bell-shaped distribution, indicating an optimal organic matter concentration to promote growth. The growth of Alteromonas and Betaproteobacteria was especially strongly correlated with organic matter supply. These data elucidate the distinctive ecological role of major bacterial taxa in organic matter cycling during open ocean phytoplankton blooms.
C1 [Tada, Yuya] Univ Tokyo, Atmosphere & Ocean Res Inst, Dept Marine Ecosyst Dynam, Kashiwa, Chiba 2778564, Japan.
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RP Tada, Y (corresponding author), Univ Tokyo, Atmosphere & Ocean Res Inst, Dept Marine Ecosyst Dynam, 5-1-5 Kashiwanoha, Kashiwa, Chiba 2778564, Japan.
EM yatada@aori.u-tokyo.ac.jp
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VL 77
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BP 4055
EP 4065
DI 10.1128/AEM.02952-10
UT WOS:000291341800018
DA 2025-07-30
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   Ciglenecki, I.
   Dautovic, J.
   Orlic, S.
TI Bacterial diversity across a highly stratified ecosystem: A salt-wedge
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SO SYSTEMATIC AND APPLIED MICROBIOLOGY
DT Article
AB Highly stratified Mediterranean estuaries are unique environments where the tidal range is low and the tidal currents are almost negligible. The main characteristics of these environments are strong salinity gradients and other environmental parameters. In this study, 454 pyrosequencing of the 16S rRNA gene in combination with catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) was used to estimate the bacterial diversity across the Krka estuary in February and July 2013. The comparison of the data derived from these two techniques resulted in a significant but weak positive correlation (R=0.28) indicating a substantial difference in the bacterial community structure, depending on the applied method. The phytoplankton bloom observed in February was identified as one of the main factors shaping the bacterial community structure between the two environmentally contrasting sampling months. Roseobacter, Bacteroidetes and Gammaproteobacteria differed substantially between February and July. Typical freshwater bacterial classes (Actinobacteria and Betaproteobacteria) showed strong vertical distribution patterns depending on the salinity gradient. Cyanobacteria decreased in abundance in February due to competition with phytoplankton, while the SAR11 Glade increased its abundance in July as a result of a better adaptation toward more oligotrophic conditions. The results provided the first detailed insight into the bacterial diversity in a highly stratified Mediterranean karstic estuary. (C) 2016 Elsevier GmbH. All rights reserved.
C1 [Korlevic, M.] Rudjer Boskovic Inst, Ctr Marine Res, Rovinj, Croatia.
   [Supraha, L.; Henderiks, J.] Uppsala Univ, Dept Earth Sci, Paleobiol, Uppsala, Sweden.
   [Ljubesic, Z.] Univ Zagreb, Fac Sci, Div Biol, Zagreb 41000, Croatia.
   [Ciglenecki, I.; Dautovic, J.] Rudjer Boskovic Inst, Div Marine & Environm Res, Zagreb, Croatia.
   [Orlic, S.] Rudjer Boskovic Inst, Div Mat Chem, Zagreb, Croatia.
   [Orlic, S.] Ctr Excellence Sci & Technol Integrating Mediterr, Microbial Ecol, Zagreb, Croatia.
RP Orlic, S (corresponding author), Rudjer Boskovic Inst, Div Mat Chem, Zagreb, Croatia.
EM sandi.orlic@irb.hr
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NR 71
TC 20
Z9 21
PD SEP
PY 2016
VL 39
IS 6
BP 398
EP 408
DI 10.1016/j.syapm.2016.06.006
UT WOS:000383305000006
DA 2025-07-30
ER

PT J
AU Cai, LL
   Zhang, R
   He, Y
   Feng, XY
   Jiao, NZ
AF Cai, Lanlan
   Zhang, Rui
   He, Ying
   Feng, Xiaoyuan
   Jiao, Nianzhi
TI Metagenomic Analysis of Virioplankton of the Subtropical Jiulong River
   Estuary, China
SO VIRUSES-BASEL
DT Article
AB Viruses are the most abundant biological entities in the oceans, and encompass a significant reservoir of genetic diversity. However, little is known about their biodiversity in estuary environments, which represent a highly dynamic and potentially more diverse habitat. Here, we report a metagenomic analysis of the dsDNA viral community from the Jiulong River Estuary (JRE), China, and provide a comparative analysis with other closely related environments. The results showed that the majority of JRE virome did not show any significant similarity to the database. For the major viral group (Caudovirales) detected in the sample, Podoviridae (44.88%) were the most abundant family, followed by Siphoviridae (32.98%) and Myoviridae (17.32%). The two most abundant viruses identified in the virome were phages HTVC010P and HMO-2011, which infect bacteria belonging to marine SAR11 and SAR116 clades, respectively. Two contigs larger than 20 kb, which show similar overall genome architectures to Celeribacter phage P12053L and Thalosomonas phage BA3, respectively, were generated during assembly. Comparative analysis showed that the JRE virome was more similar to marine viromes than to freshwater viromes, and shared a relative coarse-grain genetic overlap (averaging 14.14% +/- 1.68%) with other coastal viromes. Our study indicated that the diversity and community structure of the virioplankton found in JRE were mainly affected by marine waters, with less influence from freshwater discharge.
C1 [Cai, Lanlan; Zhang, Rui; Jiao, Nianzhi] Xiamen Univ Xiangan, Inst Marine Microbes & Ecospheres, State Key Lab Marine Environm Sci, Xiamen 361005, Peoples R China.
   [He, Ying; Feng, Xiaoyuan] Shanghai Jiao Tong Univ, Sch Life Sci & Biotechnol, State Key Lab Microbial Metab, Shanghai 200240, Peoples R China.
RP Zhang, R; Jiao, NZ (corresponding author), Xiamen Univ Xiangan, Inst Marine Microbes & Ecospheres, State Key Lab Marine Environm Sci, Xiamen 361005, Peoples R China.
EM cailanlan@stu.xmu.edu.cn; ruizhang@xmu.edu.cn; heying1982@sjtu.edu.cn;
   asdfeng131@sjtu.edu.cn; jiao@xmu.edu.cn
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NR 62
TC 39
Z9 45
PD FEB
PY 2016
VL 8
IS 2
AR 35
DI 10.3390/v8020035
UT WOS:000371831800027
DA 2025-07-30
ER

PT J
AU Bacosa, HP
   Liu, ZF
   Erdner, DL
AF Bacosa, Hernando P.
   Liu, Zhanfei
   Erdner, Deana L.
TI Natural Sunlight Shapes Crude Oil-Degrading Bacterial Communities in
   Northern Gulf of Mexico Surface Waters
SO FRONTIERS IN MICROBIOLOGY
DT Article
AB Following the Deepwater Horizon (DWH) spill in 2010, an enormous amount of oil was observed in the deep and surface waters of the northern Gulf of Mexico. Surface waters are characterized by intense sunlight and high temperature during summer. While the oil-degrading bacterial communities in the deep-sea plume have been widely investigated, the effect of natural sunlight on those in oil polluted surface waters remains unexplored to date. In this study, we incubated surface water from the DWH site with amendments of crude oil, Corexit dispersant, or both for 36 days under natural sunlight in the northern Gulf of Mexico. The bacterial community was analyzed over time for total abundance, density of alkane and polycyclic aromatic hydrocarbon degraders, and community composition via pyrosequencing. Our results showed that, for treatments with oil and/or Corexit, sunlight significantly reduced bacterial diversity and evenness and was a key driver of shifts in bacterial community structure. In samples containing oil or dispersant, sunlight greatly reduced abundance of the Cyanobacterium Synechococcus but increased the relative abundances of Alteromonas, Marinobacter, Labrenzia, Sandarakinotalea, Bartonella, and Halomonas. Dark samples with oil were represented by members of Thalassobius, Winogradskyella, Alcanivorax, Formosa, Pseudomonas, Eubacterium, Erythrobacter, Natronocella, and Coxiella. Both oil and Corexit inhibited the Candidatus Pelagibacter with or without sunlight exposure. For the first time, we demonstrated the effects of light in structuring microbial communities in water with oil and/or Corexit. Overall, our findings improve understanding of oil pollution in surface water, and provide unequivocal evidence that sunlight is a key factor in determining bacterial community composition and dynamics in oil polluted marine waters.
C1 [Bacosa, Hernando P.; Liu, Zhanfei; Erdner, Deana L.] Univ Texas Austin, Inst Marine Sci, Port Aransas, TX 78373 USA.
RP Erdner, DL (corresponding author), Univ Texas Austin, Inst Marine Sci, Port Aransas, TX 78373 USA.
EM derdner@utexas.edu
NR 0
TC 73
Z9 81
PD DEC 1
PY 2015
VL 6
AR 1326
DI 10.3389/fmicb.2015.01325
UT WOS:000366553800001
DA 2025-07-30
ER

PT J
AU Thiele, S
   Richter, M
   Balestra, C
   Glöckner, FO
   Casotti, R
AF Thiele, Stefan
   Richter, Michael
   Balestra, Cecilia
   Gloeckner, Frank Oliver
   Casotti, Raffaella
TI Taxonomic and functional diversity of a coastal planktonic bacterial
   community in a river-influenced marine area
SO MARINE GENOMICS
DT Article
AB The Gulf of Naples is a dynamical area with intense exchanges between offshore oligotrophic and coastal eutrophic waters with frequent freshwater inputs. The Sarno River, one of the most polluted rivers in Europe, strongly contributes to the pollution of the area, discharging high amounts of heavy metals and organic wastes from heavily cultivated and industrial areas. This paper reports on the diversity and community structure of the marine residential Bacteria and Archaea of the Gulf of Naples in an area close to the river Sarno plume and investigates their small-scale taxonomic diversity and expression patterns as a proxy of potential metabolic activity using metagenomics and metatranscriptomics. Bacteria and Archaea were mainly represented by marine clades, with only minor contributors from freshwater ones. The community was dominated by Alpha- and Gammaproteobacteria, of which Rhodospirillales, Pelagibacteriales, and Oceanospirilalles were most represented. However, Alteromonadales and Rhodobacterales were the most active, despite their relative lower abundance, suggesting that they are important for overall ecosystem functioning and nutrient cycling. Nitrification and a reversed form of dissimilatory sulfate reduction were the major metabolic processes found in the metatrascriptomes and were mainly associated to NitrosopuMilaleS and Pelagibacter, respectively. No clear indication of transcripts related to stress induced by heavy metals or organic pollutants was found. In general, despite the high loads of pollutants discharged continuously by the Sarno River, the microbial community did not show marks of stress-induced changes neither structural nor functional, thus suggesting that this river has little or no effect on the planktonic bacterial community of the Gulf of Naples. (C) 2016 Elsevier B.V. All rights reserved.
C1 [Thiele, Stefan; Balestra, Cecilia; Casotti, Raffaella] Stn Zool Anton Dohrn, I-80121 Naples, Italy.
   [Richter, Michael; Gloeckner, Frank Oliver] Max Planck Inst Marine Microbiol, Celsiusstr 1, D-28359 Bremen, Germany.
   [Gloeckner, Frank Oliver] Jacobs Univ Bremen gGmbH, Campus Ring 1, D-28759 Bremen, Germany.
   [Thiele, Stefan] MIT, Parsons Lab 15 Vassar St, Cambridge, MA 02139 USA.
RP Casotti, R (corresponding author), Stn Zool Anton Dohrn, I-80121 Naples, Italy.
EM raffaella.casotti@szn.it
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NR 62
TC 15
Z9 16
PD APR
PY 2017
VL 32
BP 61
EP 69
DI 10.1016/j.margen.2016.12.003
UT WOS:000399519700008
DA 2025-07-30
ER

PT J
AU Poiata, E
   Meyer, MM
   Ames, TD
   Breaker, RR
AF Poiata, Elena
   Meyer, Michelle M.
   Ames, Tyler D.
   Breaker, Ronald R.
TI A variant riboswitch aptamer class for S-adenosylmethionine
   common in marine bacteria
SO RNA
DT Article
AB Riboswitches that sense S-adenosylmethionine (SAM) are widely distributed throughout a variety of bacterial lineages. Four classes of SAM-binding riboswitches have been reported to date, constituting the most diverse collection of riboswitch classes that sense the same compound. Three of these classes, termed SAM-I, SAM-II, and SAM-III represent unique structures that form distinct binding pockets for the ligand. SAM-IV riboswitches carry different conserved sequence and structural features compared to other SAM riboswitches, but nucleotides and substructures corresponding to the ligand binding pocket are identical to SAM-I aptamers. In this article, we describe a fifth class of SAM binding aptamer, which we have termed SAM-V. SAM-V was discovered by analyzing GC-rich intergenic regions preceding metabolic genes in the marine alpha-proteobacterium "Candidatus Pelagibacter ubique.'' Although the motif is nearly unrepresented in cultured bacteria whose genomes have been completely sequenced, SAM-V is prevalent in marine metagenomic sequences. The consensus sequence and structure of SAM-V show some similarities to that of the SAM-II riboswitch, and it is likely that the two aptamers form similar ligand binding pockets. In addition, we identified numerous examples of a tandem SAM-II/SAM-V aptamer architecture. In this arrangement, the SAM-II aptamer is always positioned 5' of the SAM-V aptamer and the SAM-II aptamer is followed by a predicted intrinsic transcription terminator stem. The SAM-V aptamer, however, appears to use a ribosome binding site occlusion mechanism for genetic regulation. This tandem riboswitch arrangement exhibits an architecture that can potentially control both the transcriptional and translational stages of gene expression.
C1 [Poiata, Elena; Meyer, Michelle M.; Ames, Tyler D.; Breaker, Ronald R.] Yale Univ, Dept Mol Cellular & Dev Biol, New Haven, CT 06520 USA.
   [Breaker, Ronald R.] Yale Univ, Dept Mol Biophys & Biochem, New Haven, CT 06520 USA.
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RP Breaker, RR (corresponding author), Yale Univ, Dept Mol Cellular & Dev Biol, POB 208103, New Haven, CT 06520 USA.
EM ronald.breaker@yale.edu
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NR 48
TC 93
Z9 129
PD NOV
PY 2009
VL 15
IS 11
BP 2046
EP 2056
DI 10.1261/rna.1824209
UT WOS:000270851000012
DA 2025-07-30
ER

PT J
AU Liu, L
   Gao, X
   Dong, CJ
   Wang, HY
   Chen, XF
   Ma, XY
   Liu, SJ
   Chen, QR
   Lin, D
   Jiao, NZ
   Tang, K
AF Liu, Le
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   Wang, Huanyu
   Chen, Xiaofeng
   Ma, Xiaoyi
   Liu, Shujing
   Chen, Quanrui
   Lin, Dan
   Jiao, Nianzhi
   Tang, Kai
TI Enantioselective transformation of phytoplankton-derived
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SO ISME JOURNAL
DT Article
AB Chirality, a fundamental property of matter, is often overlooked in the studies of marine organic matter cycles. Dihydroxypropanesulfonate (DHPS), a globally abundant organosulfur compound, serves as an ecologically important currency for nutrient and energy transfer from phytoplankton to bacteria in the ocean. However, the chirality of DHPS in nature and its transformation remain unclear. Here, we developed a novel approach using chiral phosphorus-reagent labeling to separate DHPS enantiomers. Our findings demonstrated that at least one enantiomer of DHPS is present in marine diatoms and coccolithophores, and that both enantiomers are widespread in marine environments. A novel chiral-selective DHPS catabolic pathway was identified in marine Roseobacteraceae strains, where HpsO and HpsP dehydrogenases at the gateway to DHPS catabolism act specifically on R-DHPS and S-DHPS, respectively. R-DHPS is also a substrate for the dehydrogenase HpsN. All three dehydrogenases generate stable hydrogen bonds between the chirality-center hydroxyls of DHPS and highly conserved residues, and HpsP also form coordinate-covalent bonds between the chirality-center hydroxyls and Zn2+, which determines the mechanistic basis of strict stereoselectivity. We further illustrated the role of enzymatic promiscuity in the evolution of DHPS metabolism in Roseobacteraceae and SAR11. This study provides the first evidence of chirality's involvement in phytoplankton-bacteria metabolic currencies, opening a new avenue for understanding the ocean organosulfur cycle.
C1 [Liu, Le; Dong, Changjie; Wang, Huanyu; Ma, Xiaoyi; Liu, Shujing; Chen, Quanrui; Lin, Dan; Jiao, Nianzhi; Tang, Kai] Xiamen Univ, Coll Ocean & Earth Sci, State Key Lab Marine Environm Sci, Fujian Key Lab Marine Carbon Sequestrat, Xiangan South Rd, Xiamen 361102, Peoples R China.
   [Gao, Xiang] Xiamen Univ, Sch Pharmaceut Sci, State Key Lab Cellular Stress Biol, Fujian Prov Key Lab Innovat Drug Target Res, Xiamen 361102, Peoples R China.
   [Chen, Xiaofeng] Minist Nat Resources, Inst Oceanog 3, Tech Innovat Ctr Utilizat Marine Biol Resources, Xiamen 361001, Peoples R China.
RP Tang, K (corresponding author), Xiamen Univ, Coll Ocean & Earth Sci, State Key Lab Marine Environm Sci, Fujian Key Lab Marine Carbon Sequestrat, Xiangan South Rd, Xiamen 361102, Peoples R China.
EM tangkai@xmu.edu.cn
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TC 5
Z9 5
PD JAN 8
PY 2024
VL 18
IS 1
AR wrae084
DI 10.1093/ismejo/wrae084
EA MAY 2024
UT WOS:001234293900001
DA 2025-07-30
ER

PT J
AU Kamennaya, NA
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AF Kamennaya, Nina A.
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   Zubkov, Mikhail, V
TI Accumulation of ambient phosphate into the periplasm of marine bacteria
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SO NATURE COMMUNICATIONS
DT Article
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RP Zubkov, MV (corresponding author), Natl Oceanog Ctr, Southampton SO14 3ZH, Hants, England.; Zubkov, MV (corresponding author), Scottish Marine Inst, Scottish Assoc Marine Sci, Oban PA37 1QA, Argyll, Scotland.
EM Mikhail.Zubkov@sams.ac.uk
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NR 72
TC 33
Z9 34
PD MAY 26
PY 2020
VL 11
IS 1
DI 10.1038/s41467-020-16428-w
UT WOS:000538812100017
DA 2025-07-30
ER

PT J
AU Kan, J
   Suzuki, MT
   Wang, K
   Evans, SE
   Chen, F
AF Kan, Jinjun
   Suzuki, Marcelino T.
   Wang, Kui
   Evans, Sarah E.
   Chen, Feng
TI High temporal but low spatial heterogeneity of bacterioplankton in the
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
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RP Chen, F (corresponding author), Univ Maryland, Ctr Marine Biotechnol, Inst Biotechnol, Suite 236,701 E Pratt St, Baltimore, MD 21202 USA.
EM chenf@umbi.umd.edu
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NR 82
TC 68
Z9 78
PD NOV
PY 2007
VL 73
IS 21
BP 6776
EP 6789
DI 10.1128/AEM.00541-07
UT WOS:000250700600010
DA 2025-07-30
ER

PT J
AU Yanuka-Golub, K
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   Kiro, Y
AF Yanuka-Golub, Keren
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   Kiro, Yael
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SO JOURNAL OF GEOPHYSICAL RESEARCH-BIOGEOSCIENCES
DT Article
AB Submarine groundwater discharge (SGD) is a globally important process supplying nutrients and trace elements to the coastal environment, thus playing a pivotal role in sustaining marine primary productivity. Along with nutrients, groundwater also contains allochthonous microbes that are discharged from the terrestrial subsurface into the sea. Currently, little is known about the interactions between groundwater-borne and coastal seawater microbial populations, and groundwater microbes' role upon introduction to coastal seawater populations. Here, we investigated seawater microbial abundance, activity and diversity in a site strongly influenced by SGD. In addition, through laboratory-controlled bottle incubations, we mimicked different mixing scenarios between groundwater and seawater. Our results demonstrate that the addition of 0.1 mu m filtered groundwater stimulated heterotrophic activity and increased microbial abundance compared to control coastal seawater, whereas 0.22 mu m filtration treatments induced primary productivity and Synechococcus growth. 16S rRNA gene sequencing showed a strong shift from a SAR11-rich community in the control samples to Rhodobacteraceae dominance in the <0.1 mu m treatment, in agreement with Rhodobacteraceae enrichment in the SGD field site. These results suggest that microbes delivered by SGD may affect the abundance, activity and diversity of intrinsic microbes in coastal seawater, highlighting the cryptic interplay between groundwater and seawater microbes in coastal environments, which has important implications for carbon cycling.
C1 [Yanuka-Golub, Keren; Weber, Nurit; Mayyani, Meor; Levy, Yehuda; Kiro, Yael] Weizmann Inst Sci, Dept Earth & Planetary Sci, Rehovot, Israel.
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RP Yanuka-Golub, K (corresponding author), Weizmann Inst Sci, Dept Earth & Planetary Sci, Rehovot, Israel.; Yanuka-Golub, K (corresponding author), Galilee Soc, Inst Appl Res, ShefaAmr, Israel.; Yanuka-Golub, K (corresponding author), Univ Haifa, Inst Evolut IoE, Haifa, Israel.; Rahav, E (corresponding author), Israel Oceanog & Limnol Res, Natl Inst Oceanog, Haifa, Israel.
EM keren@gal-soc.org; keren@gal-soc.org
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NR 72
TC 0
Z9 0
PD FEB
PY 2024
VL 129
IS 2
AR e2023JG007610
DI 10.1029/2023JG007610
UT WOS:001173753900001
DA 2025-07-30
ER

PT J
AU Ren, YH
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   Wu, YH
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AF Ren, Yanhu
   Luo, Zhenhao
   Liu, Qian
   Wei, Bin
   Wu, Yue-Hong
   Shu, Wen-Sheng
   Xu, Xue-Wei
TI Insights into community assembly mechanisms, biogeography, and metabolic
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SO FRONTIERS IN MARINE SCIENCE
DT Article
AB Heterotrophic prokaryotes constitute the largest living biomass in the ocean and can be divided into particle-associated (PA) and free-living (FL) fractions. PA and FL prokaryotic communities play critical roles in the biogeochemical cycles of particulate and dissolved organic matter; however, their community assembly processes, biogeographical distribution patterns, and functional properties in oligotrophic surface water remain to be further elucidated. Based on 16S rRNA gene sequencing and shotgun metagenomics, we investigated the assembly mechanisms, biogeography, and functional potential of PA and FL prokaryotes in the surface waters of the West Pacific and Indian Oceans. FL prokaryotic communities were predominantly structured by deterministic processes, whereas their PA counterparts appeared to be shaped by the combined action of deterministic and stochastic processes. PA and FL prokaryotes in the tropical oligotrophic surface ocean exhibit markedly different community structures and functional potentials. Bacterial PA specialists such as Lentimonas, Alteromonas, and Pirellula as well as archaeal PA specialists Marine Group II and Marine Group III were significantly more abundant in PA assemblages, whereas lineages such as Prochlorococcus, SAR11 clade, and Candidatus Actinomarina were significantly more abundant in FL communities. The metabolic potential of the PA community was more abundant in pathways such as polyamine biosynthesis, carbohydrate metabolism, and glycosaminoglycan degradation. In contrast, the FL community was more enriched in functions related to amino acid metabolism, lipid biosynthesis, and aromatic degradation.
C1 [Ren, Yanhu; Xu, Xue-Wei] Zhejiang Univ, Ocean Coll, Zhoushan, Peoples R China.
   [Ren, Yanhu; Liu, Qian; Wu, Yue-Hong; Xu, Xue-Wei] Minist Nat Resources, Minist Nat Resources & Inst Oceanog 2, Key Lab Marine Ecosyst Dynam, Hangzhou, Peoples R China.
   [Luo, Zhenhao] Sun Yat Sen Univ, Sch Life Sci, State Key Lab Biocontrol, Guangdong Prov Key Lab Plant Resources & Southern, Guangzhou, Peoples R China.
   [Wei, Bin] Zhejiang Univ Technol, Coll Pharmaceut Sci, Hangzhou, Peoples R China.
   [Wei, Bin] Zhejiang Univ Technol, Collaborat Innovat Ctr Yangtze River Delta Reg Gre, Hangzhou, Peoples R China.
   [Shu, Wen-Sheng] South China Normal Univ, Inst Ecol Sci, Sch Life Sci, Guangzhou, Peoples R China.
RP Xu, XW (corresponding author), Zhejiang Univ, Ocean Coll, Zhoushan, Peoples R China.; Xu, XW (corresponding author), Minist Nat Resources, Minist Nat Resources & Inst Oceanog 2, Key Lab Marine Ecosyst Dynam, Hangzhou, Peoples R China.; Shu, WS (corresponding author), South China Normal Univ, Inst Ecol Sci, Sch Life Sci, Guangzhou, Peoples R China.
EM shuwensheng@m.scnu.edu.cn; xuxw@sio.org.cn
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NR 64
TC 2
Z9 2
PD SEP 15
PY 2022
VL 9
AR 923295
DI 10.3389/fmars.2022.923295
UT WOS:000862140400001
DA 2025-07-30
ER

PT J
AU Hmelo, LR
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   Mincer, TJ
AF Hmelo, L. R.
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   Mincer, T. J.
TI Characterization of bacterial epibionts on the cyanobacterium
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SO AQUATIC MICROBIAL ECOLOGY
DT Article
AB Interest in Trichodesmium, a nitrogen-fixing genus of Cyanobacteria, has been fueled by its prominent role in the marine nitrogen cycle. However, it is often overlooked that Trichodesmium occur in the ocean as colonies and are only one member of a complex microbial consortium. In the present study, we used 16S rRNA gene sequences to phylogenetically classify the communities associated with 2 morphological types of Trichodesmium colonies, tufts and puffs, which were collected at the Bermuda Atlantic Time Series (BATS) site in the Sargasso Sea. Both Trichodesmium morphotypes were most closely related to T. thiebautii at >= 99% identity. Non-cyanobacterial sequences from both types of colonies were dominated by Flavobacteria, Sphingobacteria, and Alphaproteobacteria. However, the epibiotic communities possessed significantly lower diversity than bacterioplankton; major seawater planktonic taxa, such as the SAR11 clade and Archaea, were conspicuously absent. Moreover, several epibiotic taxa appeared to be novel. Among the tuft or puff 16S rRNA clone libraries constructed in the present study, epibionts sharing common operational taxonomic units at the 97 percent sequence identity (PSI) threshold or higher were not observed, presenting the possibility that these 2 morphologies could select for different epibiotic communities. While our data are representative of a single sample point in time and space, these data suggest that Trichodesmium possess an epibiotic microbial community of relatively low diversity, distinct from that observed in bacterial picoplankton.
C1 [Hmelo, L. R.; Van Mooy, B. A. S.; Mincer, T. J.] Woods Hole Oceanog Inst, Dept Marine Chem & Geochem, Woods Hole, MA 02543 USA.
RP Mincer, TJ (corresponding author), Woods Hole Oceanog Inst, Dept Marine Chem & Geochem, Woods Hole, MA 02543 USA.
EM tmincer@whoi.edu
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TC 59
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BP 1
EP U119
DI 10.3354/ame01571
UT WOS:000308651800001
DA 2025-07-30
ER

PT J
AU Jain, A
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AF Jain, Anand
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TI Differences in free-living and particle-associated bacterial communities
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SO JOURNAL OF BASIC MICROBIOLOGY
DT Article
AB High throughput V3-16S rRNA amplicon sequencing data was used for evaluating differences between free-living (FL, <1.2-0.2m) and particle-associated (PA, >1.2m) bacterial communities, and their spatial variation between inner fjord (IF) and outer fjord (OF) of Kongsfjorden. A total of 4,454,142 high quality sequences obtained clustered into 32,058 OTUs. A majority of these sequences were affiliated with Proteobacteria (59.8%), followed by Bacteroidetes (29.02%), Firmicutes (5.9%), Actinobacteria (2.84%), Cyanobacteria (1.04%), and others (1.4%). The highest bacterial diversity was recorded in the inner fjord free-living (IF_FL) fraction whilst the lowest was observed in the outer fjord free-living (OF_FL) fraction. There was a clear spatial variation among FL bacterial communities, while PA communities remained similar at both sampling locations. The free-living bacterial community differs from particle-associated community and had relatively higher abundance (>4-fold) of Alteromonas and Pseudoalteromonas, while PA community was relatively more enriched with Balneatrix, Ulvibacter, Formosa, Candidatus Planktomarina, Sulfitobacter, Loktanella, members of SAR116, and Acidimicrobiales. In addition, two major bacterial taxa, Polaribacter and SAR11, co-occurred in both FL and PA fractions with varied proportions in IF and OF. These results suggest co-occurrence of PA specialist as well as generalist bacterial groups in Kongsfjorden. Further, high bacterial diversity in the IF_FL fraction indicates possible role of glacial inputs in modulating diversity of free-living bacterial community in Kongsfjorden.
C1 [Jain, Anand; Krishnan, Kottekkatu P.] Natl Ctr Antarctic & Ocean Res, Cryobiol Lab, Vasco Da Gama 403804, Goa, India.
RP Jain, A (corresponding author), Natl Ctr Antarctic & Ocean Res, Cryobiol Lab, Vasco Da Gama 403804, Goa, India.
EM microanand2003@gmail.com
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VL 57
IS 10
BP 827
EP 838
DI 10.1002/jobm.201700216
UT WOS:000412552300003
DA 2025-07-30
ER

PT J
AU Zhang, WH
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SO MICROBIAL ECOLOGY
DT Article
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C1 [Zhang, Weihong; Yuan, Wenke; Chen, Lu; Ye, Chen; Jiang, Ying; Yang, Yuyi] Chinese Acad Sci, Wuhan Bot Garden, Key Lab Aquat Bot & Watershed Ecol, Lumo Rd 1, Wuhan 430074, Peoples R China.
   [Zhang, Weihong; Yuan, Wenke; Chen, Lu; Ye, Chen; Jiang, Ying; Yang, Yuyi] Chinese Acad Sci, Core Bot Gardens, Ctr Plant Ecol, Wuhan 430074, Peoples R China.
   [Zhang, Weihong] Univ Chinese Acad Sci, Beijing 100049, Peoples R China.
RP Yang, YY (corresponding author), Chinese Acad Sci, Wuhan Bot Garden, Key Lab Aquat Bot & Watershed Ecol, Lumo Rd 1, Wuhan 430074, Peoples R China.; Yang, YY (corresponding author), Chinese Acad Sci, Core Bot Gardens, Ctr Plant Ecol, Wuhan 430074, Peoples R China.
EM yangyy@wbgcas.cn
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BP 985
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EA NOV 2021
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DA 2025-07-30
ER

PT J
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AF Yang, Caiyun
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TI Bacterial community dynamics during a bloom caused by Akashiwo
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SO HARMFUL ALGAE
DT Article
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C1 [Tian, Yun] Xiamen Univ, State Key Lab Marine Environm Sci, Xiamen 361005, Peoples R China.
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RP Tian, Y (corresponding author), Xiamen Univ, State Key Lab Marine Environm Sci, Xiamen 361005, Peoples R China.
EM tianyun@xmu.edu.cn; wshwzh@xmu.edu.cn
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ER

PT J
AU Morris, JJ
   Lenski, RE
   Zinser, ER
AF Morris, J. Jeffrey
   Lenski, Richard E.
   Zinser, Erik R.
TI The Black Queen Hypothesis: Evolution of Dependencies through Adaptive
   Gene Loss
SO MBIO
DT Article
AB Reductive genomic evolution, driven by genetic drift, is common in endosymbiotic bacteria. Genome reduction is less common in free-living organisms, but it has occurred in the numerically dominant open-ocean bacterioplankton Prochlorococcus and "Candidatus Pelagibacter," and in these cases the reduction appears to be driven by natural selection rather than drift. Gene loss in free-living organisms may leave them dependent on cooccurring microbes for lost metabolic functions. We present the Black Queen Hypothesis (BQH), a novel theory of reductive evolution that explains how selection leads to such dependencies; its name refers to the queen of spades in the game Hearts, where the usual strategy is to avoid taking this card. Gene loss can provide a selective advantage by conserving an organism's limiting resources, provided the gene's function is dispensable. Many vital genetic functions are leaky, thereby unavoidably producing public goods that are available to the entire community. Such leaky functions are thus dispensable for individuals, provided they are not lost entirely from the community. The BQH predicts that the loss of a costly, leaky function is selectively favored at the individual level and will proceed until the production of public goods is just sufficient to support the equilibrium community; at that point, the benefit of any further loss would be offset by the cost. Evolution in accordance with the BQH thus generates "beneficiaries" of reduced genomic content that are dependent on leaky "helpers," and it may explain the observed nonuniversality of prototrophy, stress resistance, and other cellular functions in the microbial world.
C1 [Morris, J. Jeffrey; Lenski, Richard E.] Michigan State Univ, E Lansing, MI 48824 USA.
   [Morris, J. Jeffrey; Lenski, Richard E.] BEACON Ctr Study Evolut Act, E Lansing, MI USA.
   [Zinser, Erik R.] Univ Tennessee, Knoxville, TN USA.
RP Morris, JJ (corresponding author), Michigan State Univ, E Lansing, MI 48824 USA.
EM jmorris@msu.edu
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NR 56
TC 820
Z9 926
PD MAR-APR
PY 2012
VL 3
IS 2
AR e00036-12
DI 10.1128/mBio.00036-12
UT WOS:000305297100008
DA 2025-07-30
ER

PT J
AU Jaiani, E
   Kusradze, I
   Kokashvili, T
   Geliashvili, N
   Janelidze, N
   Kotorashvili, A
   Kotaria, N
   Guchmanidze, A
   Tediashvili, M
   Prangishvili, D
AF Jaiani, Ekaterine
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   Kokashvili, Tamar
   Geliashvili, Natia
   Janelidze, Nino
   Kotorashvili, Adam
   Kotaria, Nato
   Guchmanidze, Archil
   Tediashvili, Marina
   Prangishvili, David
TI Microbial Diversity and Phage-Host Interactions in the Georgian Coastal
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SO MARINE DRUGS
DT Article
AB Viruses have the greatest abundance and highest genetic diversity in marine ecosystems. The interactions between viruses and their hosts is one of the hot spots of marine ecology. Besides their important role in various ecosystems, viruses, especially bacteriophages and their gene pool, are of enormous interest for the development of new gene products with high innovation value. Various studies have been conducted in diverse ecosystems to understand microbial diversity and phage-host interactions; however, the Black Sea, especially the Eastern coastal area, remains among the least studied ecosystems in this regard. This study was aimed at to fill this gap by analyzing microbial diversity and bacteriophage-host interactions in the waters of Eastern Black Sea using a metagenomic approach. To this end, prokaryotic and viral metagenomic DNA from two sampling sites, Poti and Gonio, were sequenced on the Illumina Miseq platform and taxonomic and functional profiles of the metagenomes were obtained using various bioinformatics tools. Our metagenomics analyses allowed us to identify the microbial communities, with Proteobacteria, Cyanobacteria, Actinibacteria, and Firmicutes found to be the most dominant bacterial phyla and Synechococcus and Candidatus Pelagibacter phages found to be the most dominant viral groups in the Black Sea. As minor groups, putative phages specific to human pathogens were identified in the metagenomes. We also characterized interactions between the phages and prokaryotic communities by determining clustered regularly interspaced short palindromic repeats (CRISPR), prophage-like sequences, and integrase/excisionase sequences in the metagenomes, along with identification of putative horizontally transferred genes in the viral contigs. In addition, in the viral contig sequences related to peptidoglycan lytic activity were identified as well. This is the first study on phage and prokaryote diversity and their interactions in the Eastern coastal area of the Black Sea using a metagenomic approach.
C1 [Jaiani, Ekaterine; Kusradze, Ia; Kokashvili, Tamar; Geliashvili, Natia; Janelidze, Nino; Tediashvili, Marina] G Eliava Inst Bacteriophages Microbiol & Virol, Tbilisi 0160, Georgia.
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   [Guchmanidze, Archil] Assoc Flora & Fauna, Batumi 6010, Georgia.
   [Prangishvili, David] Pasteur Inst, F-75015 Paris, France.
   [Prangishvili, David] Iv Javakhishvili Tbilisi State Univ, Fac Med, Tbilisi 0179, Georgia.
RP Jaiani, E (corresponding author), G Eliava Inst Bacteriophages Microbiol & Virol, Tbilisi 0160, Georgia.
EM e.jaiani@pha.ge; iakusradze@pha.ge; t.kokashvili@pha.ge;
   nageli2014@agruni.edu.ge; n.janelidze@pha.ge; A.kotorashvili@ncdc.ge;
   n.kotaria@ncdc.ge; guchmanidze@gmail.com; m.tediashvili@pha.ge;
   david.prangishvili@pasteur.fr
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NR 67
TC 11
Z9 12
PD NOV
PY 2020
VL 18
IS 11
AR 558
DI 10.3390/md18110558
UT WOS:000594009800001
DA 2025-07-30
ER

PT J
AU Liu, SG
   Luo, YR
   Huang, LF
AF Liu, SiGuang
   Luo, YuanRong
   Huang, LingFeng
TI Dynamics of size-fractionated bacterial communities during the coastal
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SO APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
DT Article
AB Everyday huge amount of treated municipal wastewater is discharged into the coastal seawater. However, microbial biomarkers for the municipal effluent instead of the fecal species from raw sewage have not been proposed. Meanwhile, bacterial taxa for degrading large amounts of input organics have not been fully understood. In this study, raw effluent and serial water samples were collected from the coastal dispersal of two sewage treatment plants in Xiamen, China. Free-living (FL) and particle-associated (PA) bacterial communities were analyzed via high-throughput sequencing of 16S rRNA gene and quantitative PCR to measure bacterial abundance. The PA bacterial communities in our samples exhibited higher cell abundance, alpha diversity, and population dynamics than the FL bacterial communities, which supports greater environmental significance of the PA bacterial communities. Two non-fecal but typical genera in activated sludge, Zoogloea and Dechloromonas, exhibited decreased but readily detectable abundance along the effluent dispersal distance. Furthermore, the dominating microbial species near the outfalls were related to well-known marine indigenous taxa, such as SAR11 clade, OM60 clade, low-GC Actinobacteria, and unclassified Flavobacteriales, as well as the less understood taxa like Pseudohongiella and Microbacteriaceae. It is interesting that these taxa exhibited two types of correlation patterns with COD concentration. Our study suggested Zoogloea as a potential indicator of municipal effluents and also proposed potential utilizers of residual effluent COD in marine environments.
C1 [Liu, SiGuang; Luo, YuanRong; Huang, LingFeng] Xiamen Univ, Fujian Prov Key Lab Coastal Ecol & Environm Studi, Xiamen 361005, Peoples R China.
   [Liu, SiGuang; Luo, YuanRong; Huang, LingFeng] Fujian Inst Oceanog, Xiamen 361005, Peoples R China.
   [Luo, YuanRong; Huang, LingFeng] Xiamen Univ, Key Lab, Coll Environm & Ecol, Minist Educ Coastal & Wetland Ecosyst, Xiamen 361005, Peoples R China.
   [Liu, SiGuang] Fujian Inst Oceanog, Lab Marine Chem, Xiamen 361000, Peoples R China.
RP Luo, YR (corresponding author), Xiamen Univ, Fujian Prov Key Lab Coastal Ecol & Environm Studi, Xiamen 361005, Peoples R China.; Luo, YR (corresponding author), Fujian Inst Oceanog, Xiamen 361005, Peoples R China.; Luo, YR (corresponding author), Xiamen Univ, Key Lab, Coll Environm & Ecol, Minist Educ Coastal & Wetland Ecosyst, Xiamen 361005, Peoples R China.
EM lyr@xmu.edu.cn
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TC 12
Z9 13
PD JUL
PY 2016
VL 100
IS 13
BP 5839
EP 5848
DI 10.1007/s00253-016-7408-9
UT WOS:000378725700015
DA 2025-07-30
ER

PT J
AU Howard, EC
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AF Howard, Erinn C.
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   Biers, Erin J.
   Moran, Mary Ann
TI Abundant and diverse bacteria involved in DMSP degradation in marine
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB An expanded analysis of oceanic metagenomic data indicates that the majority of prokaryotic cells in marine surface waters have the genetic capability to demethylate dimethylsulfoniopropionate (DMSP). The 1701 homologues of the DMSP demethylase gene, dmdA, identified in the (2007) Global Ocean Sampling (GOS) metagenome, are sufficient for 58% (+/- 9%) of sampled cells to participate in this critical step in the marine sulfur cycle. This remarkable frequency of DMSP-demethylating cells is in accordance with biogeochemical data indicating that marine phytoplankton direct up to 10% of fixed carbon to DMSP synthesis, and that most of this DMSP is subsequently degraded by bacteria via demethylation. The GOS metagenomic data also revealed a new cluster of dmdA sequences (designated Clade E) that implicates marine gammaproteobacteria in DMSP demethylation, along with previously recognized alphaproteobacterial groups Roseobacter and SAR11. Analyses of G+C content and gene order indicate that lateral gene transfer is likely responsible for the wide distribution of dmdA among diverse taxa, contributing to the homogenization of biogeochemical roles among heterotrophic marine bacterioplankton. Candidate genes for the competing bacterial degradation process that converts DMSP to the climate-active gas dimethylsulfide (DMS) (dddD and dddL) occur infrequently in the (2007) GOS metagenome, suggesting either that the key DMS-producing bacterial genes are yet to be identified or that DMS formation by free-living bacterioplankton is insignificant relative to their demethylation activity.
C1 [Sun, Shulei; Biers, Erin J.; Moran, Mary Ann] Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
   [Howard, Erinn C.] Univ Georgia, Dept Microbiol, Athens, GA 30602 USA.
RP Moran, MA (corresponding author), Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
EM mmoran@uga.edu
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TC 134
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BP 2397
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DA 2025-07-30
ER

PT J
AU Hahn, MW
AF Hahn, MW
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DT Article
AB More than 40 bacterial strains belonging to the cosmopolitan Polynucleobacter necessarius cluster (Betaproteobacteria) were isolated from a broad spectrum of freshwater habitats located in three climatic zones. Sequences affiliated with the freshwater P. necessarius cluster are among the most frequently detected in studies on bacterial diversity in freshwater ecosystems. Despite this frequent detection with culture-independent techniques and the cosmopolitan occurrence of members affiliated with this cluster, no isolates have been reported thus far. The isolated strains have been obtained from lakes, ponds, and rivers in central Europe, the People's Republic of China, and East Africa by use of the filtration-acclimatization method. The 16S rRNA gene sequences of the isolates are 98.8 to 100% identical to reference sequences obtained by various authors by use of culture-independent methods. The isolates, aerobic heterotrophs, grew on a wide range of standard complex media and formed visible colonies on agar plates. Thus, the previous lack of isolates cannot be explained by a lack of appropriate media. Most of the isolates possess, under a wide range of culture conditions, very small cells (<0.1 mum(3)), even when grown in medium containing high concentrations of organic substances. Thus, these strains are obligate ultramicrobacteria. The obtained strains have a C-shaped cell morphology which is very similar to that of recently isolated ultramicrobacterial Luna cluster strains (Actinobacteria) and the SAR11 cluster strains (Alphaproteobacteria).
C1 Austrian Acad Sci, Inst Limnol, A-5310 Mondsee, Austria.
RP Hahn, MW (corresponding author), Austrian Acad Sci, Inst Limnol, Mondseestr 9, A-5310 Mondsee, Austria.
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NR 33
TC 167
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PD SEP
PY 2003
VL 69
IS 9
BP 5248
EP 5254
DI 10.1128/AEM.69.9.5248-5254.2003
UT WOS:000185437000027
DA 2025-07-30
ER

PT J
AU Shi, RJ
   Li, JJ
   Qi, ZH
   Zhang, Z
   Liu, HX
   Huang, HH
AF Shi, Rongjun
   Li, Jiajun
   Qi, Zhanhui
   Zhang, Zhe
   Liu, Huaxue
   Huang, Honghui
TI Abundance and community composition of bacterioplankton in the Northern
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SO BIOLOGIA
DT Article
AB The abundance and composition of bacterioplankton of the Northern South China Sea (NSCS) were investigated using flow cytometry and high-throughput sequencing. The results showed that the absolute abundance of bacterioplankton retained high values in surface waters at both continental shelf and oceanic sites and Proteobacteria, Cyanobacteria, and Bacteroidetes represented the three typical dominant phyla in NSCS. The average bacterioplankton abundances at 5 m, 75 m, and 200 m were 9.55, 5.04, and 1.32 x 10(5) cells mL(-1), respectively, and there was a significantly positive correlation between bacterioplankton abundance and Chl a content (r = 0.84, p < 0.01). Drastic changes of the bacterioplankton community occurred in different water layers. Three operational taxonomic units (OTUs), whose distribution were significantly different between 5-m and 75-m water layers, all belonged to Flavobacteriales of the Bacteroidetes (p < 0.05). In addition, bacterioplankton community richness and diversity at the continental shelf (CS) was generally higher than at oceanic stations (SB and KI). Five OTUs, which favored the habitat of continental shelf, belonged to Alphaproteobacteria including the orders of the SAR11 cluster, Rhodospirillales, Rhodobacterales and other unclassified orders (p < 0.05). Two OTUs, which favored the habitat of oceanic stations, were assigned to the orders of Flavobacteriales and Alteromonadales. Furthermore, the abundances of two OTUs belonging to the Cyanobacteria phylum and Verrucomicrobiales order were significantly different between the sea basin (SB) and Kuroshio influenced area (KI) stations (p < 0.05).
C1 [Shi, Rongjun; Li, Jiajun; Qi, Zhanhui; Zhang, Zhe; Liu, Huaxue; Huang, Honghui] Chinese Acad Fishery Sci, South China Sea Fisheries Res Inst, Guangdong Prov Key Lab Fishery Ecol & Environm, 231 West Xingang Rd, Guangzhou 510300, Guangdong, Peoples R China.
   [Shi, Rongjun; Li, Jiajun; Qi, Zhanhui; Zhang, Zhe; Liu, Huaxue; Huang, Honghui] Chinese Acad Fishery Sci, South China Sea Fisheries Res Inst, Key Lab Open Sea Fishery Dev, Minist Agr, 231 West Xingang Rd, Guangzhou 510300, Guangdong, Peoples R China.
   [Shi, Rongjun] Chinese Acad Sci, South China Sea Inst Oceanol, Guangdong Prov Key Lab Appl Marine Biol, Guangzhou 510300, Guangdong, Peoples R China.
RP Huang, HH (corresponding author), Chinese Acad Fishery Sci, South China Sea Fisheries Res Inst, Guangdong Prov Key Lab Fishery Ecol & Environm, 231 West Xingang Rd, Guangzhou 510300, Guangdong, Peoples R China.; Huang, HH (corresponding author), Chinese Acad Fishery Sci, South China Sea Fisheries Res Inst, Key Lab Open Sea Fishery Dev, Minist Agr, 231 West Xingang Rd, Guangzhou 510300, Guangdong, Peoples R China.
EM shirongjun@scsfri.ac.cn; huanghh@scsfri.ac.cn
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TC 3
Z9 4
PD FEB
PY 2018
VL 73
IS 2
BP 197
EP 206
DI 10.2478/s11756-018-0023-8
UT WOS:000429144600011
DA 2025-07-30
ER

PT J
AU Giraud, C
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   Beauvais, M
   Mailliez, JR
   Ansquer, D
   Selmaoui-Folcher, N
   Pham, D
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   Boulo, V
AF Giraud, Carolane
   Callac, Nolwenn
   Beauvais, Maxime
   Mailliez, Jean-Rene
   Ansquer, Dominique
   Selmaoui-Folcher, Nazha
   Pham, Dominique
   Wabete, Nelly
   Boulo, Viviane
TI Potential lineage transmission within the active microbiota of the eggs
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SO PEERJ
DT Article
AB Background. Microbial communities associated with animals are known to be key elements in the development of their hosts. In marine environments, these communities are largely under the influence of the surrounding water. In aquaculture, understanding the interactions existing between the microbiotas of farmed species and their rearing environment could help establish precise bacterial management. Method. In light of these facts, we studied the active microbial communities associated with the eggs and the nauplii of the Pacific blue shrimp (Litopenaeus stylirostris) and their rearing water. All samples were collected in September 2018, November 2018 and February 2019. After RNA extractions, two distinct Illumina HiSeq sequencings were performed. Due to different sequencing depths and in order to compare samples, data were normalized using the Count Per Million method. Results. We found a core microbiota made of taxa related to Aestuariibacter, Al-teromonas, Vibrio, SAR11, HIMB11, AEGEAN 169 marine group and Candidatus En-dobugula associated with all the samples indicating that these bacterial communities could be transferred from the water to the animals. We also highlighted specific bacterial taxa in the eggs and the nauplii affiliated to Pseudomonas, Corynebacterium, Acinetobacter, Labrenzia, Rothia, Thalassolituus, Marinobacter, Aureispira, Oleiphilus, Profundimonas and Marinobacterium genera suggesting a possible prokaryotic vertical transmission from the breeders to their offspring. This study is the first to focus on the active microbiota associated with early developmental stages of a farmed shrimp species and could serve as a basis to comprehend the microbial interactions involved throughout the whole rearing process.
C1 [Giraud, Carolane; Callac, Nolwenn; Beauvais, Maxime; Mailliez, Jean-Rene; Ansquer, Dominique; Pham, Dominique; Wabete, Nelly; Boulo, Viviane] Univ La Reunion, Univ Nouvelle Caledonie, Ifremer, IRD,CNRS,UMR ENTROPIE 9220, Noumea, New Caledonia.
   [Giraud, Carolane; Selmaoui-Folcher, Nazha] Univ New Caledonia, Inst Sci Exactes & Appl ISEA, Noumea, New Caledonia.
   [Beauvais, Maxime] Sorbonne Univ, Lab Oceanog Microbienne, Observ Oceanol Banyuls Sur Mer, UMR 7261,CNRS, Banyuls Sur Mer, France.
   [Boulo, Viviane] Univ Perpignan, Univ Montpellier, IHPE, CNRS,Ifremer, Via Domitia, Montpellier, France.
RP Giraud, C; Callac, N (corresponding author), Univ La Reunion, Univ Nouvelle Caledonie, Ifremer, IRD,CNRS,UMR ENTROPIE 9220, Noumea, New Caledonia.; Giraud, C (corresponding author), Univ New Caledonia, Inst Sci Exactes & Appl ISEA, Noumea, New Caledonia.
EM cgiraud@ifremer.fr; ncallac@ifremer.fr
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NR 84
TC 12
Z9 12
PD NOV 15
PY 2021
VL 9
AR e12241
DI 10.7717/peerj.12241
UT WOS:000722308700003
DA 2025-07-30
ER

PT J
AU Biers, EJ
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AF Biers, Erin J.
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB The Sorcerer II Global Ocean Sampling (GOS) sequencing effort has vastly expanded the landscape of metagenomics, providing an opportunity to study the genetic potential of surface ocean water bacterioplankton on a global scale. Here we describe the habitat-based microbial diversity, both taxon evenness and taxon richness, for each GOS site and estimate genome characteristics of a typical free-living, surface ocean water bacterium. While Alphaproteobacteria and particularly SAR11 dominate the 0.1- to 0.8-mu m size fraction of surface ocean water bacteria (43% and 31%, respectively), the proportions of other taxa varied with ocean habitat type. Within each habitat type, lower-bound estimates of phylum richness ranged between 18 and 59 operational taxonomic units (OTUs). However, OTU richness was relatively low in the hypersaline lagoon community at every taxonomic level, and open-ocean communities had much more microdiversity than any other habitat. Based on the abundance of single-copy eubacterial genes from the same data set, we estimate that the genome of an average free-living surface ocean water bacterium (sized between 0.1 and 0.8 mu m) contains similar to 1,019 genes and 1.8 copies of the 16S rRNA gene, suggesting that these bacteria have relatively streamlined genomes in comparison to those of cultured bacteria and bacteria from other habitats (e. g., soil or acid mine drainage).
C1 [Biers, Erin J.; Sun, Shulei] Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
   [Howard, Erinn C.] Univ Georgia, Dept Microbiol, Athens, GA 30602 USA.
RP Biers, EJ (corresponding author), Univ S Carolina, Dept Environm Hlth Sci, Columbia, SC 29208 USA.
EM ejbiers@mailbox.sc.edu
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NR 58
TC 150
Z9 181
PD APR 1
PY 2009
VL 75
IS 7
BP 2221
EP 2229
DI 10.1128/AEM.02118-08
UT WOS:000264549400048
DA 2025-07-30
ER

PT J
AU Zhao, ZQ
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   Yan, T
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AF Zhao, Zhangqi
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TI Seasonal and Spatial Variability in the Bacterial Diversity in Haizhou
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SO DIVERSITY-BASEL
DT Article
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C1 [Zhao, Zhangqi; Zhang, Dechao] Chinese Acad Sci, Inst Oceanol, Lab Marine Organism Taxon & Phylogeny, Qingdao Key Lab Marine Biodivers & Conservat, Qingdao 266071, Peoples R China.
   [Zhao, Zhangqi; Zhang, Dechao] Univ Chinese Acad Sci, Beijing 100049, Peoples R China.
   [Zhan, Haoyu; Yan, Tian] Chinese Acad Sci, Inst Oceanol, CAS Key Lab Marine Ecol & Environm Sci, Qingdao 266071, Peoples R China.
RP Zhang, DC (corresponding author), Chinese Acad Sci, Inst Oceanol, Lab Marine Organism Taxon & Phylogeny, Qingdao Key Lab Marine Biodivers & Conservat, Qingdao 266071, Peoples R China.; Zhang, DC (corresponding author), Univ Chinese Acad Sci, Beijing 100049, Peoples R China.; Yan, T (corresponding author), Chinese Acad Sci, Inst Oceanol, CAS Key Lab Marine Ecol & Environm Sci, Qingdao 266071, Peoples R China.
EM zhaozhangqi@qdio.ac.cn; hyzhan@yeah.net; tianyan@qdio.ac.cn;
   zhangdechao@qdio.ac.cn
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NR 66
TC 0
Z9 2
PD OCT
PY 2023
VL 15
IS 10
AR 1051
DI 10.3390/d15101051
UT WOS:001094067800001
DA 2025-07-30
ER

PT J
AU Wang, M
   Sun, HF
   Ma, X
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AF Wang, Min
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   Ma, Xu
   Wang, Haibo
   Shi, Baoyou
TI Metabolic response of bacterial community to sodium hypochlorite and
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DT Article
AB The biofilm is important for the antibiotic resistance genes (ARGs) propagation in drinking water pipelines. This study investigated the influence of chlorine disinfection and ammonia nitrogen on the ARGs in pipelines biofilm using metagenomic and metabolomics analysis. Chlorine disinfection reduced the relative abundance of unclassified_c_Actinobacteria, Acidimicrobium, and Candidatus_Pelagibacter to 394-430 TPM, 114-123 TPM, and 4954 TPM, respectively. Correspondingly, the ARGs Saur_rpoC_DAP, macB, and mfd was reduced to 8-12 TPM, 81-92 TPM and 30-35 TPM, respectively. The results of metabolomics suggested that chlorine disinfection suppressed the pathways of ABC transporters, fatty acid biosynthesis, biosynthesis of unsaturated fatty acids, and biosynthesis of amino acids. These pathways were related to the cell membrane integrality and extracellular polymeric substances (EPS) secretion. Chlorine disinfection induced the decrease of EPS-related genes, resulting in the lower relative abundance of bacterial community and their antibiotic resistance. However, added approximately 0.5 mg/L NH3-N induced up-regulation of these metabolic pathways. In addition, NH3-N addition increased the relative abundance of enzymes related to inorganic and organic nitrogen metabolic pathway significantly, such as ammonia monooxygenase, glutamine synthetase, and glutamate synthase. Due to the EPS protection and nitrogen metabolism, the relative abundance of the main bacterial genera and the related ARGs increased to the level equal to that in pipelines biofilm with no disinfection. Therefore, NH3-N reduced the ARGs removal efficiency of chlorine disinfection. It is necessary to take measures to improve the removal rate of NH3-N and ARGs for preventing their risks in drinking water.
C1 [Wang, Min; Ma, Xu; Wang, Haibo; Shi, Baoyou] Chinese Acad Sci, Res Ctr Ecoenvironm Sci, Key Lab Drinking Water Sci & Technol, Beijing 100085, Peoples R China.
   [Sun, Huifang] Shanxi Univ, Inst Resources & Environm Engn, Taiyuan 030006, Shanxi, Peoples R China.
   [Shi, Baoyou] Univ Chinese Acad Sci, Beijing 100049, Peoples R China.
RP Wang, HB (corresponding author), Chinese Acad Sci, Res Ctr Ecoenvironm Sci, Key Lab Drinking Water Sci & Technol, Beijing 100085, Peoples R China.
EM hbwang@rcees.ac.cn
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NR 60
TC 8
Z9 9
PD MAR 15
PY 2024
VL 252
AR 121179
DI 10.1016/j.watres.2024.121179
EA FEB 2024
UT WOS:001178810800001
DA 2025-07-30
ER

PT J
AU Acinas, SG
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AF Acinas, SG
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DT Article
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C1 Univ Miguel Hernandez, Ctr Biol Mol & Celular, Unidad Microbiol, Alicante 03550, Spain.
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RP Rodríguez-Valera, F (corresponding author), Univ Miguel Hernandez, Ctr Biol Mol & Celular, Unidad Microbiol, Campus San Juan,Apartado 18, Alicante 03550, Spain.
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NR 44
TC 299
Z9 332
PD FEB
PY 1999
VL 65
IS 2
BP 514
EP 522
UT WOS:000078495200023
DA 2025-07-30
ER

PT J
AU Salcher, MM
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AF Salcher, Michaela M.
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TI In situ substrate preferences of abundant bacterioplankton
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DT Article
AB The substrate partitioning of sympatric populations of freshwater bacterioplankton was studied via microautoradiography and fluorescence in situ hybridization. Fourteen radiolabeled tracers were used to assess microbial acquisition spectra of low-molecular-weight (LMW) organic compounds. The most abundant group, ac1 Actinobacteria, were highly active in leucine, thymidine and glucose assimilation, whereas Alphaproteobacteria from the LD12 lineage (the freshwater sister clade of SAR11) only weakly incorporated these tracers, but exhibited a distinct preference for glutamine and glutamate. Different Bacteroidetes showed contrasting uptake patterns: Flavobacteriales did not incorporate significant amounts of any LMW compound, and Cyclobacteriaceae were clearly specialized on leucine, glucose and arginine. Betaproteobacteria represented the most active and versatile bacterioplankton fraction and >90% of them could be assigned to eight species-to genus-like populations with contrasting substrate specialization. Limnohabitans sp. were the most abundant and active Betaproteobacteria, incorporating almost all tracers. While three closely related betaproteobacterial populations substantially differed in their uptake spectra, two more distantly related lineages had very similar preferences, and one population did not incorporate any tracer. The dominant phototrophic microorganism, the filamentous cyanobacterium Planktothrix rubescens, assimilated several substrates, whereas other (pico)cyanobacteria had no heterotrophic activity. The variable extent of specialization by the studied bacterial taxa on subsets of LMW compounds contrasts theoretical considerations about non-selective microbial substrate assimilation at oligotrophic conditions. This physiological niche separation might be one explanation for the coexistence of freshwater bacterioplankton species in a seemingly uniform environment. The ISME Journal (2013) 7, 896-907; doi:10.1038/ismej.2012.162; published online 13 December 2012
C1 [Salcher, Michaela M.; Posch, Thomas; Pernthaler, Jakob] Univ Zurich, Inst Plant Biol, Limnol Stn, CH-8802 Kilchberg, Switzerland.
RP Salcher, MM (corresponding author), Univ Zurich, Inst Plant Biol, Limnol Stn, Seestr 187, CH-8802 Kilchberg, Switzerland.
EM msalcher@limnol.uzh.ch
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NR 70
TC 107
Z9 118
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PY 2013
VL 7
IS 5
BP 896
EP 907
DI 10.1038/ismej.2012.162
UT WOS:000317963300002
DA 2025-07-30
ER

PT J
AU Messer, LF
   Ostrowski, M
   Doblin, MA
   Petrou, K
   Baird, ME
   Ingleton, T
   Bissett, A
   Van de Kamp, J
   Nelson, T
   Paulsen, I
   Bodrossy, L
   Fuhrman, JA
   Seymour, JR
   Brown, MV
AF Messer, Lauren F.
   Ostrowski, Martin
   Doblin, Martina A.
   Petrou, Katherina
   Baird, Mark E.
   Ingleton, Timothy
   Bissett, Andrew
   Van de Kamp, Jodie
   Nelson, Tiffanie
   Paulsen, Ian
   Bodrossy, Levente
   Fuhrman, Jed A.
   Seymour, Justin R.
   Brown, Mark, V
TI Microbial tropicalization driven by a strengthening western ocean
   boundary current
SO GLOBAL CHANGE BIOLOGY
DT Article
AB Western boundary currents (WBCs) redistribute heat and oligotrophic seawater from the tropics to temperate latitudes, with several displaying substantial climate change-driven intensification over the last century. Strengthening WBCs have been implicated in the poleward range expansion of marine macroflora and fauna, however, the impacts on the structure and function of temperate microbial communities are largely unknown. Here we show that the major subtropical WBC of the South Pacific Ocean, the East Australian Current (EAC), transports microbial assemblages that maintain tropical and oligotrophic (k-strategist) signatures, to seasonally displace more copiotrophic (r-strategist) temperate microbial populations within temperate latitudes of the Tasman Sea. We identified specific characteristics of EAC microbial assemblages compared with non-EAC assemblages, including strain transitions within the SAR11 clade, enrichment ofProchlorococcus, predicted smaller genome sizes and shifts in the importance of several functional genes, including those associated with cyanobacterial photosynthesis, secondary metabolism and fatty acid and lipid transport. At a temperate time-series site in the Tasman Sea, we observed significant reductions in standing stocks of total carbon and chlorophylla, and a shift towards smaller phytoplankton and carnivorous copepods, associated with the seasonal impact of the EAC microbial assemblage. In light of the substantial shifts in microbial assemblage structure and function associated with the EAC, we conclude that climate-driven expansions of WBCs will expand the range of tropical oligotrophic microbes, and potentially profoundly impact the trophic status of temperate waters.
C1 [Messer, Lauren F.] Univ Queensland, Australian Ctr Ecogen, Sch Chem & Mol Biosci, Brisbane, Qld, Australia.
   [Ostrowski, Martin; Paulsen, Ian] Univ Technol Sydney, Climate Change Cluster, Sydney, NSW, Australia.
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   [Ingleton, Timothy] Off Environm & Heritage, Sydney, NSW, Australia.
   [Nelson, Tiffanie] Deakin Univ, Geelong Ctr Emerging Infect Dis, Melbourne, Vic, Australia.
   [Fuhrman, Jed A.] Univ Southern Calif, Los Angeles, CA 90007 USA.
   [Brown, Mark, V] Univ Newcastle Australia, Sch Environm & Life Sci, Callaghan, NSW, Australia.
   [Messer, Lauren F.] Queensland Univ Technol, Ctr Microbiome Res, Sch Biomed Sci, Woolloongabba, Qld, Australia.
RP Brown, MV (corresponding author), Univ Newcastle Australia, Sch Environm & Life Sci, Callaghan, NSW, Australia.
EM oceanmicrobes@gmail.com
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NR 114
TC 14
Z9 15
PD OCT
PY 2020
VL 26
IS 10
BP 5613
EP 5629
DI 10.1111/gcb.15257
EA JUL 2020
UT WOS:000552351100001
DA 2025-07-30
ER

PT J
AU Tsagaraki, TM
   Pree, B
   Leiknes, O
   Larsen, A
   Bratbak, G
   Ovreås, L
   Egge, JK
   Spanek, R
   Paulsen, ML
   Olsen, Y
   Vadstein, O
   Thingstad, TF
AF Tsagaraki, Tatiana M.
   Pree, Bernadette
   Leiknes, Oystein
   Larsen, Aud
   Bratbak, Gunnar
   Ovreas, Lise
   Egge, Jorun K.
   Spanek, Roman
   Paulsen, Maria L.
   Olsen, Yngvar
   Vadstein, Olav
   Thingstad, T. F.
TI Bacterial community composition responds to changes in copepod abundance
   and alters ecosystem function in an Arctic mesocosm study
SO ISME JOURNAL
DT Article
AB Combining a minimum food web model with Arctic microbial community dynamics, we have suggested that top-down control by copepods can affect the food web down to bacterial consumption of organic carbon. Pursuing this hypothesis further, we used the minimum model to design and analyse a mesocosm experiment, studying the effect of high (+Z) and low (-Z) copepod density on resource allocation, along an organic-C addition gradient. In the Arctic, both effects are plausible due to changes in advection patterns (affecting copepods) and meltwater inputs (affecting carbon). The model predicts a trophic cascade from copepods via ciliates to flagellates, which was confirmed experimentally. Auto-and heterotrophic flagellates affect bacterial growth rate and abundance via competition for mineral nutrients and predation, respectively. In +Z, the model predicts low bacterial abundance and activity, and little response to glucose; as opposed to clear glucose consumption effects in -Z. We observed a more resilient bacterial response to high copepods and demonstrate this was due to changes in bacterial community equitability. Species able to use glucose to improve their competitive and/or defensive properties, became predominant. The observed shift from a SAR11-to a Psychromonodaceae - dominated community suggests the latter was pivotal in this modification of ecosystem function. We argue that this group used glucose to improve its defensive or its competitive abilities (or both). Adding such flexibility in bacterial traits to the model, we show how it creates the observed resilience to top-down manipulations observed in our experiment.
C1 [Tsagaraki, Tatiana M.; Pree, Bernadette; Larsen, Aud; Bratbak, Gunnar; Ovreas, Lise; Egge, Jorun K.; Paulsen, Maria L.; Thingstad, T. F.] Univ Bergen, Dept Biol Sci, Bergen, Norway.
   [Leiknes, Oystein; Olsen, Yngvar] NTNU Norwegian Univ Sci & Technol, Dept Biol, Trondheim, Norway.
   [Larsen, Aud] Uni Res AS, Uni Res Environm, Bergen, Norway.
   [Spanek, Roman] Tech Univ Liberec, Inst Mechatron & Comp Engn, Liberec, Czech Republic.
   [Vadstein, Olav] NTNU Norwegian Univ Sci & Technol, Dept Biotechnol & Food Sci, Trondheim, Norway.
   [Ovreas, Lise] Univ Ctr Svalbard, Longyearbyen, Norway.
RP Tsagaraki, TM (corresponding author), Univ Bergen, Dept Biol Sci, Bergen, Norway.
EM tatiana.tsagaraki@uib.no
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NR 78
TC 19
Z9 21
PD NOV
PY 2018
VL 12
IS 11
BP 2694
EP 2705
DI 10.1038/s41396-018-0217-7
UT WOS:000447661300010
DA 2025-07-30
ER

PT J
AU Nogales, B
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   Bosch, R
AF Nogales, Balbina
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   Martin-Cardona, Celia
   Lalucat, Jorge
   Bosch, Rafael
TI Bacterial diversity, composition and dynamics in and around recreational
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB A comparative study on the composition of bacterial communities in a coastal area in the West Mediterranean receiving the impact of recreation-derived activities (from a marina and a beach) was performed by terminal-restriction fragment length polymorphism (T-RFLP) of 16S rDNA along spatial and temporal scales. Interpolation of concentration of hydrophobic compounds, chlorophyll and bacterial cells in seawater over the geography of the sampling area using geographic information systems techniques (GIS) allowed the delineation of two different habitats: bay and marina (with low and high levels of impact respectively), and a transition zone between them. Accordingly, the 16S rDNA T-RFLP profiles of bacterial communities in the area differed mainly spatially, with gradual changes in community composition and structure when approaching the beach and marina. Bacterial communities in impacted areas had higher diversity and equitability, as well as different composition. The main bacterial populations inferred in bay samples, which were members of the Alphaproteobacteria (mainly SAR11 and Roseobacter groups), were replaced by a different population of the Roseobacter clade, and members of the Gammaproteobacteria and Bacteroidetes in more impacted areas. There were also differences in the dynamics of bacterial communities. While temporal variations in bacterial communities in bay samples were lower and mainly determined by temperature, an important factor for the functioning of this ecosystem, variation in impacted areas was more irregular, not so much temperature-driven, and in the case of the transition zone (beach) reflected the use of the coast during warmer periods.
C1 Univ Illes Balears, Dept Biol, Grp Microbiol, Palma de Mallorca 07122, Spain.
RP Nogales, B (corresponding author), Univ Illes Balears, Dept Biol, Grp Microbiol, Palma de Mallorca 07122, Spain.
EM bnogales@uib.es
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NR 49
TC 49
Z9 58
PD AUG
PY 2007
VL 9
IS 8
BP 1913
EP 1929
DI 10.1111/j.1462-2920.2007.01308.x
UT WOS:000248451600005
DA 2025-07-30
ER

PT J
AU Wu, ZQ
   Guo, LY
   Wu, Y
   Yang, MY
   Du, S
   Shao, JB
   Zhang, ZF
   Zhao, YL
AF Wu, Zuqing
   Guo, Luyuan
   Wu, Ying
   Yang, Mingyu
   Du, Sen
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   Zhang, Zefeng
   Zhao, Yanlin
TI Novel phage infecting the Roseobacter CHUG lineage reveals a
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SO MSPHERE
DT Article
AB Bacteriophages play an essential role in shaping the diversity and metabolism of bacterial communities. Marine Roseobacter group is an abundant heterotrophic bacterial group that is involved in many major element cycles, especially carbon and sulfur. Members of the Roseobacter CHUG (Clade Hidden and Underappreciated Globally) lineage are globally distributed and are activated in pelagic marine environments. In this study, we isolated and characterized a phage, CRP-810, that infects the CHUG strain FZCC0198. The genome of CRP-810 was dissimilar to those of other known phages. Additionally, 251 uncultured viral genomes (UViGs) closely related to CRP-810 were obtained from the uncultivated marine viral contig databases. Comparative genomic and phylogenetic analyses revealed that CRP-810 and these related UViGs exhibited conserved genome synteny, representing a new phage family with at least eight subgroups. Most of the CRP-810-type phages contain an integrase gene, and CRP-810 can be integrated into the host genome. Further analysis revealed that three CRP-810-type members were prophages found in the genomes of marine SAR11, Poseidonocella, and Sphingomonadaceae. Finally, viromic read-mapping analysis showed that CRP-810-type phages were globally distributed and displayed distinct biogeographic patterns related to temperature and latitude. Many members with a lower G + C content were mainly distributed in the trade station, whereas members with a higher G + C content were mainly distributed in polar and westerlies station, indicating that the niche differentiation of phages was subject to host adaptation. Collectively, these findings identify a novel phage family and expand our understanding of phylogenetic diversity, evolution, and biogeography of marine phages.
C1 [Wu, Zuqing; Guo, Luyuan; Wu, Ying; Yang, Mingyu; Du, Sen; Shao, Jiabing; Zhang, Zefeng; Zhao, Yanlin] Fujian Agr & Forestry Univ, Coll JunCao Sci & Ecol, Fujian Prov Key Lab Agroecol Proc & Safety Monitor, Fuzhou, Peoples R China.
RP Zhang, ZF; Zhao, YL (corresponding author), Fujian Agr & Forestry Univ, Coll JunCao Sci & Ecol, Fujian Prov Key Lab Agroecol Proc & Safety Monitor, Fuzhou, Peoples R China.
EM zfengbio@126.com; yanlinzhao@fafu.edu.cn
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VL 9
IS 7
DI 10.1128/msphere.00458-24
EA JUN 2024
UT WOS:001255329700005
DA 2025-07-30
ER

PT J
AU Vila-Costa, M
   Pinhassi, J
   Alonso, C
   Pernthaler, J
   Simó, R
AF Vila-Costa, Maria
   Pinhassi, Jarone
   Alonso, Cecilia
   Pernthaler, Jakob
   Simo, Rafel
TI An annual cycle of dimethylsulfoniopropionate-sulfur and leucine
   assimilating bacterioplankton in the coastal NW Mediterranean
SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB The contribution of major phylogenetic groups to heterotrophic bacteria assimilating sulfur from dissolved dimethylsulfoniopropionate (DMSP) and assimilating leucine was analysed in surface seawaters from Blanes Bay (NW Mediterranean) over an annual study between March 2003 and April 2004. The percentage of bacteria assimilating DMSP-S showed a strong seasonal pattern, with a steady increase from winter (8 +/- 5%) to summer (23 +/- 3%). The same seasonal pattern was observed for the rate of DMSP-S assimilation. The annual average percentage of DMSP-S-assimilating bacteria (16 +/- 8%) was lower than the corresponding percentage of leucine-assimilating cells (35 +/- 16%), suggesting that not all bacteria synthesizing protein incorporated DMSP-S. Smaller differences between both percentages were recorded in summer. Members of the Alphaproteobacteria (Roseobacter and SAR11) and Gammaproteobacteria groups accounted for most of bacterial DMSP-S-assimilating cells over the year. All major bacterial groups showed an increase of the percentage of cells assimilating DMSP-S during summer, and contributed to the increase of the DMSP-S assimilation rate in this period. In these primarily P-limited waters, enrichment with P + DMSP resulted in a stimulation of bacterial heterotrophic production comparable to, or higher than, that with P + glucose in summer, while during the rest of the year P + glucose induced a stronger response. This suggested that DMSP was more important a S and C source for bacteria in the warm stratified season. Overall, our results suggest that DMSP-S assimilation is controlled by the contribution of DMSP to S (and C) sources rather than by the phylogenetic composition of the bacterioplankton.
C1 CSIC, Inst Ciencies Mar, E-08003 Barcelona, Catalonia, Spain.
   Univ Kalmar, Dept Biol & Environm Sci, SE-39182 Kalmar, Sweden.
   Max Planck Inst Marine Microbiol, D-28359 Bremen, Germany.
RP Simó, R (corresponding author), CSIC, Inst Ciencies Mar, Pg Maritim Barceloneta 37-49, E-08003 Barcelona, Catalonia, Spain.
EM rsimo@icm.csic.es
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NR 62
TC 47
Z9 51
PD OCT
PY 2007
VL 9
IS 10
BP 2451
EP 2463
DI 10.1111/j.1462-2920.2007.01363.x
UT WOS:000249222600008
DA 2025-07-30
ER

PT J
AU Siallagan, ZL
   Fadli, M
   de Fretes, CE
   Opier, RDA
   Susanto, RD
   Wei, ZX
   Suhardi, VSH
   Nugrahapraja, H
   Radjasa, OK
   Dwivany, FM
AF Siallagan, Zen Ladestam
   Fadli, Muhammad
   de Fretes, Charlie Ester
   Opier, Rafidha Dh Ahmad
   Susanto, R. Dwi
   Wei, Zexun
   Suhardi, V. Sri Harjati
   Nugrahapraja, Husna
   Radjasa, Ocky Karna
   Dwivany, Fenny M.
TI Metagenomic analysis of deep-sea bacterial communities in the Makassar
   and Lombok Straits
SO SCIENTIFIC REPORTS
DT Article
AB The extreme conditions of the deep-sea environment, including limited light, low oxygen levels, high pressure, and nutrient scarcity, create a natural habitat for deep-sea bacteria. These remarkable microorganisms have developed unique strategies to survive and adapt to their surroundings. However, research on the diversity of deep-sea bacteria, both culture-dependent and culture-independent, in Indonesian waters remains insufficient. This study focused on exploring the biodiversity of deep-sea bacteria, specifically in the Makassar and Lombok Strait, the main Indonesian throughflow pathway characterized by relatively fertile water, which serves as an important deep-sea region. High-throughput DNA sequencing of full-length 16S rRNA was employed to construct a genomic database. The results of the bioinformatic analysis revealed that two stations, 48 and 50 (Makassar Strait), exhibited a more similar community structure of deep-sea bacteria than did station 33 (Lombok Strait). Among the predominant phyla found at a depth of 1000 m, the top ten were Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Planctomycetes, Acidobacteria, Nitrospinae, Verrucomicrobia, Candidatus Melainabacteria, and Cyanobacteria. Furthermore, the genera Colwellia, Moritella, Candidatus Pelagibacter, Alteromonas, and Psychrobacter consistently appeared at all three stations, albeit with varying relative abundance values. These bacterial genera share common characteristics, such as psychrophilic, halophilic, and piezophilic tendencies, and are commonly found in deep-sea ecosystem. The environmental conditions at a depth of 1000 m were relatively stable, with an average pressure 10 MPa, temperature 4.68 degrees C, salinity 34.58 PSU, pH 8.06, chlorophyll-a 0.29 mu g/L, nitrate 3.19 mu mol/L, phosphate 6.32 mu mol/L and dissolved oxygen (DO) 2.90 mg/L. The bacterial community structures at the three sampling stations located at the same depth (1000 m) exhibited similarities, as indicated by the closely aligned similarity index values.
C1 [Siallagan, Zen Ladestam; Nugrahapraja, Husna; Dwivany, Fenny M.] Inst Teknol Bandung, Sch Life Sci & Technol, Doctoral Program Biol, Jl Ganesha 10, Bandung 40132, Indonesia.
   [Siallagan, Zen Ladestam; Fadli, Muhammad; de Fretes, Charlie Ester; Opier, Rafidha Dh Ahmad; Radjasa, Ocky Karna] Natl Res & Innovat Agcy, Res Ctr Deep Sea, Jakarta 14430, Indonesia.
   [Suhardi, V. Sri Harjati; Nugrahapraja, Husna; Radjasa, Ocky Karna; Dwivany, Fenny M.] Inst Teknol Bandung, Ctr Biosci & Biotechnol, Jl Ganesha 10, Bandung 40132, Indonesia.
   [Susanto, R. Dwi] Univ Maryland, Dept Atmospher & Ocean Sci, College Pk, MD 20742 USA.
   [Wei, Zexun] Minist Nat Resources, Inst Oceanog 1, Qingdao, Peoples R China.
   [Wei, Zexun] Minist Nat Resources, Key Lab Marine Sci & Numer Modeling, Qingdao, Peoples R China.
   [Fadli, Muhammad] Univ Pattimura, Ctr Collaborat Res Aquat Ecosyst Eastern Indonesia, Ambon 97233, Indonesia.
RP Siallagan, ZL; Dwivany, FM (corresponding author), Inst Teknol Bandung, Sch Life Sci & Technol, Doctoral Program Biol, Jl Ganesha 10, Bandung 40132, Indonesia.; Siallagan, ZL; Radjasa, OK (corresponding author), Natl Res & Innovat Agcy, Res Ctr Deep Sea, Jakarta 14430, Indonesia.; Radjasa, OK; Dwivany, FM (corresponding author), Inst Teknol Bandung, Ctr Biosci & Biotechnol, Jl Ganesha 10, Bandung 40132, Indonesia.
EM zenl001@brin.go.id; ocky001@brin.go.id; fennym@itb.ac.id
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NR 48
TC 2
Z9 2
PD OCT 26
PY 2024
VL 14
IS 1
AR 25472
DI 10.1038/s41598-024-74118-9
UT WOS:001343699800101
DA 2025-07-30
ER

PT J
AU Shilova, IN
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   Wawrik, B
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   Zehr, JP
AF Shilova, Irina N.
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   Tripp, H. James
   Turk-Kubo, Kendra
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   Hollibaugh, James T.
   Millard, Andy
   Ostrowski, Martin
   Scanlan, David J.
   Paerl, Ryan W.
   Stuart, Rhona
   Zehr, Jonathan P.
TI A microarray for assessing transcription from pelagic marine microbial
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SO ISME JOURNAL
DT Article
AB Metagenomic approaches have revealed unprecedented genetic diversity within microbial communities across vast expanses of the world's oceans. Linking this genetic diversity with key metabolic and cellular activities of microbial assemblages is a fundamental challenge. Here we report on a collaborative effort to design MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories), a high-density oligonucleotide microarray that targets functional genes of diverse taxa in pelagic and coastal marine microbial communities. MicroTOOLs integrates nucleotide sequence information from disparate data types: genomes, PCR-amplicons, metagenomes, and metatranscriptomes. It targets 19 400 unique sequences over 145 different genes that are relevant to stress responses and microbial metabolism across the three domains of life and viruses. MicroTOOLs was used in a proof-of-concept experiment that compared the functional responses of microbial communities following Fe and P enrichments of surface water samples from the North Pacific Subtropical Gyre. We detected transcription of 68% of the gene targets across major taxonomic groups, and the pattern of transcription indicated relief from Fe limitation and transition to N limitation in some taxa. Prochlorococcus (eHLI), Synechococcus (sub-cluster 5.3) and Alphaproteobacteria SAR11 clade (HIMB59) showed the strongest responses to the Fe enrichment. In addition, members of uncharacterized lineages also responded. The MicroTOOLs microarray provides a robust tool for comprehensive characterization of major functional groups of microbes in the open ocean, and the design can be easily amended for specific environments and research questions.
C1 [Shilova, Irina N.; Robidart, Julie C.; Turk-Kubo, Kendra; Zehr, Jonathan P.] Univ Calif Santa Cruz, Dept Ocean Sci, Santa Cruz, CA 95064 USA.
   [Tripp, H. James] DOE Joint Genome Inst, Walnut Creek, CA USA.
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   [Millard, Andy; Ostrowski, Martin; Scanlan, David J.] Univ Warwick, Dept Marine Microbiol, Coventry CV4 7AL, W Midlands, England.
   [Paerl, Ryan W.] Univ Calif San Diego, Marine Biol Res Div, San Diego, CA 92103 USA.
   [Stuart, Rhona] Lawrence Livermore Natl Lab, Livermore, CA USA.
RP Shilova, IN (corresponding author), Univ Calif Santa Cruz, Dept Ocean Sci, 1156 High St, Santa Cruz, CA 95064 USA.
EM iirina@ucsc.edu
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NR 116
TC 27
Z9 29
PD JUL
PY 2014
VL 8
IS 7
BP 1476
EP 1491
DI 10.1038/ismej.2014.1
UT WOS:000338213900012
DA 2025-07-30
ER

PT J
AU Shi, ZY
   Ma, LL
   Wang, YY
   Liu, J
AF Shi, Ziyue
   Ma, Lili
   Wang, Yingying
   Liu, Jie
TI Abundant and rare bacteria in anthropogenic estuary: Community
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SO ECOLOGICAL INDICATORS
DT Article
AB In estuary, bacteria are critically vital to ecosystem function and sustainability. However, the effect of geographic distance and its related factors (i.e., salinity and nutrients) on bacterial diversity, co-occurrence, as well as community assembly on the abundant and rare species scale remained to be discussed. In this study, we deci-phered the bacterial dynamics and ecological processes in the anthropogenic estuary of the Haihe River, in China. The results revealed that salinity was the major abiotic factor to shape bacterial community composition, diversity, and network complexity, and the role of biotic cytometric characteristics was considerable as well. Furthermore, the salinity gradient tended to select bacteria with low nucleic acid (LNA) such as Candidatus Pelagibacter and Longivirga, and abundant bacteria were more sensitive to the salinity gradient in comparison with rare ones. The similar keystone number and network topology values indicated that both abundant and rare bacteria played important ecological functions in degrading pollutants, developing co-occurrence networks, and maintaining compositional stability and complexity. In addition, drift and dispersion limitation dominated the ecological processes in the community assembly, suggesting that although salinity caused the migration of species, its ecological role was still weaker than that of stochastic processes. Further, niche differentiation contributed to different stochastic components of abundant and rare species. In high-salinity areas, rare bacteria with small population sizes but high diversity were enriched, which made the bacterial community more affected by ecological drift. Our study illustrated the different responses of abundant and rare bacteria to salinity and the assembly process of bacterial communities in anthropogenic estuary, deepening the understanding of their ecological processes in the estuarine ecosystem.
C1 [Shi, Ziyue; Liu, Jie] Lanzhou Univ, Coll Pastoral Agr Sci & Technol, Collaborat Innovat Ctr Western Ecol Safety, Ctr Grassland Microbiome,State Key Lab Herbage Imp, Lanzhou 730000, Peoples R China.
   [Wang, Yingying; Liu, Jie] Nankai Univ, Coll Environm Sci & Engn, Key Lab Pollut Proc & Environm Criteria, Minist Educ, Tianjin 300071, Peoples R China.
   [Ma, Lili] Southwest Petr Univ, Coll Chem & Chem Engn, Chengdu 610500, Sichuan, Peoples R China.
   [Wang, Yingying] Nankai Univ, Coll Environm Sci & Engn, 94 Weijin Rd, Tianjin 300071, Peoples R China.
   [Liu, Jie] 222 TianShui Rd South, Lanzhou, Gansu, Peoples R China.
RP Wang, YY (corresponding author), Nankai Univ, Coll Environm Sci & Engn, 94 Weijin Rd, Tianjin 300071, Peoples R China.; Liu, J (corresponding author), 222 TianShui Rd South, Lanzhou, Gansu, Peoples R China.
EM wangyy@nankai.edu.cn; jieliu@lzu.edu.cn
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ER

PT J
AU Reza, MS
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   Gojobori, Takashi
   Watabe, Shugo
TI Basin-scale seasonal changes in marine free-living bacterioplankton
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SO GENE
DT Article
AB The Ofunato Bay in the northeastern Pacific Ocean area of Japan possesses the highest biodiversity of marine organisms in the world and has attracted much attention due to its economic and environmental importance. We report here a shotgun metagenomic analysis of the year-round variation in free-living bacterioplankton collected across the entire length of the bay. Phylogenetic differences among spring, summer, autumn and winter bacterioplankton suggested that members of Proteobacteria tended to decrease at high water temperatures and increase at low temperatures. It was revealed that Candidatus Pelagibacter varied seasonally, reaching as much as 60% of all sequences at the genus level in the surface waters during winter. This increase was more evident in the deeper waters, where they reached up to 75%. The relative abundance of Planktomarina also rose during winter and fell during summer. A significant component of the winter bacterioplankton community was Archaea (mainly represented by Nitrosopumilus), as their relative abundance was very low during spring and summer but high during winter. In contrast, Actinobacteria and Cyanobacteria appeared to be higher in abundance during high-temperature periods. It was also revealed that Bacteroidetes constituted a significant component of the summer bacterioplankton community, being the second largest bacterial phylum detected in the Ofunato Bay. Its members, notably Polaribacter and Flavobacterium, were found to be high in abundance during spring and summer, particularly in the surface waters. Principal component analysis and hierarchal clustering analyses showed that the bacterial communities in the Ofunato Bay changed seasonally, likely caused by the levels of organic matter, which would be deeply mixed with surface runoff in the winter.
C1 [Reza, Md Shaheed; Kobiyama, Atsushi; Yamada, Yuichiro; Ikeda, Yuri; Ikeda, Daisuke; Mizusawa, Nanami; Ikeo, Kazuho; Sato, Shigeru; Ogata, Takehiko; Jimbo, Mitsuru; Kudo, Toshiaki; Watabe, Shugo] Kitasato Univ, Sch Marine Biosci, Minami Ku, Sagamihara, Kanagawa 2520373, Japan.
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RP Gojobori, T (corresponding author), King Abdullah Univ Sci & Technol, Computat Biosci Res Ctr, Thuwal 239556900, Saudi Arabia.; Gojobori, T (corresponding author), King Abdullah Univ Sci & Technol, Biol & Environm Sci & Engn, Thuwal 239556900, Saudi Arabia.; Watabe, S (corresponding author), Kitasato Univ, Dept Marine Biochem, Sch Marine Biosci, Minami Ku, Sagamihara, Kanagawa 2520373, Japan.
EM takashi.gojobori@kaust.edu.sa; swatabe@kitasato-u.ac.jp
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NR 42
TC 9
Z9 9
PD JUL 30
PY 2018
VL 665
BP 185
EP 191
DI 10.1016/j.gene.2018.04.074
UT WOS:000435621900023
DA 2025-07-30
ER

PT J
AU Delmont, TO
   Hammar, KM
   Ducklow, HW
   Yager, PL
   Post, AF
AF Delmont, Tom O.
   Hammar, Katherine M.
   Ducklow, Hugh W.
   Yager, Patricia L.
   Post, Anton F.
TI Phaeocystis antarctica blooms strongly influence bacterial community
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SO FRONTIERS IN MICROBIOLOGY
DT Article
AB Rising temperatures and changing winds drive the expansion of the highly productive polynyas (open water areas surrounded by sea ice) abutting the Antarctic continent. Phytoplankton blooms in polynyas are often dominated by the haptophyte Phaeocystis antarctica, and they generate the organic carbon that enters the resident microbial food web. Yet, little is known about how Phaeocystis blooms shape bacterial community structures and carbon fluxes in these systems. We identified the bacterial communities that accompanied a Phaeocystis bloom in the Amundsen Sea polynya during the austral summers of 20072008 and 20102011. These communities are distinct from those determined for the Antarctic Circumpolar Current (ACC) and off the Palmer Peninsula. Diversity patterns for most microbial taxa in the Amundsen Sea depended on location (e.g., waters abutting the pack ice near the shelf break and at the edge of the Dotson glacier) and depth, reflecting different niche adaptations within the confines of this isolated ecosystem. Inside the polynya, P. antarctica coexisted with the bacterial taxa Polaribacter sensu lato, a cryptic Oceanospirillum, SAR92 and Pelagibacter. These taxa were dominated by a single oligotype (genotypes partitioned by Shannon entropy analysis) and together contributed up to 73% of the bacterial community. Size fractionation of the bacterial community [<3 mu m (free-living bacteria) vs. >3 mu m (particle-associated bacteria)] identified several taxa (especially SAR92) that were preferentially associated with Phaeocystis colonies, indicative of a distinct role in Phaeocystis bloom ecology. In contrast, particle-associated bacteria at 250 m depth were enriched in Colwellia and members of the Cryomorphaceae suggesting that they play important roles in the decay of Phaeocystis blooms.
C1 [Delmont, Tom O.; Hammar, Katherine M.; Post, Anton F.] Josephine Bay Paul Ctr Comparat Mol Biol & Evalut, Marine Biol Lab, Woods Hole, MA 02543 USA.
   [Ducklow, Hugh W.] Columbia Univ, Lamont Doherty Earth Observ, Palisades, NY USA.
   [Yager, Patricia L.] Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
RP Post, AF (corresponding author), Josephine Bay Paul Ctr Comparat Mol Biol & Evalut, Marine Biol Lab, 7 MBL St, Woods Hole, MA 02543 USA.
EM apost@mbl.edu
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NR 72
TC 88
Z9 95
PD DEC 19
PY 2014
VL 5
AR 646
DI 10.3389/fmicb.2014.00646
UT WOS:000348523100001
DA 2025-07-30
ER

PT J
AU Chen, XW
   Ma, RJ
   Yang, YL
   Jiao, NZ
   Zhang, R
AF Chen, Xiaowei
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   Jiao, Nianzhi
   Zhang, Rui
TI Viral Regulation on Bacterial Community Impacted by Lysis-Lysogeny
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SO FRONTIERS IN MICROBIOLOGY
DT Article
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C1 [Chen, Xiaowei; Ma, Ruijie; Yang, Yunlan; Jiao, Nianzhi; Zhang, Rui] Xiamen Univ, Inst Marine Microbes & Ecospheres, State Key Lab Marine Environm Sci, Coll Ocean & Earth Sci, Xiamen, Fujian, Peoples R China.
   [Yang, Yunlan] Xiamen Univ, Coll Environm & Ecol, Xiamen, Fujian, Peoples R China.
RP Jiao, NZ; Zhang, R (corresponding author), Xiamen Univ, Inst Marine Microbes & Ecospheres, State Key Lab Marine Environm Sci, Coll Ocean & Earth Sci, Xiamen, Fujian, Peoples R China.
EM jiao@xmu.edu.cn; ruizhang@xmu.edu.cn
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NR 74
TC 28
Z9 31
PD JUL 31
PY 2019
VL 10
AR 1763
DI 10.3389/fmicb.2019.01763
UT WOS:000478001300001
DA 2025-07-30
ER

PT J
AU Neuenschwander, SM
   Salcher, MM
   Pernthaler, J
AF Neuenschwander, Stefan M.
   Salcher, Michaele M.
   Pernthaler, Jakob
TI Fluorescence in situ hybridization and sequential catalyzed
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SO FRONTIERS IN MICROBIOLOGY
DT Article
AB Flow cytometric sorting is a powerful tool to physically separate cells within mixed microbial communities. If combined with phylogenetic staining (fluorescence in situ hybridization, FISH) it allows to specifically sort defined genotypic microbial populations from complex natural samples. However, the targeted enrichment of freshwater ultramicrobacteria, such as members of the LD12 clade of Alphaproteobacteria (SAR11-IIIb), is still challenging. Current FISH protocols, even in combination with signal amplification by catalyzed reporter deposition (CARD), are not sufficiently sensitive for the distinction of these bacteria from background noise by flow cytometry, presumably due to their low ribosome content and small cell sizes. We, therefore, modified a CARD based flow sorting protocol with the aim of increasing its sensitivity to a level sufficient for ultramicrobacteria. This was achieved by a second signal amplification step mediated by horseradish peroxidase labeled antibodies targeted to the fluorophores that were previously deposited by CARD-FISH staining. The protocol was tested on samples from an oligo-mesotrophic lake. Ultramicrobacteria affiliated with LD12 Alphaproteobacteria could be successfully sorted to high purity by flow cytometry. The ratios of median fluorescence signal to background ranged around 20, and hybridization rates determined by flow cytometry were comparable to those obtained by fluorescence microscopy. Potential downstream applications of our modified cell staining approach range from the analysis of microdiversity within 16S rRNA-defined populations to that of functional properties, such as the taxon-specific incorporation rates of organic substrates.
C1 [Neuenschwander, Stefan M.; Salcher, Michaele M.; Pernthaler, Jakob] Univ Zurich, Limnol Stn, Inst Plant Biol, CH-8802 Kilchberg, Switzerland.
RP Pernthaler, J (corresponding author), Univ Zurich, Limnol Stn, Inst Plant Biol, Seestr 187, CH-8802 Kilchberg, Switzerland.
EM pernthaler@limnol.uzh.ch
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NR 37
TC 18
Z9 19
PD MAR 31
PY 2015
VL 6
AR 247
DI 10.3389/fmicb.2015.00247
UT WOS:000352537700001
DA 2025-07-30
ER

PT J
AU Arandia-Gorostidi, N
   Krabberod, AK
   Logares, R
   Deutschmann, IM
   Scharek, R
   Moran, XAG
   Gonzalez, F
   Alonso-Saez, L
AF Arandia-Gorostidi, Nestor
   Krabberod, Anders K.
   Logares, Ramiro
   Deutschmann, Ina Maria
   Scharek, Renate
   Moran, Xose Anxelu G.
   Gonzalez, Felipe
   Alonso-Saez, Laura
TI Novel Interactions Between Phytoplankton and Bacteria Shape Microbial
   Seasonal Dynamics in Coastal Ocean Waters
SO FRONTIERS IN MARINE SCIENCE
DT Article
AB Trophic interactions between marine phytoplankton and heterotrophic bacteria are at the base of the biogeochemical carbon cycling in the ocean. However, the specific interactions taking place between phytoplankton and bacterial taxa remain largely unexplored, particularly out of phytoplankton blooming events. Here, we applied network analysis to a 3.5-year time-series dataset to assess the specific associations between different phytoplankton and bacterial taxa along the seasonal scale, distinguishing between free-living and particle-attached bacteria. Using a newly developed network post-analysis technique we removed bacteria-phytoplankton correlations that were primarily driven by environmental parameters, to detect potential biotic interactions. Our results indicate that phytoplankton dynamics may be a strong driver of the inter-annual variability in bacterial community composition. We found the highest abundance of specific bacteria-phytoplankton associations in the particle-attached fraction, indicating a tighter bacteria-phytoplankton association than in the free-living fraction. In the particle-associated fraction we unveiled novel potential associations such as the one between Planctomycetes taxa and the diatom Leptocylindrus spp. Consistent correlations were also found between free-living bacterial taxa and different diatoms, including novel associations such as those between SAR11 with Naviculales diatom order, and between Actinobacteria and Cylindrotheca spp. We also confirmed previously known associations between Rhodobacteraceae and Thalassiosira spp. Our results expand our view on bacteria-phytoplankton associations, suggesting that taxa-specific interactions may largely impact the seasonal dynamics of heterotrophic bacterial communities.
C1 [Arandia-Gorostidi, Nestor; Scharek, Renate; Moran, Xose Anxelu G.; Gonzalez, Felipe; Alonso-Saez, Laura] CSIC, Ctr Oceanog Gijon Xixon, Inst Espanol Oceanog IEO, Gijon, Spain.
   [Arandia-Gorostidi, Nestor] Stanford Univ, Dept Earth Syst Sci, Stanford, CA 94305 USA.
   [Krabberod, Anders K.] Univ Oslo, Dept Biosci, Sect Genet & Evolutionary Biol EVOGENE, Oslo, Norway.
   [Logares, Ramiro; Deutschmann, Ina Maria] CSIC, Inst Ciencies Mar ICM, Barcelona, Spain.
   [Moran, Xose Anxelu G.] King Abdullah Univ Sci & Technol, Red Sea Res Ctr, Biol & Environm Sci & Engn Div, Thuwal, Saudi Arabia.
   [Alonso-Saez, Laura] Basque Res & Technol Alliance BRTA, AZTI, Marine Res, Sukarrieta, Spain.
RP Arandia-Gorostidi, N; Alonso-Saez, L (corresponding author), CSIC, Ctr Oceanog Gijon Xixon, Inst Espanol Oceanog IEO, Gijon, Spain.; Arandia-Gorostidi, N (corresponding author), Stanford Univ, Dept Earth Syst Sci, Stanford, CA 94305 USA.; Alonso-Saez, L (corresponding author), Basque Res & Technol Alliance BRTA, AZTI, Marine Res, Sukarrieta, Spain.
EM n.arandia86@gmail.com; lalonso@azti.es
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NR 85
TC 18
Z9 18
PD JUL 22
PY 2022
VL 9
AR 901201
DI 10.3389/fmars.2022.901201
UT WOS:000837257800001
DA 2025-07-30
ER

PT J
AU Alonso-Sáez, L
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AF Alonso-Saez, Laura
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TI Effect of natural sunlight on bacterial activity and differential
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB We studied the effects of natural sunlight on heterotrophic marine bacterioplankton in short-term experiments. We used a single-cell level approach involving How cytometry combined with physiological probes and microautoradiography to determine sunlight effects on the activity and integrity of the cells. After 4 h of sunlight exposure, most bacterial cells maintained membrane integrity and viability as assessed by the simultaneous staining with propidium iodide and SYBR green I. In contrast, a significant inhibition of heterotrophic bacterial activity was detected, measured by 5-cyano-2,3 ditolyl tetrazolium chloride reduction and leucine incorporation. We applied microautoradiography combined with catalyzed reporter deposition-fluorescence in situ hybridization to test the sensitivity of the different bacterial groups naturally occurring in the Northwestern Mediterranean to sunlight. Members of the Gammaproteobacteria and Bacteroidetes groups appeared to be highly resistant to solar radiation, with small changes in activity after exposure. On the contrary, Alphaproteobacteria bacteria were more sensitive to radiation as measured by the cell-specific incorporation of labeled amino acids, leucine, and ATE Within Alphaproteobacteria, bacteria belonging to the Roseobacter group showed higher resistance than members of the SAR11 cluster. The activity of Roseobacter was stimulated by exposure to photosynthetic available radiation compared to the dark treatment. Our results suggest that UV radiation can significantly affect the in situ single-cell activity of bacterioplankton and that naturally dominating phylogenetic bacterial groups have different sensitivity to natural levels of incident solar radiation.
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RP Gasol, JM (corresponding author), CSIC, CMIMA, Inst Ciencias Mar, Dept Biol Marina & Oceanog, Paseo Nacl S-N, E-08003 Barcelona, Catalunya, Spain.
EM pepgasol@icm.csic.es
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NR 56
TC 127
Z9 140
PD SEP
PY 2006
VL 72
IS 9
BP 5806
EP 5813
DI 10.1128/AEM.00597-06
UT WOS:000240474000017
DA 2025-07-30
ER

PT J
AU Zhuang, GC
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   Montgomery, A
   Montoya, JP
   Joye, SB
AF Zhuang, Guang-Chao
   Pena-Montenegro, Tito D.
   Montgomery, Andrew
   Montoya, Joseph P.
   Joye, Samantha B.
TI Significance of Acetate as a Microbial Carbon and Energy Source in the
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SO GLOBAL BIOGEOCHEMICAL CYCLES
DT Article
AB Acetate is a key intermediate of organic matter mineralization, but its metabolism remains largely unconstrained in the pelagic ocean. We conducted an integrated biogeochemical study to investigate microbial acetate cycling in the northern Gulf of Mexico with the goal of elucidating the importance of acetate as a carbon and energy source. Acetate was used primarily as an energy source, as evidenced by observed oxidation rates (rate constant k: 0.06-0.22 day(-1)) that varied between 42% and 96% of total biological acetate uptake (i.e., assimilation + oxidation; k: 0.06-0.34 day(-1)). The assimilation of acetate into biomass (k: 0.01-0.20 day(-1)) illustrated the potential significance of acetate as a biomass carbon source, particularly in nutrient-rich coastal waters. No relationship between acetate assimilation or oxidation and environmental factors, such as chlorophyll and nutrients, was observed. However, elevated acetate uptake in reduced oxygen waters characterized by particulate organic carbon mineralization suggests that acetate metabolism may be a good proxy for particulate organic carbon breakdown. Molecular genetic analysis revealed that SAR11 Alphaproteobacteria were the most abundant heterotrophic bacteria and suggest that they may utilize acetate. At some sites, acetate carbon may have accounted for up to 50.4% of the bacterial carbon production. These results suggest that acetate may serve as an important carbon and energy source for heterotrophic bacteria thus revealing a potentially significant role of acetate for dissolved organic carbon cycling in the ocean.
C1 [Zhuang, Guang-Chao; Pena-Montenegro, Tito D.; Montgomery, Andrew; Joye, Samantha B.] Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
   [Pena-Montenegro, Tito D.] Univ Georgia, Inst Bioinformat, Athens, GA 30602 USA.
   [Montoya, Joseph P.] Georgia Inst Technol, Sch Biol Sci, Atlanta, GA 30332 USA.
RP Joye, SB (corresponding author), Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
EM mjoye@uga.edu
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NR 54
TC 31
Z9 40
PD FEB
PY 2019
VL 33
IS 2
BP 223
EP 235
DI 10.1029/2018GB006129
UT WOS:000460499000007
DA 2025-07-30
ER

PT J
AU West, NJ
   Obernosterer, I
   Zemb, O
   Lebaron, P
AF West, Nyree J.
   Obernosterer, Ingrid
   Zemb, Olivier
   Lebaron, Philippe
TI Major differences of bacterial diversity and activity inside and outside
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB One of the first comparisons of a natural iron fertilized bloom with a high-nutrient low-chlorophyll (HNLC) site was undertaken during the Kerguelen ocean and plateau compared study (KEOPS) cruise. To understand better the bacteria-phytoplankton relationship in the context of natural iron fertilization, bacterial diversity and activity was investigated in the bloom and in the adjacent HNLC region by 16S rDNA clone libraries and by single strand conformation polymorphism (SSCP) analysis. Both libraries were dominated by Alphaproteobacteria, Gammaproteobacteria and the Cytophaga-Flavobacteria-Bacteroides group. Cluster analysis at 99% sequence similarity yielded several microdiverse clusters and revealed striking differences between the two libraries. In the bloom, the dominant operational taxonomic units (OTUs) were the Roseobacter NAC11-7 cluster, SAR92 and a Cytophaga-Flavobacteria-Bacteroides cluster related to the agg58 group, whereas in the HNLC region, SAR11, Roseobacter RCA and Polaribacter dominated. SSCP analysis of 16S rDNA and 16S rRNA revealed contrasting dynamics of three different Roseobacter OTUs. Roseobacter NAC11-7 and NAC11-6 had higher relative abundances and activities in the bloom compared with the HNLC site and NAC11-6 was only detected at the decline of the bloom concomitant with a shift in phytoplankton composi tion. In contrast, Roseobacter RCA was relatively abundant and active both inside and outside of the bloom. These results suggest that the different OTUs within the Roseobacter group represent functional groups that each play an important role in the cycling of carbon.
C1 [West, Nyree J.; Obernosterer, Ingrid; Zemb, Olivier; Lebaron, Philippe] Univ Paris 06, Lab Arago, F-66650 Banyuls Sur Mer, France.
   [West, Nyree J.; Obernosterer, Ingrid; Zemb, Olivier; Lebaron, Philippe] CNRS, UMR7621, Lab Oceanog Biol Banyuls, F-66650 Banyuls Sur Mer, France.
RP West, NJ (corresponding author), Univ Paris 06, Lab Arago, Ave Fontaule,BP44, F-66650 Banyuls Sur Mer, France.
EM nyree.west@obs-banyuls.fr
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NR 72
TC 139
Z9 148
PD MAR
PY 2008
VL 10
IS 3
BP 738
EP 756
DI 10.1111/j.1462-2920.2007.01497.x
UT WOS:000252712300018
DA 2025-07-30
ER

PT J
AU Kirchman, DL
   Dittel, AI
   Malmstrom, RR
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AF Kirchman, DL
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TI Biogeography of major bacterial groups in the Delaware Estuary
SO LIMNOLOGY AND OCEANOGRAPHY
DT Article
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C1 Univ Delaware, Coll Marine Studies, Lewes, DE 19958 USA.
RP Kirchman, DL (corresponding author), Univ Delaware, Coll Marine Studies, Lewes, DE 19958 USA.
EM kirchman@cms.udel.edu
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NR 42
TC 185
Z9 211
PD SEP
PY 2005
VL 50
IS 5
BP 1697
EP 1706
DI 10.4319/lo.2005.50.5.1697
UT WOS:000231932800034
DA 2025-07-30
ER

PT J
AU Garcia, SL
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   Stepanauskas, R
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   Malmstrom, RR
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AF Garcia, Sarahi L.
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   Woyke, Tanja
   Tringe, Susannah G.
   Andersson, Siv G. E.
   Bertilsson, Stefan
   Malmstrom, Rex R.
   McMahon, Katherine D.
TI Contrasting patterns of genome-level diversity across distinct
   co-occurring bacterial populations
SO ISME JOURNAL
DT Article
AB To understand the forces driving differentiation and diversification in wild bacterial populations, we must be able to delineate and track ecologically relevant units through space and time. Mapping metagenomic sequences to reference genomes derived from the same environment can reveal genetic heterogeneity within populations, and in some cases, be used to identify boundaries between genetically similar, but ecologically distinct, populations. Here we examine population-level heterogeneity within abundant and ubiquitous freshwater bacterial groups such as the acI Actinobacteria and LD12 Alphaproteobacteria (the freshwater sister clade to the marine SAR11) using 33 single-cell genomes and a 5-year metagenomic time series. The single-cell genomes grouped into 15 monophyletic clusters (termed "tribes") that share at least 97.9% 16S rRNA identity. Distinct populations were identified within most tribes based on the patterns of metagenomic read recruitments to single-cell genomes representing these tribes. Genetically distinct populations within tribes of the acI Actinobacterial lineage living in the same lake had different seasonal abundance patterns, suggesting these populations were also ecologically distinct. In contrast, sympatric LD12 populations were less genetically differentiated. This suggests that within one lake, some freshwater lineages harbor genetically discrete (but still closely related) and ecologically distinct populations, while other lineages are composed of less differentiated populations with overlapping niches. Our results point at an interplay of evolutionary and ecological forces acting on these communities that can be observed in real time.
C1 [Garcia, Sarahi L.; Stevens, Sarah L. R.; McMahon, Katherine D.] Univ Wisconsin Madison, Dept Bacteriol, Madison, WI 53706 USA.
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   [Crary, Benjamin; McMahon, Katherine D.] Univ Wisconsin Madison, Dept Civil & Environm Engn, Madison, WI 53706 USA.
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   [Stepanauskas, Ramunas] Bigelow Lab Ocean Sci, East Boothbay, ME USA.
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   [Andersson, Siv G. E.] Uppsala Univ, Dept Mol Evolut, Uppsala, Sweden.
RP McMahon, KD (corresponding author), Univ Wisconsin Madison, Dept Bacteriol, Madison, WI 53706 USA.; McMahon, KD (corresponding author), Univ Wisconsin Madison, Dept Civil & Environm Engn, Madison, WI 53706 USA.
EM Trina.mcmahon@wisc.edu
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NR 50
TC 47
Z9 54
PD MAR
PY 2018
VL 12
IS 3
BP 742
EP 755
DI 10.1038/s41396-017-0001-0
UT WOS:000427226100010
DA 2025-07-30
ER

PT J
AU Sheik, CS
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   Breier, JA
   Sylvan, JB
   Edwards, KJ
   Dick, GJ
AF Sheik, Cody S.
   Anantharaman, Karthik
   Breier, John A.
   Sylvan, Jason B.
   Edwards, Katrina J.
   Dick, Gregory J.
TI Spatially resolved sampling reveals dynamic microbial communities in
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SO ISME JOURNAL
DT Article
AB Within hydrothermal plumes, chemosynthetic processes and microbe-mineral interactions drive primary productivity in deep-ocean food webs and may influence transport of elements such as iron. However, the source of microorganisms in plumes and the factors governing how these communities assemble are poorly understood, in part due to lack of data from early stages of plume formation. In this study, we examined microbial community composition of rising hydrothermal plumes from five vent fields along the Eastern Lau Spreading Center. Seafloor and plume microbial communities were significantly dissimilar and shared few phylotypes. Plume communities were highly similar to each other with significant differences in community membership only between Kilo Moana and Mariner, two vents that are separated by extremes in depth, latitude and geochemistry. Systematic sampling of waters surrounding the vents revealed that species richness and phylogenetic diversity was typically highest near the vent orifice, implying mixing of microbial communities from the surrounding habitats. Above-plume background communities were primarily dominated by SAR11, SAR324 and MG-I Archaea, while SUP05, Sulfurovum, Sulfurimonas, SAR324 and Alteromonas were abundant in plume and near-bottom background communities. These results show that the ubiquitous water-column microorganisms populate plume communities, and that the composition of background seawater exerts primary influence on plume community composition, with secondary influence from geochemical and/or physical properties of vents. Many of these pervasive deep-ocean organisms are capable of lithotrophy, suggesting that they are poised to use inorganic electron donors encountered in hydrothermal plumes.
C1 [Sheik, Cody S.; Anantharaman, Karthik; Dick, Gregory J.] Dept Earth & Environm Sci, Ann Arbor, MI USA.
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RP Dick, GJ (corresponding author), Univ Michigan, Dept Earth & Environm Sci, 2534 CC Little Bldg,1100 North Univ Ave, Ann Arbor, MI 48109 USA.
EM gdick@umich.edu
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NR 79
TC 54
Z9 58
PD JUN
PY 2015
VL 9
IS 6
BP 1434
EP 1445
DI 10.1038/ismej.2014.228
UT WOS:000354786700014
DA 2025-07-30
ER

PT J
AU Sun, H
   Zheng, HA
   Jiang, YW
   Liang, JC
   Liao, BL
   Wang, RX
   Li, AH
   Xiao, BH
AF Sun, Hao
   Zheng, Huina
   Jiang, Yiwei
   Liang, Jinchang
   Liao, Baolin
   Wang, Ruixuan
   Li, Aihua
   Xiao, Baohua
TI Elevated temperature alters bacterial community composition and
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SO ECOLOGICAL INDICATORS
DT Article
AB The global phenomenon of coral bleaching under thermal stress has been recognized as the primary driver underlying coral reef degradation. The coral bacterial community plays an important role in the stability of coral reef ecosystem. Dimethylsulfoniopropionate (DMSP) and its associated metabolites are essential for the establishment of coral bacterial communities and provide key benefits for overall coral health and bleaching recovery. Substantial research to date has focused on the bacterial community composition, metabolism and functional properties within the coral holobiont, but less attention has been paid to the role of bacteria in seawater surrounding corals under thermal stress. Here, we investigated bacterial community composition, biological functions and DMSP metabolism changes of the seawater surrounding corals under thermal stress. We found that microbial community in seawater surrounding corals changed under thermal stress, and corals bleached eventually. The abundance of Rhodobacterales, Flavobacteriales and Rhizobiales increased while Chitinophagales and SAR11 decreased as temperature elevated. Correspondingly, stress tolerant, biofilm forming and mobile elements increased, resulting in large part from changes in Rhodobacterales and Phaeodactylibacter abundance. DMSP producing and catabolic levels in seawater surrounding corals were enhanced under thermal stress with higher dsyB (1.46-fold), dddP (2.43-fold) and dmdA (1.47-fold) detected. This study reveals the biological functions and metabolisms of bacteria in the water surrounding corals, providing valuable insight on how these communities and functions change in coral reef ecosystem under thermal stress.
C1 [Sun, Hao; Jiang, Yiwei; Liao, Baolin; Xiao, Baohua] Guangdong Ocean Univ, Shenzhen Inst, Binhai 2 Rd, Shenzhen 518120, Peoples R China.
   [Xiao, Baohua] Guangdong Ocean Univ, Coll Fisheries, Zhanjiang 524088, Peoples R China.
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   [Zheng, Huina] Guangdong Ocean Univ, Coll Food Sci & Technol, Zhanjiang 524088, Peoples R China.
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   [Wang, Ruixuan] Hanshan Normal Univ, Sch Life Sci & Food Engn, Chaozhou 521041, Peoples R China.
   [Li, Aihua; Xiao, Baohua] Guangdong Ocean Univ, China B Xiao Inst Hydrobiol, Shenzhen Inst, Binhai 2 Rd, Shenzhen 518120, Peoples R China.
RP Xiao, BH (corresponding author), Guangdong Ocean Univ, Shenzhen Inst, Binhai 2 Rd, Shenzhen 518120, Peoples R China.; Xiao, BH (corresponding author), Guangdong Ocean Univ, Coll Fisheries, Zhanjiang 524088, Peoples R China.; Li, AH (corresponding author), Chinese Acad Sci, Inst Hydrobiol, Wuhan 430072, Peoples R China.; Li, AH; Xiao, BH (corresponding author), Guangdong Ocean Univ, China B Xiao Inst Hydrobiol, Shenzhen Inst, Binhai 2 Rd, Shenzhen 518120, Peoples R China.
EM liaihua@ihb.ac.cn; xiaobh@gdou.edu.cn
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NR 90
TC 10
Z9 11
PD JUN
PY 2022
VL 139
AR 108886
DI 10.1016/j.ecolind.2022.108886
EA APR 2022
UT WOS:000795544700002
DA 2025-07-30
ER

PT J
AU Kong, LF
   Yan, KQ
   Xie, ZX
   He, YB
   Lin, L
   Xu, HK
   Liu, SQ
   Wang, DZ
AF Kong, Ling-Fen
   Yan, Ke-Qiang
   Xie, Zhang-Xian
   He, Yan-Bin
   Lin, Lin
   Xu, Hong-Kai
   Liu, Si-Qi
   Wang, Da-Zhi
TI Metaproteomics Reveals Similar Vertical Distribution of Microbial
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SO FRONTIERS IN MICROBIOLOGY
DT Article
AB Solubilized particulate organic matter (POM) rather than dissolved organic matter (DOM) has been speculated to be the major carbon and energy sources for heterotrophic prokaryotes in the ocean. However, the direct evidence is still lack. Here we characterized microbial transport proteins of POM collected from both euphotic (75 m, deep chlorophyll maximum DCM, and 100 m) and upper-twilight (200 m and 500 m) zones in three contrasting environments in the northwest Pacific Ocean using a metaproteomic approach. The proportion of transport proteins was relatively high at the bottom of the euphotic zone (200 m), indicating that this layer was the most active area of microbe-driven POM remineralization in the water column. In the upper-twilight zone, the predicted substrates of the identified transporters indicated that amino acids, carbohydrates, taurine, inorganic nutrients, urea, biopolymers, and cobalamin were essential substrates for the microbial community. SAR11, Rhodobacterales, Alteromonadales, and Enterobacteriales were the key contributors with the highest expression of transporters. Interestingly, both the taxonomy and function of the microbial communities varied among water layers and sites with different environments; however, the distribution of transporter types and their relevant organic substrates were similar among samples, suggesting that microbial communities took up similar compounds and were functionally redundant in organic matter utilization throughout the water column. The similar vertical distribution of transport proteins from the euphotic zone to the upper twilight zone among the contrasting environments indicated that solubilized POM rather than DOM was the preferable carbon and energy sources for the microbial communities.
C1 [Kong, Ling-Fen; Xie, Zhang-Xian; Lin, Lin; Wang, Da-Zhi] Xiamen Univ, Coll Environm & Ecol, State Key Lab Marine Environm Sci, Xiamen, Peoples R China.
   [Kong, Ling-Fen; Xie, Zhang-Xian; Wang, Da-Zhi] Southern Marine Sci & Engn Guangdong Lab Zhuhai, Zhuhai, Peoples R China.
   [Yan, Ke-Qiang; He, Yan-Bin; Xu, Hong-Kai; Liu, Si-Qi] BGI Shenzhen, Shenzhen, Peoples R China.
RP Wang, DZ (corresponding author), Xiamen Univ, Coll Environm & Ecol, State Key Lab Marine Environm Sci, Xiamen, Peoples R China.; Wang, DZ (corresponding author), Southern Marine Sci & Engn Guangdong Lab Zhuhai, Zhuhai, Peoples R China.
EM dzwang@xmu.edu.cn
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NR 50
TC 5
Z9 5
PD MAR 25
PY 2021
VL 12
AR 629802
DI 10.3389/fmicb.2021.629802
UT WOS:000638272700001
DA 2025-07-30
ER

PT J
AU Clingenpeel, S
   Macur, RE
   Kan, JJ
   Inskeep, WP
   Lovalvo, D
   Varley, J
   Mathur, E
   Nealson, K
   Gorby, Y
   Jiang, HC
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AF Clingenpeel, Scott
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   Varley, John
   Mathur, Eric
   Nealson, Kenneth
   Gorby, Yuri
   Jiang, Hongchen
   LaFracois, Toben
   McDermott, Timothy R.
TI Yellowstone Lake: high-energy geochemistry and rich bacterial diversity
SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Yellowstone Lake is central to the balanced functioning of the Yellowstone ecosystem, yet little is known about the microbial component of its food chain. A remotely operated vehicle provided video documentation (http://www.tbi.montana.edu/media/videos/) and allowed sampling of dilute surface zone waters and enriched lake floor hydrothermal vent fluids. Vent emissions contained substantial H2S, CH4, CO2 and H-2, although CH4 and H-2 levels were also significant throughout the lake. Pyrosequencing and near full-length sequencing of Bacteria 16S rRNA gene diversity associated with two vents and two surface water environments demonstrated that this lake contains significant bacterial diversity. Biomass was size-fractionated by sequentially filtering through 20-mu m-, 3.0-mu m-, 0.8-mu m- and 0.1-mu m-pore-size filters, with the > 0.1 to < 0.8 mu m size class being the focus of this study. Major phyla included Acidobacteria, Actinobacteria, Bacteroidetes, alpha- and beta-Proteobacteria and Cyanobacteria, with 21 other phyla represented at varying levels. Surface waters were dominated by two phylotypes: the Actinobacteria freshwater acI group and an alpha-Proteobacteria clade tightly linked with freshwater SAR11-like organisms. We also obtained evidence of novel thermophiles and recovered Prochlorococcus phylotypes (97-100% identity) in one near surface photic zone region of the lake. The combined geochemical and microbial analyses suggest that the foundation of this lake's food chain is not simple. Phototrophy presumably is an important driver of primary productivity in photic zone waters; however, chemosynthetic hydrogenotrophy and methanotrophy are likely important components of the lake's food chain.
C1 [Clingenpeel, Scott; Macur, Richard E.; Inskeep, William P.; McDermott, Timothy R.] Montana State Univ, Thermal Biol Inst, Bozeman, MT 59717 USA.
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RP McDermott, TR (corresponding author), Montana State Univ, Thermal Biol Inst, Bozeman, MT 59717 USA.
EM timmcder@montana.edu
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NR 76
TC 40
Z9 44
PD AUG
PY 2011
VL 13
IS 8
BP 2172
EP 2185
DI 10.1111/j.1462-2920.2011.02466.x
UT WOS:000294075600019
DA 2025-07-30
ER

PT J
AU Wang, K
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   Zhang, DM
AF Wang, Kai
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   Hou, Dandi
   Wang, Yanting
   Dong, Pengsheng
   Zhang, Demin
TI Archaeal biogeography and interactions with microbial community across
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DT Article
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C1 [Wang, Kai; Hu, Hanjing; Yan, Huizhen; Hou, Dandi; Wang, Yanting; Dong, Pengsheng; Zhang, Demin] Ningbo Univ, Sch Marine Sci, Ningbo, Zhejiang, Peoples R China.
   [Wang, Kai; Hu, Hanjing; Zhang, Demin] Collaborat Innovat Ctr Zhejiang Marine High Effic, Ningbo, Zhejiang, Peoples R China.
RP Wang, K (corresponding author), Ningbo Univ, Sch Marine Sci, Ningbo, Zhejiang, Peoples R China.; Zhang, DM (corresponding author), Collaborat Innovat Ctr Zhejiang Marine High Effic, Ningbo, Zhejiang, Peoples R China.
EM wangkai@nbu.edu.cn; zhangdemin@nbu.edu.cn
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NR 95
TC 29
Z9 34
PD JUN
PY 2019
VL 28
IS 12
BP 3101
EP 3118
DI 10.1111/mec.15105
UT WOS:000475983100012
DA 2025-07-30
ER

PT J
AU Vergin, KL
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DT Article
AB The Bermuda Atlantic Time-series Study site provided an opportunity to study bacterial community assembly processes at 2 different depths, the surface and 200 m, in the upper mesopelagic, just below the euphotic zone. Over 100 monthly bacterioplankton DNA samples, from each depth, were analyzed using 16S rRNA gene sequences parsed with the custom software package PhyloAssigner. Co-occurrence networks, filtered for potential autocorrelation artifacts, were constructed for each depth. Network characteristics for the 2 depths were remarkably similar, and network parameters, such as connectance, were in the same range as previously published for ecological networks. Spectral clustering applied to similarity matrices based on exact connections revealed clusters of nodal taxonomic units (NTUs) that peaked at similar times, supporting deterministic, niche-based assembly. An algorithm that used hierarchical Dirichlet processes (HDPs) to model neutral communities based on learned parameters indicated that community assembly processes fit niche-based models at the metacommunity level for both depths. However, HDP analyses restricted to SAR11, SAR86, or SAR202 NTUs supported the neutral assembly hypothesis, suggesting that neutral process models may apply within some phylogenetic domains. To understand whether phylogenetically related taxa can substitute for one another in networks, we created a new metric, phylogenetically weighted connectivity, which considered the similarity of connections among near phylogenetic neighbors. This analysis suggested that phylogenetically similar lineages share similar network connections. Overall, our findings show that niche-based community assembly models are the best fit at both depths but that the neutral model may apply at some phylogenetic scales.
C1 [Vergin, Kevin L.; Jhirad, Nicholas; Giovannoni, Stephen J.] Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
   [Dodge, Jonathon] Oregon State Univ, Dept Comp Sci, Corvallis, OR 97331 USA.
   [Carlson, Craig A.] Univ Calif Santa Barbara, Dept Ecol Evolut & Marine Biol, Santa Barbara, CA 93106 USA.
RP Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
EM steve.giovannoni@oregonstate.edu
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PY 2017
VL 79
IS 2
BP 165
EP 175
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UT WOS:000402654000007
DA 2025-07-30
ER

PT J
AU Dupont, CL
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TI Functional Tradeoffs Underpin Salinity-Driven Divergence in Microbial
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SO PLOS ONE
DT Article
AB Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity.
C1 [Dupont, Chris L.; McCrow, John P.; Allen, Lisa Zeigler; Allen, Andrew E.; Friedman, Robert; Venter, J. Craig] J Craig Venter Inst, Microbial & Environm Genom, San Diego, CA USA.
   [Larsson, John; Ininbergs, Karolina; Asplund-Samuelsson, Johannes; Celepli, Narin; Ekman, Martin; Brindefalk, Bjorn; Bergman, Birgitta] Stockholm Univ, Dept Ecol Environm & Plant Sci, S-10691 Stockholm, Sweden.
   [Yooseph, Shibu; Richter, Alexander R.; Tenney, Aaron; Badger, Jonathan H.] J Craig Venter Inst, Informat Grp, San Diego, CA USA.
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   [Nylander, Johan A. A.] Swedish Museum Nat Hist, Dept Biodivers Informat, S-10405 Stockholm, Sweden.
   [Norrby, Erling] Royal Swedish Acad Sci, Ctr Hist Sci, Stockholm, Sweden.
   [Pinhassi, Jarone] Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, Kalmar, Sweden.
RP Dupont, CL (corresponding author), J Craig Venter Inst, Microbial & Environm Genom, San Diego, CA USA.
EM cdupont@jcvi.org; john.larsson@su.se
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NR 45
TC 157
Z9 171
PD FEB 27
PY 2014
VL 9
IS 2
AR e89549
DI 10.1371/journal.pone.0089549
UT WOS:000332390800027
DA 2025-07-30
ER

PT J
AU Wu, LY
   Piedade, GJ
   Moore, RM
   Harrison, AO
   Martins, AM
   Bidle, KD
   Polson, SW
   Sakowski, EG
   Nissimov, JI
   Dums, JT
   Ferrell, BD
   Wommack, KE
AF Wu, Ling-Yi
   Piedade, Goncalo J.
   Moore, Ryan M.
   Harrison, Amelia O.
   Martins, Ana M.
   Bidle, Kay D.
   Polson, Shawn W.
   Sakowski, Eric G.
   Nissimov, Jozef I.
   Dums, Jacob T.
   Ferrell, Barbra D.
   Wommack, K. Eric
TI Ubiquitous, B12-dependent virioplankton utilizing
   ribonucleotide-triphosphate reductase demonstrate interseasonal dynamics
   and associate with a diverse range of bacterial hosts in the pelagic
   ocean
SO ISME COMMUNICATIONS
DT Article
AB Through infection and lysis of their coexisting bacterial hosts, viruses impact the biogeochemical cycles sustaining globally significant pelagic oceanic ecosystems. Currently, little is known of the ecological interactions between lytic viruses and their bacterial hosts underlying these biogeochemical impacts at ecosystem scales. This study focused on populations of lytic viruses carrying the B-12-dependent Class II monomeric ribonucleotide reductase (RNR) gene, ribonucleotide-triphosphate reductase (Class II RTPR), documenting seasonal changes in pelagic virioplankton and bacterioplankton using amplicon sequences of Class II RTPR and the 16S rRNA gene, respectively. Amplicon sequence libraries were analyzed using compositional data analysis tools that account for the compositional nature of these data. Both virio- and bacterioplankton communities responded to environmental changes typically seen across seasonal cycles as well as shorter term upwelling-downwelling events. Defining Class II RTPR-carrying viral populations according to major phylogenetic clades proved a more robust means of exploring virioplankton ecology than operational taxonomic units defined by percent sequence homology. Virioplankton Class II RTPR populations showed positive associations with a broad phylogenetic diversity of bacterioplankton including dominant taxa within pelagic oceanic ecosystems such as Prochlorococcus and SAR11. Temporal changes in Class II RTPR virioplankton, occurring as both free viruses and within infected cells, indicated possible viral-host pairs undergoing sustained infection and lysis cycles throughout the seasonal study. Phylogenetic relationships inferred from Class II RTPR sequences mirrored ecological patterns in virio- and bacterioplankton populations demonstrating possible genome to phenome associations for an essential viral replication gene.
C1 [Wu, Ling-Yi] Univ Utrecht, Theoret Biol & Bioinformat, Sci Life 4, Padualaan 8, NL-3584 CH Utrecht, Netherlands.
   [Piedade, Goncalo J.] NIOZ Royal Netherlands Inst Sea Res, Dept Marine Microbiol & Biogeochem, NL-1797 SZ Thorntje, Netherlands.
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   [Moore, Ryan M.; Harrison, Amelia O.; Polson, Shawn W.; Dums, Jacob T.; Ferrell, Barbra D.; Wommack, K. Eric] Univ Delaware, Delaware Biotechnol Inst, 590 Ave 1743, Newark, DE 19713 USA.
   [Bidle, Kay D.] Rutgers State Univ, Dept Marine & Coastal Sci, 71 Dudley Rd, New Brunswick, NJ 08901 USA.
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   [Dums, Jacob T.] North Carolina State Univ, Biotechnol Program, 2800 Faucette Dr, Raleigh, NC 27695 USA.
RP Wommack, KE (corresponding author), Univ Delaware, Delaware Biotechnol Inst, 590 Ave 1743, Newark, DE 19713 USA.
EM wommack@udel.edu
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NR 113
TC 1
Z9 1
PD OCT 3
PY 2023
VL 3
IS 1
AR 108
DI 10.1038/s43705-023-00306-9
UT WOS:001083649900001
DA 2025-07-30
ER

PT J
AU Zhao, WB
   Chen, LR
   Huang, XY
   Liu, JW
   Niu, WT
   Zhang, XH
   Thompson, F
   Xiao, JG
   Wang, XL
AF Zhao, Wenbin
   Chen, Leiran
   Huang, Xiaoyun
   Liu, Jiwen
   Niu, Wentao
   Zhang, Xiao-Hua
   Thompson, Fabiano
   Xiao, Jiaguang
   Wang, Xiaolei
TI Distinct diversity, assembly, and co-occurrence patterns of the
   prokaryotic microbiome in coral ecosystems of the South China Sea
SO ECOLOGICAL INDICATORS
DT Article
AB Coral reefs are among the most energetic marine ecosystems, taking a place in ecological balance. Microbes participate in the energy exchange in coral ecosystems, which may affect coral resistance and resilience. However, there is still a lack of understanding regarding the microbial structure between corals and seawater. In this study, microbial structure and interactions in coral and seawater were studied using quantitative PCR and high- throughput sequencing. We found that the abundance and diversity of microbes in corals were higher than those in seawater. Corals, as nonfluidic ecosystems, limited the dispersal of microbes, causing broader stochasticity in the ecological shaping process, whereas ecological drift and homogeneous selection were the most important assembly mechanisms in seawater. The microbial niche width was larger in the coral group than in the seawater group, indicating strong adaptability. A group of microbes (e.g., Caldilineaceae, , Burkholderiaceae, , and Nitrosopumilaceae) ) may become microbial indicators which differentiate seawater samples (e.g., SAR11 and SAR86 clades, Cryomorphaceae), ), which may be due to separated habitats and nutrition. Coral microbes may participate in nitrogen-metabolism to maintain a nitrogen limited microenvironment. Nodes linked in the coral co- occurrence network showed coexisting interactions and higher complexity based on the comparison of topological values. Collectively, significant differences in microbial fractions were demonstrated observed in terms of diversity, composition, co-occurrence patterns, assembly processes and predicted functions between coral and seawater samples, showing potential microbial interactions and providing in-depth insights into the meta- community diversity in coral reef ecosystems.
C1 [Zhao, Wenbin; Chen, Leiran; Huang, Xiaoyun; Liu, Jiwen; Zhang, Xiao-Hua; Wang, Xiaolei] Ocean Univ China, Coll Marine Life Sci & Frontiers Sci, Ctr Deep Ocean Multispheres & Earth Syst, Qingdao 266003, Peoples R China.
   [Niu, Wentao; Xiao, Jiaguang] Minist Nat Resources, Inst Oceanog 3, Lab Marine Biodivers Res, 178 Daxue Rd, Xiamen 361005, Peoples R China.
   [Zhao, Wenbin; Chen, Leiran; Huang, Xiaoyun; Liu, Jiwen; Zhang, Xiao-Hua; Wang, Xiaolei] Ocean Univ China, Inst Evolut & Marine Biodivers, Qingdao 266100, Peoples R China.
   [Niu, Wentao; Xiao, Jiaguang] Nansha Isl Coral Reef Ecosyst Natl Observat & Res, Guangzhou 510000, Peoples R China.
   [Zhao, Wenbin] Chinese Acad Sci, Qingdao Inst Bioenergy & Bioproc Technol, Qingdao, Peoples R China.
   [Thompson, Fabiano] Fed Univ Rio de Janeiro UFRJ, Inst Biol, Rio De Janeiro, Brazil.
   [Thompson, Fabiano] Fed Univ Rio de Janeiro UFRJ, COPPE, Rio De Janeiro, Brazil.
RP Wang, XL (corresponding author), Ocean Univ China, Coll Marine Life Sci & Frontiers Sci, Ctr Deep Ocean Multispheres & Earth Syst, Qingdao 266003, Peoples R China.; Xiao, JG (corresponding author), Minist Nat Resources, Inst Oceanog 3, Lab Marine Biodivers Res, 178 Daxue Rd, Xiamen 361005, Peoples R China.; Wang, XL (corresponding author), Ocean Univ China, Inst Evolut & Marine Biodivers, Qingdao 266100, Peoples R China.; Xiao, JG (corresponding author), Nansha Isl Coral Reef Ecosyst Natl Observat & Res, Guangzhou 510000, Peoples R China.
EM xiaojiaguang@tio.org.cn; wangxiaolei@ouc.edu.cn
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NR 107
TC 0
Z9 0
PD SEP
PY 2024
VL 166
AR 112452
DI 10.1016/j.ecolind.2024.112452
EA AUG 2024
UT WOS:001291141600001
DA 2025-07-30
ER

PT J
AU De Menezes, TA
   De Freitas, MAM
   Lima, MS
   Soares, AC
   Leal, C
   Busch, MD
   Tschoeke, DA
   Vidal, LD
   Atella, GC
   Kruger, RH
   Setubal, J
   Vasconcelos, AA
   De Mahiques, MM
   Siegle, E
   Asp, NE
   Cosenza, C
   Hajdu, E
   De Rezende, CE
   Thompson, CC
   Thompson, FL
AF De Menezes, Tatiane A.
   De Freitas, Mayanne A. M.
   Lima, Michele S.
   Soares, Ana Carolina
   Leal, Camille
   Busch, Mileane De S.
   Tschoeke, Diogo A.
   Vidal, Luciana De O.
   Atella, Georgia C.
   Kruger, Ricardo H.
   Setubal, Joao
   Vasconcelos, Agnaldo A.
   De Mahiques, Michel M.
   Siegle, Eduardo
   Asp, Nils Edvin
   Cosenza, Carlos
   Hajdu, Eduardo
   De Rezende, Carlos E.
   Thompson, Cristiane C.
   Thompson, Fabiano L.
TI Fluxes of the Amazon River plume nutrients and microbes into marine
   sponges
SO SCIENCE OF THE TOTAL ENVIRONMENT
DT Article
AB Sponges have co-evolved with microbes for over 400 myr. Previous studies have demonstrated that sponges can be classified according to the abundance of microbes in their tissues as Low Microbial Abundance (LMA) and High Microbial Abundance (HMA). While LMA sponges rely mainly on water column microbes, HMA appear to rely much more on symbiotic fermentative and autotrophic microbes maintained in their tissues. However, it is unclear if this pattern holds when comparing different species of tropical sponges under extreme nutrient conditions and sediment loads in the water column, such as the Great Amazon Reef System (GARS), which covers an area of similar to 56,000 km(2) off the Amazon River mouth. Sponges are the major GARS benthic components. However, these sponges' microbiome across the GARS is still unknown. Here, we investigated water quality, isotopic values (delta C-13 and delta N-15), metagenomic and lipidomic profiles of sponges obtained from different sectors throughout the GARS. >180 million shotgun metagenomic reads were annotated, covering 22 sponge species. Isotopic and lipidomic analyses suggested LMA sponges rely on the Amazon River Plume for nutrition. HMA sponges (N = 15) had higher Roseiflexus and Nitrospira abundance, whereas LMA sponges (N= 7) had higher Prochlorococcus and Pelagibacter abundance. Functional data revealed that the LMA sponge microbiomes had greater number of sequences related to phages and prophages as well as electron transport and photophosphorylation which may be related to photosynthetic processes associated with the Prochlorococcus and Synechococcus found in the LMA. The higher phages abundance in LMA sponges could be related to these holobionts' reduced defense towards phage infection. Meanwhile, HMA sponge microbiomes had higher Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR abundance, which may be involved in defense against phage infection. This study sheds light on the nutrient fluxes and microbes from the Amazon River plume into the sponge holobionts.
C1 [De Menezes, Tatiane A.; De Freitas, Mayanne A. M.; Lima, Michele S.; Leal, Camille; Thompson, Cristiane C.; Thompson, Fabiano L.] Fed Univ Rio De Janeiro UFRJ, Biol Inst, Microbiol Lab, Rio De Janeiro, Brazil.
   [Busch, Mileane De S.; Atella, Georgia C.] Fed Univ Rio De Janeiro UFRJ, Biochem Inst Leopoldo De Meis, Lab Lipids Biochem & Lipoprot, Rio De Janeiro, Brazil.
   [Tschoeke, Diogo A.] Fed Univ Rio De Janeiro UFRJ, Biomed Engn Program COPPE, Rio De Janeiro, Brazil.
   [Cosenza, Carlos; Thompson, Fabiano L.] Fed Univ Rio De Janeiro UFRJ, Ctr Technol CT2, SAGE COPPE, Rio De Janeiro, Brazil.
   [Vidal, Luciana De O.; De Rezende, Carlos E.] Univ Estadual Norte Fluminense Darcy Ribeiro UENF, Biosci & Biotechnol Ctr, Environm Sci Lab, Campos Goytacazes, Rio De Janeiro, Brazil.
   [Vidal, Luciana De O.] Univ Fed Estado Rio De Janeiro UNIRIO, Inst Biosci, Dept Ecol & Marine Resources, Rio De Janeiro, Brazil.
   [Kruger, Ricardo H.] Univ Brasilia UNB, Lab Enzymol, Brasilia, DF, Brazil.
   [Vasconcelos, Agnaldo A.] Greenpeace Brazil, Rio De Janeiro, Brazil.
   [De Mahiques, Michel M.; Siegle, Eduardo] Univ Sao Paulo, Oceanog Inst IO, Sao Paulo, Brazil.
   [Asp, Nils Edvin] Fed Univ Para, Inst Coastal Studies IECOS, Braganca Campus, Braganca, PA, Brazil.
   [Hajdu, Eduardo] Fed Univ Rio De Janeiro UFRJ, Dept Invertebrates, Natl Museum, Rio De Janeiro, Brazil.
   [Soares, Ana Carolina; Setubal, Joao] Univ Sao Paulo, Inst Chem, Dept Biochem, Bioinformat Lab, Sao Paulo, Brazil.
RP De Rezende, CE; Thompson, CC; Thompson, FL (corresponding author), Univ Fed Rio de Janeiro, Biol Inst, CCS, Ave Carlos Chagas Filho,Bloco A, BR-21941902 Rio de Janeiro, RJ, Brazil.
EM crezende@uenf.br; thompsoncristiane@gmail.com;
   fabianothompson1@gmail.com
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NR 91
TC 8
Z9 10
PD NOV 15
PY 2022
VL 847
AR 157474
DI 10.1016/j.scitotenv.2022.157474
EA AUG 2022
UT WOS:000884273800005
DA 2025-07-30
ER

PT J
AU Georges, AA
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AF Georges, Anna A.
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TI Metaproteomic analysis of a winter to spring succession in coastal
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DT Article
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RP Walsh, DA (corresponding author), Concordia Univ, Dept Biol, 7141 Sherbrooke St West, Montreal, PQ H4B 1R6, Canada.
EM david.walsh@concordia.ca
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PD JUN
PY 2014
VL 8
IS 6
BP 1301
EP 1313
DI 10.1038/ismej.2013.234
UT WOS:000336836200013
DA 2025-07-30
ER

PT J
AU Liu, ST
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SO LIMNOLOGY AND OCEANOGRAPHY
DT Article
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C1 [Liu, Shuting; Opalk, Keri; Baetge, Nicholas; Halewood, Elisa; Carlson, Craig A.] Univ Calif Santa Barbara, Marine Sci Inst, Dept Ecol Evolut & Marine Biol, Santa Barbara, CA 93106 USA.
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RP Liu, ST (corresponding author), Univ Calif Santa Barbara, Marine Sci Inst, Dept Ecol Evolut & Marine Biol, Santa Barbara, CA 93106 USA.
EM shutingliu@ucsb.edu
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NR 153
TC 41
Z9 46
PD JUL
PY 2020
VL 65
IS 7
BP 1532
EP 1553
DI 10.1002/lno.11405
EA JAN 2020
UT WOS:000508963300001
DA 2025-07-30
ER

PT J
AU Connelly, TL
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AF Connelly, Tara L.
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   Wawrik, Boris
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
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C1 [Connelly, Tara L.] Univ Texas Austin, Inst Marine Sci, Port Aransas, TX USA.
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RP Wawrik, B (corresponding author), Univ Oklahoma, Dept Microbiol & Plant Biol, Norman, OK 73019 USA.
EM bwawrik@ou.edu
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NR 70
TC 54
Z9 63
PD OCT
PY 2014
VL 80
IS 19
BP 6013
EP 6022
DI 10.1128/AEM.01431-14
UT WOS:000341887100015
DA 2025-07-30
ER

PT J
AU Yeo, SK
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AF Yeo, Sara K.
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DT Article
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C1 [Yeo, Sara K.; Huggett, Megan J.; Eiler, Alexander; Rappe, Michael S.] Univ Hawaii, Sch Ocean & Earth Sci & Technol, Hawaii Inst Marine Biol, Kaneohe, HI 96744 USA.
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RP Rappé, MS (corresponding author), Univ Hawaii, Sch Ocean & Earth Sci & Technol, Hawaii Inst Marine Biol, Kaneohe, HI 96744 USA.
EM rappe@hawaii.edu
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NR 58
TC 68
Z9 83
PD FEB 7
PY 2013
VL 8
IS 2
AR e56207
DI 10.1371/journal.pone.0056207
UT WOS:000315157200122
DA 2025-07-30
ER

PT J
AU Connon, SA
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AF Connon, SA
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DT Article
AB Microbial diversity studies based on the cloning and sequencing of DNA from nature support the conclusion that only a fraction of the microbial diversity is currently represented in culture collections. Out of over 40 known prokaryotic phyla, only half have cultured representatives. In an effort to culture the uncultured phylotypes from oligotrophic marine ecosystems, we developed high-throughput culturing procedures that utilize the concept of extinction culturing to isolate cultures in small volumes of low-nutrient media. In these experiments, marine bacteria were isolated and cultivated at in situ substrate concentrations-typically 3 orders of magnitude less than common laboratory media. Microtiter plates and a newly developed procedure for making cell arrays were employed to raise the throughput rate and lower detection sensitivity, permitting cell enumeration from 200-mul aliquots of cultures with densities as low as 10(3) cells/ml. Approximately 2,500 extinction cultures from 11 separate samplings of marine bacterio plankton were screened over the course of 3 years. Up to 14% of the cells collected from coastal seawater were cultured by this method, which was 14- to 1,400-fold higher than the numbers obtained by traditional microbiological culturing techniques. Among the microorganisms cultured were four unique cell lineages that belong to previously uncultured or undescribed marine Proteobacteria clades known from environmental gene cloning studies. These cultures are related to the clades SAR11 (alpha subclass), OM43 (beta subclass), SAR92 (gamma subclass), and OM60/OM241 (gamma subclass). This method proved successful for the cultivation of previously uncultured marine bacterioplankton that have consistently been found in marine clone libraries.
C1 Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
RP Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
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NR 40
TC 531
Z9 658
PD AUG
PY 2002
VL 68
IS 8
BP 3878
EP 3885
DI 10.1128/AEM.68.8.3878-3885.2002
UT WOS:000177260500028
DA 2025-07-30
ER

PT J
AU Cram, JA
   Hollins, A
   Mccarty, AJ
   Martinez, G
   Cui, MM
   Gomes, ML
   Fuchsman, CA
AF Cram, Jacob A.
   Hollins, Ashley
   Mccarty, Alexandra J.
   Martinez, Grace
   Cui, Minming
   Gomes, Maya L.
   Fuchsman, Clara A.
TI Microbial diversity and abundance vary along salinity, oxygen, and
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DT Article
AB Marine snow and other particles are abundant in estuaries, where they drive biogeochemical transformations and elemental transport. Particles range in size, thereby providing a corresponding gradient of habitats for marine microorganisms. We used standard normalized amplicon sequencing, verified with microscopy, to characterize taxon-specific microbial abundances, (cells per litre of water and per milligrams of particles), across six particle size classes, ranging from 0.2 to 500 mu m, along the main stem of the Chesapeake Bay estuary. Microbial communities varied in salinity, oxygen concentrations, and particle size. Many taxonomic groups were most densely packed on large particles (in cells/mg particles), yet were primarily associated with the smallest particle size class, because small particles made up a substantially larger portion of total particle mass. However, organisms potentially involved in methanotrophy, nitrite oxidation, and sulphate reduction were found primarily on intermediately sized (5-180 mu m) particles, where species richness was also highest. All abundant ostensibly free-living organisms, including SAR11 and Synecococcus, appeared on particles, albeit at lower abundance than in the free-living fraction, suggesting that aggregation processes may incorporate them into particles. Our approach opens the door to a more quantitative understanding of the microscale and macroscale biogeography of marine microorganisms.
   Overview of the particle size fractionation approach, and of the microbial community structure of free living bacteria and ones attached to small, intermediate and large particles. Arrows at the bottom indicate that bacterial abundance is highest in the planktonic stages and on smaller particles, and that small particles are more abundance than large ones.image
C1 [Cram, Jacob A.; Hollins, Ashley; Mccarty, Alexandra J.; Fuchsman, Clara A.] Univ Maryland, Ctr Environm Sci, Horn Point Lab, Cambridge, MD 21613 USA.
   [Mccarty, Alexandra J.] Virginia Inst Marine Sci, Marine Advisory Program, Gloucester, VA USA.
   [Martinez, Grace] Maryland Sea Grant, College Pk, MD USA.
   [Cui, Minming; Gomes, Maya L.] Johns Hopkins Univ, Earth & Planetary Sci, Baltimore, MD USA.
RP Cram, JA (corresponding author), Univ Maryland, Ctr Environm Sci, Horn Point Lab, Cambridge, MD 21613 USA.
EM jcram@umces.edu
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NR 127
TC 8
Z9 8
PD JAN
PY 2024
VL 26
IS 1
DI 10.1111/1462-2920.16557
EA JAN 2024
UT WOS:001135805600001
DA 2025-07-30
ER

PT J
AU Sebastián, M
   Pitta, P
   González, JM
   Thingstad, TF
   Gasol, JM
AF Sebastian, Marta
   Pitta, Paraskevi
   Gonzalez, Jose M.
   Thingstad, T. Frede
   Gasol, Josep M.
TI Bacterioplankton groups involved in the uptake of phosphate and
   dissolved organic phosphorus in a mesocosm experiment with P-starved
   Mediterranean waters
SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB The use of inorganic phosphate (Pi) and dissolved organic phosphorus (DOP) by different bacterial groups was studied in experimental mesocosms of P-starved eastern Mediterranean waters in the absence (control mesocosms) and presence of additional Pi (P-amended mesocosms). The low Pi turnover times in the control mesocosms and the increase in heterotrophic prokaryotic abundance and production upon Pi addition confirmed that the bacterial community was originally P-limited. The bacterioplankton groups taking up Pi and DOP were identified by means of microautoradiography combined with catalysed reporter deposition fluorescence in situ hybridization. Incubations with leucine were also performed for comparative purposes. All the probe-identified groups showed a high percentage of cells taking up Pi and DOP in the control, P-limited, mesocosms throughout the experiment. However, in response to Pi addition two contrasting scenarios in Pi use were observed: (i) on day 1 of the experiment Pi addition caused a clear reduction in the percentage of SAR11 cells taking up Pi, whereas Gammaproteobacteria, Roseobacter and Bacteroidetes showed similar percentages to the ones in the control mesocosms and (ii) on day 4 of the experiment, probably when the bacterial community had fully responded to the P input, all the probe-identified groups showed low percentages of cells taking up the substrate as compared with the control mesocosms. These differences are likely related to different P requirements among the bacterial groups and point out to the existence of two contrasting strategies in P use.
C1 [Sebastian, Marta; Gasol, Josep M.] CSIC, Inst Ciencies Mar, Dept Biol Marina & Oceanog, E-08003 Barcelona, Catalunya, Spain.
   [Pitta, Paraskevi] Hellen Ctr Marine Res, Oceanog Inst, Iraklion 71003, Crete, Greece.
   [Gonzalez, Jose M.] Univ La Laguna, Dept Microbiol, ES-38206 Tenerife, Spain.
   [Thingstad, T. Frede] Univ Bergen, Dept Biol, N-5020 Bergen, Norway.
RP Sebastián, M (corresponding author), CSIC, Inst Ciencies Mar, Dept Biol Marina & Oceanog, Pg Maritim Barceloneta 37-49, E-08003 Barcelona, Catalunya, Spain.
EM msebastian@icm.csic.es
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NR 91
TC 30
Z9 33
PD SEP
PY 2012
VL 14
IS 9
SI SI
BP 2334
EP 2347
DI 10.1111/j.1462-2920.2012.02772.x
UT WOS:000308300600008
DA 2025-07-30
ER

PT J
AU Mou, XZ
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AF Mou, Xiaozhen
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   Moran, Mary Ann
TI Bacterioplankton assemblages transforming dissolved organic compounds in
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB To characterize bacterioplankton functional assemblages that transform specific components of the coastal seawater dissolved organic carbon (DOC) pool, bromodeoxyuridine (BrdU) was used to label the bacterioplankton cells that were active following addition of single-DOC model compounds: two organic osmolytes [dimethylsulfoniopropionate (DMSP) and glycine betaine (GIyB)] and two aromatic monomers [para-hydroxybenzoic acid (pHBA) and vanillic acid (VanA)]. Bacterial populations were analysed based on in situ fluorescent immunodetection of BrdU incorporation followed by fluorescence-activated cell sorting (FACS). Sorted cells were then characterized by 16S rDNA-based analysis. Populations with high BrdU incorporation level (HI) developed within 8 h of introduction of 100 nM model compound. Terminal restriction fragment length polymorphisms (T-RFLP) analysis indicated that the HI populations in all four amendments were composed of bacteria from the same major taxa (phylum and subphylum levels), but the relative abundance of each differed. High-resolution clone libraries (each containing similar to 200 clones) showed that the HI populations in the GIyB and VanA amendments consisted of both metabolic generalists and specialists within the alpha-Proteobacteria (mainly members of the Roseobacter clade), beta-Proteobacteria and gamma-Proteobacteria (mainly members of Altermonadaceae, Chromatiaceae, Oceanospirillaceae and Pseudomonadaceae). The presence of members of OM60/241, OM185, SAR11, SAR86 and SAR116 in the HI populations indicated that members of these groups can assimilate the model DOC compounds, providing some of the first glimpses into heterotrophy by members of these poorly understood environmental clusters.
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RP Moran, MA (corresponding author), Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
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NR 38
TC 52
Z9 58
PD AUG
PY 2007
VL 9
IS 8
BP 2025
EP 2037
DI 10.1111/j.1462-2920.2007.01318.x
UT WOS:000248451600013
DA 2025-07-30
ER

PT J
AU Tout, J
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AF Tout, Jessica
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TI Variability in Microbial Community Composition and Function Between
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SO MICROBIAL ECOLOGY
DT Article
AB To explore how microbial community composition and function varies within a coral reef ecosystem, we performed metagenomic sequencing of seawater from four niches across Heron Island Reef, within the Great Barrier Reef. Metagenomes were sequenced from seawater samples associated with (1) the surface of the coral species Acropora palifera, (2) the surface of the coral species Acropora aspera, (3) the sandy substrate within the reef lagoon and (4) open water, outside of the reef crest. Microbial composition and metabolic function differed substantially between the four niches. The taxonomic profile showed a clear shift from an oligotroph-dominated community (e.g. SAR11, Prochlorococcus, Synechococcus) in the open water and sandy substrate niches, to a community characterised by an increased frequency of copiotrophic bacteria (e.g. Vibrio, Pseudoalteromonas, Alteromonas) in the coral seawater niches. The metabolic potential of the four microbial assemblages also displayed significant differences, with the open water and sandy substrate niches dominated by genes associated with core house-keeping processes such as amino acid, carbohydrate and protein metabolism as well as DNA and RNA synthesis and metabolism. In contrast, the coral surface seawater metagenomes had an enhanced frequency of genes associated with dynamic processes including motility and chemotaxis, regulation and cell signalling. These findings demonstrate that the composition and function of microbial communities are highly variable between niches within coral reef ecosystems and that coral reefs host heterogeneous microbial communities that are likely shaped by habitat structure, presence of animal hosts and local biogeochemical conditions.
C1 [Tout, Jessica; Jeffries, Thomas C.; Ralph, Peter J.; Seymour, Justin R.] Univ Technol Sydney, Plant Funct Biol & Climate Change Cluster, Sydney, NSW 2007, Australia.
   [Webster, Nicole S.] Australian Inst Marine Sci, Townsville, Qld 4810, Australia.
   [Stocker, Roman] MIT, Ralph M Parsons Lab, Dept Civil & Environm Engn, Cambridge, MA 02139 USA.
RP Tout, J (corresponding author), Univ Technol Sydney, Plant Funct Biol & Climate Change Cluster, Sydney, NSW 2007, Australia.
EM jessica.tout@student.uts.edu.au
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NR 104
TC 65
Z9 74
PD APR
PY 2014
VL 67
IS 3
BP 540
EP 552
DI 10.1007/s00248-013-0362-5
UT WOS:000333348900004
DA 2025-07-30
ER

PT J
AU Eiler, A
   Hayakawa, DH
   Rappé, MS
AF Eiler, Alexander
   Hayakawa, Darin H.
   Rappe, Michael S.
TI Non-random assembly of bacterioplankton communities in the subtropical
   North Pacific Ocean
SO FRONTIERS IN MICROBIOLOGY
DT Article
AB The exploration of bacterial diversity in the global ocean has revealed new taxa and previously unrecognized metabolic potential; however, our understanding of what regulates this diversity is limited. Using terminal restriction fragment length polymorphism (T-RFLP) data from bacterial small-subunit ribosomal RNA genes we show that, independent of depth and time, a large fraction of bacterioplankton co-occurrence patterns are non-random in the oligotrophic North Pacific subtropical gyre (NPSG). Pair-wise correlations of all identified operational taxonomic units (OTUs) revealed a high degree of significance, with 6.6% of the pair-wise co-occurrences being negatively correlated and 20.7% of them being positive. The most abundant OTUs, putatively identified as Prochlorococcus, SAR11, and SAR116 bacteria, were among the most correlated OTUs. As expected, bacterial community composition lacked statistically significant patterns of seasonality in the mostly stratified water column except in a few depth horizons of the sunlit surface waters, with higher frequency variations in community structure apparently related to populations associated with the deep chlorophyll maximum. Communities were structured vertically into epipelagic, mesopelagic, and bathypelagic populations. Permutation-based statistical analyses of T-RFLP data and their corresponding metadata revealed a broad range of putative environmental drivers controlling bacterioplankton community composition in the NPSG, including concentrations of inorganic nutrients and phytoplankton pigments. Together, our results suggest that deterministic forces such as environmental filtering and interactions among taxa determine bacterioplankton community patterns, and consequently affect ecosystem functions in the NPSG.
C1 [Eiler, Alexander; Hayakawa, Darin H.; Rappe, Michael S.] Univ Hawaii, Sch Ocean & Earth Sci & Technol, Hawaii Inst Marine Biol, Kaneohe, HI USA.
   [Eiler, Alexander] Uppsala Univ, Dept Ecol & Genet, Uppsala, Sweden.
   [Hayakawa, Darin H.] Univ Hawaii, Dept Microbiol, Honolulu, HI 96822 USA.
RP Eiler, A (corresponding author), Dept Ecol & Genet, Norbyvagen 18D, SE-75236 Uppsala, Sweden.
EM alexander.eiler@ebc.uu.se
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NR 53
TC 36
Z9 45
PY 2011
VL 2
AR 140
DI 10.3389/fmicb.2011.00140
UT WOS:000208863500150
DA 2025-07-30
ER

PT J
AU Li, B
   Liang, J
   Baniasadi, HR
   Phillips, MA
   Michael, AJ
AF Li, Bin
   Liang, Jue
   Baniasadi, Hamid R.
   Phillips, Margaret A.
   Michael, Anthony J.
TI Functional polyamine metabolic enzymes and pathways encoded by the
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SO PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
   AMERICA
DT Article
AB Viruses produce more viruses by manipulating the metabolic and replication systems of their host cells. Many have acquired metabolic genes from ancestral hosts and use the encoded enzymes to subvert host metabolism. The polyamine spermidine is required for bacteriophage and eukaryotic virus replication, and herein, we have identified and func-tionally characterized diverse phage-and virus-encoded polyamine metabolic enzymes and pathways. These include pyridoxal 5 '-phosphate (PLP)-dependent ornithine decarboxylase (ODC), pyruvoyl-dependent ODC and arginine decarboxylase (ADC), arginase, S-adenosylmethionine decarboxylase (AdoMetDC/speD), spermidine synthase, homospermidine synthase, spermidine N-acetyltransferase, and N-acetylspermidine amidohydrolase. We identified homologs of the spermidine-modified translation fac-tor eIF5a encoded by giant viruses of the Imitervirales. Although AdoMetDC/speD is prevalent among marine phages, some homologs have lost AdoMetDC activity and have evolved into pyruvoyl-dependent ADC or ODC. The pelagiphages that encode the pyruvoyl-dependent ADCs infect the abundant ocean bacterium Candidatus Pelagibacter ubique, which we have found encodes a PLP-dependent ODC homolog that has evolved into an ADC, indicating that infected cells would contain both PLP-and pyruvoyl-dependent ADCs. Complete or partial spermidine or homospermidine biosynthetic pathways are found encoded in the giant viruses of the Algavirales and Imitervirales, and in addition, some viruses of the Imitervirales can release spermidine from the inactive N-acetylspermidine. In contrast, diverse phages encode spermidine N-acetyltransferase that can sequester spermidine into its inactive N-acetyl form. Together, the virome-en-coded enzymes and pathways for biosynthesis and release or biochemical sequestration of spermidine or its structural analog homospermidine consolidate and expand evidence supporting an important and global role of spermidine in virus biology.
C1 [Li, Bin; Liang, Jue; Baniasadi, Hamid R.; Phillips, Margaret A.; Michael, Anthony J.] Univ Texas Southwestern Med Ctr, Dept Biochem, Dallas, TX 75214 USA.
RP Michael, AJ (corresponding author), Univ Texas Southwestern Med Ctr, Dept Biochem, Dallas, TX 75214 USA.
EM anthony.michael@utsouthwestern.edu
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TI Optimal Defense Strategies in an Idealized Microbial Food Web under
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SO PLOS ONE
DT Article
AB Trophic mechanisms that can generate biodiversity in food webs include bottom-up (growth rate regulating) and top-down (biomass regulating) factors. The top-down control has traditionally been analyzed using the concepts of "Keystone Predation'' (KP) and "Killing-the-Winner'' (KtW), predominately occuring in discussions of macro- and micro-biological ecology, respectively. Here we combine the classical diamond-shaped food web structure frequently discussed in KP analyses and the KtW concept by introducing a defense strategist capable of partial defense. A formalized description of a trade-off between the defense-strategist's competitive and defensive ability is included. The analysis reveals a complex topology of the steady state solution with strong relationships between food web structure and the combination of trade-off, defense strategy and the system's nutrient content. Among the results is a difference in defense strategies corresponding to maximum biomass, production, or net growth rate of invading individuals. The analysis thus summons awareness that biomass or production, parameters typically measured in field studies to infer success of particular biota, are not directly acted upon by natural selection. Under coexistence with a competition specialist, a balance of competitive and defensive ability of the defense strategist was found to be evolutionarily stable, whereas stronger defense was optimal under increased nutrient levels in the absence of the pure competition specialist. The findings of success of different defense strategies are discussed with respect to SAR11, a highly successful bacterial clade in the pelagic ocean.
C1 [Vage, Selina; Storesund, Julia E.; Giske, Jarl; Thingstad, T. Frede] Univ Bergen, Dept Biol, Hjort Ctr Marine Ecosyst Dynam, Bergen, Norway.
RP Våge, S (corresponding author), Univ Bergen, Dept Biol, Hjort Ctr Marine Ecosyst Dynam, Bergen, Norway.
EM Selina.Vage@bio.uib.no
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NR 80
TC 32
Z9 35
PD JUL 7
PY 2014
VL 9
IS 7
AR e101415
DI 10.1371/journal.pone.0101415
UT WOS:000338637300041
DA 2025-07-30
ER

PT J
AU Li, JQ
   Liu, XP
   Xie, ND
   Bai, MH
   Liu, L
   Sen, B
   Wang, GY
AF Li, Jiaqian
   Liu, Xiuping
   Xie, Ningdong
   Bai, Mohan
   Liu, Lu
   Sen, Biswarup
   Wang, Guangyi
TI Subsurface Bacterioplankton Structure and Diversity in the
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SO MICROORGANISMS
DT Article
AB The consequences of climate change may directly or indirectly impact the marine biosphere. Although ocean stratification has been recognized as one of the crucial consequences of ocean warming, its impacts on several critical aspects of marine microbes remain largely unknown in the Indian Ocean. Here, we investigate the effects of water stratification, in both surface and subsurface layers, on hydrogeographic parameters and bacterioplankton diversity within the equatorial eastern Indian Ocean (EIO). Strong stratification in the upper 200 m of equatorial EIO was detected with evidential low primary productivity. The vertical bacterioplankton diversity of the whole water columns displayed noticeable variation, with lower diversity occurring in the surface layer than in the subsurface layers. Horizontal heterogeneity of bacterioplankton communities was also in the well-mixed layer among different stations. SAR11 and Prochlorococcus displayed uncharacteristic low abundance in the surface water. Some amplicon sequence variants (ASVs) were identified as potential biomarkers for their specific depths in strongly-stratified water columns. Thus, barriers resulting from stratification are proposed to function as an 'ASV filter' to regulate the vertical bacterioplankton community diversity along the water columns. Overall, our results suggest that the effects of stratification on the structure and diversity of bacterioplankton can extend up to the bathypelagic zone in the strongly-stratified waters of the equatorial EIO. This study provides the first insight into the effect of stratification on the subsurface microbial communities in the equatorial eastern Indian Ocean.
C1 [Li, Jiaqian; Liu, Xiuping; Xie, Ningdong; Bai, Mohan; Liu, Lu; Sen, Biswarup; Wang, Guangyi] Tianjin Univ, Ctr Marine Environm Ecol, Sch Environm Sci & Engn, Tianjin 300072, Peoples R China.
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RP Sen, B; Wang, GY (corresponding author), Tianjin Univ, Ctr Marine Environm Ecol, Sch Environm Sci & Engn, Tianjin 300072, Peoples R China.; Wang, GY (corresponding author), Tianjin Univ, Key Lab Syst Bioengn, Minist Educ, Tianjin 300072, Peoples R China.; Wang, GY (corresponding author), Tianjin Univ, Ctr Biosafety Res & Strategy, Tianjin 300072, Peoples R China.
EM bsen@tju.edu.cn; gywang@tju.edu.cn
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NR 72
TC 6
Z9 6
PD MAR
PY 2023
VL 11
IS 3
AR 592
DI 10.3390/microorganisms11030592
UT WOS:000958461100001
DA 2025-07-30
ER

PT J
AU Zehnpfennig, JR
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   Wankel, SD
   Sheik, CS
   Horton, DJ
   Lamborg, CH
   Learman, DR
AF Zehnpfennig, Jessica R.
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TI Diel Patterns in Marine Microbial Metatranscriptomes Reflect Differences
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SO FRONTIERS IN MARINE SCIENCE
DT Article
AB Microbial community dynamics are influenced not only by biological but also physical and chemical phenomena (e.g., temperature, sunlight, pH, wave energy) that vary on both short and long-time scales. In this study, samples of continental shelf waters of the northwest Atlantic Ocean were periodically collected from pre-sunrise to post-sunset and at multiple depths over summers of 2016 and 2017. Metatranscriptomic analyses revealed expression of photosynthetic genes in surface water samples corresponding to a diel relationship with sunlight. Photosynthetic genes originated from known phototrophs including Aureococcus, Ostreococcous, Synechocococus, and Prochlorococcus. Photosynthetic gene expression occurred pre-sunrise, suggesting the community initiates transcription before sunlight exposure, ostensibly to harvest energy more efficiently when the anticipated increase in light occurs. Transcripts from photoheterotrophic members of the SAR11 clade were also documented in surface samples, with rhodopsin expression being more abundant pre-sunrise and post-sunrise. Conversely, samples taken from the aphotic layer exhibited expression of transcripts related to nitrification that did not vary over the diel cycle. Nitrification gene transcripts, specifically amoA, nirK, hao, and norAB, were taxonomically related to well-known genera of ammonia oxidizers, such as Nitrospira, Candidatus Nitrosomarinus, Nitrosospira, and Nitrosopumilus. Overall, this study documents the role of light (varying with time and depth) in shaping the photosynthetic microbial community activity in the surface ocean, and further demonstrates that this diel regulation of photosynthesis is decoupled from the activity of the nitrifying microbial community in deeper and darker waters.
C1 [Zehnpfennig, Jessica R.; Horton, Dean J.; Learman, Deric R.] Cent Michigan Univ, Dept Biol, Inst Great Lakes Res, Mt Pleasant, MI 48859 USA.
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   [Sheik, Cody S.] Univ Minnesota Duluth, Dept Biol, Large Lakes Observ, Duluth, MN USA.
   [Lamborg, Carl H.] Univ Calif Santa Cruz, Ocean Sci Dept, Santa Cruz, CA 95064 USA.
RP Learman, DR (corresponding author), Cent Michigan Univ, Dept Biol, Inst Great Lakes Res, Mt Pleasant, MI 48859 USA.
EM deric.learman@cmich.edu
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NR 53
TC 3
Z9 3
PD FEB 3
PY 2022
VL 9
AR 798877
DI 10.3389/fmars.2022.798877
UT WOS:000759935200001
DA 2025-07-30
ER

PT J
AU Apprill, A
   Holm, H
   Santoro, AE
   Becker, C
   Neave, M
   Hughen, K
   Doná, AR
   Aeby, G
   Work, T
   Weber, L
   McNally, S
AF Apprill, Amy
   Holm, Henry
   Santoro, Alyson E.
   Becker, Cynthia
   Neave, Matthew
   Hughen, Konrad
   Dona, Angela Richards
   Aeby, Greta
   Work, Thierry
   Weber, Laura
   McNally, Sean
TI Microbial ecology of coral-dominated reefs in the Federated States of
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SO AQUATIC MICROBIAL ECOLOGY
DT Article
AB Microorganisms are central to the functioning of coral reef ecosystems, but their dynamics are unstudied on most reefs. We examined the microbial ecology of shallow reefs within the Federated States of Micronesia. We surveyed 20 reefs surrounding 7 islands and atolls (Yap, Woleai, Olimarao, Kosrae, Kapingamarangi, Nukuoro, and Pohnpei), spanning 875 053 km(2). On the reefs, we found consistently higher coral coverage (mean +/- SD = 36.9 +/- 22.2%; max 77 %) compared to macroalgae coverage (15.2 +/- 15.5 %; max 58 %), and low abundances of fish. Reef waters had low inorganic nutrient concentrations and were dominated by Synechococcus, Prochiorococcus, and SAR11 bacteria. The richness of bacterial and archaeal communities was significantly related to interactions between island/atoll and depth. High coral coverage on reefs was linked to higher relative abundances of Flavobacteriaceae, Leisingera, Owenweeksia, Vibrio, and the OM27 clade, as well as other heterotrophic bacterial groups, consistent with communities residing in waters near corals and within coral mucus. Microbial community structure at reef depth was significantly correlated with geographic distance, suggesting that island biogeography influences reef microbial communities. Reefs at Kosrae Island, which hosted the highest coral abundance and diversity, were unique compared to other locations; seawater from Kosrae reefs had the lowest organic carbon (59.8-67.9 mu M), highest organic nitrogen (4.5-5.3 mu M), and harbored consistent microbial communities (>85% similar), which were dominated by heterotrophic cells. This study suggests that the reef-water microbial ecology on Micronesian reefs is influenced by the density and diversity of corals as well as other biogeographical features.
C1 [Apprill, Amy; Holm, Henry; Becker, Cynthia; Neave, Matthew; Hughen, Konrad; Weber, Laura; McNally, Sean] Woods Hole Oceanog Inst, Marine Chem & Geochem Dept, Woods Hole, MA 02543 USA.
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   [Santoro, Alyson E.] Univ Calif Santa Barbara, Dept Ecol Evolut & Marine Biol, Santa Barbara, CA 93106 USA.
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   [Neave, Matthew] CSIRO, Australian Anim Hlth Lab, Geelong, Vic 3219, Australia.
   [Weber, Laura; McNally, Sean] Univ Massachusetts, Sch Environm, Boston, MA 02125 USA.
RP Apprill, A (corresponding author), Woods Hole Oceanog Inst, Marine Chem & Geochem Dept, Woods Hole, MA 02543 USA.
EM aapprill@whoi.edu
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NR 77
TC 13
Z9 15
PY 2021
VL 86
BP 115
EP 136
DI 10.3354/ame01961
UT WOS:000665451400009
DA 2025-07-30
ER

PT J
AU Schwalbach, MS
   Brown, M
   Fuhrman, JA
AF Schwalbach, MS
   Brown, M
   Fuhrman, JA
TI Impact of light on marine bacterioplankton community structure
SO AQUATIC MICROBIAL ECOLOGY
DT Article
AB Reports of widespread proteorhodopsin and bacteriochlorophyll a genes suggest that light may facilitate the growth of many marine bacteria. We tested this hypothesis by conducting 3 light manipulation experiments with bacterial communities obtained off the Southern California coast. In each experiment, duplicate 20 l mesocosms were subjected to either 14:10 h light:dark or continual darkness for 5 to 10 d. Automated Ribosomal Intergenic Spacer Analysis (ARISA), a whole-community fingerprinting technique, was used to determine how light affects bacterial community structure. Light removal resulted in only minor changes in ARISA profiles (mean decrease in similarity between treatments: 6 +/- 1 % via Sorenson's index [only considers presence/absence of taxa], 15 +/- 7 % via Pearson's coefficient [considers relative abundance of taxa]) at the conclusion of the experiments. Oligotrophic communities responded nearly twice as strongly to light removal compared to mesotrophic communities. Phototrophs such as cyanobacteria exhibited consistent, sharp declines in dark treatments, indicating whatever heterotrophic abilities they possess were not sufficient to sustain them when faced with natural removal processes such as grazing or viral lysis. Members of the broad SAR86, SAR11, SAR116, CFB and Roseobacter phylogenetic groups exhibited minor, mixed responses to light removal, suggesting that only a few select members may rely on phototrophy to a measurable extent. Our results indicate that the majority of non-cyanobacterial bacteria in the ocean do not depend heavily on light to maintain themselves over 5 or 10 d periods in the presence of natural removal processes, and hint that proteorhodopsin and bacteriochlorophyll a genes may have alternative, undetermined ecological benefits besides phototrophy.
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   Univ So Calif, Wrigley Inst Marine Studies, Los Angeles, CA 90089 USA.
RP Univ So Calif, Dept Biol Sci, Los Angeles, CA 90089 USA.
EM schwalba@usc.edu
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NR 42
TC 47
Z9 50
PD JUN 20
PY 2005
VL 39
IS 3
BP 235
EP 245
DI 10.3354/ame039235
UT WOS:000230467100003
DA 2025-07-30
ER

PT J
AU Garner, RE
   Gregory-Eaves, I
   Walsh, DA
AF Garner, Rebecca E.
   Gregory-Eaves, Irene
   Walsh, David A.
TI Sediment Metagenomes as Time Capsules of Lake Microbiomes
SO MSPHERE
DT Article
AB The reconstruction of ecological time series from lake sediment archives can retrace the environmental impact of human activities. Molecular genetic approaches in paleolimnology have provided unprecedented access to DNA time series, which record evidence of the microbial ecologies that underlaid historical lake ecosystems. Such studies often rely on single-gene surveys, and consequently, the full diversity of preserved microorganisms remains unexplored. In this study, we probed the diversity archived in contemporary and preindustrial sediments by comparative shotgun metagenomic analysis of surface water and sediment samples from three eastern Canadian lakes. In a strategy that was aimed at disentangling historical DNA from the indigenous sediment background, microbial preservation signals were captured by mapping sequence similarities between sediment metagenome reads and reference surface water metagenome assemblies. We detected preserved Cyanobacteria, diverse bacterioplankton, microeukaryotes, and viruses in sediment metagenomes. Among the preserved microorganisms were important groups never before reported in paleolimnological reconstructions, including bacteriophages (Caudoviroles) and ubiquitous freshwater Betaproteobacteria (Polynucleobacter and Limnohabitans). In contrast, ultramicroscopic Actinobacteria ("Candidatus Nanopelagicales") and Alphaproteobacteria (Pelagibacterales) were apparently not well preserved in sediment metagenomes even though they were numerically dominant in surface water metagenomes. Overall, our study explored a novel application of whole-metagenome shotgun sequencing for discovering the DNA remains of a broad diversity of microorganisms preserved in lake sediments. The recovery of diverse microbial time series supports the taxonomic expansion of microbiome reconstructions and the development of novel microbial paleoindicators.
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C1 [Garner, Rebecca E.; Walsh, David A.] Concordia Univ, Dept Biol, Montreal, PQ, Canada.
   [Gregory-Eaves, Irene] McGill Univ, Dept Biol, Montreal, PQ, Canada.
   [Garner, Rebecca E.; Gregory-Eaves, Irene; Walsh, David A.] Grp Rech Interuniv Limnol, Montreal, PQ, Canada.
RP Walsh, DA (corresponding author), Concordia Univ, Dept Biol, Montreal, PQ, Canada.; Walsh, DA (corresponding author), Grp Rech Interuniv Limnol, Montreal, PQ, Canada.
EM david.walsh@concordia.ca
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NR 78
TC 23
Z9 23
PD NOV-DEC
PY 2020
VL 5
IS 6
AR e00512-20
DI 10.1128/mSphere.00512-20
UT WOS:000588447300001
DA 2025-07-30
ER

PT J
AU Pelve, EA
   Fontanez, KM
   DeLong, EF
AF Pelve, Erik A.
   Fontanez, Kristina M.
   DeLong, Edward F.
TI Bacterial Succession on Sinking Particles in the Ocean's Interior
SO FRONTIERS IN MICROBIOLOGY
DT Article
AB Sinking particles formed in the photic zone and moving vertically through the water column are a main mechanism for nutrient transport to the deep ocean, and a key component of the biological carbon pump. The particles appear to be processed by a microbial community substantially different from the surrounding waters. Single cell genomics and metagenomics were employed to describe the succession of dominant bacterial groups during particle processing. Sinking particles were extracted from sediment traps at Station Aloha in the North Pacific Subtropical Gyre (NPSG) during two different trap deployments conducted in July and August 2012. The microbial communities in poisoned vs. live sediment traps differed significantly from one another, consistent with prior observations by Fontanez et al. (2015). Partial genomes from these communities were sequenced from cells belonging to the genus Arcobacter (commensalists potentially associated with protists such as Radiolaria), and Vibrio carnpbellii (a group previously reported to be associated with crustacea). These bacteria were found in the particle-associated communities at specific depths in both trap deployments, presumably due to their specific host-associations. Partial genomes were also sequenced from cells belonging to Idiomarina and Kangiella that were enriched in live traps over a broad depth range, that represented a motile copiotroph and a putatively non-motile algicidal saprophyte, respectively. Planktonic bacterial cells most likely caught in the wake of the particles belonging to Actinomarina and the SAR11 Glade were also sequenced. Our results suggest that similar groups of eukaryote-associated bacteria are consistently found on sinking particles at different times, and that particle remineralization involves specific, reproducible bacterial succession events in oligotrophic ocean waters.
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RP DeLong, EF (corresponding author), Univ Hawaii Manoa, Dept Oceanog, Daniel K Inoue Ctr Microbial Oceanog Res & Educ, Honolulu, HI 96822 USA.
EM edelong@hawaii.edu
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NR 48
TC 49
Z9 52
PD NOV 24
PY 2017
VL 8
AR 2269
DI 10.3389/fmicb.2017.02269
UT WOS:000416109000001
DA 2025-07-30
ER

PT J
AU Stirrup, R
   Mausz, MA
   Silvano, E
   Murphy, A
   Guillonneau, R
   Quareshy, M
   Rihtman, B
   Ferretjans, MA
   He, R
   Todd, JD
   Chen, F
   Scanlan, DJ
   Chen, Y
AF Stirrup, Rachel
   Mausz, Michaela A.
   Silvano, Eleonora
   Murphy, Andrew
   Guillonneau, Richard
   Quareshy, Mussa
   Rihtman, Branko
   Ferretjans, Maria Aguilo
   He, Ruo
   Todd, Jonathan D.
   Chen, Feng
   Scanlan, David J.
   Chen, Yin
TI Aminolipids elicit functional trade-offs between competitiveness and
   bacteriophage attachment in Ruegeria pomeroyi
SO ISME JOURNAL
DT Article
AB Lipids play a crucial role in maintaining cell integrity and homeostasis with the surrounding environment. Cosmopolitan marine roseobacter clade (MRC) and SAR11 clade bacteria are unique in that, in addition to glycerophospholipids, they also produce an array of amino acid-containing lipids that are conjugated with beta-hydroxy fatty acids through an amide bond. Two of these aminolipids, the ornithine aminolipid (OL) and the glutamine aminolipid (QL), are synthesized using the O-acetyltransferase OlsA. Here, we demonstrate that OL and QL are present in both the inner and outer membranes of the Gram-negative MRC bacterium Ruegeria pomeroyi DSS-3. In an olsA mutant, loss of these aminolipids is compensated by a concurrent increase in glycerophospholipids. The inability to produce aminolipids caused significant changes in the membrane proteome, with the membrane being less permeable and key nutrient transporters being downregulated while proteins involved in the membrane stress response were upregulated. Indeed, the import of C-14-labelled choline and dimethylsulfoniopropionate, as a proxy for the transport of key marine nutrients across membranes, was significantly impaired in the olsA mutant. Moreover, the olsA mutant was significantly less competitive than the wild type (WT) being unable to compete with the WT strain in co-culture. However, the olsA mutant unable to synthesize these aminolipids is less susceptible to phage attachment. Together, these data reveal a critical role for aminolipids in the ecophysiology of this important clade of marine bacteria and a trade-off between growth and avoidance of bacteriophage attachment.
C1 [Stirrup, Rachel; Mausz, Michaela A.; Silvano, Eleonora; Murphy, Andrew; Guillonneau, Richard; Quareshy, Mussa; Rihtman, Branko; Ferretjans, Maria Aguilo; Scanlan, David J.; Chen, Yin] Univ Warwick, Sch Life Sci, Coventry CV4 7AL, England.
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   [Todd, Jonathan D.] Univ East Anglia, Sch Biol Sci, Norwich Res Pk, Norwich NR4 7TJ, England.
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RP Chen, Y (corresponding author), Univ Warwick, Sch Life Sci, Coventry CV4 7AL, England.
EM Y.chen.25@warwick.ac.uk
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NR 37
TC 7
Z9 8
PD MAR
PY 2023
VL 17
IS 3
BP 315
EP 325
DI 10.1038/s41396-022-01346-0
EA DEC 2022
UT WOS:000894983600001
DA 2025-07-30
ER

PT J
AU Cordone, A
   D'Errico, G
   Magliulo, M
   Bolinesi, F
   Selci, M
   Basili, M
   de Marco, R
   Saggiomo, M
   Rivaro, P
   Giovannelli, D
   Mangoni, O
AF Cordone, Angelina
   D'Errico, Giuseppe
   Magliulo, Maria
   Bolinesi, Francesco
   Selci, Matteo
   Basili, Marco
   de Marco, Rocco
   Saggiomo, Maria
   Rivaro, Paola
   Giovannelli, Donato
   Mangoni, Olga
TI Bacterioplankton Diversity and Distribution in Relation to Phytoplankton
   Community Structure in the Ross Sea Surface Waters
SO FRONTIERS IN MICROBIOLOGY
DT Article
AB Primary productivity in the Ross Sea region is characterized by intense phytoplankton blooms whose temporal and spatial distribution are driven by changes in environmental conditions as well as interactions with the bacterioplankton community. However, the number of studies reporting the simultaneous diversity of the phytoplankton and bacterioplankton in Antarctic waters are limited. Here, we report data on the bacterial diversity in relation to phytoplankton community structure in the surface waters of the Ross Sea during the Austral summer 2017. Our results show partially overlapping bacterioplankton communities between the stations located in the Terra Nova Bay (TNB) coastal waters and the Ross Sea Open Waters (RSOWs), with a dominance of members belonging to the bacterial phyla Bacteroidetes and Proteobacteria. In the TNB coastal area, microbial communities were characterized by a higher abundance of sequences related to heterotrophic bacterial genera such as Polaribacter spp., together with higher phytoplankton biomass and higher relative abundance of diatoms. On the contrary, the phytoplankton biomass in the RSOW were lower, with relatively higher contribution of haptophytes and a higher abundance of sequences related to oligotrophic and mixothrophic bacterial groups like the Oligotrophic Marine Gammaproteobacteria (OMG) group and SAR11. We show that the rate of diversity change between the two locations is influenced by both abiotic (salinity and the nitrogen to phosphorus ratio) and biotic (phytoplankton community structure) factors. Our data provide new insight into the coexistence of the bacterioplankton and phytoplankton in Antarctic waters, suggesting that specific rather than random interaction contribute to the organic matter cycling in the Southern Ocean.
C1 [Cordone, Angelina; Magliulo, Maria; Bolinesi, Francesco; Selci, Matteo; Giovannelli, Donato; Mangoni, Olga] Univ Naples Federico II, Dept Biol, Naples, Italy.
   [D'Errico, Giuseppe; Giovannelli, Donato] Polytech Univ Marche, Dept Life Sci, DISVA, Ancona, Italy.
   [Basili, Marco; de Marco, Rocco; Giovannelli, Donato] Inst Marine Biol Resources & Biotechnol CNR IRBIM, Natl Res Council, Ancona, Italy.
   [Saggiomo, Maria] Stn Zool Anton Dohrn, Naples, Italy.
   [Rivaro, Paola] Univ Genoa, Dept Chem & Ind Chem, Genoa, Italy.
   [Giovannelli, Donato] Rutgers State Univ, Dept Marine & Coastal Sci, New Brunswick, NJ 08901 USA.
   [Giovannelli, Donato] Woods Hole Oceanog Inst, Dept Marine Chem & Geochem, Woods Hole, MA 02543 USA.
   [Giovannelli, Donato] Tokyo Inst Technol, Earth Life Sci Inst, Tokyo, Japan.
   Consorzio Nazl Interuniv Sci Mare CoNISMa, Rome, Italy.
   [Magliulo, Maria] Univ Essex, Colchester, Essex, England.
RP Bolinesi, F; Giovannelli, D (corresponding author), Univ Naples Federico II, Dept Biol, Naples, Italy.; Giovannelli, D (corresponding author), Polytech Univ Marche, Dept Life Sci, DISVA, Ancona, Italy.; Giovannelli, D (corresponding author), Inst Marine Biol Resources & Biotechnol CNR IRBIM, Natl Res Council, Ancona, Italy.; Giovannelli, D (corresponding author), Rutgers State Univ, Dept Marine & Coastal Sci, New Brunswick, NJ 08901 USA.; Giovannelli, D (corresponding author), Woods Hole Oceanog Inst, Dept Marine Chem & Geochem, Woods Hole, MA 02543 USA.; Giovannelli, D (corresponding author), Tokyo Inst Technol, Earth Life Sci Inst, Tokyo, Japan.
EM francesco.bolinesi@unina.it; donato.giovannelli@unina.it
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NR 136
TC 14
Z9 15
PD JAN 27
PY 2022
VL 13
AR 722900
DI 10.3389/fmicb.2022.722900
UT WOS:000753189400001
DA 2025-07-30
ER

PT J
AU Morán, XAG
   Alonso-Sáez, L
   Nogueira, E
   Ducklow, HW
   González, N
   López-Urrutia, A
   Díaz-Pérez, L
   Calvo-Díaz, A
   Arandia-Gorostidi, N
   Huete-Stauffer, TM
AF Moran, Xose Anxelu G.
   Alonso-Saez, Laura
   Nogueira, Enrique
   Ducklow, Hugh W.
   Gonzalez, Natalia
   Lopez-Urrutia, Angel
   Diaz-Perez, Laura
   Calvo-Diaz, Alejandra
   Arandia-Gorostidi, Nestor
   Huete-Stauffer, Tamara M.
TI More, smaller bacteria in response to ocean's warming?
SO PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
DT Article
AB Heterotrophic bacteria play a major role in organic matter cycling in the ocean. Although the high abundances and relatively fast growth rates of coastal surface bacterioplankton make them suitable sentinels of global change, past analyses have largely overlooked this functional group. Here, time series analysis of a decade of monthly observations in temperate Atlantic coastal waters revealed strong seasonal patterns in the abundance, size and biomass of the ubiquitous flow-cytometric groups of low (LNA) and high nucleic acid (HNA) content bacteria. Over this relatively short period, we also found that bacterioplankton cells were significantly smaller, a trend that is consistent with the hypothesized temperature-driven decrease in body size. Although decadal cell shrinking was observed for both groups, it was only LNA cells that were strongly coherent, with ecological theories linking temperature, abundance and individual size on both the seasonal and interannual scale. We explain this finding because, relative to their HNA counterparts, marine LNA bacteria are less diverse, dominated by members of the SAR11 clade. Temperature manipulation experiments in 2012 confirmed a direct effect of warming on bacterial size. Concurrent with rising temperatures in spring, significant decadal trends of increasing standing stocks (3% per year) accompanied by decreasing mean cell size (-1% per year) suggest a major shift in community structure, with a larger contribution of LNA bacteria to total biomass. The increasing prevalence of these typically oli-gotrophic taxa may severely impact marine food webs and carbon fluxes by an overall decrease in the efficiency of the biological pump.
C1 [Moran, Xose Anxelu G.] King Abdullah Univ Sci & Technol, Div Biol & Environm Sci & Engn, Red Sea Res Ctr, Thuwal 239556900, Saudi Arabia.
   [Moran, Xose Anxelu G.; Alonso-Saez, Laura; Nogueira, Enrique; Lopez-Urrutia, Angel; Diaz-Perez, Laura; Calvo-Diaz, Alejandra; Arandia-Gorostidi, Nestor; Huete-Stauffer, Tamara M.] Ctr Oceanog Xixon, Inst Espanol Oceanog, Xixon 33212, Asturies, Spain.
   [Alonso-Saez, Laura] AZTI Tecnalia, Marine Res Div, Sukarrieta 48395, Bizkaia, Spain.
   [Ducklow, Hugh W.] Columbia Univ, Lamont Doherty Earth Observ, Palisades, NY 10964 USA.
   [Gonzalez, Natalia] Univ Rey Juan Carlos, Dept Biol & Geol Fis & Quim Inorgan, Madrid 28933, Spain.
RP Morán, XAG (corresponding author), King Abdullah Univ Sci & Technol, Div Biol & Environm Sci & Engn, Red Sea Res Ctr, Thuwal 239556900, Saudi Arabia.
EM xelu.moran@kaust.edu.sa
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NR 65
TC 81
Z9 82
PD JUL 7
PY 2015
VL 282
IS 1810
AR 20150371
DI 10.1098/rspb.2015.0371
UT WOS:000357719500011
DA 2025-07-30
ER

PT J
AU DeLorenzo, S
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   Zuber, P
AF DeLorenzo, Suzanne
   Braeuer, Suzanna L.
   Edgmont, Chelsea A.
   Herfort, Lydie
   Tebo, Bradley M.
   Zuber, Peter
TI Ubiquitous Dissolved Inorganic Carbon Assimilation by Marine Bacteria in
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SO PLOS ONE
DT Article
AB In order to identify bacteria that assimilate dissolved inorganic carbon (DIC) in the northeast Pacific Ocean, stable isotope probing (SIP) experiments were conducted on water collected from 3 different sites off the Oregon and Washington coasts in May 2010, and one site off the Oregon Coast in September 2008 and March 2009. Samples were incubated in the dark with 2 mM C-13-NaHCO3, doubling the average concentration of DIC typically found in the ocean. Our results revealed a surprising diversity of marine bacteria actively assimilating DIC in the dark within the Pacific Northwest coastal waters, indicating that DIC fixation is relevant for the metabolism of different marine bacterial lineages, including putatively heterotrophic taxa. Furthermore, dark DIC-assimilating assemblages were widespread among diverse bacterial classes. Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes dominated the active DIC-assimilating communities across the samples. Actinobacteria, Betaproteobacteria, Deltaproteobacteria, Planctomycetes, and Verrucomicrobia were also implicated in DIC assimilation. Alteromonadales and Oceanospirillales contributed significantly to the DIC-assimilating Gammaproteobacteria within May 2010 clone libraries. 16S rRNA gene sequences related to the sulfur-oxidizing symbionts Arctic96BD-19 were observed in all active DIC assimilating clone libraries. Among the Alphaproteobacteria, clones related to the ubiquitous SAR11 clade were found actively assimilating DIC in all samples. Although not a dominant contributor to our active clone libraries, Betaproteobacteria, when identified, were predominantly comprised of Burkholderia. DIC-assimilating bacteria among Deltaproteobacteria included members of the SAR324 cluster. Our research suggests that DIC assimilation is ubiquitous among many bacterial groups in the coastal waters of the Pacific Northwest marine environment and may represent a significant metabolic process.
C1 [DeLorenzo, Suzanne; Braeuer, Suzanna L.; Edgmont, Chelsea A.; Herfort, Lydie; Tebo, Bradley M.; Zuber, Peter] Oregon Hlth & Sci Univ, Ctr Coastal Margin Observat & Predict, Beaverton, OR USA.
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   [Braeuer, Suzanna L.] Appalachian State Univ, Boone, NC 28608 USA.
RP DeLorenzo, S (corresponding author), Oregon Hlth & Sci Univ, Ctr Coastal Margin Observat & Predict, Beaverton, OR USA.
EM delorenz@ebs.ogi.edu
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NR 59
TC 41
Z9 44
PD OCT 3
PY 2012
VL 7
IS 10
AR e46695
DI 10.1371/journal.pone.0046695
UT WOS:000309454000075
DA 2025-07-30
ER

PT J
AU Vila-Costa, M
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   Sun, SL
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   Poretsky, R
   Moran, MA
AF Vila-Costa, Maria
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DT Article
AB Dimethylsulfoniopropionate (DMSP) is an important source of reduced sulfur and carbon for marine microbial communities, as well as the precursor of the climate-active gas dimethylsulfide (DMS). In this study, we used metatranscriptomic sequencing to analyze gene expression profiles of a bacterial assemblage from surface waters at the Bermuda Atlantic Time-series Study (BATS) station with and without a short-term enrichment of DMSP (25 nM for 30 min). An average of 303 143 reads were obtained per treatment using 454 pyrosequencing technology, of which 51% were potential protein-encoding sequences. Transcripts from Gammaproteobacteria and Bacteroidetes increased in relative abundance on DMSP addition, yet there was little change in the contribution of two bacterioplankton groups whose cultured members harbor known DMSP degradation genes, Roseobacter and SAR11. The DMSP addition led to an enrichment of transcripts supporting heterotrophic activity, and a depletion of those encoding light-related energy generation. Genes for the degradation of C3 compounds were significantly overrepresented after DMSP addition, likely reflecting the metabolism of the C3 component of DMSP. Mapping these transcripts to known biochemical pathways indicated that both acetyl-CoA and succinyl-CoA may be common entry points of this moiety into the tricarboxylic acid cycle. In a short time frame (30 min) in the extremely oligotrophic Sargasso Sea, different gene expression patterns suggest the use of DMSP by a diversity of marine bacterioplankton as both carbon and sulfur sources. The ISME Journal (2010) 4, 1410-1420; doi: 10.1038/ismej.2010.62; published online 13 May 2010
C1 [Vila-Costa, Maria; Rinta-Kanto, Johanna M.; Sun, Shulei; Sharma, Shalabh; Poretsky, Rachel; Moran, Mary Ann] Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
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RP Moran, MA (corresponding author), Univ Georgia, Dept Marine Sci, Marine Sci Bldg, Athens, GA 30602 USA.
EM mmoran@uga.edu
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NR 64
TC 55
Z9 63
PD NOV
PY 2010
VL 4
IS 11
BP 1410
EP 1420
DI 10.1038/ismej.2010.62
UT WOS:000285793700006
DA 2025-07-30
ER

PT J
AU Lu, XX
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   Hollibaugh, JT
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AF Lu, Xinxin
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TI Temporal and Vertical Distributions of Bacterioplankton at the Gray's
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DT Article
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C1 [Lu, Xinxin; Zhang, Yu-Qin; Mou, Xiaozhen] Kent State Univ, Dept Biol Sci, Kent, OH 44242 USA.
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RP Mou, XZ (corresponding author), Kent State Univ, Dept Biol Sci, Kent, OH 44242 USA.
EM xmou@kent.edu
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NR 40
TC 17
Z9 21
PD FEB
PY 2015
VL 81
IS 3
BP 910
EP 917
DI 10.1128/AEM.02802-14
UT WOS:000347914800012
DA 2025-07-30
ER

PT J
AU Davey, KE
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AF Davey, KE
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DT Article
AB Distinct profiles of extracellular proteolytic enzyme activity were observed in the water column of the North Atlantic, with maximum potential proteolytic activity occurring in the top 35 m. The proteolytic enzyme V(max) values varied significantly and decreased from 1.46 nM min(-1) in surface waters to 0.365 nM min(-1) at 100 m. In contrast, K(m) values increased with depth from about 70 to 360 muM. Cell-associated enzymes accounted for the majority of the observed proteolytic activity. Dissolved enzymes comprised only 30-40% of the total extracellular enzyme activity and exhibited a low substrate affinity (K(m) = similar to 1000 muM). These observations indicate clear stratification of bacterial associated extracellular enzyme activity, with the maximum activity in surface waters. This is consistent with some environmental changes in the water column, especially algal biomass and nitrate concentration. Bacterial mediated nitrogen remineralization in surface waters was approximately three times the total nitrogen demand of phytoplankton and bacteria. We determined bacterial population diversity using 16S rRNA sequence analysis and found evidence for stratification, with a higher representation of the Cytophaga/Flexibacter/Bacteriodes group at 5 m compared to 100 m. No similar stratification was observed among the alpha -proteobacterial SAR11 cluster, which were especially prevalent in the PRIME eddy. However, sequences phylogenetically related to another marine cluster, SAR122, were only observed at 100 m. We suggest that stratification of proteolytic activity within the water column may be explained at least in part, by differences in the composition of the bacterial community. (C) 2001 Elsevier Science Ltd. All rights reserved.
C1 Plymouth Marine Lab, Plymouth PL1 3DH, Devon, England.
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RP Davey, KE (corresponding author), Plymouth Marine Lab, Prospect Pl,The Hoe, Plymouth PL1 3DH, Devon, England.
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NR 66
TC 49
Z9 59
PY 2001
VL 48
IS 4-5
BP 1003
EP 1017
DI 10.1016/S0967-0645(00)00106-5
UT WOS:000166204500018
DA 2025-07-30
ER

PT J
AU Cerro-Gálvez, E
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AF Cerro-Galvez, Elena
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   Vila-Costa, Maria
TI Responses of Coastal Marine Microbiomes Exposed to Anthropogenic
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SO ENVIRONMENTAL SCIENCE & TECHNOLOGY
DT Article
AB Coastal seawaters receive thousands of organic pollutants. However, we have little understanding of the response of microbiomes to this pool of anthropogenic dissolved organic carbon (ADOC). In this study, coastal microbial communities were challenged with ADOC at environmentally relevant concentrations. Experiments were performed at two Mediterranean sites with different impact by pollutants and nutrients: off the Barcelona harbor ("BCN"), and at the Blanes Bay ("BL"). ADOC additions stimulated prokaryotic leucine incorporation rates at both sites, indicating the use of ADOC as growth substrate. The percentage of "membranecompromised" cells increased with increasing ADOC, indicating concurrent toxic effects of ADOC. Metagenomic analysis of the BCN community challenged with ADOC showed a significant growth of Methylophaga and other gammaproteobacterial taxa belonging to the rare biosphere. Gene expression profiles showed a taxon-dependent response, with significantly enrichments of transcripts from SAR11 and Glaciecola spp. in BCN and BL, respectively. Further, the relative abundance of transposon-related genes (in BCN) and transcripts (in BL) correlated with the number of differentially abundant genes (in BCN) and transcripts (in BLA), suggesting that microbial responses to pollution may be related to pre-exposure to pollutants, with transposons playing a role in adaptation to ADOC. Our results point to a taxon-specific response to low concentrations of ADOC that impact the functionality, structure and plasticity of the communities in coastal seawaters. This work contributes to address the influence of pollutants on microbiomes and their perturbation to ecosystem services and ocean health.
C1 [Cerro-Galvez, Elena; Dachs, Jordi; Fernandez-Pinos, Maria-Carmen; Vila-Costa, Maria] IDAEA CSIC, Dept Environm Chem, Catalunya 08034, Spain.
   [Lundin, Daniel] Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, EEMiS, S-35195 Kalmar, Sweden.
   [Sebastian, Marta] ICM CSIC, Dept Marine Biol & Oceanog, Catalunya 08003, Spain.
RP Vila-Costa, M (corresponding author), IDAEA CSIC, Dept Environm Chem, Catalunya 08034, Spain.
EM maria.vila@idaea.csic.es
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NR 102
TC 18
Z9 21
PD JUL 20
PY 2021
VL 55
IS 14
SI SI
BP 9609
EP 9621
DI 10.1021/acs.est.0c07262
EA FEB 2021
UT WOS:000677482500023
DA 2025-07-30
ER

PT J
AU Clifford, EL
   De Corte, D
   Amano, C
   Paliaga, P
   Ivancic, I
   Ortiz, V
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   Herndl, GJ
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AF Clifford, Elisabeth L.
   De Corte, Daniele
   Amano, Chie
   Paliaga, Paolo
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   Najdek, Mirjana
   Herndl, Gerhard J.
   Sintes, Eva
TI Mesozooplankton taurine production and prokaryotic uptake in the
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SO LIMNOLOGY AND OCEANOGRAPHY
DT Article
AB Dissolved free taurine, an important osmolyte in phytoplankton and metazoans, has been shown to be a significant carbon and energy source for prokaryotes in the North Atlantic throughout the water column. However, the extent of the coupling between taurine production and consumption over a seasonal cycle has not been examined yet. We determined taurine production by abundant crustacean zooplankton and its role as a carbon and energy source for several prokaryotic taxa in the northern Adriatic Sea over a seasonal cycle. Taurine concentrations were generally in the low nanomolar range, reaching a maximum of 22 nmol L(-1)in fall during aPseudonitzschiabloom and coinciding with the highest zooplankton taurine release rates. Taurine accounted for up to 5% of the carbon, 11% of the nitrogen, and up to 71% of the sulfur requirements of heterotrophic prokaryotes. Members of theRoseobacterclade,Alteromonas, Thaumarchaeota, and Euryarchaeota exhibited higher cell-specific taurine assimilation rates than SAR11 cells. However, cell-specific taurine and leucine assimilation were highly variable in all taxa, suggesting species and/or ecotype specific utilization patterns of taurine and dissolved free amino acids. Copepods were able to cover the bulk taurine requirements of the prokaryotic communities in fall and winter and partly in the spring-summer period. Overall, our study emphasizes the significance of taurine as a carbon and energy source for the prokaryotic community in the northern Adriatic Sea and the importance of crustacean zooplankton as a significant source of taurine and other organic compounds for the heterotrophic prokaryotic community.
C1 [Clifford, Elisabeth L.; Amano, Chie; Ortiz, Victor; Herndl, Gerhard J.; Sintes, Eva] Univ Vienna, Dept Funct & Evolutionary Ecol, Vienna, Austria.
   [De Corte, Daniele] Japan Agcy Marine Earth Sci & Technol JAMSTEC, Res & Dev Ctr Marine Biosci, Yokosuka, Kanagawa, Japan.
   [Paliaga, Paolo] Juraj Dobrila Univ Pula, Dept Nat & Hlth Sci, Pula, Croatia.
   [Ivancic, Ingrid; Najdek, Mirjana] Rudjer Boskovic Inst, Ctr Marine Res, Rovinj, Croatia.
   [Herndl, Gerhard J.] Univ Utrecht, Royal Netherlands Inst Sea Res NIOZ, Dept Marine Microbiol & Biogeochem, Den Burg, Netherlands.
   [Sintes, Eva] Inst Espanol Oceanog IEO, Ctr Oceanog Baleares, Palma De Mallorca, Spain.
RP Sintes, E (corresponding author), Univ Vienna, Dept Funct & Evolutionary Ecol, Vienna, Austria.; Sintes, E (corresponding author), Inst Espanol Oceanog IEO, Ctr Oceanog Baleares, Palma De Mallorca, Spain.
EM eva.sintes@ieo.es
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NR 81
TC 7
Z9 9
PD NOV
PY 2020
VL 65
IS 11
BP 2730
EP 2747
DI 10.1002/lno.11544
EA JUN 2020
UT WOS:000542820900001
DA 2025-07-30
ER

PT J
AU Obeid, K
   Kanellopoulos, P
   Abouzayed, A
   Mattsson, A
   Tolmachev, V
   Nock, BA
   Maina, T
   Orlova, A
AF Obeid, Karim
   Kanellopoulos, Panagiotis
   Abouzayed, Ayman
   Mattsson, Adam
   Tolmachev, Vladimir
   Nock, Berthold A.
   Maina, Theodosia
   Orlova, Anna
TI GRPR-Antagonists Carrying DOTAGA-Chelator via Positively Charged
   Linkers: Perspectives for Prostate Cancer Theranostics
SO PHARMACEUTICS
DT Article
AB Gastrin-releasing peptide receptor (GRPR)-antagonists have served as motifs in the development of theranostic radioligands for prostate cancer. Our efforts have been focused on the development of radiolabeled RM26 (H-DPhe6-Gln7-Trp8-Ala9-Val10-Gly11-His12-Sta13-Leu14-NH2) analogs, such as [111In]In-DOTAGA-PEG2-RM26. We recently showed that its Gly11/Sar11-substituted version, [111In]In-AU-RM26-M1, resisted degradation by neprilysin (NEP) while in circulation and achieved higher tumor uptake in mice. We herein introduce the following three new AU-RM26-M1 mimics labeled with In-111, with basic residues in the linker: (i) AU-RM26-M2 (PEG2-Pip), (ii) AU-RM26-M3 (PEG2-Arg), and (iii) AU-RM26-M4 (Arg-Arg-Pip). These analogs were compared in PC-3 cells and animal models vs. AU-RM26-M1 (reference). The new analogs showed high affinity and specificity for the GRPR, exhibiting an uptake and distribution pattern in PC-3 cells typical for a radiolabeled GRPR-antagonist. They showed high stability in peripheral mice blood, except for [111In]In-AU-RM26-M3. AU-RM26-M4 achieved the highest tumor uptake and promising background clearance, followed by [111In]In-RM26-M2, showing lower background levels. These findings were confirmed for [111In]In-AU-RM26-M2 and [111In]In-AU-RM26-M4 by micro-SPECT/CT at 4 and 24 h post-injection. Hence, the type of positively charged residues in the linker of AU-RM26-M1 mimics strongly influenced biological behavior. The analogs with Pip next to DPhe6 demonstrated the best overall characteristics and warrant further investigation.
C1 [Obeid, Karim; Kanellopoulos, Panagiotis; Abouzayed, Ayman; Mattsson, Adam; Orlova, Anna] Uppsala Univ, Dept Med Chem, S-75183 Uppsala, Sweden.
   [Kanellopoulos, Panagiotis; Nock, Berthold A.; Maina, Theodosia] NCSR Demokritos, Mol Radiopharm, INRaSTES, Athens 15341, Greece.
   [Tolmachev, Vladimir] Uppsala Univ, Dept Immunol Genet & Pathol, S-75183 Uppsala, Sweden.
   [Orlova, Anna] Uppsala Univ, Sci Life Lab, Uppsala, Sweden.
RP Orlova, A (corresponding author), Uppsala Univ, Dept Med Chem, S-75183 Uppsala, Sweden.; Orlova, A (corresponding author), Uppsala Univ, Sci Life Lab, Uppsala, Sweden.
EM karim.obeid.1838@student.uu.se; panagiotis.kanellopoulos@ilk.uu.se;
   ayman.abouzayed@ilk.uu.se; adam.mattsson.4918@student.uu.se;
   vladimir.tolmachev@igp.uu.se; nock_berthold.a@hotmail.com;
   maina_thea@hotmail.com; anna.orlova@ilk.uu.se
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NR 41
TC 4
Z9 4
PD APR
PY 2024
VL 16
IS 4
AR 513
DI 10.3390/pharmaceutics16040513
UT WOS:001210289800001
DA 2025-07-30
ER

PT J
AU Riemann, L
   Steward, GF
   Fandino, LB
   Campbell, L
   Landry, MR
   Azam, F
AF Riemann, L
   Steward, GF
   Fandino, LB
   Campbell, L
   Landry, MR
   Azam, F
TI Bacterial community composition during two consecutive NE Monsoon
   periods in the Arabian Sea studied by denaturing gradient gel
   electrophoresis (DGGE) of rRNA genes
SO DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY
DT Article
AB Horizontal and vertical variations in bacterial community composition were examined in samples collected during two Joint Global Ocean Flux Study (JGOFS) Arabian Sea cruises in 1995, The cruises, 11 months apart, took place during two consecutive NE Monsoon periods (January and December). Bacteria were harvested by filtration from samples collected in the mixed layer, mid-water, and deep sea at stations across the study area, Total bacterial community genomic DNA was analyzed by PCR amplification of 16S rRNA gene fragments, followed by denaturing gradient gel electrophoresis (DGGE). In total, 20 DGGE bands reflecting unique or varying phylotypes were excised, cloned and sequenced. Amplicons were dominated by bacterial groups commonly found in oceanic waters (e.g,, the SAR11 cluster of alpha-Proteobacteria and cyanobacteria), but surprisingly none of the sequenced amplicons were related to gamma-Proteobacteria or to members of the Cytophaga-Flavobacter-Bacteroides phylum, Amplicons related to magnetotactic bacteria were found for the first time in pelagic oceanic waters. The DGGE banding patterns revealed a dominance of approximate to 15 distinguishable amplicons in all samples. In the mixed layer the bacterial community was dominated by the same approximate to 15 phylotypes at all stations, but unique phylotypes were found with increasing depth. Except for cyanobacteria, comparison of the bacterial community composition in surface waters from January and December 1995 showed only minor differences, despite significant differences in environmental parameters. These data suggest a horizontal homogeneity and some degree of seasonal predictability of bacterial community composition in the Arabian Sea. (C) 1999 Elsevier Science Ltd. All rights reserved.
C1 Univ Calif San Diego, Scripps Inst Oceanog, Div Marine Biol Res, La Jolla, CA 92093 USA.
   Texas A&M Univ, Dept Oceanog, College Stn, TX 77843 USA.
   Univ Hawaii Manoa, Dept Oceanog, Honolulu, HI 96822 USA.
RP Univ Copenhagen, Freshwater Biol Lab, 51 Helsingorsgade, DK-3400 Hillerod, Denmark.
EM bkb9457@vip.cybercity.dk
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NR 63
TC 110
Z9 129
PY 1999
VL 46
IS 8-9
BP 1791
EP 1811
DI 10.1016/S0967-0645(99)00044-2
UT WOS:000081781000011
DA 2025-07-30
ER

PT J
AU Sun, MQ
   Zhan, YC
   Marsan, D
   Páez-Espino, D
   Cai, LL
   Chen, F
AF Sun, Mengqi
   Zhan, Yuanchao
   Marsan, David
   Paez-Espino, David
   Cai, Lanlan
   Chen, Feng
TI Uncultivated Viral Populations Dominate Estuarine Viromes on the
   Spatiotemporal Scale
SO MSYSTEMS
DT Article
AB Viruses are ubiquitous and abundant in the oceans, and viral metagenomes (viromes) have been investigated extensively via several large-scale ocean sequencing projects. However, there have not been any systematic viromic studies in estuaries. Here, we investigated the viromes of the Delaware Bay and Chesapeake Bay, two Mid-Atlantic estuaries. Deep sequencing generated a total of 48,190 assembled viral sequences (>5 kb) and 26,487 viral populations (9,204 virus clusters and 17,845 singletons), including 319 circular viral contigs between 7.5 kb and 161.8 kb. Unknown viruses represented the vast majority of the dominant populations, while the composition of known viruses, such as pelagiphage and cyanophage, appeared to be relatively consistent across a wide range of salinity gradients and in different seasons. A difference between estuarine and ocean viromes was reflected by the proportions of Myoviridae, Podoviridae, Siphoviridae, Phycodnaviridae, and a few well-studied virus representatives. The difference in viral community between the Delaware Bay and Chesapeake Bay is significantly more pronounced than the difference caused by temperature or salinity, indicating strong local profiles caused by the unique ecology of each estuary. Interestingly, a viral contig similar to phages infecting Acinetobacter baumannii ("Iraqibacter") was found to be highly abundant in the Delaware Bay but not in the Chesapeake Bay, the source of which is yet to be identified. Highly abundant viruses in both estuaries have close hits to viral sequences derived from the marine single-cell genomes or long-read single-molecule sequencing, suggesting that important viruses are still waiting to be discovered in the estuarine environment.
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C1 [Sun, Mengqi; Zhan, Yuanchao; Marsan, David; Chen, Feng] Univ Maryland, Ctr Environm Sci, Inst Marine & Environm Technol, Baltimore, MD 21201 USA.
   [Paez-Espino, David] Joint Genome Inst, Dept Energy, Berkeley, CA USA.
   [Paez-Espino, David] Mammoth Biosci Inc, San Francisco, CA USA.
   [Cai, Lanlan] Xiamen Univ Xiangan, Inst Marine Microbes & Ecospheres, State Key Lab Marine Environm Sci, Xiamen, Peoples R China.
RP Chen, F (corresponding author), Univ Maryland, Ctr Environm Sci, Inst Marine & Environm Technol, Baltimore, MD 21201 USA.
EM chenf@umces.edu
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NR 87
TC 19
Z9 20
PD MAR
PY 2021
VL 6
IS 2
AR e01020-20
DI 10.1128/mSystems.01020-20
UT WOS:000665831100008
DA 2025-07-30
ER

PT J
AU Dobal-Amador, V
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AF Dobal-Amador, Vladimir
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TI Vertical stratification of bacterial communities driven by multiple
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SO DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS
DT Article
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C1 [Dobal-Amador, Vladimir; Guerrero-Feijoo, Elisa; Varela, Marta M.] IEO, Ctr Oceanog A Coruna, Apdo 130, La Coruna 15080, Spain.
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RP Varela, MM (corresponding author), IEO, Ctr Oceanog A Coruna, Apdo 130, La Coruna 15080, Spain.
EM marta.varela@co.ieo.es
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NR 61
TC 19
Z9 22
PD AUG
PY 2016
VL 114
BP 1
EP 11
DI 10.1016/j.dsr.2016.04.009
UT WOS:000381531500001
DA 2025-07-30
ER

PT J
AU Milke, F
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AF Milke, Felix
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TI Composition and Biogeography of Planktonic Pro- and Eukaryotic
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SO FRONTIERS IN MICROBIOLOGY
DT Article
AB Basin-scale biogeographic observations of marine pelagic pro- and eukaryotic communities are necessary to understand forces driving community composition and for providing a baseline to monitor global change. Deep sequencing of rRNA genes provides community composition at high resolution; yet, it is unclear how the choice of primers affects biogeographic patterns. Here, we re-amplified 16S rRNA genes from DNA sampled during R/V Polarstern Cruise ANT28-5 over a latitudinal transect across the Atlantic Ocean from 52 degrees S to 47 degrees N using universal V4-V5 primers and compared the results with those obtained previously with V5-V6 bacteria-specific primers. For validation of our results, we inferred community composition based on 16S rRNA genes of metagenomes from the same stations and single amplified genomes (SAGs) from the Global Ocean Reference Genome (GORG) database. We found that the universal V4-V5 primers retrieved SAR11 clades with similar relative proportions as those found in the GORG database while the V5-V6 primers recovered strongly diverging clade abundances. We confirmed an inverse bell-shaped distance-decay relationship and a latitudinal diversity gradient that did not decline linearly with absolute latitude in the Atlantic Ocean. Patterns were modified by sampling depth, sequencing depth, choice of primers, and abundance filtering. Especially richness patterns were not robust to methodological change. This study offers a detailed picture of the Atlantic Ocean microbiome using a universal set of PCR primers that allow for the conjunction of biogeographical patterns among organisms from different domains of life.
C1 [Milke, Felix; Dlugosch, Leon; Simon, Meinhard] Carl von Ossietzky Univ Oldenburg, Inst Chmistry & Biol Marine Environm, Oldenburg, Germany.
   [Sanchez-Garcia, Selene; Wagner-Doebler, Irene] Tech Univ Carolo Wilhelmina Braunschweig, Inst Microbiol, Braunschweig, Germany.
   [McNichol, Jesse; Fuhrman, Jed] Univ Southern Calif, Dept Biol Sci, Los Angeles, CA USA.
   [Simon, Meinhard] Helmholtz Inst Funct Marine Biodivers, Oldenburg, Germany.
RP Wagner-Doebler, I (corresponding author), Tech Univ Carolo Wilhelmina Braunschweig, Inst Microbiol, Braunschweig, Germany.
EM I.Wagner-Doebler@tu-braunschweig.de
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NR 72
TC 6
Z9 6
PD JUN 28
PY 2022
VL 13
AR 895875
DI 10.3389/fmicb.2022.895875
UT WOS:000824496400001
DA 2025-07-30
ER

PT J
AU Schattenhofer, M
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AF Schattenhofer, Martha
   Wulf, Joerg
   Kostadinov, Ivalyo
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TI Phylogenetic characterisation of picoplanktonic populations with high
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SO SYSTEMATIC AND APPLIED MICROBIOLOGY
DT Article
AB In flow cytometric analyses of marine prokaryotic picoplankton often two populations with distinct differences in their apparent nucleic acid content are discernable, one with a high and one with a low nucleic acid content (HNA and LNA, respectively). In this study we determined the phylogenetic composition of flow cytometrically sorted HNA and LNA populations, collected at six stations along a transect across three oceanic provinces from Iceland to the Azores. Catalysed reporter deposition fluorescence in situ hybridisation (CARD-FISH) analysis of sorted cells revealed distinct differences in phylogenetic composition between the LNA and HNA populations with only little overlap. At all stations the LNA population was dominated by the alphaproteobacterial clade SAR11 (45-74%). Also, Betaproteobacteria were always present at 2-4%. While the LNA composition was rather stable, the HNA populations were composed of distinct phylogenetic clades in the different oceanic provinces of Arctic and Tropics. For example Cyanobacteria dominated the North Atlantic Gyre HNA population (29-44%) with Prochlorococcus as the major clade (34-44%), but were low in Arctic and Polar waters (1% and 5%, respectively). In contrast, Bacteroidetes accounted for the majority of HNA cells in the Polar and Arctic province (26% and 32%, respectively), but were low in the Gyre region (3-10%). The DNA content of the HNA population was about 3.5 times higher than that of the LNA populations. This reflects differences in the genome sizes of closely related cultured representatives of HNA clades (3-6 Mbp) and LNA clades (1.3-1.5 Mbp). (C) 2011 Elsevier GmbH. All rights reserved.
C1 [Schattenhofer, Martha; Wulf, Joerg; Fuchs, Bernhard M.] Max Planck Inst Marine Microbiol, Dept Mol Ecol, Bremen, Germany.
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   [Kostadinov, Ivalyo; Gloeckner, Frank Oliver] Univ Bremen, Bremen, Germany.
RP Fuchs, BM (corresponding author), Celsiusstr 1, D-28359 Bremen, Germany.
EM bfuchs@mpi-bremen.de
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NR 35
TC 71
Z9 80
PD SEP
PY 2011
VL 34
IS 6
BP 470
EP 475
DI 10.1016/j.syapm.2011.01.008
UT WOS:000295743800013
DA 2025-07-30
ER

PT J
AU Satinsky, BM
   Zielinski, BL
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   Crump, BC
   Moran, MA
AF Satinsky, Brandon M.
   Zielinski, Brian L.
   Doherty, Mary
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   Moran, Mary Ann
TI The Amazon continuum dataset: quantitative metagenomic and
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SO MICROBIOME
DT Article
AB Background: The Amazon River is by far the world's largest in terms of volume and area, generating a fluvial export that accounts for about a fifth of riverine input into the world's oceans. Marine microbial communities of the Western Tropical North Atlantic Ocean are strongly affected by the terrestrial materials carried by the Amazon plume, including dissolved (DOC) and particulate organic carbon (POC) and inorganic nutrients, with impacts on primary productivity and carbon sequestration.
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RP Moran, MA (corresponding author), Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
EM mmoran@uga.edu
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TC 47
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PD MAY 15
PY 2014
VL 2
AR 17
DI 10.1186/2049-2618-2-17
UT WOS:000363192000001
DA 2025-07-30
ER

PT J
AU Gifford, SM
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SO FRONTIERS IN MICROBIOLOGY
DT Article
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RP Moran, MA (corresponding author), Univ Georgia, Dept Marine Sci, 220 Marine Sci Bldg, Athens, GA 30602 USA.
EM mmoran@uga.eduu
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PD APR 24
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VL 5
AR 185
DI 10.3389/fmicb.2014.00185
UT WOS:000334854400001
DA 2025-07-30
ER

PT J
AU Saidi, A
   Banchi, E
   Fonti, V
   Manna, V
   De Vittor, C
   Giani, M
   Malfatti, F
   Celussi, M
AF Saidi, Amira
   Banchi, Elisa
   Fonti, Viviana
   Manna, Vincenzo
   De Vittor, Cinzia
   Giani, Michele
   Malfatti, Francesca
   Celussi, Mauro
TI Microbial dynamics in shallow CO2 seeps system off Panarea
   Island (Italy)
SO MARINE BIOLOGY
DT Article
AB Shallow-water hydrothermal vents are extreme environments characterized by high temperatures, low pH, and high CO2 concentrations; therefore, they are considered as suitable laboratories for studying the effect of global changes on marine microbes. We hypothesized a direct effect of vents on prokaryotic community structure and functioning in the Panarea Island's hydrothermal system. Sampling was conducted along a 9-station transect characterized by three active emission points. The water column was stratified with a thermocline at 25 m depth and a deep chlorophyll maximum between 50 and 100 m. Prokaryotic abundance ranged from 0.2 to 1.5 x 10(9) cells L-1, prokaryotic carbon production from 2.4 to 75.4 ng C L-1 h(-1), and exoenzymatic activities degrading proteins, phosphorylated compounds, and polysaccharides were on the order of 4-28, 2-31 and 0.2-4.16 nM h(-1), respectively. While microbial abundance and production were shaped by the water column's physical structure, alkaline phosphatase and beta-glucosidase activities seemed to be enhanced by hydrothermal fluids. The 16S rRNA gene amplicon sequencing analysis identified a surface, a deep, and a vent-influenced microbial community. In terms of relative abundance members of the SAR11 group dominated the water column, alongside Synechococcus and Prochlorococcus in surface and bottom samples, respectively. Vent-influenced stations were characterized by the presence of Thiomicrorhabdus, a sulfur-oxidizer chemolithoautotroph. Overall, this study provides insights on the coupling between microbial community structure and the biogeochemical cycling of nutrients in low-pH conditions (CO2 and H2S-based), thus addressing some of the opened questions about the response of microbes to acidification.
C1 [Saidi, Amira; Banchi, Elisa; Fonti, Viviana; Manna, Vincenzo; De Vittor, Cinzia; Giani, Michele; Malfatti, Francesca; Celussi, Mauro] Ist Nazl Oceanog E Geofis Sperimentale, OGS, Trieste, Italy.
   [Saidi, Amira] CaFoscari Univ Venezia, Venice, Italy.
   [Malfatti, Francesca] Univ Trieste, Trieste, Italy.
RP Saidi, A; Malfatti, F; Celussi, M (corresponding author), Ist Nazl Oceanog E Geofis Sperimentale, OGS, Trieste, Italy.; Saidi, A (corresponding author), CaFoscari Univ Venezia, Venice, Italy.; Malfatti, F (corresponding author), Univ Trieste, Trieste, Italy.
EM asaidi@ogs.it; fmalfatti@units.it; mcelussi@ogs.it
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NR 97
TC 3
Z9 3
PD AUG
PY 2023
VL 170
IS 8
AR 97
DI 10.1007/s00227-023-04247-8
UT WOS:001017472700001
DA 2025-07-30
ER

PT J
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NR 66
TC 33
Z9 36
PD APR
PY 2010
VL 33
IS 3
BP 128
EP 138
DI 10.1016/j.syapm.2009.12.006
UT WOS:000278007200004
DA 2025-07-30
ER

PT J
AU Poretsky, RS
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   Moran, MA
AF Poretsky, Rachel S.
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TI Comparative day/night metatranscriptomic analysis of microbial
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Metatranscriptomic analyses of microbial assemblages (< 5 mu m) from surface water at the Hawaiian Ocean Time-Series (HOT) revealed community-wide metabolic activities and day/night patterns of differential gene expression. Pyrosequencing produced 75 558 putative mRNA reads from a day transcriptome and 75 946 from a night transcriptome. Taxonomic binning of annotated mRNAs indicated that Cyanobacteria contributed a greater percentage of the transcripts (54% of annotated sequences) than expected based on abundance (35% of cell counts and 21% 16S rRNA of libraries), and may represent the most actively transcribing cells in this surface ocean community in both the day and night. Major heterotrophic taxa contributing to the community transcriptome included alpha-Proteobacteria (19% of annotated sequences, most of which were SAR11-related) and gamma-Proteobacteria (4%). The composition of transcript pools was consistent with models of prokaryotic gene expression, including operon-based transcription patterns and an abundance of genes predicted to be highly expressed. Metabolic activities that are shared by many microbial taxa (e.g. glycolysis, citric acid cycle, amino acid biosynthesis and transcription and translation machinery) were well represented among the community transcripts. There was an overabundance of transcripts for photosynthesis, C1 metabolism and oxidative phosphorylation in the day compared with night, and evidence that energy acquisition is coordinated with solar radiation levels for both autotrophic and heterotrophic microbes. In contrast, housekeeping activities such as amino acid biosynthesis, membrane synthesis and repair, and vitamin biosynthesis were overrepresented in the night transcriptome. Direct sequencing of these environmental transcripts has provided detailed information on metabolic and biogeochemical responses of a microbial community to solar forcing.
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RP Moran, MA (corresponding author), Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
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NR 51
TC 220
Z9 259
PD JUN
PY 2009
VL 11
IS 6
BP 1358
EP 1375
DI 10.1111/j.1462-2920.2008.01863.x
UT WOS:000266597200005
DA 2025-07-30
ER

PT J
AU Lemonnier, C
   Perennou, M
   Eveillard, D
   Fernandez-Guerra, A
   Leynaert, A
   Marié, L
   Morrison, HG
   Memery, L
   Paillard, C
   Maignien, L
AF Lemonnier, Clarisse
   Perennou, Morgan
   Eveillard, Damien
   Fernandez-Guerra, Antonio
   Leynaert, Aude
   Marie, Louis
   Morrison, Hilary G.
   Memery, Laurent
   Paillard, Christine
   Maignien, Lois
TI Linking Spatial and Temporal Dynamic of Bacterioplankton Communities
   With Ecological Strategies Across a Coastal Frontal Area
SO FRONTIERS IN MARINE SCIENCE
DT Article
AB Ocean frontal systems are widespread hydrological features defining the transition zone between distinct water masses. They are generally of high biological importance as they are often associated with locally enhanced primary production by phytoplankton. However, the composition of bacterial communities in the frontal zone remains poorly understood. In this study, we investigate how a coastal tidal front in Brittany (France) structures the free-living bacterioplankton communities in a spatio-temporal survey across four cruises, five stations and three depths. We used 16S rRNA gene surveys to compare bacterial community structures across 134 seawater samples and defined groups of co-varying taxa (modules) exhibiting coherent ecological patterns across space and time. We found that bacterial communities composition was strongly associated with the biogeochemical characteristics of the different water masses and that the front act as an ecological boundary for free-living bacteria. Seasonal variations in primary producers and their distribution in the water column appeared as the most salient parameters controlling heterotrophic bacteria which dominated the free-living community. Different dynamics of modules observed in this environment were strongly consistent with a partitioning of heterotrophic bacterioplankton in oligotroph and copiotroph ecological strategies. Oligotroph taxa, dominated by SAR11 Clade members, were relatively more abundant in low phytoplankton, high inorganic nutrients water masses, while copiotrophs and particularly opportunist taxa such as Tenacibaculum sp. or Pseudoalteromonas sp. reached their highest abundances during the more productive period. Overall, this study shows a remarkable coupling between bacterioplankton communities dynamics, trophic strategies, and seasonal cycles in a complex coastal environment.
C1 [Lemonnier, Clarisse; Maignien, Lois] Univ Brest UBO, Lab Microbiol Environm Extremes, CNRS, IFREMER, Plouzane, France.
   [Lemonnier, Clarisse; Perennou, Morgan; Leynaert, Aude; Memery, Laurent; Paillard, Christine] Univ Brest UBO, Lab Sci Environm Mann, CNRS, IRD,Ifremer, Plouzane, France.
   [Eveillard, Damien] Univ Nantes, Lab Sci Numer Nantes, CNRS, Cent Nantes,IMTA, Nantes, France.
   [Fernandez-Guerra, Antonio] Max Planck Inst Marine Microbiol, Microbial Genom & Bioinformat Res Grp, Bremen, Germany.
   [Fernandez-Guerra, Antonio] Univ Copenhagen, GLOBE Inst, Lundbeck Fdn GeoGenet Ctr, Copenhagen, Denmark.
   [Fernandez-Guerra, Antonio] Univ Bremen, Ctr Marine Environm Sci, Bremen, Germany.
   [Marie, Louis] Univ Brest, CNRS, IRD, Ifremer,Lab Oceanog Phys & Spatiale, Plouzane, France.
   [Morrison, Hilary G.; Maignien, Lois] Josephine Bay Paul Ctr Comparat Mol Biol & Evolut, Marine Biol Lab, Woods Hole, MA 02543 USA.
RP Lemonnier, C; Maignien, L (corresponding author), Univ Brest UBO, Lab Microbiol Environm Extremes, CNRS, IFREMER, Plouzane, France.; Lemonnier, C (corresponding author), Univ Brest UBO, Lab Sci Environm Mann, CNRS, IRD,Ifremer, Plouzane, France.; Maignien, L (corresponding author), Josephine Bay Paul Ctr Comparat Mol Biol & Evolut, Marine Biol Lab, Woods Hole, MA 02543 USA.
EM clarisse.lemonnier@univ-brest.fr; lois.maignien@univ-brest.fr
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NR 84
TC 10
Z9 10
PD JUN 9
PY 2020
VL 7
AR 376
DI 10.3389/fmars.2020.00376
UT WOS:000538994800001
DA 2025-07-30
ER

PT J
AU Rappe, MS
   Kemp, PF
   Giovannoni, SJ
AF Rappe, MS
   Kemp, PF
   Giovannoni, SJ
TI Phylogenetic diversity of marine coastal picoplankton 16S rRNA genes
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SO LIMNOLOGY AND OCEANOGRAPHY
DT Article
AB The phylogenetic diversity of a continental-shelf picoplankton community was examined by analyzing 16S ribosomal RNA (rRNA) genes amplified from environmental DNA with bacterial-specific primers and the polymerase chain reaction (PCR). Picoplankton populations collected from the pycnocline (10 m) over the eastern continental shelf of the United States near Cape Hatteras, North Carolina, served as the source of bulk nucleic acids used in this study. A large proportion of the 169 rDNA clones recovered (33%) were related to plastid 16S rRNA genes, including plastids from both chromophyte and chlorophyte algae. Most bacterial gene clones (75% of bacterial clones, 50% of the total) were closely related to rRNA gene lineages that had been discovered previously in clone libraries from open-ocean marine habitats, including the SAR86 cluster (gamma-Proteobacteria), SAR83, SAR11, and SAR116 clusters (all or-Proteobacteria), as well as the marine Gram-positive cluster (high G+C Gram-positive). Most of the remaining bacterial clones recovered were phylogenetically related to the gamma and beta subclasses of the Proteobacteria, including an rDNA lineage within the type 1 methylotroph clade of the beta subclass. The abundance of plastid rDNAs and the lack of cyanobacterial-related clones, as well as the presence of beta-Proteobacteria, are features of this coastal picoplankton gene clone library that distinguish it from similar studies of oligotrophic open-ocean sites. Overall, however, these data indicate that a limited number of as yet uncultured bacterioplankton lineages, related to those previously observed in the open ocean, can account for most cells in this coastal marine bacterioplankton assemblage.
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PY 1997
VL 42
IS 5
BP 811
EP 826
DI 10.4319/lo.1997.42.5.0811
UT WOS:A1997YK66100003
DA 2025-07-30
ER

PT J
AU Dupont, CL
   McCrow, JP
   Valas, R
   Moustafa, A
   Walworth, N
   Goodenough, U
   Roth, R
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   Bai, J
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AF Dupont, Chris L.
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   Bai, Jing
   Johnson, Zackary I.
   Mann, Elizabeth
   Palenik, Brian
   Barbeau, Katherine A.
   Venter, J. Craig
   Allen, Andrew E.
TI Genomes and gene expression across light and productivity gradients in
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SO ISME JOURNAL
DT Article
AB Transitions in community genomic features and biogeochemical processes were examined in surface and subsurface chlorophyll maximum (SCM) microbial communities across a trophic gradient from mesotrophic waters near San Diego, California to the oligotrophic Pacific. Transect end points contrasted in thermocline depth, rates of nitrogen and CO2 uptake, new production and SCM light intensity. Relative to surface waters, bacterial SCM communities displayed greater genetic diversity and enrichment in putative sulfur oxidizers, multiple actinomycetes, low-light-adapted Prochlorococcus and cell-associated viruses. Metagenomic coverage was not correlated with transcriptional activity for several key taxa within Bacteria. Low-light-adapted Prochlorococcus, Synechococcus, and low abundance gamma-proteobacteria enriched in the > 3.0-mu m size fraction contributed disproportionally to global transcription. The abundance of these groups also correlated with community functions, such as primary production or nitrate uptake. In contrast, many of the most abundant bacterioplankton, including SAR11, SAR86, SAR112 and high-light-adapted Prochlorococcus, exhibited low levels of transcriptional activity and were uncorrelated with rate processes. Eukaryotes such as Haptophytes and non-photosynthetic Aveolates were prevalent in surface samples while Mamielles and Pelagophytes dominated the SCM. Metatranscriptomes generated with ribosomal RNA-depleted mRNA (total mRNA) coupled to in vitro polyadenylation compared with polyA-enriched mRNA revealed a trade-off in detection eukaryotic organelle and eukaryotic nuclear origin transcripts, respectively. Gene expression profiles of SCM eukaryote populations, highly similar in sequence identity to the model pelagophyte Pelagomonas sp. CCMP1756, suggest that pelagophytes are responsible for a majority of nitrate assimilation within the SCM.
C1 [Dupont, Chris L.; McCrow, John P.; Valas, Ruben; Walworth, Nathan; Bai, Jing; Venter, J. Craig; Allen, Andrew E.] J Craig Venter Inst, Microbial & Environm Genom Grp, La Jolla, CA 92037 USA.
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RP Allen, AE (corresponding author), J Craig Venter Inst, Microbial & Environm Genom Grp, 4120 Capricorn Lane, La Jolla, CA 92037 USA.
EM aallen@jcvi.org
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NR 68
TC 84
Z9 97
PD MAY
PY 2015
VL 9
IS 5
BP 1076
EP 1092
DI 10.1038/ismej.2014.198
UT WOS:000353354100003
DA 2025-07-30
ER

PT J
AU Djurhuus, A
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AF Djurhuus, Anni
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   Hatun, Hjalmar
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TI Seasonal progression of microbial communities on the Faroe shelf
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DT Article
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RP Djurhuus, A (corresponding author), Faroe Marine Res Inst, Noatun 1, FO-100 Torshavn, Faroe Islands, Denmark.
EM anni.djurhuus@gmail.com
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NR 78
TC 2
Z9 2
PY 2015
VL 11
IS 9
BP 895
EP 908
DI 10.1080/17451000.2015.1041532
UT WOS:000362342500001
DA 2025-07-30
ER

PT J
AU Walsh, EA
   Smith, DC
   Sogin, ML
   D'Hondt, S
AF Walsh, Emily A.
   Smith, David C.
   Sogin, Mitchell L.
   D'Hondt, Steven
TI Bacterial and archaeal biogeography of the deep chlorophyll maximum in
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SO AQUATIC MICROBIAL ECOLOGY
DT Article
AB We used 16S rRNA gene tag pyro sequencing to examine the biogeography of bacterial and archaeal community composition in the deep chlorophyll maximum (DCM) of the South Pacific Gyre (SPG), the largest and most oligotrophic region of the world ocean. Dominant DCM bacterial taxa, including Prochlorococcus, SAR11, SAR406, and SAR86, were present at each sampled site in similar proportions, although the sites are separated by thousands of kilometers and up to 100 m in water depth. Marine Group II (MGII) and MGIII Euryarcheota dominated the archaeal assemblages of the DCM at these sites. Bray-Curtis indices show that assemblage composition of these sites is > 70% similar for Bacteria and > 80% similar for Archaea. Despite these similarities, communities of the central SPG, the western SPG margin, and the southern SPG margin are distinguishable from each other. Comparison of our bacterial results to samples from the DCM of the North Pacific Gyre (NPG) and the relatively nutrient-and chlorophyll-rich Equatorial Pacific (EQP) shows that DCM bacterial assemblage composition is > 50% similar throughout all 3 regions. Nonetheless, the SPG, NPG, and EQP assemblages are statistically distinct from each other (ANOSIM, p = 0.001), with the communities of the 2 gyres resembling each other more closely than either resembles the EQP community (which lives geographically between them). Variation in assemblage composition correlates with sea-surface chlorophyll concentration (r(2) = 0.71, p < 0.003). This study demonstrates that the DCM horizons of different oceanic regions harbor statistically distinct communities that are consistent within regions for thousands of kilometers.
C1 [Walsh, Emily A.; Smith, David C.; D'Hondt, Steven] Univ Rhode Isl, Grad Sch Oceanog, Narragansett, RI 02882 USA.
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RP Walsh, EA (corresponding author), Univ Rhode Isl, Grad Sch Oceanog, Narragansett Bay Campus,215 South Ferry Rd, Narragansett, RI 02882 USA.
EM ewalsh@gso.uri.edu
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NR 51
TC 22
Z9 26
PY 2015
VL 75
IS 1
BP 1
EP 13
DI 10.3354/ame01746
UT WOS:000354392600001
DA 2025-07-30
ER

PT J
AU Sowell, SM
   Abraham, PE
   Shah, M
   Verberkmoes, NC
   Smith, DP
   Barofsky, DF
   Giovannoni, SJ
AF Sowell, Sarah M.
   Abraham, Paul E.
   Shah, Manesh
   Verberkmoes, Nathan C.
   Smith, Daniel P.
   Barofsky, Douglas F.
   Giovannoni, Stephen J.
TI Environmental proteomics of microbial plankton in a highly productive
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SO ISME JOURNAL
DT Article
AB Metaproteomics is one of a suite of new approaches providing insights into the activities of microorganisms in natural environments. Proteins, the final products of gene expression, indicate cellular priorities, taking into account both transcriptional and posttranscriptional control mechanisms that control adaptive responses. Here, we report the proteomic composition of the < 1.2 mu m fraction of a microbial community from Oregon coast summer surface waters, detected with two-dimensional liquid chromatography coupled with electrospray tandem mass spectrometry. Spectra corresponding to proteins involved in protein folding and biosynthesis, transport, and viral capsid structure were the most frequently detected. A total of 36% of all the detected proteins were best matches to the SAR11 clade, and other abundant coastal microbial clades were also well represented, including the Roseobacter clade (17%), oligotrophic marine gammaproteobacteria group (6%), OM43 clade (1%). Viral origins were attributed to 2.5% of proteins. In contrast to oligotrophic waters, phosphate transporters were not highly detected in this nutrient-rich system. However, transporters for amino acids, taurine, polyamines and glutamine synthetase were among the most highly detected proteins, supporting predictions that carbon and nitrogen are more limiting than phosphate in this environment. Intriguingly, one of the highly detected proteins was methanol dehydrogenase originating from the OM43 clade, providing further support for recent reports that the metabolism of one-carbon compounds by these streamlined methylotrophs might be an important feature of coastal ocean biogeochemistry. The ISME Journal (2011) 5, 856-865; doi:10.1038/ismej.2010.168; published online 11 November 2010
C1 [Giovannoni, Stephen J.] Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
   [Sowell, Sarah M.; Smith, Daniel P.] Oregon State Univ, Mol & Cellular Biol Program, Corvallis, OR 97331 USA.
   [Abraham, Paul E.; Shah, Manesh; Verberkmoes, Nathan C.] Oak Ridge Natl Lab, Div Chem, Oak Ridge, TN 37831 USA.
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   [Barofsky, Douglas F.] Oregon State Univ, Dept Chem, Corvallis, OR 97331 USA.
RP Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, 220 Nash Hall, Corvallis, OR 97331 USA.
EM steve.giovannoni@oregonstate.edu
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NR 52
TC 129
Z9 142
PD MAY
PY 2011
VL 5
IS 5
BP 856
EP 865
DI 10.1038/ismej.2010.168
UT WOS:000290022500009
DA 2025-07-30
ER

PT J
AU López-Pérez, M
   Haro-Moreno, JM
   Gonzalez-Serrano, R
   Parras-Moltó, M
   Rodriguez-Valera, F
AF Lopez-Perez, Mario
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   Parras-Molto, Marcos
   Rodriguez-Valera, Francisco
TI Genome diversity of marine phages recovered from Mediterranean
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SO PLOS GENETICS
DT Article
AB Marine viruses play a critical role not only in the global geochemical cycles but also in the biology and evolution of their hosts. Despite their importance, viral diversity remains under-explored mostly due to sampling and cultivation challenges. Direct sequencing approaches such as viromics has provided new insights into the marine viral world. As a complementary approach, we analysed 24 microbial metagenomes (> 0.2 mu m size range) obtained from six sites in the Mediterranean Sea that vary by depth, season and filter used to retrieve the fraction. Filter-size comparison showed a significant number of viral sequences that were retained on the larger-pore filters and were different from those found in the viral fraction from the same sample, indicating that some important viral information is missing using only assembly from viromes. Besides, we were able to describe 1,323 viral genomic fragments that were more than 10Kb in length, of which 36 represented complete viral genomes including some of them retrieved from a cross-assembly from different metagenomes. Host prediction based on sequence methods revealed new phage groups belonging to marine prokaryotes like SAR11, Cyanobacteria or SAR116. We also identified the first complete vir-ophage from deep seawater and a new endemic clade of the recently discovered Marine group II Euryarchaeota virus. Furthermore, analysis of viral distribution using metagenomes and viromes indicated that most of the new phages were found exclusively in the Mediterranean Sea and some of them, mostly the ones recovered from deep metagenomes, do not recruit in any database probably indicating higher variability and endemicity in Mediterranean bathypelagic waters. Together these data provide the first detailed picture of genomic diversity, spatial and depth variations of viral communities within the Mediterranean Sea using metagenome assembly.
C1 [Lopez-Perez, Mario; Haro-Moreno, Jose M.; Gonzalez-Serrano, Rafael; Rodriguez-Valera, Francisco] Univ Miguel Hernandez, Div Microbiol, Evolutionary Genom Grp, Campus San Juan, Alacant, Spain.
   [Parras-Molto, Marcos] CSIC, Ctr Biol Mol Severo Ochoa, Madrid, Spain.
   [Parras-Molto, Marcos] Univ Autonoma Madrid, Madrid, Spain.
RP Rodriguez-Valera, F (corresponding author), Univ Miguel Hernandez, Div Microbiol, Evolutionary Genom Grp, Campus San Juan, Alacant, Spain.
EM frvalera@umh.es
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UT WOS:000411976100038
DA 2025-07-30
ER

PT J
AU Zhang, XL
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TI Abundance, Diversity and Functional Potentials of Planktonic Bacteria
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SO JOURNAL OF OCEAN UNIVERSITY OF CHINA
DT Article
AB Corals influence microorganisms within the surrounding seawater, yet the diversities and functions of seawater bacteria and microeukaryotes in coral-reef systems have not been well addressed. We collected 40 seawater samples in outer coral reef flats and semi-closed inner lagoons from the surface, middle and bottom layers in the pristine coral-reef system of Xisha Islands, South China Sea. We detected the abundance, composition and distribution of bacteria and microeukaryotes using flow cytometry, qPCR and high throughput sequencing techniques, and profiled the potential ecological roles based on the information of 16S and 18S rDNA sequencing. In terms of flow cytometry, Prochlorococcus dominated the autotrophs with cell abundance ranging from 5.8 x 10(2) to 5.44 x 10(3) cells mL(-1) seawater. Based on qPCR, the 16S rDNA copies were much higher in coral reef flats than in lagoons (P=0.003). The bacterial communities held significantly lower diversity in bottom waters compared with surface and middle waters (P < 0.05), which were dominated by SAR11, Flavobacteriales, and Synechococcus. Alveolata represented most of the microeukaryotic communities with Dinophyceae and Syndiniales well represented in all samples. Neither bacterial nor microeukaryotic community exhibited distinct layer or niche pattern, however, Haptophyta and Picozoa decreased with depth and SAR 86, MAST-3 and Picozoa were enriched in lagoons (P <0.05). To adapt the nutrient-poor and organic matter-rich environment, bacterial nitrogen fixation and assimilatory/dissimilatory nitrate reduction were active in the system, and mixotrophy was the most important trophic strategy among microeukaryotes. The study highlighted the ecological adaptability of seawater microbes to the unique coral-reef environments.
C1 [Zhang Xiaoli; Wang Lei; Peng Saijun; Wuzhong Qiyue; Dong Zhijun; Sun Tingting; Liu Ping; Zhang Qianqian; Zhao Jiamnin] Chinese Acad Sci, Yantai Inst Coastal Zone Res, Yantai 264003, Peoples R China.
   [Peng Saijun; Sun Tingting] Univ Chinese Acad Sci, Beijing 100049, Peoples R China.
   [Wuzhong Qiyue] Hainan Univ, Coll Marine Sci, State Key Lab Marine Resource Utilizat South Chin, Haikou 570228, Hainan, Peoples R China.
   [Zhang Lei] Yantai Univ, Coll Life Sci, Yantai 264005, Peoples R China.
RP Dong, ZJ; Zhao, JN (corresponding author), Chinese Acad Sci, Yantai Inst Coastal Zone Res, Yantai 264003, Peoples R China.
EM zjdong@yic.ac.cn; jmzhao@yic.ac.cn
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NR 90
TC 2
Z9 2
PD JUN
PY 2022
VL 21
IS 3
BP 748
EP 762
DI 10.1007/s11802-022-5107-y
UT WOS:000795139600022
DA 2025-07-30
ER

PT J
AU Chen, SZ
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DT Article
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RP Hou, SW; Zhang, CL (corresponding author), Southern Univ Sci & Technol, Dept Ocean Sci & Engn, Shenzhen Key Lab Marine Archaea Geoom, Shenzhen 518000, Peoples R China.; Hou, SW (corresponding author), Shanghai Jiao Tong Univ, Shanghai Key Lab Polar Life & Environm Sci, Shanghai 200030, Peoples R China.; Hou, SW (corresponding author), Shanghai Jiao Tong Univ, Key Lab Polar Ecosyst & Climate Change, Shanghai 200030, Peoples R China.; Zhang, CL (corresponding author), Shanghai Earthquake Agcy, Shanghai Sheshan Natl Geophys Observ, Shanghai 200062, Peoples R China.
EM housw@sustech.edu.cn; zhangcl@sustech.edu.cn
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NR 71
TC 1
Z9 1
PD APR 16
PY 2024
VL 3
AR 0044
DI 10.34133/olar.0044
UT WOS:001524155200001
DA 2025-07-30
ER

PT J
AU Gronniger, JL
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   Hunt, DE
AF Gronniger, Jessica L.
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TI A Gulf Stream frontal eddy harbors a distinct microbiome compared to
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SO PLOS ONE
DT Article
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C1 [Gronniger, Jessica L.; Gray, Patrick C.; Johnson, Zackary I.; Hunt, Dana E.] Duke Univ, Marine Lab, Beaufort, NC 28516 USA.
   [Niebergall, Alexandria K.] Duke Univ, Nicholas Sch Environm, Durham, NC USA.
   [Johnson, Zackary I.; Hunt, Dana E.] Duke Univ, Biol & Civil & Environm Engn, Durham, NC 27708 USA.
RP Hunt, DE (corresponding author), Duke Univ, Marine Lab, Beaufort, NC 28516 USA.; Hunt, DE (corresponding author), Duke Univ, Biol & Civil & Environm Engn, Durham, NC 27708 USA.
EM dana.hunt@duke.edu
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NR 65
TC 3
Z9 4
PD NOV 9
PY 2023
VL 18
IS 11
AR e0293334
DI 10.1371/journal.pone.0293334
UT WOS:001124300500033
DA 2025-07-30
ER

PT J
AU Wienhausen, G
   Dlugosch, L
   Jarling, R
   Wilkes, H
   Giebel, HA
   Simon, M
AF Wienhausen, Gerrit
   Dlugosch, Leon
   Jarling, Rene
   Wilkes, Heinz
   Giebel, Helge-A.
   Simon, Meinhard
TI Availability of vitamin B12 and its lower ligand intermediate
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SO ISME JOURNAL
DT Article
AB Genome analyses predict that the cofactor cobalamin (vitamin B-12, called B-12 herein) is produced by only one-third of all prokaryotes but almost all encode at least one B-12-dependent enzyme, in most cases methionine synthase. This implies that the majority of prokaryotes relies on exogenous B-12 supply and interacts with producers. B-12 consists of a corrin ring centred around a cobalt ion and the lower ligand 5'6-dimethylbenzimidazole (DMB). It has never been tested whether availability of this pivotal cofactor, DMB or its intermediate alpha-ribazole affect growth and composition of prokaryotic microbial communities. Here we show that in the subtropical, equatorial and polar frontal Pacific Ocean supply of B-12 and alpha-ribazole enhances heterotrophic prokaryotic production and alters the composition of prokaryotic and heterotrophic protist communities. In the polar frontal Pacific, the SAR11 clade and Oceanospirillales increased their relative abundances upon B-12 supply. In the subtropical Pacific, Oceanospirillales increased their relative abundance upon B-12 supply as well but also downregulated the transcription of the btuB gene, encoding the outer membrane permease for B-12. Surprisingly, Prochlorococcus, known to produce pseudo-B-12 and not B-12, exhibited significant upregulation of genes encoding key proteins of photosystem I + II, carbon fixation and nitrate reduction upon B-12 supply in the subtropical Pacific. These findings show that availability of B-12 and alpha-ribazole affect growth and composition of prokaryotic and protist communities in oceanic systems thus revealing far-reaching consequences of methionine biosynthesis and other B-12-dependent enzymatic reactions on a community level.
C1 [Wienhausen, Gerrit; Dlugosch, Leon; Jarling, Rene; Wilkes, Heinz; Giebel, Helge-A.; Simon, Meinhard] Carl von Ossietzky Univ Oldenburg, Inst Chem & Biol Marine Environm, Carl von Ossietzky Str 9-11, D-26129 Oldenburg, Germany.
   [Simon, Meinhard] Univ Oldenburg HIFMB, Helmholtz Inst Funct Marine Biodivers, Ammerlander Heerstr 231, D-26129 Oldenburg, Germany.
   [Jarling, Rene] Thuenen Inst Forest Genet, Eberswalder Chaussee 3a, D-15377 Waldsleversdorf, Germany.
RP Simon, M (corresponding author), Carl von Ossietzky Univ Oldenburg, Inst Chem & Biol Marine Environm, Carl von Ossietzky Str 9-11, D-26129 Oldenburg, Germany.; Simon, M (corresponding author), Univ Oldenburg HIFMB, Helmholtz Inst Funct Marine Biodivers, Ammerlander Heerstr 231, D-26129 Oldenburg, Germany.
EM m.simon@icbm.de
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NR 85
TC 29
Z9 31
PD AUG
PY 2022
VL 16
IS 8
BP 2002
EP 2014
DI 10.1038/s41396-022-01250-7
EA MAY 2022
UT WOS:000797293000001
DA 2025-07-30
ER

PT J
AU Fadeev, E
   Salter, I
   Schourup-Kristensen, V
   Nothig, EM
   Metfies, K
   Engels, A
   Piontek, J
   Boetiuso, A
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AF Fadeev, Eduard
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   Boetiuso, Antje
   Bienhold, Christina
TI Microbial Communities in the East and West Fram Strait During Sea Ice
   Melting Season
SO FRONTIERS IN MARINE SCIENCE
DT Article
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C1 [Fadeev, Eduard; Salter, Ian; Schourup-Kristensen, Vibe; Nothig, Eva-Maria; Metfies, Katja; Boetiuso, Antje; Bienhold, Christina] Helmholtz Ctr Polar & Marine Res, Alfred Wegener Inst, Bremerhaven, Germany.
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   [Metfies, Katja] Helmholtz Inst Funct Marine Biodivers, Oldenburg, Germany.
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RP Fadeev, E; Bienhold, C (corresponding author), Helmholtz Ctr Polar & Marine Res, Alfred Wegener Inst, Bremerhaven, Germany.; Fadeev, E; Bienhold, C (corresponding author), Max Planck Inst Marine Microbiol, Bremen, Germany.
EM eduard.fadeev@awi.de; Christina.Bienhold@awi.de
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PD NOV 22
PY 2018
VL 5
AR 429
DI 10.3389/fmars.2018.00429
UT WOS:000457485300001
DA 2025-07-30
ER

PT J
AU Jing, HM
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AF Jing, Hongmei
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   Liu, Hongbin
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SO PLOS ONE
DT Article
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C1 [Jing, Hongmei; Xia, Xiaomin; Liu, Hongbin] Hong Kong Univ Sci & Technol, Div Life Sci, Kowloon, Hong Kong, Peoples R China.
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RP Liu, HB (corresponding author), Hong Kong Univ Sci & Technol, Div Life Sci, Kowloon, Hong Kong, Peoples R China.
EM liuhb@ust.hk
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ER

PT J
AU Oggerin, M
   Viver, T
   Brüwer, J
   Voss, D
   García-Llorca, M
   Zielinski, O
   Orellana, LH
   Fuchs, BM
AF Oggerin, Monike
   Viver, Tomeu
   Bruwer, Jan
   Voss, Daniela
   Garcia-Llorca, Marina
   Zielinski, Oliver
   Orellana, Luis H.
   Fuchs, Bernhard M.
TI Niche differentiation within bacterial key-taxa in stratified surface
   waters of the Southern Pacific Gyre
SO ISME JOURNAL
DT Article
AB One of the most hostile marine habitats on Earth is the surface of the South Pacific Gyre (SPG), characterized by high solar radiation, extreme nutrient depletion, and low productivity. During the SO-245 "UltraPac" cruise through the center of the ultra-oligotrophic SPG, the marine alphaproteobacterial group AEGEAN169 was detected by fluorescence in situ hybridization at relative abundances up to 6% of the total microbial community in the uppermost water layer, with two distinct populations (Candidatus Nemonibacter and Ca. Indicimonas). The high frequency of dividing cells combined with high transcript levels suggests that both clades may be highly metabolically active. Comparative metagenomic and metatranscriptomic analyses of AEGEAN169 revealed that they encoded subtle but distinct metabolic adaptions to this extreme environment in comparison to their competitors SAR11, SAR86, SAR116, and Prochlorococcus. Both AEGEAN169 clades had the highest percentage of transporters per predicted proteins (9.5% and 10.6%, respectively). In particular, the high expression of ABC transporters in combination with proteorhodopsins and the catabolic pathways detected suggest a potential scavenging lifestyle for both AEGEAN169 clades. Although both AEGEAN169 clades may share the genomic potential to utilize phosphonates as a phosphorus source, they differ in their metabolic pathways for carbon and nitrogen. Ca. Nemonibacter potentially use glycine-betaine, whereas Ca. Indicimonas may catabolize urea, creatine, and fucose. In conclusion, the different potential metabolic strategies of both clades suggest that both are well adapted to thrive resource-limited conditions and compete well with other dominant microbial clades in the uppermost layers of SPG surface waters.
C1 [Oggerin, Monike; Viver, Tomeu; Bruwer, Jan; Garcia-Llorca, Marina; Orellana, Luis H.; Fuchs, Bernhard M.] Max Planck Inst Marine Microbiol, Dept Mol Ecol, Celsiusstr 1, D-28359 Bremen, Germany.
   [Voss, Daniela; Zielinski, Oliver] Carl von Ossietzky Univ Oldenburg, Inst Chem & Biol Marine Environm, Wilhelmshafen, Germany.
   [Zielinski, Oliver] Leibniz Inst Balt Sea Res Warnemunde, D-18119 Rostock, Germany.
RP Oggerin, M; Fuchs, BM (corresponding author), Max Planck Inst Marine Microbiol, Dept Mol Ecol, Celsiusstr 1, D-28359 Bremen, Germany.
EM moggerin@mpi-bremen.de; bfuchs@mpi-bremen.de
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NR 104
TC 0
Z9 0
PD AUG 30
PY 2024
VL 18
IS 1
AR wrae155
DI 10.1093/ismejo/wrae155
UT WOS:001302053600001
DA 2025-07-30
ER

PT J
AU Park, BS
   Lee, M
   Shin, K
   Baek, SH
AF Park, Bum Soo
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   Shin, Kyoungsoon
   Baek, Seung Ho
TI Response of the bacterioplankton composition to inorganic nutrient
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SO MARINE ECOLOGY-AN EVOLUTIONARY PERSPECTIVE
DT Article
AB In Korean coastal waters (KCW), nutrient loading from the four major rivers usually peaks in summer, probably due to the large amount of water discharge in rainy seasons, but little is known about the responses of the bacterial community composition to inorganic nutrient loading. To gain deeper understanding of variations in marine microbial biodiversity and function with inorganic nutrient loading, a large-scale mesocosm (1,000 L) experiment was conducted in southern KCW for 10 days in summer (July 27 through August 6, 2015) and the bacterioplankton community composition (BCC) was investigated using 16S rRNA amplicon pyrosequencing method. The bioassays established in the mesocosm were designed with the following each nutrient dosing treatments: nitrate (+N), phosphate (+P), and nitrate plus phosphate (+NP). Among the three treatments, the +NP and +N treatments exhibited the largest and second-largest increases in phytoplankton abundance, respectively, whereas there was relatively less variation under the +P treatment. Enhanced growth of phytoplankton not only induced increases in pH and bacterial abundance (p < .05) but also led to changes in the BCC: the orders Flavobacteria, Micrococcales, Oceanospirillales, and Rhodobacterales exhibited increases in relative abundance, whereas Methylophilales, Puniceicoccales, SAR11, SAR116, and SAR86 showed a decreasing trend. Inorganic nutrients may directly contribute to variation in the BCC, as the relative abundance of Sphingobacteriales, containing members that undergo chemotaxis toward inorganic nutrients, was increased by the +N treatment. Given that these findings, changes in phytoplankton abundance due to nutrient addition may be the most crucial component resulting in variation in the BCC.
C1 [Park, Bum Soo] Korea Inst Ocean Sci & Technol, Marine Ecosyst Res Ctr, Busan, South Korea.
   [Lee, Minji; Baek, Seung Ho] Korea Inst Ocean Sci & Technol, Risk Assessment Res Ctr, Geoje 53201, South Korea.
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RP Baek, SH (corresponding author), Korea Inst Ocean Sci & Technol, Risk Assessment Res Ctr, Geoje 53201, South Korea.
EM baeksh@kiost.ac.kr
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NR 92
TC 13
Z9 14
PD JUN
PY 2020
VL 41
IS 3
AR e12591
DI 10.1111/maec.12591
EA APR 2020
UT WOS:000527793000001
DA 2025-07-30
ER

PT J
AU Hernandez-Magana, AE
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AF Hernandez-Magana, Alejandra Elisa
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TI Prokaryotic diversity and activity in contrasting productivity regimes
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SO JOURNAL OF MARINE SYSTEMS
DT Article
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C1 [Hernandez-Magana, Alejandra Elisa; Liu, Yan; Debeljak, Pavla; Crispi, Olivier; Marie, Barbara; Koedooder, Coco; Obernosterer, Ingrid] Sorbonne Univ, CNRS, Lab Oceanog Microbienne, LOMIC, F-66650 Banyuls Sur Mer, France.
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RP Obernosterer, I (corresponding author), Sorbonne Univ, CNRS, Microbial Oceanog Lab LOMIC, 1 Ave Pierre Fabre, F-66650 Banyuls Sur Mer, France.
EM ingrid.obernosterer@obs-banyuls.fr
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TC 8
Z9 9
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PY 2021
VL 221
AR 103561
DI 10.1016/j.jmarsys.2021.103561
EA JUN 2021
UT WOS:000658513500002
DA 2025-07-30
ER

PT J
AU Kallistova, AY
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   Rusanov, II
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AF Kallistova, A. Yu.
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   Yusupov, S. K.
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TI Methane Production in a Temperate Freshwater Lake during an Intense
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SO MICROBIOLOGY
DT Article
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C1 [Kallistova, A. Yu.; Kosyakova, A. I.; Rusanov, I. I.; Kadnikov, V. V.; Beletsky, A. V.; Koval, D. D.; Yusupov, S. K.; Pimenov, N. V.] Russian Acad Sci, Fed Res Ctr Biotechnol, Moscow 119071, Russia.
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RP Kallistova, AY (corresponding author), Russian Acad Sci, Fed Res Ctr Biotechnol, Moscow 119071, Russia.
EM kallistoanna@mail.ru
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BP 638
EP 649
DI 10.1134/S0026261723601586
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DA 2025-07-30
ER

PT J
AU Zhang, Y
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AF Zhang, Yu
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C1 [Zhang, Yu; Lu, Ye; Wang, Jiahua; Xu, Lei; Xiao, Xiang; Xu, Jun] Shanghai Jiao Tong Univ, Sch Oceanog, State Key Lab Ocean Engn, Shanghai 200240, Peoples R China.
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RP Xu, J (corresponding author), Shanghai Jiao Tong Univ, Sch Oceanog, State Key Lab Ocean Engn, Shanghai 200240, Peoples R China.
EM xujunn@sjtu.edu.cn
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PT J
AU Morando, M
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AF Morando, Michael
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NR 78
TC 14
Z9 15
PD DEC 2
PY 2016
VL 7
AR 1932
DI 10.3389/fmicb.2016.01932
UT WOS:000389265100001
DA 2025-07-30
ER

PT J
AU Chun, SJ
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   Baek, SH
   Ahn, CY
   Oh, HM
AF Chun, Seong-Jun
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   Baek, Seung Ho
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TI Seasonal succession of microbes in different size-fractions and their
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SO SCIENCE OF THE TOTAL ENVIRONMENT
DT Article
AB Microbes interact with each other in response to various environmental changes in coastal marine ecosystems. To explore how the macroenvironment (environmental filtering) and species-engineered microenvironment (niche construction) affect the ecological network of the marine microbiome in the highly dynamic coastal waters of Korea, we analyzed the modular structures of the microbial community and identified microbial interconnections in different size fractions for a year. Fluctuations in the macroenvironment, such as temperature and nutrient concentrations driven by seasonal changes, are the major factors in determining successive microbial modules. Compared to particle-associated (PA) microbes, free-living (FL) microbes seemed to be more affected by macroenvironmental filtering. Modules related to nutrients were further divided into various modules according to different lifestyles. In addition, a large transient discharge of the Changjiang (Yangtze River) in summer also formed a distinct microbial module, which was related to the high ammonia concentration arising from phytoplankton degradation. Microbes belonging to the SAR11, SAR86, and SAR116 clades, Flavobacteriaceae, and MG IIa-L showed repeated interconnections in temperature-related modules, while the SAR202 clade, Marinimicrobia, DEV007 clade, and Arctic97B-4 and Sva0996 marine groups displayed repeated connections in nutrient-related modules. These 'skeleton'-forming microbes created species-engineered microenvironments, further fine-tuning microbial modular structures. Furthermore, they serve as keystone species for module stability by linking interdependent microbial partners within their own modules through universally beneficial met abolic activities. Therefore, they could reinforce the ecological resilience of microbial communities under abiotic and biotic perturbations in dynamic coastal waters. In conclusion, both macro-and micro-environmental filtering were important for determining the seasonal succession of microbial community structures.
   (c) 2021 Elsevier B.V. All rights reserved.
C1 [Chun, Seong-Jun] Natl Inst Ecol, LMO Res Team, 1210 Geumgang Ro, Maseo Myeon 33657, Seocheon, South Korea.
   [Chun, Seong-Jun; Cui, Yingshun; Ahn, Chi-Yong; Oh, Hee-Mock] Korea Res Inst Biosci & Biotechnol KRIBB, Cell Factory Res Ctr, 125 Gwahak Ro, Daejeon 34141, South Korea.
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   [Ahn, Chi-Yong; Oh, Hee-Mock] Korea Univ Sci & Technol UST, KRIBB Sch Biotechnol, Dept Environm Biotechnol, 217 Gajeong Ro, Daejeon 34113, South Korea.
RP Ahn, CY; Oh, HM (corresponding author), Korea Res Inst Biosci & Biotechnol KRIBB, Cell Factory Res Ctr, 125 Gwahak Ro, Daejeon 34141, South Korea.
EM cyahn@kribb.re.kr; heemock@kribb.re.kr
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NR 106
TC 23
Z9 23
PD AUG 25
PY 2021
VL 784
AR 147046
DI 10.1016/j.scitotenv.2021.147046
EA APR 2021
UT WOS:000657591600014
DA 2025-07-30
ER

PT J
AU Forth, M
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AF Forth, Michael
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DT Article
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C1 [Forth, Michael; Treusch, Alexander H.] Univ Southern Denmark, Nord Ctr Earth Evolut, Dept Biol, DK-5230 Odense M, Denmark.
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RP Treusch, AH (corresponding author), Univ Southern Denmark, Dept Biol, Campusvej 55, DK-5230 Odense M, Denmark.
EM atreusch@biology.sdu.dk
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TC 18
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PD MAR
PY 2015
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BP 656
EP 669
DI 10.1038/ismej.2014.172
UT WOS:000349850600011
DA 2025-07-30
ER

PT J
AU Lanfranconi, MP
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AF Lanfranconi, Mariana P.
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   Nogales, Balbina
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DT Article
AB The changes caused by diesel oil pollution in the metabolically active bacterioplankton from an oligotrophic coastal location were analysed in laboratory microcosms (44 l) using 16S ribosomal RNA (16S rRNA) as molecular marker. The aim was to simulate typical hydrocarbon pollution events in a coastal area exploited for seasonal touristic activities. The experiment consisted in addition of low amounts of diesel oil without nutrients to seawater collected at different times (winter and summer). Bacterial diversity was analysed by terminal-restriction fragment length polymorphism (T-RFLP) profiling of 16S rRNAs after reverse transcription polymerase chain reaction (RTPCR), and by generation of 16S rRNA clone libraries in control and diesel-polluted microcosms. Diesel addition caused a twofold increase in prokaryotic numbers in comparison with controls at the end of the experiment, both in winter and summer microcosms. Bacterioplankton composition, determined by 16S rRNA T-RFLP data, changed rapidly (within 17 h) in response to treatment. The resulting communities were different in microcosms with water collected in summer and winter. A reduction in diversity (Shannon index, calculated on the basis of T-RFLP data) was observed only in summer microcosms. This was due to the rapid increase of phylotypes affiliated to the Oceanospirillaceae, not observed in winter microcosms. After diesel treatment there was a reduction in the number of phylotypes related to SAR11, SAR86 and picocyanobacteria, while phylotypes of the Roseobacter clade, and the OMG group seemed to be favoured. Our results show that diesel pollution alone caused profound effects on the bacterioplankton of oligotrophic seawater, and explained many of the differences in diversity reported previously in pristine and polluted sites in this coastal area.
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RP Nogales, B (corresponding author), Univ Illes Balears, Dept Biol, Palma De Mallorca 07122, Spain.
EM bnogales@uib.es
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SI SI
BP 607
EP 621
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UT WOS:000289739300013
DA 2025-07-30
ER

PT J
AU Zubkov, MV
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AF Zubkov, Mikhail V.
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DT Article
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C1 Natl Oceanog Ctr, Southampton SO14 3ZH, Hants, England.
   Plymouth Marine Lab, Plymouth PL1 3DH, Devon, England.
   Max Planck Inst Marine Microbiol, D-28359 Bremen, Germany.
   Univ Warwick, Dept Biol Sci, Coventry CV4 7AL, W Midlands, England.
   Sir Alister Hardy Fdn Ocean Sci, Plymouth PL1 2PB, Devon, England.
   Univ Plymouth, Marine Inst, Plymouth PL4 8AA, Devon, England.
RP Zubkov, MV (corresponding author), Natl Oceanog Ctr, Southampton SO14 3ZH, Hants, England.
EM mvz@noc.soton.ac.uk
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TC 99
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PD AUG
PY 2007
VL 9
IS 8
BP 2079
EP 2089
DI 10.1111/j.1462-2920.2007.01324.x
UT WOS:000248451600017
DA 2025-07-30
ER

PT J
AU Li, HF
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AF Li, Hongfei
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   Li, Denghui
   Lin, Senjie
TI In situ community transcriptomics illuminates
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DT Article
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C1 [Li, Hongfei; Yu, Liying; Li, Tangcheng; Li, Ling; Yuan, Huatao; Wang, Jingtian; Wang, Cong; Lin, Senjie] Xiamen Univ, State Key Lab Marine Environm Sci, Xiamen, Fujian, Peoples R China.
   [Li, Hongfei] Zhejiang Ocean Univ, Natl Engn Res Ctr Marine Aquaculture, Zhoushan, Zhejiang, Peoples R China.
   [Li, Hongfei; Lin, Senjie] Univ Connecticut, Dept Marine Sci, Groton, CT 06340 USA.
   [Chen, Jianwei; Fan, Guangyi; Li, Denghui] BGI Res, Qingdao Key Lab Marine Genom, Qingdao, Shandong, Peoples R China.
   [Fan, Guangyi] BGI Res, State Key Lab Agr Genom, Shenzhen, Guangdong, Peoples R China.
   [Li, Denghui] Qingdao Innovat Ctr Seaweed Biotechnol, Qingdao, Shandong, Peoples R China.
RP Lin, SJ (corresponding author), Xiamen Univ, State Key Lab Marine Environm Sci, Xiamen, Fujian, Peoples R China.; Lin, SJ (corresponding author), Univ Connecticut, Dept Marine Sci, Groton, CT 06340 USA.
EM senjie.lin@uconn.edu
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NR 82
TC 2
Z9 2
PD MAR 5
PY 2024
VL 12
IS 3
DI 10.1128/spectrum.02177-23
EA FEB 2024
UT WOS:001158281100004
DA 2025-07-30
ER

PT J
AU Gilbert, JA
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AF Gilbert, Jack A.
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   Smyth, Tim
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   Joint, Ian
TI The seasonal structure of microbial communities in the Western English
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB P>Very few marine microbial communities are well characterized even with the weight of research effort presently devoted to it. Only a small proportion of this effort has been aimed at investigating temporal community structure. Here we present the first report of the application of high-throughput pyrosequencing to investigate intra-annual bacterial community structure. Microbial diversity was determined for 12 time points at the surface of the L4 sampling site in the Western English Channel. This was performed over 11 months during 2007. A total of 182 560 sequences from the V6 hyper-variable region of the small-subunit ribosomal RNA gene (16S rRNA) were obtained; there were between 11 327 and 17 339 reads per sample. Approximately 7000 genera were identified, with one in every 25 reads being attributed to a new genus; yet this level of sampling far from exhausted the total diversity present at any one time point. The total data set contained 17 673 unique sequences. Only 93 (0.5%) were found at all time points, yet these few lineages comprised 50% of the total reads sequenced. The most abundant phylum was Proteobacteria (50% of all sequenced reads), while the SAR11 clade comprised 21% of the ubiquitous reads and similar to 12% of the total sequenced reads. In contrast, 78% of all operational taxonomic units were only found at one time point and 67% were only found once, evidence of a large and transient rare assemblage. This time series shows evidence of seasonally structured community diversity. There is also evidence for seasonal succession, primarily reflecting changes among dominant taxa. These changes in structure were significantly correlated to a combination of temperature, phosphate and silicate concentrations.
C1 [Gilbert, Jack A.; Smyth, Tim; Somerfield, Paul J.; Joint, Ian] Plymouth Marine Lab, Plymouth PL1 3DH, Devon, England.
   [Field, Dawn; Swift, Paul; Newbold, Lindsay; Oliver, Anna] CEH Oxford, NERC, Ctr Ecol & Hydrol, Oxford OX1 3SR, England.
   [Huse, Sue] Marine Biol Lab, Josephine Bay Paul Ctr Comparat Mol Biol & Evolut, Woods Hole, MA 02543 USA.
RP Gilbert, JA (corresponding author), Plymouth Marine Lab, Prospect Pl, Plymouth PL1 3DH, Devon, England.
EM jagi@pml.ac.uk
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NR 27
TC 322
Z9 378
PD DEC
PY 2009
VL 11
IS 12
BP 3132
EP 3139
DI 10.1111/j.1462-2920.2009.02017.x
UT WOS:000273182500017
DA 2025-07-30
ER

PT J
AU Campoverde, NCG
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AF Campoverde, Nataly Carolina Guevara
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TI Characterization of bacterioplankton communities and quantification of
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SO PEERJ
DT Article
AB Bacteria play a crucial role in the marine carbon cycle, contributing to the production and degradation of organic carbon. Here, we investigated organic carbon pools, aggregate formation, and bacterioplankton communities in three contrasting oceanographic settings in the Galapagos Archipelago. We studied a submarine CO2 vent at Roca Redonda (RoR), an upwelling site at Bolivar Channel (BoC) subjected to a weak El Nino event at the time of sampling in October 2014, as well as a site without volcanic or upwelling influence at Cowley Islet (CoI). We recorded physico-chemical parameters, and quantified particulate and dissolved organic carbon, transparent exopolymeric particles, and the potential of the water to form larger marine aggregates. Free-living and particle-attached bacterial communities were assessed via 16S rRNA gene sequencing. Both RoR and BoC exhibited temperatures elevated by 1-1.5 degrees C compared to CoI. RoR further experienced reduced pH between 6.8 and 7.4. We observed pronounced differences in organic carbon pools at each of the three sites, with highest dissolved organic carbon concentrations at BoC and RoR, and highest particulate organic carbon concentrations and aggregate formation at BoC. Bacterioplankton communities at BoC were dominated by opportunistic copiotrophic taxa, such as Alteromonas and Roseobacter, known to thrive in phytoplankton blooms, as opposed to oligotrophic taxa dominating at CoI, such as members of the SAR11 clade. Therefore, we propose that bacterial communities were mainly influenced by the availability of organic carbon at the investigated sites. Our study provides a comprehensive characterization of organic carbon pools and bacterioplankton communities, highlighting the high heterogeneity of various components of the marine carbon cycle around the Galapagos Archipelago.
C1 [Campoverde, Nataly Carolina Guevara] Univ San Francisco Quito, Galapagos Sci Ctr, Colegio Ciencias Biol & Ambientales, Quito, Ecuador.
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RP Hassenrück, C (corresponding author), Leibniz Ctr Trop Marine Res, Dept Biogeochem & Geol, Trop Marine Microbiol, Bremen, Germany.
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NR 96
TC 6
Z9 7
PD DEC 3
PY 2018
VL 6
AR e5984
DI 10.7717/peerj.5984
UT WOS:000452458500003
DA 2025-07-30
ER

PT J
AU Dong, HP
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AF Dong, Hong-Po
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TI Metaproteomic characterization of high molecular weight dissolved
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SO GEOCHIMICA ET COSMOCHIMICA ACTA
DT Article
AB Dissolved organic matter (DOM) is an important reservoir of carbon and energy in the marine environment and plays a key role in regulating the global carbon cycle. This study characterized proteins of high-molecular-weight DOM (size between 5 kDa and <0.2 mu m, HMW-DOM) collected from the surface seawaters in the South China Sea using a shotgun proteomic approach in combination with the global ocean sampling combined assembly protein database. A total of 367 protein groups matched by 993 unique peptides from 1991 spectra were identified from four surface HMW-DOM samples. Proteins with unknown taxonomic classification and function dominated the dissolved protein pool (43-53%) while the remaining proteins presented close similarity in biological origin among the four sampling sites. Rhodospirillaceae, Prochlorococcus, SAR11 clade and viruses were the major contributors to dissolved proteins in the HMW-DOM from surface seawaters while very few proteins were from the eukaryotic phytoplankton and no archaeal proteins were detected. Transporters with substrate specificities for nitrogen-and carbon-containing compounds (1.5% of the total spectra for each) were highly detected while no phosphate transporters were found, suggesting that carbon and nitrogen might be more limiting than phosphorus in the surface seawater. Viral proteins were assigned into three families: Myoviridae, Podoviridae and Siphoviridae, and the Myoviridae proteins were the most abundant. Among them, structure proteins were the most abundant viral proteins. This study indicated that the dissolved proteins of HMW-DOM presented compositional and biologically original homogeneity in the surface seawaters of the South China Sea, and bacteria and viruses dominated the dissolved protein pool. (C) 2013 Elsevier Ltd. All rights reserved.
C1 [Dong, Hong-Po; Wang, Da-Zhi; Xie, Zhang-Xian; Dai, Min-Han; Hong, Hua-Sheng] Xiamen Univ, Coll Environm & Ecol, State Key Lab Marine Environm Sci, Xiamen, Peoples R China.
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RP Wang, DZ (corresponding author), Xiamen Univ, Coll Environm & Ecol, State Key Lab Marine Environm Sci, Xiamen, Peoples R China.
EM wangdz66@yahoo.com
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NR 45
TC 12
Z9 15
PD MAY 15
PY 2013
VL 109
BP 51
EP 61
DI 10.1016/j.gca.2013.01.041
UT WOS:000317269600005
DA 2025-07-30
ER

PT J
AU Stevens, H
   Ulloa, O
AF Stevens, Heike
   Ulloa, Osvaldo
TI Bacterial diversity in the oxygen minimum zone of the eastern tropical
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB The structure and diversity of bacterial communities associated with the oxygen minimum zone (OMZ) of the eastern tropical South Pacific was studied through phylogenetic analysis. Clone libraries of 16S rRNA gene fragments were constructed using environmental DNA collected from the OMZ (60 m and 200 m), the sea surface (10 m), and the deep oxycline (450 m). At the class level, the majority of sequences affiliated to the gamma- (53.7%) and alpha-Proteobacteria (19.7%), and to the Bacteroidetes (11.2%). A vertical partitioning of the bacterial communities was observed, with main differences between the suboxic OMZ and the more oxygenated surface and deep oxycline waters. At the surface, the microbial community was predominantly characterized by SAR86, Loktanella and unclassified Flavobacteriaceae, whereas the deeper layer was dominated by Sulfitobacter and unclassified Alteromonadaceae. In the OMZ, major constituents affiliated to the marine SAR11 clade and to thiotrophic gamma-symbionts (25% of all sequences), a group not commonly found in pelagic waters. Sequences affiliating to the phylum Chloroflexi, to the AGG47 and SAR202 clades, to the delta-Proteobacteria, to the Acidobacteria, and to the 'anammox group' of the Planctomycetes were found exclusively in the OMZ. The bacterial richness in the OMZ was higher than in the oxic surface and deeper oxycline, as revealed by rarefaction analysis and the Chao1 richness estimator (surface: 45 +/- 8, deeper oxycline: 76 +/- 26; OMZ(60m): 97 +/- 33, OMZ(200m): 109 +/- 31). OMZ bacterial diversity indices (Fisher's: similar to 30 +/- 5, Shannon's: similar to 3.31, inverse Simpson's: similar to 20) were similar to those found in other pelagic marine environments. Thus, our results indicate a distinct and diverse bacterial community within the OMZ, with presumably novel and yet uncultivated bacterial lineages.
C1 Univ Concepcion, Lab Proc Oceanog & Clima, Dept Oceanog, Concepcion, Chile.
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RP Stevens, H (corresponding author), Univ Concepcion, Lab Proc Oceanog & Clima, Dept Oceanog, Casilla 160-C, Concepcion, Chile.
EM h.stevens@profc.udec.cl
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NR 85
TC 190
Z9 204
PD MAY
PY 2008
VL 10
IS 5
BP 1244
EP 1259
DI 10.1111/j.1462-2920.2007.01539.x
UT WOS:000254666700013
DA 2025-07-30
ER

PT J
AU Babic, I
   Mucko, M
   Petric, I
   Bosak, S
   Mihanovic, H
   Vilibic, I
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   Cetinic, I
   Balestra, C
   Casotti, R
   Ljubesic, Z
AF Babic, Ivana
   Mucko, Maja
   Petric, Ines
   Bosak, Suncica
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   Vilibic, Ivica
   Radic, Iris Dupcic
   Cetinic, Ivona
   Balestra, Cecilia
   Casotti, Raffaella
   Ljubesic, Zrinka
TI Multilayer approach for characterization of bacterial diversity in a
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SO JOURNAL OF MARINE SYSTEMS
DT Article
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C1 [Babic, Ivana; Mucko, Maja; Bosak, Suncica; Ljubesic, Zrinka] Univ Zagreb, Fac Sci, Dept Biol, Rooseveltov Trg 6, Zagreb 10000, Croatia.
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   [Mihanovic, Hrvoje; Vilibic, Ivica] Inst Oceanog & Fisheries, Phys Oceanog Lab, Setaliste I Mestrovica 63, Split 21000, Croatia.
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   [Balestra, Cecilia; Casotti, Raffaella] Dept Integrat Marine Ecol, Stn Zool Anton Dohrn, I-80121 Naples, Italy.
RP Petric, I (corresponding author), Rudjer Boskovic Inst, Div Marine & Environm Res, Bijenicka Cesta 54, Zagreb 10000, Croatia.
EM ipetric@irb.hr
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NR 68
TC 8
Z9 8
PD AUG
PY 2018
VL 184
BP 15
EP 27
DI 10.1016/j.jmarsys.2018.04.002
UT WOS:000434749000002
DA 2025-07-30
ER

PT J
AU Molina, V
   Cornejo-D'Ottone, M
   Soto, EH
   Quiroga, E
   Alarcón, G
   Silva, D
   Acuña, C
   Silva, N
AF Molina, Veronica
   Cornejo-D'Ottone, Marcela
   Soto, Eulogio H.
   Quiroga, Eduardo
   Alarcon, Guillermo
   Silva, Daniela
   Acuna, Carla
   Silva, Nelson
TI Biogeochemical Responses and Seasonal Dynamics of the Benthic Boundary
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   Boundary Upwelling System
SO WATER
DT Article
AB The Eastern South Pacific coastal zone is characterized by seasonal and interannual variability, driven by upwelling and El Nino Southern Oscillation (ENSO), respectively. These oceanographical conditions influence microbial communities and their contribution to nutrient and greenhouse gases recycling, especially in bottom waters due to oxygenation. This article addresses the seasonal hydrographic and biogeochemical conditions in the water and sediments during El Nino 2015. Bottom water active microbial communities, including nitrifiers, were studied using amplicon sequencing of 16S rRNA (cDNA) and RT-qPCR, respectively. The results of the hydrographic analysis showed changes in the water column associated with the predominance of sub-Antarctic Waters characterized by warmed and low nutrients in the surface and more oxygenated conditions at the bottom in comparison with El Nino 2014. The organic matter quantity and quality decreased during fall and winter. The bottom water active microbial assemblages were dominated by archaea (Ca. Poseidoniales) and putative ammonia oxidizing archaea. Active bacteria affiliated to SAR11, Marinimicrobia and Nitrospina, and oxygen deficient realms (Desulfobacterales, SUP05 clade and anammox) suffered variations, possibly associated with oxygen and redox conditions in the benthic boundary layer. Nitrifying functional groups contributed significantly more during late fall and winter which was consistent with higher bottom water oxygenation. Relationships between apparent oxygen utilization nitrate and nitrous oxide in the water support the contribution of nitrification to this greenhouse gas distribution in the water. In general, our study suggests that seasonal oceanographic variability during an El Nino year influences the microbial community and thus remineralization potential, which supports the need to carry out longer time series to identify the relevance of seasonality under ENSO in Eastern Boundary Upwelling Systems (EBUS) areas.
C1 [Molina, Veronica; Silva, Daniela; Acuna, Carla] Univ Playa Ancha, Observ Ecol Microbiana, Dept Biol, Fac Ciencias Nat & Exactas, Ave Leopoldo Carvallo 270, Valparaiso 2340000, Chile.
   [Molina, Veronica] Univ Playa Ancha, HUB Ambiental UPLA, Ave Leopoldo Carvallo 200, Valparaiso 2340000, Chile.
   [Cornejo-D'Ottone, Marcela; Quiroga, Eduardo; Alarcon, Guillermo; Silva, Nelson] Pontificia Univ Catolica Valparaiso, Escuela Ciencias Mar, Altamirano 1480, Valparaiso 2360007, Chile.
   [Cornejo-D'Ottone, Marcela; Quiroga, Eduardo; Alarcon, Guillermo; Silva, Nelson] Pontificia Univ Catolica Valparaiso, Inst Milenio Oceanog, Altamirano 1480, Valparaiso 2360007, Chile.
   [Soto, Eulogio H.] Univ Valparaiso, Fac Ciencias Mar & Recursos Nat, Ctr Observ Marino Estudios Riesgos Ambiente Coste, Casilla 5080, Vina Del Mar 2520000, Chile.
   [Soto, Eulogio H.] Univ Valparaiso, Lab Bentos, Escuela Biol Marina, Vina Del Mar 2520000, Chile.
RP Molina, V (corresponding author), Univ Playa Ancha, Observ Ecol Microbiana, Dept Biol, Fac Ciencias Nat & Exactas, Ave Leopoldo Carvallo 270, Valparaiso 2340000, Chile.; Molina, V (corresponding author), Univ Playa Ancha, HUB Ambiental UPLA, Ave Leopoldo Carvallo 200, Valparaiso 2340000, Chile.; Cornejo-D'Ottone, M (corresponding author), Pontificia Univ Catolica Valparaiso, Escuela Ciencias Mar, Altamirano 1480, Valparaiso 2360007, Chile.; Cornejo-D'Ottone, M (corresponding author), Pontificia Univ Catolica Valparaiso, Inst Milenio Oceanog, Altamirano 1480, Valparaiso 2360007, Chile.
EM veronica.molina@upla.cl; marcela.cornejo@pucv.cl; eulogio.soto@uv.cl;
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NR 71
TC 5
Z9 6
PD JAN
PY 2021
VL 13
IS 2
AR 180
DI 10.3390/w13020180
UT WOS:000611784400001
DA 2025-07-30
ER

PT J
AU Rasse, R
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AF Rasse, Rafael
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TI The suspended small-particle layer in the oxygen-poor Black Sea: a proxy
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SO BIOGEOSCIENCES
DT Article
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C1 [Rasse, Rafael; Claustre, Herve; Poteau, Antoine] Sorbonne Univ, F-06230 Villefranche Sur Mer, France.
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RP Rasse, R (corresponding author), Sorbonne Univ, F-06230 Villefranche Sur Mer, France.
EM rafael.rasse@obs-vlfr.fr
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NR 98
TC 7
Z9 7
PD DEC 23
PY 2020
VL 17
IS 24
BP 6491
EP 6505
DI 10.5194/bg-17-6491-2020
UT WOS:000603350700001
DA 2025-07-30
ER

PT J
AU Ferrera, I
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AF Ferrera, Isabel
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   Fraile-Nuez, Eugenio
   Gasol, Josep M.
TI Transient Changes in Bacterioplankton Communities Induced by the
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SO PLOS ONE
DT Article
AB The submarine volcanic eruption occurring near El Hierro (Canary Islands) in October 2011 provided a unique opportunity to determine the effects of such events on the microbial populations of the surrounding waters. The birth of a new underwater volcano produced a large plume of vent material detectable from space that led to abrupt changes in the physicalchemical properties of the water column. We combined flow cytometry and 454-pyrosequencing of 16S rRNA gene amplicons (V1-V3 regions for Bacteria and V3-V5 for Archaea) to monitor the area around the volcano through the eruptive and post-eruptive phases (November 2011 to April 2012). Flow cytometric analyses revealed higher abundance and relative activity (expressed as a percentage of high-nucleic acid content cells) of heterotrophic prokaryotes during the eruptive process as compared to post-eruptive stages. Changes observed in populations detectable by flow cytometry were more evident at depths closer to the volcano (similar to 70-200 m), coinciding also with oxygen depletion. Alpha-diversity analyses revealed that species richness (Chao1 index) decreased during the eruptive phase; however, no dramatic changes in community composition were observed. The most abundant taxa during the eruptive phase were similar to those in the post-eruptive stages and to those typically prevalent in oceanic bacterioplankton communities (i.e. the alphaproteobacterial SAR11 group, the Flavobacteriia class of the Bacteroidetes and certain groups of Gammaproteobacteria). Yet, although at low abundance, we also detected the presence of taxa not typically found in bacterioplankton communities such as the Epsilonproteobacteria and members of the candidate division ZB3, particularly during the eruptive stage. These groups are often associated with deep-sea hydrothermal vents or sulfur-rich springs. Both cytometric and sequence analyses showed that once the eruption ceased, evidences of the volcano-induced changes were no longer observed.
C1 [Ferrera, Isabel; Gasol, Josep M.] CSIC, Inst Ciencias Mar, Dept Biol Marina & Oceanog, Barcelona, Spain.
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RP Ferrera, I (corresponding author), CSIC, Inst Ciencias Mar, Dept Biol Marina & Oceanog, Barcelona, Spain.
EM iferrera@icm.csic.es
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NR 44
TC 21
Z9 23
PD FEB 11
PY 2015
VL 10
IS 2
AR e0118136
DI 10.1371/journal.pone.0118136
UT WOS:000349545300085
DA 2025-07-30
ER

PT J
AU Mizuno, CM
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AF Megumi Mizuno, Carolina
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   Ghai, Rohit
TI Expanding the Marine Virosphere Using Metagenomics
SO PLOS GENETICS
DT Article
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C1 [Megumi Mizuno, Carolina; Rodriguez-Valera, Francisco; Kimes, Nikole E.; Ghai, Rohit] Univ Miguel Hernandez, Evolutionary Genom Grp, Dept Prod Vegetal & Microbiol, Alicante, Spain.
RP Rodriguez-Valera, F (corresponding author), Univ Miguel Hernandez, Evolutionary Genom Grp, Dept Prod Vegetal & Microbiol, Alicante, Spain.
EM frvalera@umh.es
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NR 86
TC 186
Z9 202
PD DEC
PY 2013
VL 9
IS 12
AR e1003987
DI 10.1371/journal.pgen.1003987
UT WOS:000330533300030
DA 2025-07-30
ER

PT J
AU Poretsky, RS
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AF Poretsky, Rachel S.
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TI Transporter genes expressed by coastal bacterioplankton in response to
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DT Article
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RP Moran, MA (corresponding author), Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
EM mmoran@uga.edu
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NR 41
TC 185
Z9 205
PD MAR
PY 2010
VL 12
IS 3
BP 616
EP 627
DI 10.1111/j.1462-2920.2009.02102.x
UT WOS:000274942300006
DA 2025-07-30
ER

PT J
AU Danhorn, T
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AF Danhorn, Thomas
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TI Comparison of large-insert, small-insert and pyrosequencing libraries
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DT Article
AB The development of DNA sequencing methods for characterizing microbial communities has evolved rapidly over the past decades. To evaluate more traditional, as well as newer methodologies for DNA library preparation and sequencing, we compared fosmid, short-insert shotgun and 454 pyrosequencing libraries prepared from the same metagenomic DNA samples. GC content was elevated in all fosmid libraries, compared with shotgun and 454 libraries. Taxonomic composition of the different libraries suggested that this was caused by a relative underrepresentation of dominant taxonomic groups with low GC content, notably Prochlorales and the SAR11 cluster, in fosmid libraries. While these abundant taxa had a large impact on library representation, we also observed a positive correlation between taxon GC content and fosmid library representation in other low-GC taxa, suggesting a general trend. Analysis of gene category representation in different libraries indicated that the functional composition of a library was largely a reflection of its taxonomic composition, and no additional systematic biases against particular functional categories were detected at the level of sequencing depth in our samples. Another important but less predictable factor influencing the apparent taxonomic and functional library composition was the read length afforded by the different sequencing technologies. Our comparisons and analyses provide a detailed perspective on the influence of library type on the recovery of microbial taxa in metagenomic libraries and underscore the different uses and utilities of more traditional, as well as contemporary 'next-generation' DNA library construction and sequencing technologies for exploring the genomics of the natural microbial world. The ISME Journal (2012) 6, 2056-2066; doi: 10.1038/ismej.2012.35; published online 26 April 2012
C1 [Danhorn, Thomas; Young, Curtis R.; DeLong, Edward F.] MIT, Dept Civil & Environm Engn, Cambridge, MA 02139 USA.
RP DeLong, EF (corresponding author), MIT, Dept Civil & Environm Engn, 48-427 MIT,15 Vassar St, Cambridge, MA 02139 USA.
EM delong@mit.edu
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NR 43
TC 16
Z9 17
PD NOV
PY 2012
VL 6
IS 11
BP 2056
EP 2066
DI 10.1038/ismej.2012.35
UT WOS:000310056400008
DA 2025-07-30
ER

PT J
AU Martinez-Gutierrez, CA
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   Aylward, FO
AF Martinez-Gutierrez, Carolina A.
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TI A timeline of bacterial and archaeal diversification in the ocean
SO ELIFE
DT Article
AB Microbial plankton play a central role in marine biogeochemical cycles, but the timing in which abundant lineages diversified into ocean environments remains unclear. Here, we reconstructed the timeline in which major clades of bacteria and archaea colonized the ocean using a high-resolution benchmarked phylogenetic tree that allows for simultaneous and direct comparison of the ages of multiple divergent lineages. Our findings show that the diversification of the most prevalent marine clades spans throughout a period of 2.2 Ga, with most clades colonizing the ocean during the last 800 million years. The oldest clades - SAR202, SAR324, Ca. Marinimicrobia, and Marine Group II - diversified around the time of the Great Oxidation Event, during which oxygen concentration increased but remained at microaerophilic levels throughout the Mid-Proterozoic, consistent with the prevalence of some clades within these groups in oxygen minimum zones today. We found the diversification of the prevalent heterotrophic marine clades SAR11, SAR116, SAR92, SAR86, and Roseobacter as well as the Marine Group I to occur near to the Neoproterozoic Oxygenation Event (0.8-0.4 Ga). The diversification of these clades is concomitant with an overall increase of oxygen and nutrients in the ocean at this time, as well as the diversification of eukaryotic algae, consistent with the previous hypothesis that the diversification of heterotrophic bacteria is linked to the emergence of large eukaryotic phytoplankton. The youngest clades correspond to the widespread phototrophic clades Prochlorococcus, Synechococcus, and Crocosphaera, whose diversification happened after the Phanerozoic Oxidation Event (0.45-0.4 Ga), in which oxygen concentrations had already reached their modern levels in the atmosphere and the ocean. Our work clarifies the timing at which abundant lineages of bacteria and archaea colonized the ocean, thereby providing key insights into the evolutionary history of lineages that comprise the majority of prokaryotic biomass in the modern ocean.
C1 [Martinez-Gutierrez, Carolina A.; Uyeda, Josef C.; Aylward, Frank O.] Virginia Tech, Dept Biol Sci, Blacksburg, VA 24061 USA.
   [Aylward, Frank O.] Virginia Tech, Ctr Emerging Zoonot & Arthropod Borne Pathogens, Blacksburg, VA 24061 USA.
RP Martinez-Gutierrez, CA; Aylward, FO (corresponding author), Virginia Tech, Dept Biol Sci, Blacksburg, VA 24061 USA.; Aylward, FO (corresponding author), Virginia Tech, Ctr Emerging Zoonot & Arthropod Borne Pathogens, Blacksburg, VA 24061 USA.
EM cmartinez@vt.edu; faylward@vt.edu
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NR 104
TC 6
Z9 6
PD DEC 7
PY 2023
VL 12
AR RP88268
DI 10.7554/eLife.88268
UT WOS:001134856900001
DA 2025-07-30
ER

PT J
AU Hattenrath-Lehmann, TK
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   Koch, F
   Gobler, CJ
AF Hattenrath-Lehmann, Theresa K.
   Jankowiak, Jennifer
   Koch, Florian
   Gobler, Christopher J.
TI Prokaryotic and eukaryotic microbiomes associated with blooms of the
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SO PLOS ONE
DT Article
AB While harmful algal blooms caused by the ichthyotoxic dinoflagellate, Cochlodinium (Margalefidinium) polykrikoides, are allelopathic and may have unique associations with bacteria, a comprehensive assessment of the planktonic communities associated with these blooms has been lacking. Here, we used high-throughput amplicon sequencing to assess size fractionated (0.2 and 5 mu m) bacterial (16S) and phytoplankton assemblages (18S) associated with blooms of C. polykrikoides during recurrent blooms in NY, USA. Over a three-year period, samples were collected inside ('patch') and outside ('non-patch') dense accumulations of C. polykrikoides to assess the microbiome associated with these blooms. Eukaryotic plankton communities of blooms had significantly lower diversity than non-bloom samples, and non-bloom samples hosted 30 eukaryotic operational taxonomic units (OTUs) not found within blooms, suggesting they may have been allelopathically excluded from blooms. Differential abundance analyses revealed that C. polykrikoides blooms were significantly enriched in dinoflagellates (p<0.001) and the experimental enrichment of C. polykrikoides led to a significant increase in the relative abundance of eight genera of dinoflagellates but a significant decline in other eukaryotic plankton. Amoebophrya co-dominated both within- and near- C. polykrikoides blooms and was more abundant in bloom patches. The core bacterial microbiome of the >0.2 mu m fraction of blooms was dominated by an uncultured bacterium from the SAR11 clade, while the >5 mu m size fraction was co-dominated by an uncultured bacterium from Rhodobacteraceae and Coraliomargarita. Two bacterial lineages within the >0.2 mu m fraction, as well as the Gammaproteobacterium, Halioglobus, from the >5 mu m fraction were unique to the microbiome of blooms, while there were 154 bacterial OTUs only found in non-bloom waters. Collectively, these findings reveal the unique composition and potential function of eukaryotic and prokaryotic communities associated with C. polykrikoides blooms.
C1 [Hattenrath-Lehmann, Theresa K.; Jankowiak, Jennifer; Koch, Florian; Gobler, Christopher J.] SUNY Stony Brook, Sch Marine & Atmospher Sci, Southampton, NY 11968 USA.
   [Jankowiak, Jennifer] New York State Dept Hlth, Wadsworth Ctr, Empire State Plaza, Albany, NY USA.
   [Koch, Florian] Helmholtz Zentrum Polar & Meeresforsch, Alfred Wegener Inst, Marine Biogeosci, Bremerhaven, Germany.
RP Gobler, CJ (corresponding author), SUNY Stony Brook, Sch Marine & Atmospher Sci, Southampton, NY 11968 USA.
EM christopher.gobler@stonybrook.edu
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NR 97
TC 21
Z9 22
PD NOV 7
PY 2019
VL 14
IS 11
AR e0223067
DI 10.1371/journal.pone.0223067
UT WOS:000532694400010
DA 2025-07-30
ER

PT J
AU Pushkarev, A
   Hevroni, G
   Roitman, S
   Shim, JG
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AF Pushkarev, Alina
   Hevroni, Gur
   Roitman, Sheila
   Shim, Jin-gon
   Choi, Ahreum
   Jung, Kwang-Hwan
   Beja, Oded
TI The Use of a Chimeric Rhodopsin Vector for the Detection of New
   Proteorhodopsins Based on Color
SO FRONTIERS IN MICROBIOLOGY
DT Article
AB Student microbial ecology laboratory courses are often conducted as condensed courses in which theory and wet lab work are combined in a very intensive short time period. In last decades, the study of marine microbial ecology is increasingly reliant on molecular-based methods, and as a result many of the research projects conducted in such courses require sequencing that is often not available on site and may take more time than a typical course allows. In this work, we describe a protocol combining molecular and functional methods for analyzing proteorhodopsins (PRs), with visible results in only 4-5 days that do not rely on sequencing. PRs were discovered in oceanic surface waters two decades ago, and have since been observed in different marine environments and diverse taxa, including the abundant alphaproteobacterial SAR11 group. PR subgroups are currently known to absorb green and blue light, and their distribution was previously explained by prevailing light conditions - green pigments at the surface and blue pigments in deeper waters, as blue light travels deeper in the water column. To detect PR in environmental samples, we created a chimeric plasmid suitable for direct expression of PRs using PCR amplification and functional analysis in Escherichia coli cells. Using this assay, we discovered several exceptional cases of PRs whose phenotypes differed from those predicted based on sequence only, including a previously undescribed yellow-light absorbing PRs. We applied this assay in two 10-days marine microbiology courses and found it to greatly enhance students' laboratory experience, enabling them to gain rapid visual feedback and colorful reward for their work. Furthermore we expect this assay to promote the use of functional assays for the discovery of new rhodopsin variants.
C1 [Pushkarev, Alina; Hevroni, Gur; Roitman, Sheila; Beja, Oded] Technion Israel Inst Technol, Fac Biol, Haifa, Israel.
   [Shim, Jin-gon; Choi, Ahreum; Jung, Kwang-Hwan] Sogang Univ, Dept Life Sci, Seoul, South Korea.
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RP Béjà, O (corresponding author), Technion Israel Inst Technol, Fac Biol, Haifa, Israel.
EM beja@tx.technion.ac.il
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NR 25
TC 16
Z9 16
PD MAR 13
PY 2018
VL 9
AR 439
DI 10.3389/fmicb.2018.00439
UT WOS:000427266100001
DA 2025-07-30
ER

PT J
AU Korlevic, M
   Ristova, PP
   Garic, R
   Amann, R
   Orlic, S
AF Korlevic, M.
   Ristova, P. Pop
   Garic, R.
   Amann, R.
   Orlic, S.
TI Bacterial Diversity in the South Adriatic Sea during a Strong, Deep
   Winter Convection Year
SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB The South Adriatic Sea is the deepest part of the Adriatic Sea and represents a key area for both the Adriatic Sea and the deep eastern Mediterranean. It has a role in dense water formation for the eastern Mediterranean deep circulation cell, and it represents an entry point for water masses originating from the Ionian Sea. The biodiversity and seasonality of bacterial picoplankton before, during, and after deep winter convection in the oligotrophic South Adriatic waters were assessed by combining comparative 16S rRNA sequence analysis and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). The picoplankton communities reached their maximum abundance in the spring euphotic zone when the maximum value of the chlorophyll a in response to deep winter convection was recorded. The communities were dominated by Bacteria, while Archaea were a minor constituent. A seasonality of bacterial richness and diversity was observed, with minimum values occurring during the winter convection and spring postconvection periods and maximum values occurring under summer stratified conditions. The SAR11 clade was the main constituent of the bacterial communities and reached the maximum abundance in the euphotic zone in spring after the convection episode. Cyanobacteria were the second most abundant group, and their abundance strongly depended on the convection event, when minimal cyanobacterial abundance was observed. In spring and autumn, the euphotic zone was characterized by Bacteroidetes and Gammaproteobacteria. Bacteroidetes clades NS2b, NS4, and NS5 and the gamma-proteobacterial SAR86 clade were detected to co-occur with phytoplankton blooms. The SAR324, SAR202, and SAR406 clades were present in the deep layer, exhibiting different seasonal variations in abundance. Overall, our data demonstrate that the abundances of particular bacterial clades and the overall bacterial richness and diversity are greatly impacted by strong winter convection.
C1 [Korlevic, M.; Orlic, S.] Rudjer Boskovic Inst, Zagreb, Croatia.
   [Ristova, P. Pop] Univ Bremen, MARUM Ctr Marine Environm Sci, D-28359 Bremen, Germany.
   [Garic, R.] Univ Dubrovnik, Inst Marine & Coastal Res, Dubrovnik, Croatia.
   [Amann, R.] Max Planck Inst Marine Microbiol, Bremen, Germany.
RP Orlic, S (corresponding author), Rudjer Boskovic Inst, Zagreb, Croatia.
EM sandi.orlic@irb.hr
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Z9 39
PD MAR
PY 2015
VL 81
IS 5
BP 1715
EP 1726
DI 10.1128/AEM.03410-14
UT WOS:000349547200020
DA 2025-07-30
ER

PT J
AU Nimnoi, P
   Pongsilp, N
AF Nimnoi, Pongrawee
   Pongsilp, Neelawan
TI Marine bacterial communities in the upper gulf of Thailand assessed by
   Illumina next-generation sequencing platform
SO BMC MICROBIOLOGY
DT Article
AB Background The total bacterial community plays an important role in aquatic ecosystems. In this study, bacterial communities and diversity along the shores of the Upper Gulf of Thailand were first characterized. The association between bacterial communities and types of land use was also evaluated. Results The bacterial communities and diversity of seawater in the Upper Gulf of Thailand, with regard to types of land use, were first revealed by using Illumina next-generation sequencing. A total of 4953 OTUs were observed from all samples in which 554 OTUs were common. The bacterial communities in sampling sites were significantly different from each other. The run-off water from three types of land use significantly affected the community richness and diversity of marine bacteria. Aquaculture sites contained the highest levels of community richness and diversity, followed by mangrove forests and tourist sites. Seawater physicochemical parameters including salinity, turbidity, TSS, total N, and BOD5, were significantly different when grouped by land use. The bacterial communities were mainly determined by salinity, total N, and total P. The species richness estimators and OTUs were positively correlated with turbidity. The top ten most abundant phyla and genera as well as the distribution of bacterial classes were characterized. The Proteobacteria constituted the largest proportions in all sampling sites, ranging between 67.31 and 78.80%. The numbers of the Marinobacterium, Neptuniibacter, Synechococcus, Candidatus Thiobios, hgcI clade (Actinobacteria), and Candidatus Pelagibacter were significantly different when grouped by land use. Conclusions Type of land use significantly affected bacterial communities and diversity along the Upper Gulf of Thailand. Turbidity was the most influential parameter affecting the variation in bacterial community composition. Salinity, total N, and P were the ones of the important factors that shaped the bacterial communities. In addition, the variations of bacterial communities from site-to-site were greater than within-site. The Proteobacteria, Bacteroidetes, Actinobacteria, Cyanobacteria, Verrucomicrobia, Euryarchaeota, Planctomycetes, Firmicutes, Deep Sea DHVEG-6, and Marinimicrobia were the most and common phyla distributed across the Upper Gulf of Thailand.
C1 [Nimnoi, Pongrawee] Kasetsart Univ, Dept Microbiol, Fac Liberal Arts & Sci, Nakhon Pathom, Thailand.
   [Pongsilp, Neelawan] Silpakorn Univ, Dept Microbiol, Fac Sci, Nakhon Pathom, Thailand.
RP Pongsilp, N (corresponding author), Silpakorn Univ, Dept Microbiol, Fac Sci, Nakhon Pathom, Thailand.
EM pongsilp_n@su.ac.th
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NR 44
TC 32
Z9 34
PD JAN 23
PY 2020
VL 20
IS 1
AR 19
DI 10.1186/s12866-020-1701-6
UT WOS:000511978700001
DA 2025-07-30
ER

PT J
AU Seo, JH
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AF Seo, Ji-Hui
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DT Article
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RP Cho, JC (corresponding author), Inha Univ, Dept Biol Sci, Incheon, South Korea.
EM chojc@inha.ac.kr
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DA 2025-07-30
ER

PT J
AU Vipindas, PV
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RP Vipindas, PV (corresponding author), Minist Earth Sci, Natl Ctr Polar & Ocean Res, Arctic Ecol & Biogeochem Div, Vasco Da Gama 403804, Goa, India.
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NR 93
TC 1
Z9 1
PD JAN
PY 2024
VL 40
IS 1
AR 25
DI 10.1007/s11274-023-03850-7
UT WOS:001115493200012
DA 2025-07-30
ER

PT J
AU Namsaraev, Z
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   Makarov, I
   Bezgreshnov, A
   Melnikova, A
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   Toshchakov, S
AF Namsaraev, Zorigto
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   Tuzov, Fedor
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   Izotova, Anna
   Makarov, Ivan
   Bezgreshnov, Andrei
   Melnikova, Anna
   Trofimova, Anna
   Kuzmin, Denis
   Patrushev, Maksim
   Toshchakov, Stepan
TI Biogeographic Analysis Suggests Two Types of Planktonic Prokaryote
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SO BIOLOGY-BASEL
DT Article
AB Simple Summary Of all the Arctic seas, the prokaryotic communities of the Barents Sea are the most affected by climate change and are strongly influenced by microbiota from the Atlantic Ocean. Using 16S metabarcoding, we analyzed samples of prokaryotic plankton communities in the Barents Sea and found two types of communities. The origin of these communities is discussed in terms of biogeography.Abstract The Barents Sea is one of the most rapidly changing Arctic regions, with an unprecedented sea ice decline and increase in water temperature and salinity. We have studied the diversity of prokaryotic communities using 16S metabarcoding in the western and northeastern parts of the Barents Sea along the Kola Section and the section from Novaya Zemlya to Franz Joseph Land. The hypothesis-independent clustering method revealed the existence of two distinct types of communities. The most common prokaryotic taxa were shared between two types of communities, but their relative abundance was different. It was found that the geographic location of the sampling sites explained more than 30% of the difference between communities, while no statistically significant correlation between environmental parameters and community composition was found. The representatives of the Psychrobacter, Sulfitobacter and Polaribacter genera were dominant in samples from both types of communities. The first type of community was also dominated by members of Halomonas, Pseudoalteromonas, Planococcaceae and an unclassified representative of the Alteromonadaceae family. The second type of community also had a significant proportion of Nitrincolaceae, SAR92, SAR11 Clade I, NS9, Cryomorphaceae and SUP05 representatives. The origin of these communities can be explained by the influence of environmental factors or by the different origins of water masses. This research highlights the importance of studying biogeographic patterns in the Barents Sea in comparison with those in the North Atlantic and Arctic Ocean prokaryote communities.
C1 [Namsaraev, Zorigto; Kozlova, Aleksandra; Krylova, Anastasia; Izotova, Anna; Melnikova, Anna; Patrushev, Maksim; Toshchakov, Stepan] Kurchatov Inst, Natl Res Ctr, Kurchatov Ctr Genome Res, Moscow 123182, Russia.
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   [Tuzov, Fedor] Lomonosov Moscow State Univ, Fac Geog, Dept Oceanol, Moscow 119991, Russia.
   [Tuzov, Fedor] All Russian Res Inst Civil Def & Emergencies, Moscow 121352, Russia.
   [Bezgreshnov, Andrei] Arctic & Antarctic Res Inst, St Petersburg 199397, Russia.
   [Trofimova, Anna] Northern Arctic Fed Univ, Higher Sch Nat Sci & Technol, Dept Geog & Hydrometeorol, Arkhangelsk 163002, Russia.
RP Namsaraev, Z (corresponding author), Kurchatov Inst, Natl Res Ctr, Kurchatov Ctr Genome Res, Moscow 123182, Russia.; Namsaraev, Z (corresponding author), Moscow Inst Phys & Technol, Dolgoprudnyi 141701, Russia.
EM zorigto@gmail.com
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TC 2
Z9 2
PD OCT
PY 2023
VL 12
IS 10
AR 1310
DI 10.3390/biology12101310
UT WOS:001092492400001
DA 2025-07-30
ER

PT J
AU Liu, HB
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AF Liu, Hongbin
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DT Article
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C1 [Liu, Hongbin; Tan, Shangjin; Guo, Wang; Xia, Xiaomin; Cheung, Shun Yan] Hong Kong Univ Sci & Technol, Div Life Sci, Kowloon, Hong Kong, Peoples R China.
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RP Liu, HB (corresponding author), Hong Kong Univ Sci & Technol, Div Life Sci, Kowloon, Hong Kong, Peoples R China.
EM liuhb@ust.hk
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NR 68
TC 10
Z9 12
PD NOV
PY 2017
VL 62
SU 1
BP S364
EP S380
DI 10.1002/lno.10612
UT WOS:000415924700024
DA 2025-07-30
ER

PT J
AU Liu, ST
   Longnecker, K
   Kujawinski, EB
   Vergin, K
   Bolanos, LM
   Giovannoni, SJ
   Parsons, R
   Opalk, K
   Halewood, E
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   Curry, R
   Carlson, CA
AF Liu, Shuting
   Longnecker, Krista
   Kujawinski, Elizabeth B.
   Vergin, Kevin
   Bolanos, Luis M.
   Giovannoni, Stephen J.
   Parsons, Rachel
   Opalk, Keri
   Halewood, Elisa
   Hansell, Dennis A.
   Johnson, Rod
   Curry, Ruth
   Carlson, Craig A.
TI Linkages Among Dissolved Organic Matter Export, Dissolved Metabolites,
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SO FRONTIERS IN MICROBIOLOGY
DT Article
AB Deep convective mixing of dissolved and suspended organic matter from the surface to depth can represent an important export pathway of the biological carbon pump. The seasonally oligotrophic Sargasso Sea experiences annual winter convective mixing to as deep as 300 m, providing a unique model system to examine dissolved organic matter (DOM) export and its subsequent compositional transformation by microbial oxidation. We analyzed biogeochemical and microbial parameters collected from the northwestern Sargasso Sea, including bulk dissolved organic carbon (DOC), total dissolved amino acids (TDAA), dissolved metabolites, bacterial abundance and production, and bacterial community structure, to assess the fate and compositional transformation of DOM by microbes on a seasonal time-scale in 2016-2017. DOM dynamics at the Bermuda Atlantic Time-series Study site followed a general annual trend of DOC accumulation in the surface during stratified periods followed by downward flux during winter convective mixing. Changes in the amino acid concentrations and compositions provide useful indices of diagenetic alteration of DOM. TDAA concentrations and degradation indices increased in the mesopelagic zone during mixing, indicating the export of a relatively less diagenetically altered (i.e., more labile) DOM. During periods of deep mixing, a unique subset of dissolved metabolites, such as amino acids, vitamins, and benzoic acids, was produced or lost. DOM export and compositional change were accompanied by mesopelagic bacterial growth and response of specific bacterial lineages in the SAR11, SAR202, and SAR86 clades, Acidimicrobiales, and Flavobacteria, during and shortly following deep mixing. Complementary DOM biogeochemistry and microbial measurements revealed seasonal changes in DOM composition and diagenetic state, highlighting microbial alteration of the quantity and quality of DOM in the ocean.
C1 [Liu, Shuting; Opalk, Keri; Halewood, Elisa; Carlson, Craig A.] Univ Calif, Inst Marine Sci, Dept Ecol, Evolut & Marine Biol, Santa Barbara, CA USA.
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   [Hansell, Dennis A.] Univ Miami, Rosenstiel Sch Marine & Atmospher Sci, Miami, FL USA.
RP Liu, ST (corresponding author), Univ Calif, Inst Marine Sci, Dept Ecol, Evolut & Marine Biol, Santa Barbara, CA USA.
EM shutingliu@ucsb.edu
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NR 159
TC 19
Z9 19
PD MAR 8
PY 2022
VL 13
AR 833252
DI 10.3389/fmicb.2022.833252
UT WOS:000777286700001
DA 2025-07-30
ER

PT J
AU Fourquez, M
   Beier, S
   Jongmans, E
   Hunter, R
   Obernosterer, I
AF Fourquez, Marion
   Beier, Sara
   Jongmans, Elanor
   Hunter, Robert
   Obernosterer, Ingrid
TI Uptake of Leucine, Chitin, and Iron by Prokaryotic Groups during Spring
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   Island (Southern Ocean)
SO FRONTIERS IN MARINE SCIENCE
DT Article
AB Iron and carbon are essential for microbial heterotrophic activity, but the bioavailability of these elements is low in surface waters of the Southern Ocean. Whether the access to iron and carbon differs among phylogenetic groups of prokaryotes is barely known. To address this question we used iron ((FeCl3)-Fe-55), and the carbon compounds chitin (H-3-Diacetylchitobiose) and leucine (H-3-leucine) as model substrates in combination with MICRO-CARD-FISH during spring phytoplankton blooms induced by natural iron fertilization off Kerguelen Island (KErguelen Ocean and Plateau compared Study 2 - KEOPS2; October-November 2011). The application of probes at broad phylogenetic levels indicated an overall similar community composition in surface waters at the 8 investigated sites. The relative contributions of the prokaryotic groups to abundance revealed a strong positive relationship with their respective contributions to the leucine-active community (p < 0.0001; r = 0.93). This relationship was much weaker for chitin (p < 0.001; r = 0.51) and absent for iron (p > 0.05; r = 0.26). These results suggest preferential uptake of iron and chitin by some prokaryotic groups. SAR11 and Cytophaga-Flavobacterium-Bacteroides (CFB) were the dominant contributors to the leucine-active community, while CFB and Archaea had the highest contributions to the chitin-active community. By contrast, Gammaproteobacteria, including SAR86, and CFB revealed the highest contributions to the iron-active community. We found several correlations between the group-specific fractions of active cells for a given substrate and most of them included CFB, pointing to the potential importance of microbial interactions for iron and carbon cycling in the Southern Ocean.
C1 [Fourquez, Marion] Univ Tasmania, Antarctic Climate & Ecosyst Cooperat Res Ctr, Hobart, Tas, Australia.
   [Fourquez, Marion; Beier, Sara; Jongmans, Elanor; Hunter, Robert; Obernosterer, Ingrid] UPMC Univ Paris 06, Sorbonne Univ, Lab Oceanog Microbienne LOMIC, Observ Oceanol,CNRS, Banyuls Sur Mer, France.
   [Beier, Sara] Letbniz Inst Balt Sea Res Warnemunde IOW, Dept Biol Oceanog, Rostock, Germany.
RP Fourquez, M (corresponding author), Univ Tasmania, Antarctic Climate & Ecosyst Cooperat Res Ctr, Hobart, Tas, Australia.; Fourquez, M (corresponding author), UPMC Univ Paris 06, Sorbonne Univ, Lab Oceanog Microbienne LOMIC, Observ Oceanol,CNRS, Banyuls Sur Mer, France.
EM marion.fourquez@gmail.com
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NR 82
TC 11
Z9 11
PY 2016
VL 3
AR 256
DI 10.3389/fmars.2016.00256
UT WOS:000457358000252
DA 2025-07-30
ER

PT J
AU Vinogradov, SN
   Tinajero-Trejo, M
   Poole, RK
   Hoogewijs, D
AF Vinogradov, Serge N.
   Tinajero-Trejo, Mariana
   Poole, Robert K.
   Hoogewijs, David
TI Bacterial and archaeal globins - A revised perspective
SO BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
DT Article
AB A bioinformatics survey of putative globins in over 2200 bacterial and some 140 archaeal genomes revealed that over half the bacterial and approximately one fifth of archaeal genomes contain genes encoding globins that were classified into three families: the M (myoglobin-like), and S (sensor) families all exhibiting the canonical 3/3 myoglobin fold, and the T family (truncated myoglobin fold). Although the M family comprises 2 subfamilies, flavohemoglobins (FHbs) and single domain globins (SDgbs), the S family encompasses chimeric globin-coupled sensors (GCSs), single domain Pgbs (protoglobins) and SSDgbs (sensor single domain globins). The T family comprises three classes TrHb1s, TrHb2s and TrHb3s, characterized by the abbreviated 2/2 myoglobin fold. The Archaea contain only Pgbs, GCSs and TrHb1s. The smallest globin-bearing genomes are the streamlined genomes (similar to 1.3 Mbp) of the SAR11 clade of alphaproteobacteria and the slightly larger (ca.1.7 Mbp) genomes of Aquificae. The smallest genome with members of all three families is the 23 Mbp genome of the extremophile Methylacidiphilum infernorum (Verrumicrobia). Of the 147 possible combinations of the eight globin subfamilies, only 83 are observed. Although binary combinations are infrequent and ternary combinations are rare, the FHb + TrHb2 combination is the most commonly observed. Of the possible functions of bacterial globins we discuss the two principal - ones nitric oxide detoxification via the NO dioxygenase or denitrosylase activities and the sensing of oxygen concentration in the environmental niche. In only few cases has a physiological role been demonstrated in vivo. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins. (c) 2013 Elsevier B.V. All rights reserved.
C1 [Vinogradov, Serge N.] Wayne State Univ, Sch Med, Dept Biochem & Mol Biol, Detroit, MI 48201 USA.
   [Tinajero-Trejo, Mariana; Poole, Robert K.] Univ Sheffield, Dept Mol Biol & Biotechnol, Inst Biol & Biotechnol, Sheffield S10 2TN, S Yorkshire, England.
   [Hoogewijs, David] Univ Zurich, Inst Physiol, CH-8057 Zurich, Switzerland.
   [Hoogewijs, David] Univ Zurich, Zurich Ctr Integrat Human Physiol, CH-8057 Zurich, Switzerland.
RP Hoogewijs, D (corresponding author), Univ Zurich, Inst Physiol, Winterthurerstr 190, CH-8057 Zurich, Switzerland.
EM david.hoogewijs@access.uzh.ch
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Z9 101
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PY 2013
VL 1834
IS 9
SI SI
BP 1789
EP 1800
DI 10.1016/j.bbapap.2013.03.021
UT WOS:000323191800014
DA 2025-07-30
ER

PT J
AU Pearman, JK
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   Thompson, L
   Waters, S
   Vandergoes, MJ
   Howarth, JD
   Duggan, IC
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AF Pearman, John K.
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   Thompson, Lucy
   Waters, Sean
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   Duggan, Ian C.
   Hogg, Ian D.
   Wood, Susanna A.
TI Human access and deterministic processes play a major role in
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SO PEERJ
DT Article
AB Lakes provide habitat for a diverse array of species and offer a wide range of ecosystem services for humanity. However, they are highly vulnerable as they are not only impacted by adverse actions directly affecting them, but also those on the surrounding environment. Improving knowledge on the processes responsible for community assembly in different biotic components will aid in the protection and restoration of lakes. Studies to date suggested a combination of deterministic (where biotic/abiotic factors act on fitness differences amongst taxa) and stochastic (where dispersal plays a larger factor in community assembly) processes are responsible for structuring biotic communities, but there is no consensus on the relative roles these processes play, and data is lacking for lakes. In the present study, we sampled different biotic components in 34 lakes located on the South Island of New Zealand. To obtain a holistic view of assembly processes in lakes we used metabarcoding to investigate bacteria in the sediment and surface waters, and eukaryotes in the sediment and two different size fractions of the water column. Physicochemical parameters were collected in parallel. Results showed that deterministic processes dominated the assembly of lake communities although the relative importance of variable and homogeneous selection differed among the biotic components. Variable selection was more important in the sediment (SSbact and SSeuks) and for the bacterioplankton (Pbact) while the assembly of the eukaryotic plankton (SPeuks, LPeuks) was driven more by homogeneous selection. The ease of human access to the lakes had a significant effect on lake communities. In particular, clade III of SAR11 and Daphnia pulex were only present in lakes with public access. This study provides insights into the distribution patterns of different biotic components and highlights the value in understanding the drivers of different biological communities within lakes.
C1 [Pearman, John K.; Thomson-Laing, Georgia; Thompson, Lucy; Waters, Sean; Wood, Susanna A.] Cawthron Inst, Nelson, New Zealand.
   [Vandergoes, Marcus J.] GNS Sci, Lower Hutt, New Zealand.
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RP Pearman, JK (corresponding author), Cawthron Inst, Nelson, New Zealand.
EM John.Pearman@cawthron.org.nz
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NR 90
TC 4
Z9 4
PD NOV 11
PY 2022
VL 10
AR e14378
DI 10.7717/peerj.14378
UT WOS:000965006400004
DA 2025-07-30
ER

PT J
AU Rasmussen, AN
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   Eloe-Fadrosh, EA
   Francis, CA
AF Rasmussen, Anna N.
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   Francis, Christopher A.
TI In-depth Spatiotemporal Characterization of Planktonic Archaeal and
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SO MICROBIAL ECOLOGY
DT Article
AB Despite being the largest estuary on the west coast of North America, no in-depth survey of microbial communities in San Francisco Bay (SFB) waters currently exists. In this study, we analyze bacterioplankton and archaeoplankton communities at several taxonomic levels and spatial extents (i.e., North versus South Bay) to reveal patterns in alpha and beta diversity. We assess communities using high-throughput sequencing of the 16S rRNA gene in 177 water column samples collected along a 150-km transect over a 2-year monthly time-series. In North Bay, the microbial community is strongly structured by spatial salinity changes while in South Bay seasonal variations dominate community dynamics. Along the steep salinity gradient in North Bay, we find that operational taxonomic units (OTUs; 97% identity) have higher site specificity than at coarser taxonomic levels and turnover ("species" replacement) is high, revealing a distinct brackish community (in oligo-, meso-, and polyhaline samples) from fresh and marine end-members. At coarser taxonomic levels (e.g., phylum, class), taxa are broadly distributed across salinity zones (i.e., present/abundant in a large number of samples) and brackish communities appear to be a mix of fresh and marine communities. We also observe variations in brackish communities between samples with similar salinities, likely related to differences in water residence times between North and South Bay. Throughout SFB, suspended particulate matter is positively correlated with richness and influences changes in beta diversity. Within several abundant groups, including the SAR11 clade (comprising up to 30% of reads in a sample), OTUs appear to be specialized to a specific salinity range. Some other organisms also showed pronounced seasonal abundance, including Synechococcus, Ca. Actinomarina, and Nitrosopumilus-like OTUs. Overall, this study represents the first in-depth spatiotemporal survey of SFB microbial communities and provides insight into how planktonic microorganisms have specialized to different niches along the salinity gradient.
C1 [Rasmussen, Anna N.; Damashek, Julian; Francis, Christopher A.] Stanford Univ, Dept Earth Syst Sci, 473 Via Ortega,Y2E2 Bldg Rm 140, Stanford, CA 94305 USA.
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RP Francis, CA (corresponding author), Stanford Univ, Dept Earth Syst Sci, 473 Via Ortega,Y2E2 Bldg Rm 140, Stanford, CA 94305 USA.
EM caf@stanfond.edu
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NR 101
TC 12
Z9 13
PD APR
PY 2021
VL 81
IS 3
BP 601
EP 616
DI 10.1007/s00248-020-01621-7
EA NOV 2020
UT WOS:000585738000001
DA 2025-07-30
ER

PT J
AU Lekunberri, I
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   Herndl, GJ
AF Lekunberri, Itziar
   Sintes, Eva
   de Corte, Daniele
   Yokokawa, Taichi
   Herndl, Gerhard J.
TI Spatial patterns of bacterial and archaeal communities along the
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SO FEMS MICROBIOLOGY ECOLOGY
DT Article
AB The composition of prokaryotic communities was determined in the meso- and bathypelagic waters funneled through the Romanche Fracture Zone (RFZ, 2 degrees 7'S, 31 degrees 79'W to 0 degrees 6'N, 14 degrees 33'W) in the tropical Atlantic. Distinct water masses were identified based on their physical and chemical characteristics. The bacterial and archaeal communities were depth-stratified with a total of 116 and 25 operational taxonomic units (OTUs), respectively, distributed among the distinct water masses as revealed by terminal restriction fragment length polymorphism, and cloning and sequencing. The relative abundance of Thaumarchaeota, determined by catalyzed reporter deposition-fluorescence in situ hybridization, was significantly higher in deeper layers (Antarctic Bottom Water, AABW, > 4000 m depth), contributing up to 31% to the total prokaryotic community, than in the mesopelagic and lower euphotic layer. Although the contribution of SAR11 to bacterial abundance did not increase with depth, SAR202, SAR324, SAR406 and Alteromonas did increase with depth. Terminal restriction fragment length polymorphism analysis revealed successional changes in the bacterial and archaeal community composition of the North Atlantic Deep Water (NADW) with a passage time through the RFZ of c. 4 months but not in the under- and overlying water masses. Our results indicate that specific water masses harbor distinct bacterial and archaeal communities and that the prokaryotic community of the NADW undergoes successional changes in this conduit between the western and eastern Atlantic basin. Apparently, in the absence of major input of organic matter to specific deep-water masses, the indigenous prokaryotic community adapts to subtle physical and biogeochemical changes in the water mass within a time frame of weeks, similar to the reported seasonal changes in surface water prokaryotic communities.
C1 [Lekunberri, Itziar; Sintes, Eva; de Corte, Daniele; Herndl, Gerhard J.] Univ Vienna, Dept Marine Biol, Fac Ctr Ecol, A-1090 Vienna, Austria.
   [Yokokawa, Taichi] Ehime Univ, CMES, Matsuyama, Ehime, Japan.
   [Herndl, Gerhard J.] Royal Netherlands Inst Sea Res NIOZ, Dept Biol Oceanog, Texel, Netherlands.
   [Herndl, Gerhard J.] Univ Groningen, CEES, Groningen, Netherlands.
RP Sintes, E (corresponding author), Univ Vienna, Dept Marine Biol, Fac Ctr Ecol, Althanstr 14, A-1090 Vienna, Austria.
EM eva.sintes@univie.ac.at
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NR 52
TC 14
Z9 15
PD SEP
PY 2013
VL 85
IS 3
BP 537
EP 552
DI 10.1111/1574-6941.12142
UT WOS:000323200400011
DA 2025-07-30
ER

PT J
AU Reintjes, G
   Heins, A
   Wang, C
   Amann, R
AF Reintjes, Greta
   Heins, Anneke
   Wang, Cheng
   Amann, Rudolf
TI Abundance and composition of particles and their attached microbiomes
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SO FRONTIERS IN MARINE SCIENCE
DT Article
AB Particulate organic matter plays a significant role in the marine carbon cycle. Its sinking exports organic carbon from the surface to deep oceans. Using fractionated filtration, we analysed particles of 3 - 10 mu m and >10 mu m and their microbiomes in thirty-five stations along a latitudinal transect of the Atlantic Ocean and provide new insights into the composition, community dynamics, and catabolic potential of particle-attached bacteria. Samples were taken during an Atlantic Meridional Transect (AMT22), which traversed six distinctive ocean provinces. Using 16S rRNA amplicon sequencing and fluorescence in situ hybridisation, we could show a strong variation between particle-attached and free-living bacterial communities at each station and across the biogeographical provinces - a dynamic likely driven by chlorophyll a concentrations, temperature, and the oxygen content of the respective biogeographical provinces. Whereas the <3 mu m fraction was primarily composed of SAR11, SAR86, Prochlorococcus and Bacteroidetes of the NS9 and NS5 clades, particle-attached communities were dominated by other Bacteroidetes (Polaribacter spp.), diverse Gammaproteobacteria including members of the genera Alteromonas and Vibrio, Alphaproteobacteria, Planctomycetes, OM27 and Verrucomicrobia. In three provinces, we quantified particle abundance and analysed their glycan composition using four lectins targeting fucose, galactose, N-acetylgalactosamine and mannose. Particles were mainly composed of fucose glycans with only a minor abundance of the other glycans, and particle abundance was directly correlated with the chlorophyll a concentrations. Functional analysis of 54 metagenome-assembled genomes retrieved from bacterial communities attached to small particles showed that particle-attached Bacteroidetes, Planctomycetes and Verrucomicrobia displayed key roles in the degradation of sulfated fucose-containing polysaccharides. We also identified gene clusters potentially encoding the utilisation of mannan and laminarin, suggesting an adaptation to the glycan composition of the particles, potentially resulting in niche diversification. Together, our results provide insights into particle-attached bacteria and their ecological strategies in the Atlantic.
C1 [Reintjes, Greta; Heins, Anneke; Wang, Cheng; Amann, Rudolf] Max Planck Inst Marine Microbiol, Dept Mol Ecol, Bremen, Germany.
   [Wang, Cheng] Sun Yat sen Univ, Guangzhou, Guangdong, Peoples R China.
RP Reintjes, G (corresponding author), Max Planck Inst Marine Microbiol, Dept Mol Ecol, Bremen, Germany.
EM greintje@mpi-bremen.de
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NR 100
TC 13
Z9 13
PD MAR 7
PY 2023
VL 10
AR 1051510
DI 10.3389/fmars.2023.1051510
UT WOS:000950888700001
DA 2025-07-30
ER

PT J
AU Balestra, C
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SO AQUATIC MICROBIAL ECOLOGY
DT Article
AB Polyunsaturated aldehydes (PUAs), produced as secondary metabolites by diatoms, have been shown to induce toxic effects on a variety of organisms, including copepods and phyto- and bacterioplankton. However, the nature of and the players in this interaction remain poorly understood. We tested the effect of 3 PUAs commonly produced by marine diatoms-2E, 4E/Z-heptadienal (HEPTA), 2E, 4E/Z-octadienal (OCTA), 2E, 4E/Z-decadienal (DECA) and a mix of HEPTA and OCTA (MIX)-on a natural bacterial community from a coastal area of the NW Mediterranean Sea (Blanes Bay, Spain). Little effect on total or relative cell abundance or bulk bacterial production was observed after 6 or 24 h exposure to 7.5 nM of the 3 different PUAs for the different bacterial phylogenetic groups (Gammaproteobacteria, Bacteroidetes, Rhodobacteraceae and SAR11), assessed by catalysed reporter deposition (CARD)-fluorescence in situ hybridisation (FISH). Metabolic activity, i.e. single-cell activity as determined by microautoradiography combined with CARD-FISH (MAR-CARD-FISH), was least affected by the addition of single PUAs in Gammaproteobacteria, markedly in Bacteroidetes and most markedly in Rhodobacteraceae, leading to a decrease in Rhodobacteraceae abundance by 21% (by 38% of the active cells assessed by leucine uptake) compared to the control. Bacteroidetes, although markedly affected in single-cell activity, were the most abundant group (54% of total cell counts). The addition of a mixture of OCTA and HEPTA produced a more pronounced decrease in the metabolic activity of all groups than the incubation with the single PUAs, suggesting a synergistic effect. Our results demonstrate that PUAs have a differential effect on the single-cell activity of distinct bacterial groups in natural communities. PUAs may therefore play an important role in shaping bacterial community composition by conferring a competitive advantage to PUA-resistant groups, allowing them to preferentially use the organic matter released by diatoms.
C1 [Balestra, Cecilia; Casotti, Raffaella] Stn Zool A Dohrn, I-80121 Naples, Italy.
   [Alonso-Saez, Laura; Gasol, Josep M.] CSIC, Inst Ciencies Mar, E-08003 Barcelona, Catalonia, Spain.
RP Casotti, R (corresponding author), Stn Zool A Dohrn, Villa Comunale, I-80121 Naples, Italy.
EM raffa@szn.it
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NR 45
TC 47
Z9 48
PY 2011
VL 63
IS 2
BP 123
EP 131
DI 10.3354/ame01486
UT WOS:000289577600003
DA 2025-07-30
ER

PT J
AU Hurtado-McCormick, V
   Krix, D
   Tschitschko, B
   Siboni, N
   Ralph, PJ
   Seymour, JR
AF Hurtado-McCormick, V.
   Krix, D.
   Tschitschko, B.
   Siboni, N.
   Ralph, P. J.
   Seymour, J. R.
TI Shifts in the seagrass leaf microbiome associated with wasting disease
   in Zostera muelleri
SO MARINE AND FRESHWATER RESEARCH
DT Article
AB Seagrass wasting disease (SWD), an infection believed to be caused by Labyrinthula zosterae, has been linked to seagrass declines in several places around the world. However, there is uncertainty about the mechanisms of disease and the potential involvement of opportunistic colonising microorganisms. Using 16S rRNA gene amplicon sequencing, we compared the microbiome of SWD lesions in leaves of Zostera muelleri with communities in adjacent asymptomatic tissues and healthy leaves. The microbiome of healthy leaf tissues was dominated by Pseudomonas and Burkholderia, whereas the most predominant taxa within adjacent tissues were Pseudomonas and Rubidimonas. Members of the Saprospiraceae, potential macroalgal pathogens, were over-represented within SWD lesions. These pronounced changes in microbiome structure were also apparent when we examined the core microbiome of different tissue types. Although the core microbiome associated with healthy leaves included three operational taxonomic units (OTUs) classified as Burkholderia, Cryomorphaceae and the SAR11 clade, a single core OTU from the Arenicella was found within adjacent tissues. Burkholderia are diazotrophic microorganisms and may play an important role in seagrass nitrogen acquisition. In contrast, some members of the Arenicella have been implicated in necrotic disease in other benthic animals. Moreover, microbiome structure was maintained across sites within healthy tissues, but not within SWD lesions or the tissues immediately adjacent to lesions. Predicted functional profiles revealed increased photoautotrophic functions in SWD tissues relative to healthy leaves, but no increase in pathogenicity or virulence. Notably, we demonstrated the presence of L. zosterae in SWD lesions by polymerase chain reaction, but only in one of the two sampled locations, which indicates that other microbiological factors may be involved in the initiation or development of SWD-like symptoms. This study suggests that the dynamics of the seagrass microbiome should be considered within the diagnosis and management of SWD.
C1 [Hurtado-McCormick, V.; Tschitschko, B.; Siboni, N.; Ralph, P. J.; Seymour, J. R.] Univ Technol Sydney, Climate Change Cluster, Fac Sci, Ultimo, NSW 2007, Australia.
   [Krix, D.] Univ Technol Sydney, Sch Life Sci, Fac Sci, Ultimo, NSW 2007, Australia.
   [Tschitschko, B.] Max Planck Inst Marine Microbiol, Celsiusstr 1, D-28359 Bremen, Germany.
RP Hurtado-McCormick, V (corresponding author), Univ Technol Sydney, Climate Change Cluster, Fac Sci, Ultimo, NSW 2007, Australia.
EM valentina.hurtadomccormick@uts.edu.au
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NR 144
TC 2
Z9 3
PY 2021
VL 72
IS 9
BP 1303
EP 1320
DI 10.1071/MF20209
EA APR 2021
UT WOS:000635523900001
DA 2025-07-30
ER

PT J
AU Stewart, FJ
   Dalsgaard, T
   Young, CR
   Thamdrup, B
   Revsbech, NP
   Ulloa, O
   Canfield, DE
   DeLong, EF
AF Stewart, Frank J.
   Dalsgaard, Tage
   Young, Curtis R.
   Thamdrup, Bo
   Revsbech, Niels Peter
   Ulloa, Osvaldo
   Canfield, Don E.
   DeLong, Edward F.
TI Experimental Incubations Elicit Profound Changes in Community
   Transcription in OMZ Bacterioplankton
SO PLOS ONE
DT Article
AB Sequencing of microbial community RNA (metatranscriptome) is a useful approach for assessing gene expression in microorganisms from the natural environment. This method has revealed transcriptional patterns in situ, but can also be used to detect transcriptional cascades in microcosms following experimental perturbation. Unambiguously identifying differential transcription between control and experimental treatments requires constraining effects that are simply due to sampling and bottle enclosure. These effects remain largely uncharacterized for "challenging" microbial samples, such as those from anoxic regions that require special handling to maintain in situ conditions. Here, we demonstrate substantial changes in microbial transcription induced by sample collection and incubation in experimental bioreactors. Microbial communities were sampled from the water column of a marine oxygen minimum zone by a pump system that introduced minimal oxygen contamination and subsequently incubated in bioreactors under near in situ oxygen and temperature conditions. Relative to the source water, experimental samples became dominated by transcripts suggestive of cell stress, including chaperone, protease, and RNA degradation genes from diverse taxa, with strong representation from SAR11-like alphaproteobacteria. In tandem, transcripts matching facultative anaerobic gammaproteobacteria of the Alteromonadales (e. g., Colwellia) increased 4-13 fold up to 43% of coding transcripts, and encoded a diverse gene set suggestive of protein synthesis and cell growth. We interpret these patterns as taxon-specific responses to combined environmental changes in the bioreactors, including shifts in substrate or oxygen availability, and minor temperature and pressure changes during sampling with the pump system. Whether such changes confound analysis of transcriptional patterns may vary based on the design of the experiment, the taxonomic composition of the source community, and on the metabolic linkages between community members. These data highlight the impressive capacity for transcriptional changes within complex microbial communities, underscoring the need for caution when inferring in situ metabolism based on transcript abundances in experimental incubations.
C1 [Stewart, Frank J.] Georgia Inst Technol, Atlanta, GA 30332 USA.
   [Dalsgaard, Tage] Aarhus Univ, Dept Biosci, Silkeborg, Denmark.
   [Young, Curtis R.; DeLong, Edward F.] MIT, Dept Civil & Environm Engn, Cambridge, MA 02139 USA.
   [Thamdrup, Bo; Canfield, Don E.] Univ So Denmark, Inst Biol, Odense, Denmark.
   [Thamdrup, Bo; Canfield, Don E.] Univ So Denmark, Nord Ctr Earth Evolut NordCEE, Odense, Denmark.
   [Revsbech, Niels Peter] Aarhus Univ, Dept Biosci, Aarhus, Denmark.
   [Ulloa, Osvaldo] Univ Concepcion, Dept Oceanog, Concepcion, Chile.
   [Ulloa, Osvaldo] Univ Concepcion, Ctr Invest Oceanog Pacifico S Oriental, Concepcion, Chile.
RP Stewart, FJ (corresponding author), Georgia Inst Technol, Atlanta, GA 30332 USA.
EM frank.stewart@biology.gatech.edu
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NR 59
TC 60
Z9 66
PD MAY 16
PY 2012
VL 7
IS 5
SI 1
AR e37118
DI 10.1371/journal.pone.0037118
UT WOS:000305341300074
DA 2025-07-30
ER

PT J
AU Hunt, DE
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AF Hunt, Dana E.
   Lin, Yajuan
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   Izzo, Lisa K.
   Johnson, Zackary I.
TI Relationship between Abundance and Specific Activity of Bacterioplankton
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Marine microbial communities are complex and dynamic, and their ecology impacts biogeochemical cycles in pelagic ecosystems. Yet, little is known about the relative activities of different microbial populations within genetically diverse communities. We used rRNA as a proxy for activity to quantify the relative specific activities (rRNA/ribosomal DNA [rDNA or rRNA genes]) of the eubacterial populations and to identify locations or clades for which there are uncouplings between specific activity and abundance. After analyzing 1.6 million sequences from 16S rDNA and rRNA (cDNA) libraries from two euphotic depths from a representative site in the Pacific Ocean, we show that although there is an overall positive relationship between the abundances (rDNAs) and activities (rRNAs) among populations of the bacterial community, for some populations these measures are uncoupled. Different ecological strategies are exemplified by the two numerically dominant clades at this site: the cyanobacterium Prochlorococcus is abundant but disproportionately more active, while the heterotrophic SAR11 is abundant but less active. Other rare populations, such as Alteromonas, have high specific activities in spite of their low abundances, suggesting intense population regulation. More detailed analyses using a complementary quantitative PCR (qPCR)-based approach of measuring relative specific activity for Prochlorococcus populations in the Pacific and Atlantic Oceans also show that specific activity, but not abundance, reflects the key drivers of light and nutrients in this system; our results also suggest substantial top-down regulation (e.g., grazing, viruses, or organismal interactions) or transport (e.g., mixing, immigration, or emigration) of these populations. Thus, we show here that abundance and specific activity can be uncoupled in open ocean systems and that describing both is critical to characterizing microbial communities and predicting marine ecosystem functioning and responses to change.
C1 [Hunt, Dana E.; Lin, Yajuan; Izzo, Lisa K.; Johnson, Zackary I.] Duke Univ, Marine Lab, Nicholas Sch Environm, Beaufort, NC 28516 USA.
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RP Johnson, ZI (corresponding author), Duke Univ, Marine Lab, Nicholas Sch Environm, Beaufort, NC 28516 USA.
EM zij@duke.edu
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NR 46
TC 113
Z9 131
PD JAN
PY 2013
VL 79
IS 1
BP 177
EP 184
DI 10.1128/AEM.02155-12
UT WOS:000312931600020
DA 2025-07-30
ER

PT J
AU Wietz, M
   Gram, L
   Jorgensen, B
   Schramm, A
AF Wietz, Matthias
   Gram, Lone
   Jorgensen, Bo
   Schramm, Andreas
TI Latitudinal patterns in the abundance of major marine bacterioplankton
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SO AQUATIC MICROBIAL ECOLOGY
DT Article
AB The present study describes the abundance of major marine bacterioplankton groups and 2 bacterial genera (Pseudoalteromonas and Vibrio) in surface seawater at 24 stations around the world. Catalyzed reporter deposition-fluorescence in situ hybridization showed that Alphaproteobacteria (average relative abundance 37%, average absolute abundance 3.7 x 10(5) cells ml(-1)) including SAR11 [30% / (3 x 10(5))], Gammaproteobacteria [14% / (1.2 x 10(5))] and Bacteroidetes [12% / (1.3 x 10(5))] globally dominated the bacterioplankton. The SAR86 clade [4.6% / (4.1 x 10(4))] and Actinobacteria [4.5% / (4 x 10(4))] were detected ubiquitously, whereas Archaea were scarce [0.6% / (4.2 x 10(3))]. The Roseobacter clade [averaging 3.8% / (3.5 x 10(4))], Pseudoalteromonas [2.6% / (2.1 x 10(4))] and Vibrio [1.5% / (1.3 x 10(4))] showed cosmopolitan occurrence. Principal component analysis revealed a latitudinal pattern in bacterial abundances by clustering samples according to lower and higher latitudes. This was related to significantly different relative abundances of Bacteroidetes (peaking at higher latitudes) and of unclassified Bacteria and Vibrio (both peaking at lower latitudes) between warmer and colder oceans. Relative abundances of Alphaproteobacteria (peaking at subtropical) and Gammaproteobacteria (polar stations) varied between major oceanic biomes, as did absolute abundances of Roseobacter (peaking at temperate and polar stations). For almost all groups, absolute abundances were positively correlated with nutrient concentrations in warmer oceans and negatively correlated with oxygen saturation in colder oceans. On a global scale, Roseobacter and SAR86 were correlated with chlorophyll a. Linkages of environmental parameters with relative abundances were more complex, with e. g. Bacteroidetes being associated with chlorophyll a. The finding of differing communities in warmer and colder oceans underlined the presence of biogeographical patterns among marine bacteria and the influence of environmental parameters on bacterial distribution.
C1 [Wietz, Matthias; Gram, Lone; Jorgensen, Bo] Tech Univ Denmark, Natl Food Inst, DK-2800 Lyngby, Denmark.
   [Schramm, Andreas] Aarhus Univ, Dept Biol Sci, DK-8000 Aarhus, Denmark.
RP Wietz, M (corresponding author), Tech Univ Denmark, Natl Food Inst, DK-2800 Lyngby, Denmark.
EM mwi@aqua.dtu.dk
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NR 58
TC 100
Z9 108
PY 2010
VL 61
IS 2
BP 179
EP 189
DI 10.3354/ame01443
UT WOS:000284005000007
DA 2025-07-30
ER

PT J
AU Davis, JJ
   Olsen, GJ
AF Davis, James J.
   Olsen, Gary J.
TI Characterizing the Native Codon Usages of a Genome: An Axis Projection
   Approach
SO MOLECULAR BIOLOGY AND EVOLUTION
DT Article
AB Codon usage can provide insights into the nature of the genes in a genome. Genes that are "native" to a genome (have not been recently acquired by horizontal transfer) range in codon usage from a low-bias "typical" usage to a more biased "high-expression" usage characteristic of genes encoding abundant proteins. Genes that differ from these native codon usages are candidates for foreign genes that have been recently acquired by horizontal gene transfer. In this study, we present a method for characterizing the codon usages of native genes-both typical and highly expressed-within a genome. Each gene is evaluated relative to a half line (or axis) in a 59D space of codon usage. The axis begins at the modal codon usage, the usage that matches the largest number of genes in the genome, and it passes through a point representing the codon usage of a set of genes with expression-related bias. A gene whose codon usage matches (does not significantly differ from) a point on this axis is a candidate native gene, and the location of its projection onto the axis provides a general estimate of its expression level. A gene that differs significantly from all points on the axis is a candidate foreign gene. This automated approach offers significant improvements over existing methods. We illustrate this by analyzing the genomes of Pseudomonas aeruginosa PAO1 and Bacillus anthracis A0248, which can be difficult to analyze with commonly used methods due to their biased base compositions. Finally, we use this approach to measure the proportion of candidate foreign genes in 923 bacterial and archaeal genomes. The organisms with the most homogeneous genomes (containing the fewest candidate foreign genes) are mostly endosymbionts and parasites, though with exceptions that include Pelagibacter ubique and Beutenbergia cavernae. The organisms with the most heterogeneous genomes (containing the most candidate foreign genes) include members of the genera Bacteroides, Corynebacterium, Desulfotalea, Neisseria, Xylella, and Thermobaculum.
C1 [Davis, James J.; Olsen, Gary J.] Univ Illinois, Dept Microbiol, Urbana, IL 61801 USA.
   [Davis, James J.; Olsen, Gary J.] Univ Illinois, Inst Genom Biol, Urbana, IL 61801 USA.
RP Olsen, GJ (corresponding author), Univ Illinois, Dept Microbiol, 131 Burrill Hall, Urbana, IL 61801 USA.
EM gary@life.illinois.edu
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NR 50
TC 19
Z9 31
PD JAN
PY 2011
VL 28
IS 1
BP 211
EP 221
DI 10.1093/molbev/msq185
UT WOS:000285418600026
DA 2025-07-30
ER

PT J
AU Hill, PG
   Heywood, JL
   Holland, RJ
   Purdie, DA
   Fuchs, BM
   Zubkov, MV
AF Hill, Polly G.
   Heywood, Jane L.
   Holland, Ross J.
   Purdie, Duncan A.
   Fuchs, Bernhard M.
   Zubkov, Mikhail V.
TI Internal and External Influences on Near-Surface Microbial Community
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SO MICROBIAL ECOLOGY
DT Article
AB Microbial community structure in the subtropical north-east Atlantic Ocean was compared between 2 years and variation attributed to environmental variables. Surface seawater communities were analysed by flow cytometry and fluorescence in situ hybridisation. Probes specific to Alphaproteobacteria, Cyanobacteria, Gammaproteobacteria and Bacteroidetes identified 67-100% of cells. Due to natural variation in the study region due to the occurrence of major currents and islands, data could not be pooled but were instead divided between distinct water masses. Community structure did not differ greatly around the Cape Verde Islands between sampling periods but varied substantially in the open ocean, suggesting different environmental perturbations favour specific bacterial groups. Wind speed varied significantly between years, with moderate to strong breeze in winter 2008 and gales in winter 2006 (8.9 +/- 0.2 ms(-1) and 16.0 +/- 0.4 ms(-1), respectively). Enhanced wind-driven turbulence was associated with domination by the SAR11 clade of Alphaproteobacteria, which were present at 2.4-fold in the abundance of Prochlorococcus (41.8 +/- 1.6% cells, compared to 17.7 +/- 7.1%). Conversely, the calmer conditions of 2008 seemed to favour Prochlorococcus (40.0 +/- 1.2% cells). Prochlorococcus high-light adapted clade HLI were only numerous during wind-driven turbulence, whereas oligotrophic-adapted clade HLII dominated under calm conditions. Bacteroidetes were most prominent in turbulent conditions (9.5 +/- 1.3% cells as opposed to 4.7 +/- 0.3%), as were Synechococcus. In 2008, a considerable dust deposition event occurred in the region, which may have led to the substantial Gammaproteobacteria population (22.5 +/- 4.0% cells compared to 4.6 +/- 0.6% in 2006). Wind-driven turbulence may have a significant impact on microbial community structure in the surface ocean. Therefore, community change following dust storm events may be linked to associated wind in addition to dust-derived nutrients.
C1 [Hill, Polly G.; Purdie, Duncan A.] Univ Southampton, Natl Oceanog Ctr, Southampton SO14 3ZH, Hants, England.
   [Heywood, Jane L.] Univ Bremen, Fac Biol Chem, D-28359 Bremen, Germany.
   [Fuchs, Bernhard M.] Max Planck Inst Microbiol, D-28359 Bremen, Germany.
RP Hill, PG (corresponding author), Univ Southampton, Natl Oceanog Ctr, European Way, Southampton SO14 3ZH, Hants, England.
EM polly.hill@noc.ac.uk
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TC 7
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PY 2012
VL 63
IS 1
BP 139
EP 148
DI 10.1007/s00248-011-9952-2
UT WOS:000299084000014
DA 2025-07-30
ER

PT J
AU Han, MAX
   Sun, JH
   Yang, QW
   Liang, YT
   Jiang, Y
   Gao, C
   Gu, CX
   Liu, Q
   Chen, XC
   Liu, G
   Shao, HB
   Guo, C
   He, H
   Wang, HL
   Sung, YY
   Mok, WJ
   Wong, LL
   Wang, ZL
   McMinn, A
   Wang, M
AF Han, Meiaoxue
   Sun, Jianhua
   Yang, Qingwei
   Liang, Yantao
   Jiang, Yong
   Gao, Chen
   Gu, Chengxiang
   Liu, Qian
   Chen, Xuechao
   Liu, Gang
   Shao, Hongbing
   Guo, Cui
   He, Hui
   Wang, Hualong
   Sung, Yeong Yik
   Mok, Wen Jye
   Wong, Li Lian
   Wang, Zongling
   McMinn, Andrew
   Wang, Min
TI Spatiotemporal Dynamics of Coastal Viral Community Structure and
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SO MSYSTEMS
DT Article
AB To the best of our knowledge, this study is the first to investigate the responses of viruses to the world's largest macroalgal green tide. It revealed the spatiotemporal dynamics of the unique viral assemblages and auxiliary metabolic genes (AMGs) following the variation and degradation of Ulva prolifera. These findings demonstrate a tight coupling between viral assemblages, and prokaryotic and eukaryotic abundances were influenced by the green tide.
   The world's largest macroalgal green tide, caused by Ulva prolifera, has resulted in serious consequences for coastal waters of the Yellow Sea, China. Although viruses are considered to be one of the key factors in controlling microalgal bloom demise, understanding of the relationship between viral communities and the macroalgal green tide is still poor. Here, a Qingdao coastal virome (QDCV) time-series data set was constructed based on the metagenomic analysis of 17 DNA viromes along three coastal stations of the Yellow Sea, covering different stages of the green tide from Julian days 165 to 271. A total of 40,076 viral contigs were detected and clustered into 28,058 viral operational taxonomic units (vOTUs). About 84% of the vOTUs could not be classified, and 62% separated from vOTUs in other ecosystems. Green tides significantly influenced the spatiotemporal dynamics of the viral community structure, diversity, and potential functions. For the classified vOTUs, the relative abundance of Pelagibacter phages declined with the arrival of the bloom and rebounded after the bloom, while Synechococcus and Roseobacter phages increased, although with a time lag from the peak of their hosts. More than 80% of the vOTUs reached peaks in abundance at different specific stages, and the viral peaks were correlated with specific hosts at different stages of the green tide. Most of the viral auxiliary metabolic genes (AMGs) were associated with carbon and sulfur metabolism and showed spatiotemporal dynamics relating to the degradation of the large amount of organic matter released by the green tide.IMPORTANCE To the best of our knowledge, this study is the first to investigate the responses of viruses to the world's largest macroalgal green tide. It revealed the spatiotemporal dynamics of the unique viral assemblages and auxiliary metabolic genes (AMGs) following the variation and degradation of Ulva prolifera. These findings demonstrate a tight coupling between viral assemblages, and prokaryotic and eukaryotic abundances were influenced by the green tide.
C1 [Han, Meiaoxue; Sun, Jianhua; Yang, Qingwei; Liang, Yantao; Jiang, Yong; Gao, Chen; Gu, Chengxiang; Liu, Qian; Chen, Xuechao; Liu, Gang; Shao, Hongbing; Guo, Cui; He, Hui; Wang, Hualong; McMinn, Andrew; Wang, Min] Ocean Univ China, Inst Evolut & Marine Biodivers, Coll Marine Life Sci, Key Lab Polar Oceanog & Global Ocean Change, Qingdao, Peoples R China.
   [Liang, Yantao; Shao, Hongbing; Guo, Cui; He, Hui; Wang, Hualong; Sung, Yeong Yik; Mok, Wen Jye; Wong, Li Lian; Wang, Min] Univ Malaysia Terengganu Ocean Univ China Joint Ct, Qingdao, Peoples R China.
   [Sung, Yeong Yik; Mok, Wen Jye; Wong, Li Lian] Univ Malaysia Terengganu, Inst Marine Biotechnol, Kuala Nerus, Malaysia.
   [Wang, Zongling] Minist Nat Resources, Inst Oceanog 1, Key Lab Marine Ecoenvironm Sci & Technol, Qingdao, Peoples R China.
   [McMinn, Andrew] Univ Tasmania, Inst Marine & Antarctic Studies, Hobart, Tas, Australia.
   [Wang, Min] Ocean Univ China, Haide Coll, Qingdao, Peoples R China.
   [Wang, Min] Qingdao Univ, Affiliated Hosp, Qingdao, Peoples R China.
RP Liang, YT; McMinn, A; Wang, M (corresponding author), Ocean Univ China, Inst Evolut & Marine Biodivers, Coll Marine Life Sci, Key Lab Polar Oceanog & Global Ocean Change, Qingdao, Peoples R China.; Liang, YT; Wang, M (corresponding author), Univ Malaysia Terengganu Ocean Univ China Joint Ct, Qingdao, Peoples R China.; Wang, ZL (corresponding author), Minist Nat Resources, Inst Oceanog 1, Key Lab Marine Ecoenvironm Sci & Technol, Qingdao, Peoples R China.; McMinn, A (corresponding author), Univ Tasmania, Inst Marine & Antarctic Studies, Hobart, Tas, Australia.; Wang, M (corresponding author), Ocean Univ China, Haide Coll, Qingdao, Peoples R China.; Wang, M (corresponding author), Qingdao Univ, Affiliated Hosp, Qingdao, Peoples R China.
EM liangyantao@ouc.edu.cn; wangzl@fio.org.cn; andrew.mcminn@utas.edu.au;
   mingwang@ouc.edu.cn
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TC 5
Z9 6
PD APR 27
PY 2023
VL 8
IS 2
DI 10.1128/msystems.01211-22
EA FEB 2023
UT WOS:000937495400001
DA 2025-07-30
ER

PT J
AU Guo, RY
   Ma, X
   Zhang, JJ
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   Wang, Pengbin
TI Microbial community structures and important taxa across oxygen
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SO FRONTIERS IN MICROBIOLOGY
DT Article
AB In oceanic oxygen minimum zones (OMZs), the abundances of aerobic organisms significantly decrease and energy shifts from higher trophic levels to microorganisms, while the microbial communities become critical drivers of marine biogeochemical cycling activities. However, little is known of the microbial ecology of the Andaman Sea and eastern Bay of Bengal (BoB) OMZs. In the present study, a total of 131 samples which from the Andaman Sea and eastern BoB epipelagic waters were analyzed. The microbial community distribution patterns across oxygen gradients, including oxygenic zones (OZs, dissolved oxygen [DO] >= 2 mg/L), oxygen limited zones (OLZs, 0.7 mg/L < DO < 2 mg/L), and OMZs (DO <= 0.7 mg/L), were investigated. Mantel tests and Spearman's correlation analysis revealed that DO was the most important driver of microbial community structures among several environmental factors. Microbial diversity, richness, and evenness were highest in the OLZs and lowest in the OZs. The microbial community compositions of OZ and OMZ waters were significantly different. Random forest analysis revealed 24 bioindicator taxa that differentiated OZ, OLZ, and OMZ water communities. These bioindicator taxa included Burkholderiaceae, HOC36, SAR11 Clade IV, Thioglobaceae, Nitrospinaceae, SAR86, and UBA10353. Further, co-occurrence network analysis revealed that SAR202, AEGEAN-169, UBA10353, SAR406, and Rhodobacteraceae were keystone taxa among the entire interaction network of the microbial communities. Functional prediction further indicated that the relative abundances of microbial populations involved in nitrogen and sulfur cycling were higher in OMZs. Several microbial taxa, including the Thioglobaceae, Nitrospinaceae, SAR202, SAR406, WPS-2, UBA10353, and Woeseiaceae, may be involved in nitrogen and/or sulfur cycling, while also contributing to oxygen consumption in these waters. This study consequently provides new insights into the microbial community structures and potentially important taxa that contribute to oxygen consumption in the Andaman Sea and eastern BoB OMZ.
C1 [Guo, Ruoyu; Zhang, Jingjing; Liu, Chenggang; Li, Hongliang; Wang, Pengbin] Minist Nat Resources, Inst Oceanog 2, Key Lab Marine Ecosyst Dynam, Hangzhou, Peoples R China.
   [Guo, Ruoyu; Ma, Xiao; Zhou, Feng; Wang, Pengbin] Minist Nat Resources, Observat & Res Stn Yangtze River Delta Marine Ecos, Zhoushan, Peoples R China.
   [Ma, Xiao; Zhou, Feng] Minist Nat Resources, Inst Oceanog 2, State Key Lab Satellite Ocean Environm Dynam, Hangzhou, Peoples R China.
   [Thu, Chit Aung] Res & Dev Sect, Dept Fisheries, Naypyidaw, Myanmar.
   [Win, Tun Naing] Minist Transport & Commun, Dept Meteorol & Hydrol, Naypyidaw, Myanmar.
   [Aung, Nyan Lin] Minist Nat Resources & Environm Conservat, Environm Conservat Dept, Naypyidaw, Myanmar.
   [Win, Hlaing Swe] Minist Educ, Dept Res Innovat, Natl Analyt Lab, Naypyidaw, Myanmar.
   [Naing, Sanda] Myanmar Maritime Univ, Port & Harbour Engn Dept, Thanlyin, Myanmar.
RP Wang, PB (corresponding author), Minist Nat Resources, Inst Oceanog 2, Key Lab Marine Ecosyst Dynam, Hangzhou, Peoples R China.; Zhou, F; Wang, PB (corresponding author), Minist Nat Resources, Observat & Res Stn Yangtze River Delta Marine Ecos, Zhoushan, Peoples R China.; Zhou, F (corresponding author), Minist Nat Resources, Inst Oceanog 2, State Key Lab Satellite Ocean Environm Dynam, Hangzhou, Peoples R China.
EM zhoufeng@sio.org.cn; algae@sio.org.cn
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TC 18
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PD NOV 2
PY 2022
VL 13
AR 1041521
DI 10.3389/fmicb.2022.1041521
UT WOS:000886482000001
DA 2025-07-30
ER

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RP Woebken, D (corresponding author), Max Planck Inst Marine Microbiol, Celsiusstr 1, D-28359 Bremen, Germany.
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NR 69
TC 195
Z9 224
PD JUL
PY 2007
VL 73
IS 14
BP 4648
EP 4657
DI 10.1128/AEM.02774-06
UT WOS:000248197400030
DA 2025-07-30
ER

PT J
AU Hewson, I
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AF Hewson, Ian
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DT Article
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C1 Univ So Calif, Dept Ocean Sci, Wrigley Inst Environm Studies, Los Angeles, CA 90089 USA.
RP Hewson, I (corresponding author), Univ So Calif, Dept Ocean Sci, Wrigley Inst Environm Studies, 1156 High St E & MS D446,3616 Trousdale Pkwy AHF, Los Angeles, CA 90089 USA.
EM hewson@ucsc.edu
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NR 65
TC 21
Z9 26
PD MAY
PY 2007
VL 53
IS 4
BP 631
EP 638
DI 10.1007/s00248-006-9148-3
UT WOS:000246565500012
DA 2025-07-30
ER

PT J
AU Li, WKW
   Andersen, RA
   Gifford, DJ
   Incze, LS
   Martin, JL
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AF Li, William K. W.
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   Martin, Jennifer L.
   Pilskaln, Cynthia H.
   Rooney-Varga, Juliette N.
   Sieracki, Michael E.
   Wilson, William H.
   Wolff, Nicholas H.
TI Planktonic Microbes in the Gulf of Maine Area
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DT Article
AB In the Gulf of Maine area (GoMA), as elsewhere in the ocean, the organisms of greatest numerical abundance are microbes. Viruses in GoMA are largely cyanophages and bacteriophages, including podoviruses which lack tails. There is also evidence of Mimivirus and Chlorovirus in the metagenome. Bacteria in GoMA comprise the dominant SAR11 phylotype cluster, and other abundant phylotypes such as SAR86-like cluster, SAR116-like cluster, Roseobacter, Rhodospirillaceae, Acidomicrobidae, Flavobacteriales, Cytophaga, and unclassified Alphaproteobacteria and Gammaproteobacteria clusters. Bacterial epibionts of the dinoflagellate Alexandrium fundyense include Rhodobacteraceae, Flavobacteriaceae, Cytophaga spp., Sulfitobacter spp., Sphingomonas spp., and unclassified Bacteroidetes. Phototrophic prokaryotes in GoMA include cyanobacteria that contain chlorophyll (mainly Synechococcus), aerobic anoxygenic phototrophs that contain bacteriochlorophyll, and bacteria that contain proteorhodopsin. Eukaryotic microalgae in GoMA include Bacillariophyceae, Dinophyceae, Prymnesiophyceae, Prasinophyceae, Trebouxiophyceae, Cryptophyceae, Dictyochophyceae, Chrysophyceae, Eustigmatophyceae, Pelagophyceae, Synurophyceae, and Xanthophyceae. There are no records of Bolidophyceae, Aurearenophyceae, Raphidophyceae, and Synchromophyceae in GoMA. In total, there are records for 665 names and 229 genera of microalgae. Heterotrophic eukaryotic protists in GoMA include Dinophyceae, Alveolata, Apicomplexa, amoeboid organisms, Labrynthulida, and heterotrophic marine stramenopiles (MAST). Ciliates include Strombidium, Lohmaniella, Tontonia, Strobilidium, Strombidinopsis and the mixotrophs Laboea strobila and Myrionecta rubrum (ex Mesodinium rubra). An inventory of selected microbial groups in each of 14 physiographic regions in GoMA is made by combining information on the depth-dependent variation of cell density and the depth-dependent variation of water volume. Across the entire GoMA, an estimate for the minimum abundance of cell-based microbes is 1.7x10(25) organisms. By one account, this number of microbes implies a richness of 10 5 to 10 6 taxa in the entire water volume of GoMA. Morphological diversity in microplankton is well-described but the true extent of taxonomic diversity, especially in the femtoplankton, picoplankton and nanoplankton - whether autotrophic, heterotrophic, or mixotrophic, is unknown.
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   [Gifford, Dian J.] Univ Rhode Isl, Grad Sch Oceanog, Narragansett, RI 02882 USA.
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   [Martin, Jennifer L.] Fisheries & Oceans Canada, Biol Stn, St Andrews, NB E0G 2X0, Canada.
   [Pilskaln, Cynthia H.] Univ Massachusetts, Sch Marine Sci & Technol, N Dartmouth, MA USA.
   [Rooney-Varga, Juliette N.] Univ Massachusetts, Dept Biol Sci, Lowell, MA USA.
RP Li, WKW (corresponding author), Fisheries & Oceans Canada, Bedford Inst Oceanog, POB 1006, Dartmouth, NS B2Y 4A2, Canada.
EM Bill.Li@dfo-mpo.gc.ca
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NR 83
TC 17
Z9 21
PD JUN 15
PY 2011
VL 6
IS 6
AR e20981
DI 10.1371/journal.pone.0020981
UT WOS:000291730000036
DA 2025-07-30
ER

PT J
AU Preston, CM
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   Scholin, Christopher A.
TI Underwater Application of Quantitative PCR on an Ocean Mooring
SO PLOS ONE
DT Article
AB The Environmental Sample Processor (ESP) is a device that allows for the underwater, autonomous application of DNA and protein probe array technologies as a means to remotely identify and quantify, in situ, marine microorganisms and substances they produce. Here, we added functionality to the ESP through the development and incorporation of a module capable of solid-phase nucleic acid extraction and quantitative PCR (qPCR). Samples collected by the instrument were homogenized in a chaotropic buffer compatible with direct detection of ribosomal RNA (rRNA) and nucleic acid purification. From a single sample, both an rRNA community profile and select gene abundances were ascertained. To illustrate this functionality, we focused on bacterioplankton commonly found along the central coast of California and that are known to vary in accordance with different oceanic conditions. DNA probe arrays targeting rRNA revealed the presence of 16S rRNA indicative of marine crenarchaea, SAR11 and marine cyanobacteria; in parallel, qPCR was used to detect 16S rRNA genes from the former two groups and the large subunit RuBisCo gene (rbcL) from Synecchococcus. The PCR-enabled ESP was deployed on a coastal mooring in Monterey Bay for 28 days during the spring-summer upwelling season. The distributions of the targeted bacterioplankon groups were as expected, with the exception of an increase in abundance of marine crenarchaea in anomalous nitrate-rich, low-salinity waters. The unexpected co-occurrence demonstrated the utility of the ESP in detecting novel events relative to previously described distributions of particular bacterioplankton groups. The ESP can easily be configured to detect and enumerate genes and gene products from a wide range of organisms. This study demonstrated for the first time that gene abundances could be assessed autonomously, underwater in near real-time and referenced against prevailing chemical, physical and bulk biological conditions.
C1 [Preston, Christina M.; Harris, Adeline; Ryan, John P.; Roman, Brent; Marin, Roman, III; Jensen, Scott; Everlove, Cheri; Birch, James; Pargett, Douglas; Scholin, Christopher A.] Monterey Bay Aquarium Res Inst, Moss Landing, CA 95039 USA.
   [Dzenitis, John M.] Lawrence Livermore Natl Lab, Livermore, CA USA.
   [Adachi, Masao] Kochi Univ, Lab Aquat Environm Sci, Kochi 780, Japan.
   [Turk, Kendra; Zehr, Jonathon P.] Univ Calif Santa Cruz, Dept Ocean Sci & Earth & Marine Sci, Santa Cruz, CA 95064 USA.
RP Preston, CM (corresponding author), Monterey Bay Aquarium Res Inst, Moss Landing, CA 95039 USA.
EM preston@mbari.org
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NR 58
TC 75
Z9 85
PD AUG 1
PY 2011
VL 6
IS 8
AR e22522
DI 10.1371/journal.pone.0022522
UT WOS:000293511200011
DA 2025-07-30
ER

PT J
AU Wang, HL
   Chen, F
   Zhang, CL
   Wang, M
   Kan, JJ
AF Wang, Hualong
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   Zhang, Chuanlun
   Wang, Min
   Kan, Jinjun
TI Estuarine gradients dictate spatiotemporal variations of microbiome
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SO ENVIRONMENTAL MICROBIOME
DT Article
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C1 [Wang, Hualong; Wang, Min] Ocean Univ China, Coll Marine Life Sci, Qingdao, Peoples R China.
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   [Zhang, Chuanlun] Southern Marine Sci & Engn Guangdong Lab, Guangzhou, Peoples R China.
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RP Kan, JJ (corresponding author), Stroud Water Res Ctr, Div Microbiol, Avondale, PA 19311 USA.; Kan, JJ (corresponding author), Southern Univ Sci & Technol, Acad Adv Interdisciplinary Studies, Shenzhen, Peoples R China.
EM jkan@stroudcenter.org
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NR 113
TC 39
Z9 39
PD NOV 27
PY 2021
VL 16
IS 1
AR 22
DI 10.1186/s40793-021-00392-z
UT WOS:000722993600001
DA 2025-07-30
ER

PT J
AU Wang, YB
   Hu, XK
   Sun, YY
   Wang, CX
AF Wang, Yibo
   Hu, Xiaoke
   Sun, Yanyu
   Wang, Caixia
TI Influence of the cold bottom water on taxonomic and functional
   composition and complexity of microbial communities in the southern
   Yellow Sea during the summer
SO SCIENCE OF THE TOTAL ENVIRONMENT
DT Article
AB The formation and presence of the cold bottomwater (Yellow Sea Cold WaterMass, YSCWM) is a striking hydrological phenomenon in the southern Yellow Sea during the summer and has important effects on themarine ecosystem. To better understand its influence on microbial community structure and function, we compared the bacterial, archaeal and microeukaryotic communities in the cold water mass area (CWMA) and the southern area (SA) during the summer using amplicon and metagenomic sequencings. The habitat environment in the deep waters of the CWMA was characterized by higher salinity/DO/PO4-P, greater depth/distance to the coast, and lower levels of temperature/chlorophyll a/DIN/SiO3-Si/N:P ratio compared to that of the SA. Pure depth or distance to the coast explained a small portion of the microbial community variance, while environment explained a significant fraction of the variance when partialling the effects of depth and distance to the coast. Oligotrophic taxa (e.g. SAR11 clade Ia, Nitrosopumilus, Chloropicophyceae) dominated the deepwater communities in the CWMA, while the common coastal taxa (e.g. Roseobacter strain HIMB11, Bacillariophyta, Noctilucophyceae) were more dominant in the deep waters of the SA, suggesting the great impact of the oligotrophic condition in the YSCWM on microbial communities. The microbial co-occurrence networks in the CWMA were less complex but contained a higher proportion of mutual exclusion relationship among prokaryotes; the prokaryotic a-diversity in the CWMA was significantly lower than in the SA while the microeukaryotic a-diversity was significantly higher in the CWMA, implying that prokaryotes and microeukaryotes respond to the cold water mass differently and the competition among prokaryotes was intensified under the impact of the YSCWM. Genes that relate to replication and repair accounted for a significantly lower proportion in the CWMA, which was likely an adaptation to the low carbon environment. (C) 2020 Published by Elsevier B.V.
C1 [Wang, Yibo; Hu, Xiaoke; Sun, Yanyu; Wang, Caixia] Chinese Acad Sci, Key Lab Coastal Biol & Bioresource Utilizat, Yantai Inst Coastal Zone Res, Yantai 264003, Peoples R China.
   [Wang, Yibo; Hu, Xiaoke; Sun, Yanyu; Wang, Caixia] Qingdao Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao 266237, Peoples R China.
   [Wang, Yibo; Sun, Yanyu] Chinese Acad Sci, Ctr Ocean Megasci, Qingdao 266071, Peoples R China.
   [Wang, Yibo; Hu, Xiaoke; Sun, Yanyu; Wang, Caixia] Univ Chinese Acad Sci, Beijing 100049, Peoples R China.
RP Hu, XK (corresponding author), Chinese Acad Sci, Key Lab Coastal Biol & Bioresource Utilizat, Yantai Inst Coastal Zone Res, Yantai 264003, Peoples R China.
EM xkhu@yic.ac.cn
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NR 89
TC 16
Z9 17
PD MAR 10
PY 2021
VL 759
AR 143496
DI 10.1016/j.scitotenv.2020.143496
EA JAN 2021
UT WOS:000605764100054
DA 2025-07-30
ER

PT J
AU Guo, J
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AF Guo, Jun
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DT Article
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C1 [Guo, Jun; Zheng, Yuanyuan; Teng, Jinhao; Wang, Xumin; Song, Jiaxiu] Shanghai Normal Univ, Sch Environm & Geog Sci, Dept Environm Engn, Shanghai 200234, Peoples R China.
   [Guo, Jun; Zheng, Yuanyuan; Teng, Jinhao; Wang, Xumin; Song, Jiaxiu] Wetland Ecosyst Observat & Res Field Stn, Shanghai 201799, Peoples R China.
RP Song, JX (corresponding author), Shanghai Normal Univ, Sch Environm & Geog Sci, Dept Environm Engn, Shanghai 200234, Peoples R China.
EM songjiaxiu@shnu.edu.cn
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PD AUG 15
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VL 311
AR 127697
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EA JUN 2021
UT WOS:000668106900006
DA 2025-07-30
ER

PT J
AU Sánchez, O
   Ferrera, I
   Mabrito, I
   Gazulla, CR
   Sebastián, M
   Auladell, A
   Marín-Vindas, C
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   Marrasé, C
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   Gasol, JM
AF Sanchez, Olga
   Ferrera, Isabel
   Mabrito, Isabel
   Gazulla, Carlota R.
   Sebastian, Marta
   Auladell, Adria
   Marin-Vindas, Carolina
   Cardelus, Clara
   Sanz-Saez, Isabel
   Pernice, Massimo C.
   Marrase, Celia
   Sala, M. Montserrat
   Gasol, Josep M.
TI Seasonal impact of grazing, viral mortality, resource availability and
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   bacterioplankton
SO SCIENTIFIC REPORTS
DT Article
AB Estimation of prokaryotic growth rates is critical to understand the ecological role and contribution of different microbes to marine biogeochemical cycles. However, there is a general lack of knowledge on what factors control the growth rates of different prokaryotic groups and how these vary between sites and along seasons at a given site. We carried out several manipulation experiments during the four astronomical seasons in the coastal NW Mediterranean in order to evaluate the impact of grazing, viral mortality, resource competition and light on the growth and loss rates of prokaryotes. Gross and net growth rates of different bacterioplankton groups targeted by group-specific CARD-FISH probes and infrared microscopy (for aerobic anoxygenic phototrophs, AAP), were calculated from changes in cell abundances. Maximal group-specific growth rates were achieved when both predation pressure and nutrient limitation were experimentally minimized, while only a minimal effect of viral pressure on growth rates was observed; nevertheless, the response to predation removal was more remarkable in winter, when the bacterial community was not subjected to nutrient limitation. Although all groups showed increases in their growth rates when resource competition as well as grazers and viral pressure were reduced, Alteromonadaceae consistently presented the highest rates in all seasons. The response to light availability was generally weaker than that to the other factors, but it was variable between seasons. In summer and spring, the growth rates of AAP were stimulated by light whereas the growth of the SAR11 clade (likely containing proteorhodopsin) was enhanced by light in all seasons. Overall, our results set thresholds on bacterioplankton group-specific growth and mortality rates and contribute to estimate the seasonally changing contribution of various bacterioplankton groups to the function of microbial communities. Our results also indicate that the least abundant groups display the highest growth rates, contributing to the recycling of organic matter to a much greater extent than what their abundances alone would predict.
C1 [Sanchez, Olga; Mabrito, Isabel; Gazulla, Carlota R.] Univ Autonoma Barcelona, Dept Genet & Microbiol, Bellaterra 08193, Catalunya, Spain.
   [Ferrera, Isabel] Inst Espanol Oceanog, Ctr Oceanog Malaga, Malaga 29640, Spain.
   [Ferrera, Isabel; Gazulla, Carlota R.; Sebastian, Marta; Auladell, Adria; Marin-Vindas, Carolina; Cardelus, Clara; Sanz-Saez, Isabel; Pernice, Massimo C.; Marrase, Celia; Sala, M. Montserrat; Gasol, Josep M.] ICM CSIC, Dept Biol Marina & Oceanog, Inst Ciencies Mar, Barcelona 08003, Catalunya, Spain.
   [Sebastian, Marta] Univ Las Palmas de Gran Canaria ULPGC, Inst Oceanog & Cambio Global IOCAG, Telde 35214, Spain.
   [Marin-Vindas, Carolina] Univ Nacional, Escuela Ciencias Biol, Heredia 40101, Costa Rica.
RP Sánchez, O (corresponding author), Univ Autonoma Barcelona, Dept Genet & Microbiol, Bellaterra 08193, Catalunya, Spain.; Ferrera, I (corresponding author), Inst Espanol Oceanog, Ctr Oceanog Malaga, Malaga 29640, Spain.; Ferrera, I (corresponding author), ICM CSIC, Dept Biol Marina & Oceanog, Inst Ciencies Mar, Barcelona 08003, Catalunya, Spain.
EM olga.sanchez@uab.es; isabel.ferrera@ieo.es
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NR 82
TC 18
Z9 18
PD NOV 13
PY 2020
VL 10
IS 1
AR 19773
DI 10.1038/s41598-020-76590-5
UT WOS:000594640400001
DA 2025-07-30
ER

PT J
AU Gifford, SM
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AF Gifford, Scott M.
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   Marchetti, Adrian
TI Microbial Niche Diversification in the Galapagos Archipelago and Its
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SO FRONTIERS IN MICROBIOLOGY
DT Article
AB The Galapagos Archipelago is located at the intersection of several major oceanographic features that produce diverse environmental conditions around the islands, and thus has the potential to serve as a natural laboratory for discerning the underlying environmental factors that structure marine microbial communities. Here we used quantitative metagenomics to characterize microbial communities in relation to archipelago marine habitats, and how those populations shift due to substantial environmental changes brought on by El Nino. Environmental conditions such as temperature, salinity, inorganic dissolved nutrients, and dissolved organic carbon (DOC) concentrations varied throughout the archipelago, revealing a diversity of potential microbial niches arising from upwelling, oligotrophic to eutrophic gradients, physical isolation, and potential island mass effects. The volumetric abundances of microbial community members shifted with these environmental changes and revealed several taxonomic indicators of different water masses. This included a transition from a Synechococcus dominated system in the west to an even mix of Synechococcus and Prochlorococcus in the east, mirroring the archipelago's mesotrophic to oligotrophic and productivity gradients. Several flavobacteria groups displayed characteristic habitat distributions, including enrichment of Polaribacter and Tenacibaculum clades in the relatively nutrient rich western waters, Leeuwenhoekiella spp. that were enriched in the more nutrient-deplete central and eastern sites, and the streamlined MS024-2A group found to be abundant across all sites. During the 2015/16 El Nino event, both environmental conditions and microbial community composition were substantially altered, primarily on the western side of the archipelago due to the reduction of upwelling from the Equatorial Undercurrent. When the upwelling resumed, concentrations of inorganic nutrients and DOC at the western surface sites were more typical of mesopelagic depths. Correspondingly, Synechococcus abundances decreased by an order of magnitude, while groups associated with deeper water masses were enriched, including streamlined roseobacters HTCC2255 and HIMB11, Thioglobacaceae, methylotrophs (Methylophilaceae), archaea (Nitrosopumilaceae), and distinct subpopulations of Pelagibaceriales (SAR11 clade). These results provide a quantitative framework to connect community-wide microbial volumetric abundances to their environmental drivers, and thus incorporation into biogeochemical and ecological models.
C1 [Gifford, Scott M.; Zhao, Liang; Seim, Harvey; Marchetti, Adrian] Univ N Carolina, Dept Marine Sci, Chapel Hill, NC 27515 USA.
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   [Medeiros, Patricia M.] Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
RP Gifford, SM (corresponding author), Univ N Carolina, Dept Marine Sci, Chapel Hill, NC 27515 USA.
EM sgifford@email.unc.edu
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NR 50
TC 8
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PD OCT 23
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VL 11
AR 575194
DI 10.3389/fmicb.2020.575194
UT WOS:000615671000001
DA 2025-07-30
ER

PT J
AU Li, JY
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AF Li, Jiyun
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   Guo, Jianhua
TI Dynamic carbon flux network of a diverse marine microbial community
SO ISME COMMUNICATIONS
DT Article
AB The functioning of microbial ecosystems has important consequences from global climate to human health, but quantitative mechanistic understanding remains elusive. The components of microbial ecosystems can now be observed at high resolution, but interactions still have to be inferred e.g., a time-series may show a bloom of bacteria X followed by virus Y suggesting they interact. Existing inference approaches are mostly empirical, like correlation networks, which are not mechanistically constrained and do not provide quantitative mass fluxes, and thus have limited utility. We developed an inference method, where a mechanistic model with hundreds of species and thousands of parameters is calibrated to time series data. The large scale, nonlinearity and feedbacks pose a challenging optimization problem, which is overcome using a novel procedure that mimics natural speciation or diversification e.g., stepwise increase of bacteria species. The method allows for curation using species-level information from e.g., physiological experiments or genome sequences. The product is a mass-balancing, mechanistically-constrained, quantitative representation of the ecosystem. We apply the method to characterize phytoplankton-heterotrophic bacteria interactions via dissolved organic matter in a marine system. The resulting model predicts quantitative fluxes for each interaction and time point (e.g., 0.16 & mu;molC/L/d of chrysolaminarin to Polaribacter on April 16, 2009). At the system level, the flux network shows a strong correlation between the abundance of bacteria species and their carbon flux during blooms, with copiotrophs being relatively more important than oligotrophs. However, oligotrophs, like SAR11, are unexpectedly high carbon processors for weeks into blooms, due to their higher biomass. The fraction of exudates (vs. grazing/death products) in the DOM pool decreases during blooms, and they are preferentially consumed by oligotrophs. In addition, functional similarity of phytoplankton i.e., what they produce, decouples their association with heterotrophs. The methodology is applicable to other microbial ecosystems, like human microbiome or wastewater treatment plants.
C1 [Li, Jiyun; Wang, Chengwen; Bai, Ge] Tsinghua Univ, Sch Environm, Beijing, Peoples R China.
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RP Wang, CW (corresponding author), Tsinghua Univ, Sch Environm, Beijing, Peoples R China.; Zheng, M; Guo, JH (corresponding author), Univ Queensland, Fac Engn Architecture & Informat Technol, Adv Water Management Ctr, Brisbane, Qld, Australia.
EM wangcw@tsinghua.edu.cn; m.zheng@awmc.uq.edu.au; j.guo@awmc.uq.edu.au
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SO MSYSTEMS
DT Article
AB Designing primers for PCR-based taxonomic surveys that amplify a broad range of phylotypes in varied community samples is a difficult challenge, and the comparability of data sets amplified with varied primers requires attention. Here, we examined the performance of modified 16S rRNA gene and internal transcribed spacer (ITS) primers for archaea/bacteria and fungi, respectively, with nonaquatic samples. We moved primer bar codes to the 5' end, allowing for a range of different 3' primer pairings, such as the 515f/926r primer pair, which amplifies variable regions 4 and 5 of the 16S rRNA gene. We additionally demonstrated that modifications to the 515f/806r (variable region 4) 16S primer pair, which improves detection of Thaumarchaeota and clade SAR11 in marine samples, do not degrade performance on taxa already amplified effectively by the original primer set. Alterations to the fungal ITS primers did result in differential but overall improved performance compared to the original primers. In both cases, the improved primers should be widely adopted for amplicon studies.
   IMPORTANCE We continue to uncover a wealth of information connecting microbes in important ways to human and environmental ecology. As our scientific knowledge and technical abilities improve, the tools used for microbiome surveys can be modified to improve the accuracy of our techniques, ensuring that we can continue to identify groundbreaking connections between microbes and the ecosystems they populate, from ice caps to the human body. It is important to confirm that modifications to these tools do not cause new, detrimental biases that would inhibit the field rather than continue to move it forward. We therefore demonstrated that two recently modified primer pairs that target taxonomically discriminatory regions of bacterial and fungal genomic DNA do not introduce new biases when used on a variety of sample types, from soil to human skin. This confirms the utility of these primers for maintaining currently recommended microbiome research techniques as the state of the art.
C1 [Walters, William] Cornell Univ, Dept Mol Biol & Genet, Ithaca, NY USA.
   [Hyde, Embriette R.; Ackermann, Gail; Humphrey, Greg; Knight, Rob] Univ Calif San Diego, Dept Pediat, La Jolla, CA 92093 USA.
   [Berg-Lyons, Donna] Univ Colorado, BioFrontiers Inst, Boulder, CO 80309 USA.
   [Parada, Alma; Fuhrman, Jed A.] Univ Southern Calif, Dept Biol Sci, Los Angeles, CA 90089 USA.
   [Gilbert, Jack A.] Argonne Natl Lab, Biosci Div BIO, 9700 S Cass Ave, Argonne, IL 60439 USA.
   [Gilbert, Jack A.] Univ Chicago, Dept Ecol & Evolut, 940 E 57th St, Chicago, IL 60637 USA.
   [Gilbert, Jack A.] Univ Chicago, Dept Surg, 5841 S Maryland Ave, Chicago, IL 60637 USA.
   [Gilbert, Jack A.] Univ Chicago, Inst Genom & Syst Biol, Chicago, IL 60637 USA.
   [Gilbert, Jack A.] Marine Biol Lab, Woods Hole, MA 02543 USA.
   [Gilbert, Jack A.] Field Museum Nat Hist, Chicago, IL 60605 USA.
   [Jansson, Janet K.] Pacific Northwest Natl Lab, Earth & Biol Sci Directorate, Richland, WA 99352 USA.
   [Caporaso, J. Gregory] No Arizona Univ, Dept Biol Sci, Box 5640, Flagstaff, AZ 86011 USA.
   [Apprill, Amy] Woods Hole Oceanog Inst, Dept Marine Chem & Geochem, Woods Hole, MA 02543 USA.
   [Knight, Rob] Univ Calif San Diego, Dept Comp Sci, La Jolla, CA 92093 USA.
   [Knight, Rob] Univ Calif San Diego, Dept Engn, La Jolla, CA 92093 USA.
RP Knight, R (corresponding author), Univ Calif San Diego, Dept Pediat, La Jolla, CA 92093 USA.; Knight, R (corresponding author), Univ Calif San Diego, Dept Comp Sci, La Jolla, CA 92093 USA.; Knight, R (corresponding author), Univ Calif San Diego, Dept Engn, La Jolla, CA 92093 USA.
EM robknight@ucsd.edu
CR [Anonymous], SCIENCE
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NR 18
TC 1565
Z9 1788
PD JAN-FEB
PY 2016
VL 1
IS 1
AR e00009
DI 10.1128/mSystems.00009-15
UT WOS:000408190500004
HC Y
HP N
DA 2025-07-30
ER

PT J
AU Raghukumar, S
AF Raghukumar, Seshagiri
TI Marine microbial eukaryotic diversity, with particular reference to
   fungi: Lessons from prokaryotes
SO INDIAN JOURNAL OF MARINE SCIENCES
DT Article
AB Novel molecular, analytical and culturing techniques have resulted in dramatic changes in our approaches towards marine eukaryotic diversity in recent years. This article reviews marine fungal diversity in the light of current knowledge, citing examples of how progress in understanding marine prokaryotes has often contributed to this new approach. Both 'true fungi' (termed mycenaean fungi in this review) and straminipilan fungi are considered. Molecular phylogenetic studies of prokaryotes has resulted in their redefinition as belonging to the Kingdoms Bacteria and Archaea. Likewise, major refinements have taken place in the phylogenetic classification of eukaryotes. In the case of fungi, it has now been realized that they are polyphyletic, belonging to the Kingdom Mycenae (Fungi), as well as the Kingdom Strairtinipila or Chromista. Although the total number of fungi on earth is estimated to be about 1.5 million, only a meagre number of obligate marine fungi, about 450 mycenaean and 50 straminipilan fungi have been described so far. It is likely that most of the true marine fungi have not yet been discovered. These are likely to have evolved between 1,500 million years ago (Ma) when fungi probably evolved in the sea and 900 Ma when they conquered land together with green plants. It now appears that most of the true marine fungi have not been cultured so far, similar to the 'great plate count anomaly' of bacteria. Thraustochytrids, which are abundant in the water column, but not easily culturable from that source is an example. Intelligent and novel culture methods might bring forth unusual and new marine fungi, as happened in the case of Pelagibacter ubique belonging to the SAR 11 group of bacteria. Molecular techniques might bring to light novel marine fungi, as is happening with bacteria. Such fungi may defy our conventional wisdom regarding these organisms in terms of morphology. Thus, several recent studies using 18S rRNA gene community profiles have discovered picoplanktonic marine fungi in the water column. Studies such as those on molecular diversity of eukaryotes in permanently anoxic habitats have also indicated that fungi may be abundant in exotic habitats and possess unusual physiology. A search for fungi in biodiversity-rich habitats, such as the coral reefs and the deep-sea, using a combination of molecular and novel culture methods is likely to reveal a fascinating diversity of marine fungi.
C1 Myko Tech Pvt Ltd, Panaji 403004, Goa, India.
RP Raghukumar, S (corresponding author), Myko Tech Pvt Ltd, 313 Vainguinnim Valley, Panaji 403004, Goa, India.
EM sraghu865@yahoo.co.in
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NR 45
TC 5
Z9 6
PD DEC
PY 2006
VL 35
IS 4
BP 388
EP 398
UT WOS:000244268700013
DA 2025-07-30
ER

PT J
AU Anderson, SR
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AF Anderson, Sean R.
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TI Estuarine microbial networks and relationships vary between
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SO PEERJ
DT Article
AB Microbial interactions have profound impacts on biodiversity, biogeochemistry, and ecosystem functioning, and yet, they remain poorly understood in the ocean and with respect to changing environmental conditions. We applied hierarchical clustering of an annual 16S and 18S amplicon dataset in the Skidaway River Estuary, which revealed two similar clusters for prokaryotes (Bacteria and Archaea) and protists: Cluster 1 (March-May and November-February) and Cluster 2 (June-October). We constructed co-occurrence networks from each cluster to explore how microbial networks and relationships vary between environmentally distinct periods in the estuary. Cluster 1 communities were exposed to significantly lower temperature, sunlight, NO3, and SiO4; only NH4 was higher at this time. Several network properties (e.g., edge number, degree, and centrality) were elevated for networks constructed with Cluster 1 vs. 2 samples. There was also evidence that microbial nodes in Cluster 1 were more connected (e.g., higher edge density and lower path length) compared to Cluster 2, though opposite trends were observed when networks considered Prokaryote-Protist edges only. The number of Prokaryote-Prokaryote and Prokaryote-Protist edges increased by >100% in the Cluster 1 network, mainly involving Flavobacteriales, Rhodobacterales, Peridiniales, and Cryptomonadales associated with each other and other microbial groups (e.g., SAR11, Bacillariophyta, and Strombidiida). Several Protist-Protist associations, including Bacillariophyta correlated with Syndiniales (Dino-Groups I and II) and an Unassigned Dinophyceae group, were more prevalent in Cluster 2. Based on the type and sign of associations that increased in Cluster 1, our findings indicate that mutualistic, competitive, or predatory relationships may have been more representative among microbes when conditions were less favorable in the estuary; however, such relationships require further exploration and validation in the field and lab. Coastal networks may also be driven by shifts in the abundance of certain taxonomic or functional groups. Sustained monitoring of microbial communities over environmental gradients, both spatial and temporal, is critical to predict microbial dynamics and biogeochemistry in future marine ecosystems.
C1 [Anderson, Sean R.] Mississippi State Univ, Northern Gulf Inst, Mississippi State, MS 39762 USA.
   [Anderson, Sean R.] NOAA, Ocean Chem & Ecosyst Div, Atlantic Oceanog & Meteorol Lab, Miami, FL 33149 USA.
   [Harvey, Elizabeth L.] Univ New Hampshire, Dept Biol Sci, Durham, NH 03824 USA.
RP Anderson, SR (corresponding author), Mississippi State Univ, Northern Gulf Inst, Mississippi State, MS 39762 USA.; Anderson, SR (corresponding author), NOAA, Ocean Chem & Ecosyst Div, Atlantic Oceanog & Meteorol Lab, Miami, FL 33149 USA.; Harvey, EL (corresponding author), Univ New Hampshire, Dept Biol Sci, Durham, NH 03824 USA.
EM sean.r.anderson@noaa.gov; elizabeth.harvey@unh.edu
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TC 6
Z9 6
PD SEP 20
PY 2022
VL 10
AR e14005
DI 10.7717/peerj.14005
UT WOS:000964563500007
DA 2025-07-30
ER

PT J
AU Luna, GM
AF Luna, Gian Marco
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SO RENDICONTI LINCEI-SCIENZE FISICHE E NATURALI
DT Article
AB Unicellular microbes are fundamental players in the ecosystem functioning and biogeochemistry of the Mediterranean Sea. Due to the unique hydrological, geological and geomorphological features, the basin is a biodiversity hot-spot of multicellular organisms, and likewise can harbor peculiar assemblages of microbes if compared to other oceans. However, we still know little about the diversity of Mediterranean microbes, due to past methodological constraints only recently conquerable with next generation sequencing of DNA and metagenomics. This review aims at summarizing the knowledge on microbial diversity in the basin, by focusing on prokaryotes (bacteria and archaea) in pelagic and benthic habitats. Richness of bacterioplankton and archaeoplankton assemblages is high in surface and deep waters, and shows consistent horizontal and vertical patterns. Members of the SAR11 clade of Alphaproteobacteria dominate surface bacterial assemblages, followed by other Alphaproteobacteria, Cyanobacteria, Bacteroidetes and uncultured Gammaproteobacteria, with a different contribution according to distance from land and human impact. Meso- and bathypelagic bacterial assemblages are conversely dominated by Gammaproteobacteria, the most representative being the Mediterranean Alteromonas macleodii "deepecotype", followed by other taxa such as Delta- Betaproteobacteria, Acidobacteria, Planctomycetes and Chloroflexi. Archaeoplankton richness is lower, and assemblages differ between water layers, with higher abundance and diversity of Euryarchaeota in the surface, and of Crenarchaeota Marine Group (MG) I, among which specific Mediterranean ecotypes, in deeper layers. In the sediments, abundance and richness of bacteria are always higher than archaea. Surface benthic bacterial assemblages are dominated by Gamma- and Deltaproteobacteria, followed by Acidobacteria and Planctomycetes, and display community composition changes between coastal and deep-sea settings. Benthic archaea show dominance of Crenarchaeota MGI in deep-sea sediments, but their phylogenetic diversity is still poorly known. Pelagic and benthic assemblages include a large proportion of rare taxa, the contribution of which to the ecosystem functioning is unknown. Continuing the exploration of Mediterranean microbes will provide a "next generation" body of knowledge, which needs to be put into the context of climate change and the anthropogenic pressure affecting this highly vulnerable basin.
C1 Natl Res Council ISMAR, Inst Marine Sci, CNR, I-30122 Venice, Italy.
RP Luna, GM (corresponding author), Natl Res Council ISMAR, Inst Marine Sci, CNR, Castello 2737-F,Arsenale Tesa 104, I-30122 Venice, Italy.
EM gianmarco.luna@ve.ismar.cnr.it
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NR 80
TC 19
Z9 20
PD MAR
PY 2015
VL 26
IS 1
BP 49
EP 58
DI 10.1007/s12210-014-0333-x
UT WOS:000351639100006
DA 2025-07-30
ER

PT J
AU Sow, SLS
   van de Poll, WH
   Eveleth, R
   Rich, JJ
   Ducklow, HW
   Rozema, PD
   Luria, CM
   Bolhuis, H
   Meredith, MP
   Amaral-Zettler, LA
   Engelmann, JC
AF Sow, Swan L. S.
   van de Poll, Willem H.
   Eveleth, Rachel
   Rich, Jeremy J.
   Ducklow, Hugh W.
   Rozema, Patrick D.
   Luria, Catherine M.
   Bolhuis, Henk
   Meredith, Michael P.
   Amaral-Zettler, Linda A.
   Engelmann, Julia C.
TI Spatial and temporal variation of Antarctic microbial interactions: a
   study around the west Antarctic Peninsula
SO ENVIRONMENTAL MICROBIOME
DT Article
AB Background The west Antarctic Peninsula (WAP) is a region of rapid environmental changes, with regional differences in climate warming along the north-south axis of the peninsula. Along the WAP, Palmer corresponds to a warmer region with lesser sea ice extent in the north compared to Rothera similar to 400 km to the south. Comprehensive and comparative, year-round assessments of the WAP microbial community dynamics in coastal surface waters at these two locations are imperative to understand the effects of regional climate warming variations on microbial community dynamics, but this is still lacking.
   Results We report on the seasonal diversity, taxonomic overview, as well as predicted inter-and intra-domain causal effects (interactions) of the bacterial and microbial eukaryotic communities close to the Palmer station and at the Rothera time-series site between July 2013 and April 2014. Our 16S- and 18S-rRNA gene amplicon sequencing data showed that across all seasons, both bacteria and microbial eukaryotic communities were considerably different between the two sites which could be attributed to seawater temperature, and sea ice coverage in combination with sea ice type differences. Overall, in terms of biotic drivers, causal-effect modelling suggests that bacteria were stronger drivers of ecosystem dynamics at Palmer, while microbial eukaryotes played a stronger role at Rothera. The parasitic taxa Syndiniales persevered at both sites across the seasons, with Palmer and Rothera harbouring different key groups. Up to 62.3% of the negative causal effects were driven by Syndiniales at Rothera compared to only 13.5% at Palmer, suggesting that parasitism drives community dynamics at Rothera more strongly than at Palmer. Conversely, SAR11 Clade II, which was less abundant but persistent year-round at both sites, was the dominant driver at Palmer, evidenced by many (28.2% and 37.4% of positive and negative effects respectively) strong causal effects. Article note: Kindly check first page article notes are correct.
   Conclusions Our research has shed light on the dynamics of microbial community composition and correlative interactions at two sampling locations that represent different climate regimes along the WAP.
C1 [Sow, Swan L. S.; Bolhuis, Henk; Amaral-Zettler, Linda A.; Engelmann, Julia C.] NIOZ Royal Netherlands Inst Sea Res, Dept Marine Microbiol & Biogeochem, POB 59, NL-1790 AB Den Burg, Netherlands.
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   [Ducklow, Hugh W.] Columbia Univ, Dept Earth & Environm Sci, New York, NY USA.
   [Ducklow, Hugh W.] Columbia Univ, Lamont Doherty Earth Observ, Palisades, NY USA.
   [Luria, Catherine M.] Harvard Med Sch, Lab Syst Pharmacol, Boston, MA USA.
   [Meredith, Michael P.] British Antarctic Survey, Cambridge, England.
   [Amaral-Zettler, Linda A.] Univ Amsterdam, Inst Biodivers & Ecosyst Dynam, Dept Freshwater & Marine Ecol, Amsterdam, Netherlands.
   [Amaral-Zettler, Linda A.] Josephine Bay Paul Ctr, Marine Biol Lab, Woods Hole, MA 02543 USA.
   [Sow, Swan L. S.] Nantes Univ, Ecole Cent Nantes, CNRS, UMR 6004,LS2N, F-44000 Nantes, France.
RP Sow, SLS; Amaral-Zettler, LA; Engelmann, JC (corresponding author), NIOZ Royal Netherlands Inst Sea Res, Dept Marine Microbiol & Biogeochem, POB 59, NL-1790 AB Den Burg, Netherlands.; Amaral-Zettler, LA (corresponding author), Univ Amsterdam, Inst Biodivers & Ecosyst Dynam, Dept Freshwater & Marine Ecol, Amsterdam, Netherlands.; Amaral-Zettler, LA (corresponding author), Josephine Bay Paul Ctr, Marine Biol Lab, Woods Hole, MA 02543 USA.; Sow, SLS (corresponding author), Nantes Univ, Ecole Cent Nantes, CNRS, UMR 6004,LS2N, F-44000 Nantes, France.
EM swan.lisan@gmail.com; linda.amaral-zettler@nioz.nl;
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NR 112
TC 0
Z9 0
PD FEB 8
PY 2025
VL 20
IS 1
AR 21
DI 10.1186/s40793-025-00663-z
UT WOS:001416630600002
DA 2025-07-30
ER

PT J
AU Ai, DM
   Li, XX
   Pan, HF
   Chen, JM
   Cram, JA
   Xia, LC
AF Ai, Dongmei
   Li, Xiaoxin
   Pan, Hongfei
   Chen, Jiamin
   Cram, Jacob A.
   Xia, Li C.
TI Explore mediated co-varying dynamics in microbial community using
   integrated local similarity and liquid association analysis
SO BMC GENOMICS
DT Article; Proceedings Paper
CT 17th Asia Pacific Bioinformatics Conference (APBC) - Genomics
CY JAN 16, 2019
CL Wuhan, PEOPLES R CHINA
AB BackgroundDiscovering the key microbial species and environmental factors of microbial community and characterizing their relationships with other members are critical to ecosystem studies. The microbial co-occurrence patterns across a variety of environmental settings have been extensively characterized. However, previous studies were limited by their restriction toward pairwise relationships, while there was ample evidence of third-party mediated co-occurrence in microbial communities.MethodsWe implemented and applied the triplet-based liquid association analysis in combination with the local similarity analysis procedure to microbial ecology data. We developed an intuitive scheme to visualize those complex triplet associations along with pairwise correlations. Using a time series from the marine microbial ecosystem as example, we identified pairs of operational taxonomic units (OTUs) where the strength of their associations appeared to relate to the values of a third mediator variable. These mediator variables appear to modulate the associations between pairs of bacteria.ResultsUsing this analysis, we were able to assess the OTUs' ability to regulate its functional partners in the community, typically not manifested in the pairwise correlation patterns. For example, we identified Flavobacteria as a multifaceted player in the marine microbial ecosystem, and its clades were involved in mediating other OTU pairs. By contrast, SAR11 clades were not active mediators of the community, despite being abundant and highly correlated with other OTUs. Our results suggested that Flavobacteria are more likely to respond to situations where particles and unusual sources of dissolved organic material are prevalent, such as after a plankton bloom. On the other hand, SAR11s are oligotrophic chemoheterotrophs with inflexible metabolisms, and their relationships with other organisms may be less governed by environmental or biological factors.ConclusionsBy integrating liquid association with local similarity analysis to explore the mediated co-varying dynamics, we presented a novel perspective and a useful toolkit to analyze and interpret time series data from microbial community. Our augmented association network analysis is thus more representative of the true underlying dynamic structure of the microbial community. The analytic software in this study was implemented as new functionalities of the ELSA (Extended local similarity analysis) tool, which is available for free download (http://bitbucket.org/charade/elsa).
C1 [Ai, Dongmei; Li, Xiaoxin; Pan, Hongfei] Univ Sci & Technol Beijing, Sch Math & Phys, Xueyuan Rd, Beijing 100001, Peoples R China.
   [Chen, Jiamin; Xia, Li C.] Stanford Univ, Sch Med, Dept Med, 269 Campus Dr, Stanford, CA 94305 USA.
   [Cram, Jacob A.] Univ Maryland, Ctr Environm Sci, Cambridge, MA 21613 USA.
RP Xia, LC (corresponding author), Stanford Univ, Sch Med, Dept Med, 269 Campus Dr, Stanford, CA 94305 USA.; Cram, JA (corresponding author), Univ Maryland, Ctr Environm Sci, Cambridge, MA 21613 USA.
EM jcram@umces.edu; l.c.xia@stanford.edu
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NR 52
TC 11
Z9 11
PD APR 4
PY 2019
VL 20
SU 2
AR 185
DI 10.1186/s12864-019-5469-8
UT WOS:000464120900003
DA 2025-07-30
ER

PT J
AU Haro-Moreno, JM
   López-Pérez, M
   de la Torre, JR
   Picazo, A
   Camacho, A
   Rodriguez-Valera, F
AF Haro-Moreno, Jose M.
   Lopez-Perez, Mario
   de la Torre, Jose R.
   Picazo, Antonio
   Camacho, Antonio
   Rodriguez-Valera, Francisco
TI Fine metagenomic profile of the Mediterranean stratified and mixed water
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SO MICROBIOME
DT Article
AB Background: The photic zone of aquatic habitats is subjected to strong physicochemical gradients. To analyze the fine-scale variations in the marine microbiome, we collected seven samples from a single offshore location in the Mediterranean at 15 m depth intervals during a period of strong stratification, as well as two more samples during the winter when the photic water column was mixed. We were able to recover 94 new metagenome-assembled genomes (MAGs) from these metagenomes and examine the distribution of key marine microbes within the photic zone using metagenomic recruitment.
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C1 [Haro-Moreno, Jose M.; Lopez-Perez, Mario; Rodriguez-Valera, Francisco] Univ Miguel Hernandez, Evolutionary Genom Grp, Div Microbiol, Apartado 18, Alicante 03550, Spain.
   [de la Torre, Jose R.] San Francisco State Univ, Dept Biol, San Francisco, CA 94132 USA.
   [Picazo, Antonio; Camacho, Antonio] Univ Valencia, Cavanilles Inst Biodivers & Evolutionary Biol, E-46100 Valencia, Spain.
RP Rodriguez-Valera, F (corresponding author), Univ Miguel Hernandez, Evolutionary Genom Grp, Div Microbiol, Apartado 18, Alicante 03550, Spain.
EM frvalera@umh.es
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NR 111
TC 66
Z9 72
PD JUL 10
PY 2018
VL 6
AR 128
DI 10.1186/s40168-018-0513-5
UT WOS:000438419000001
DA 2025-07-30
ER

PT J
AU Delpech, LM
   Vonnahme, TR
   McGovern, M
   Gradinger, R
   Præbel, K
   Poste, AE
AF Delpech, Lisa-Marie
   Vonnahme, Tobias R.
   McGovern, Maeve
   Gradinger, Rolf
   Praebel, Kim
   Poste, Amanda E.
TI Terrestrial Inputs Shape Coastal Bacterial and Archaeal Communities in a
   High Arctic Fjord (Isfjorden, Svalbard)
SO FRONTIERS IN MICROBIOLOGY
DT Article
AB The Arctic is experiencing dramatic changes including increases in precipitation, glacial melt, and permafrost thaw, resulting in increasing freshwater runoff to coastal waters. During the melt season, terrestrial runoff delivers carbon- and nutrient-rich freshwater to Arctic coastal waters, with unknown consequences for the microbial communities that play a key role in determining the cycling and fate of terrestrial matter at the land-ocean interface. To determine the impacts of runoff on coastal microbial (bacteria and archaea) communities, we investigated changes in pelagic microbial community structure between the early (June) and late (August) melt season in 2018 in the Isfjorden system (Svalbard). Amplicon sequences of the 16S rRNA gene were generated from water column, river and sediment samples collected in Isfjorden along fjord transects from shallow river estuaries and glacier fronts to the outer fjord. Community shifts were investigated in relation to environmental gradients, and compared to river and marine sediment microbial communities. We identified strong temporal and spatial reorganizations in the structure and composition of microbial communities during the summer months in relation to environmental conditions. Microbial diversity patterns highlighted a reorganization from rich communities in June toward more even and less rich communities in August. In June, waters enriched in dissolved organic carbon (DOC) provided a niche for copiotrophic taxa including Sulfitobacter and Octadecabacter. In August, lower DOC concentrations and Atlantic water inflow coincided with a shift toward more cosmopolitan taxa usually associated with summer stratified periods (e.g., SAR11 Clade Ia), and prevalent oligotrophic marine clades (OM60, SAR92). Higher riverine inputs of dissolved inorganic nutrients and suspended particulate matter also contributed to spatial reorganizations of communities in August. Sentinel taxa of this late summer fjord environment included taxa from the class Verrucomicrobiae (Roseibacillus, Luteolibacter), potentially indicative of a higher fraction of particle-attached bacteria. This study highlights the ecological relevance of terrestrial runoff for Arctic coastal microbial communities and how its impacts on biogeochemical conditions may make these communities susceptible to climate change.
C1 [Delpech, Lisa-Marie] Univ Lyon, Ecole Normale Super Lyon, Dept Biol, Lyon, France.
   [Delpech, Lisa-Marie; Vonnahme, Tobias R.; McGovern, Maeve; Gradinger, Rolf] UiT Arctic Univ Norway, Dept Arctic & Marine Biol, Tromso, Norway.
   [Delpech, Lisa-Marie; Poste, Amanda E.] Norwegian Inst Water Res NIVA, Tromso, Norway.
   [Praebel, Kim] UiT Arctic Univ Norway, Norwegian Coll Fishery Sci, Tromso, Norway.
RP Delpech, LM (corresponding author), Univ Lyon, Ecole Normale Super Lyon, Dept Biol, Lyon, France.; Delpech, LM; Vonnahme, TR (corresponding author), UiT Arctic Univ Norway, Dept Arctic & Marine Biol, Tromso, Norway.; Delpech, LM (corresponding author), Norwegian Inst Water Res NIVA, Tromso, Norway.
EM lisa-marie.delpech@ens-lyon.fr; tobias.vonnahme@uit.no
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NR 121
TC 23
Z9 23
PD FEB 26
PY 2021
VL 12
AR 614634
DI 10.3389/fmicb.2021.614634
UT WOS:000627768400001
DA 2025-07-30
ER

PT J
AU Mucko, M
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   Casotti, R
   Balestra, C
   Ljubesic, Z
AF Mucko, Maja
   Bosak, Suncica
   Casotti, Raffaella
   Balestra, Cecilia
   Ljubesic, Zrinka
TI Winter picoplankton diversity in an oligotrophic marginal sea
SO MARINE GENOMICS
DT Article
AB Marine picoplankton, unicellular organisms with cell sizes up to 3 mu m in diameter, numerically dominate marine ecosystems, encompassing Archaea, Bacteria, Eukarya (protists and fungi) as well as viruses. Autotrophic and heterotrophic picoplankton abundance and community composition with a focus on picoeukaryotes (PEs) were investigated in the winter of 2016 at three stations along a coast-to-offshore transect in the southern Adriatic Sea. Abundances were estimated by flow cytometry, while community composition by Illumina High Throughput Sequencing (HTS) of 16S and 18S rRNA genes. The photosynthetic picoplankton diversity was also investigated by High-Performance Liquid Chromatography (HPLC) of liposoluble pigments. Heterotrophic bacteria and cyanobacteria (Prochlorococcus and Synechococcus) accounted for up to 7 x 10(5); 2.3 x 10(4) and 2.5 x 10(4) cells mL(-1), respectively, while photosynthetic picoeukaryotes peaked with 3 x 10(3) cells mL(-1). Prokaryotes, as revealed by HTS were dominated by Aiphaproteobacteria (mainly SAR11, 44.91% of total 16S sequence reads), followed by Gammaproteobacteria (Oceanospirillales and Pseudomonadales, 14.96%), Bacteroidetes (mainly Flavobacteriales, 13%), Cyanobacteria (Prochlorococcus and Synechococcus, 9.52%), Marinimicrobia (SAR406, 7.97%), Deltaproteobacteria (SAR324, 3.83%), Actinobacteria (2.24%) and Chloroflezi (SAR202, 1.90%). Photosynthetic pigment concentrations were very low (12.12 mu gL(-1) at the most) and taxonomic pigments could be attributed to Prochlorococcus, Synechococcus, Prymnesiophyceae, Bacillariophyceae, Chrysophyceae, and Prasinophyceae. HTS data revealed that PEs were dominated by heterotrophs, such as Syndiniophyceae, parasitic dinoflagellates (79.67% of total 18S sequence reads), Dinophyceae (8.7%) and the radiolarians Collodaria belonging to Sphaerozoidae (22.1%) and Spumellaria (5.0%). On the other hand, photoautotrophs, including Chlorophyta (Mamiellophyceae, Prasinophyceae, Trebouxiophyceae, and Ulvophyceae), Stramenopiles (Bacillariophyta, Chrysophyceae, Dictyochophyceae, Pelagophyceae), photoautotrophic Cryptophyta and some Haptophyta (Prymnesiophyceae), did not exceed 5% of total sequence reads. This study provides the first snapshot of the PEs diversity in oligotrophic euphotic waters of the southern Adriatic Sea, hence setting the stage for large-scale surveying and characterization of the eukaryotic diversity in the entire basin.
C1 [Mucko, Maja; Bosak, Suncica; Ljubesic, Zrinka] Univ Zagreb, Fac Sci, Dept Biol, Rooseveltov Trg 6, Zagreb 10000, Croatia.
   [Casotti, Raffaella; Balestra, Cecilia] Dept Integrat Marine Ecol, Stn Zool Anton Dohrn, I-80121 Naples, Italy.
RP Ljubesic, Z (corresponding author), Univ Zagreb, Fac Sci, Dept Biol, Rooseveltov Trg 6, Zagreb 10000, Croatia.
EM zrinka.ljubesic@biol.pmf.hr
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NR 92
TC 10
Z9 10
PD DEC
PY 2018
VL 42
BP 14
EP 24
DI 10.1016/j.margen.2018.09.002
UT WOS:000454376100002
DA 2025-07-30
ER

PT J
AU Ng, C
   Le, TH
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AF Ng, Charmaine
   Le, Thai-Hoang
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TI A Comparison of Microbial Water Quality and Diversity for Ballast and
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SO PLOS ONE
DT Article
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C1 [Ng, Charmaine; Le, Thai-Hoang; Goh, Shin Giek; Liang, Liang; Yew-Hoong, Karina Gin] Natl Univ Singapore, Dept Civil & Environm Engn, Singapore 117548, Singapore.
   [Kim, Yiseul; Rose, Joan B.] Michigan State Univ, Dept Microbiol & Mol Genet, E Lansing, MI 48824 USA.
   [Yew-Hoong, Karina Gin] Natl Univ Singapore, Environm Res Inst NERI, Singapore 117548, Singapore.
RP Yew-Hoong, KG (corresponding author), Natl Univ Singapore, Dept Civil & Environm Engn, Singapore 117548, Singapore.
EM ceeginyh@nus.edu.sg
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TC 46
Z9 52
PD NOV 17
PY 2015
VL 10
IS 11
AR e0143123
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UT WOS:000365153400043
DA 2025-07-30
ER

PT J
AU Vila-Costa, M
   Gasol, JM
   Sharma, S
   Moran, MA
AF Vila-Costa, Maria
   Gasol, Josep M.
   Sharma, Shalabh
   Moran, Mary Ann
TI Community analysis of high- and low-nucleic acid-containing bacteria in
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
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C1 [Vila-Costa, Maria] Ctr Estudis Avancats Blanes CSIC, Grp Limnol, Dept Continental Ecol, Blanes 17300, Catalonia, Spain.
   [Vila-Costa, Maria; Sharma, Shalabh; Moran, Mary Ann] Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
   [Gasol, Josep M.] Inst Ciencies Mar CSIC, Barcelona 08003, Catalonia, Spain.
RP Vila-Costa, M (corresponding author), Ctr Estudis Avancats Blanes CSIC, Grp Limnol, Dept Continental Ecol, Acces Cala St Francesc 14, Blanes 17300, Catalonia, Spain.
EM mariavila@ceab.csic.es
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TC 104
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PY 2012
VL 14
IS 6
BP 1390
EP 1402
DI 10.1111/j.1462-2920.2012.02720.x
UT WOS:000304866600004
DA 2025-07-30
ER

PT J
AU Yu, J
   Wang, S
   Lai, JG
   Tian, JY
   Zhang, HQ
   Yang, GP
   Chen, R
AF Yu, Juan
   Wang, Su
   Lai, Jing-Guang
   Tian, Ji-Yuan
   Zhang, Hao-Quan
   Yang, Gui-Peng
   Chen, Rong
TI The Effect of Zooplankton on the Distributions of Dimethyl Sulfide and
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DT Article
AB Dimethyl sulfide (DMS) and its precursor dimethylsulfoniopropionate (DMSP) are ubiquitous sulfur compounds in the ocean. DMS is emitted into the atmosphere and has potential climatic effects. The distributions of DMS and DMSP are affected by various biological factors (i.e., bacterial catabolism and phytoplankton and zooplankton community composition). The horizontal and vertical distributions of DMSP, DMSP lyase activity (DLA), DMS, and the abundances of bacteria, DMSP-consuming bacteria, dimethyl sulfoxide-consuming bacteria, and picophytoplankton were investigated in the Bohai Sea (BS) and Yellow Sea (YS) during autumn 2020. DLA was significantly correlated with chlorophyll a, DMS, and dissolved DMSP concentrations. Our data show that bacteria Clade_I SAR11 was a significant contributor to DLA. A dilution experiment indicated that the highest microzooplankton grazing rate coincided with the highest DMS concentration and DMS production rate. A proportion of 16%-62% of the DMSPt was converted to DMS in the dilution experiment. Copepods dominated the mesozooplankton community. Calanus sinicus was the predominant copepod in the BS and YS. C. sinicus grazing stimulated DMS production. DMS concentration increased 299% after C. sinicus grazing on physically broken algal cells for 48 hr. These results will help with a better understanding of the control of DMS and DMSP concentrations by zooplankton and the DMS release mechanisms that occur through zooplankton grazing.Plain Language Summary Dimethylsulfoniopropionate (DMSP) and dimethyl sulfide (DMS) are transferred and transformed in the food web and are affected by zooplankton, phytoplankton, and bacteria. This study investigated spatial distributions of DMS, DMSP, DMSP lyase activity (DLA), the abundances of bacteria, DMSP-consuming bacteria, and dimethyl sulfoxide-consuming bacteria in the surface seawater of the Bohai Sea and Yellow Sea. As results, the distributions of DMS and dissolved DMSP were significantly correlated with DLA. A deck incubation experiment indicated that grazing by microzooplankton promoted the conversion of DMSP to DMS and that mesozooplankton copepod grazing stimulated DMS production. These results provide a more comprehensive way to understand the possible DMS release mechanisms via zooplankton grazing.
C1 [Yu, Juan; Wang, Su; Lai, Jing-Guang; Zhang, Hao-Quan; Yang, Gui-Peng; Chen, Rong] Ocean Univ China, Coll Chem & Chem Engn, Frontiers Sci Ctr Deep Ocean Multispheres & Earth, Key Lab Marine Chem Theory & Technol, Qingdao, Peoples R China.
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   [Tian, Ji-Yuan] Qingdao Agr Univ, Coll Food Sci & Engn, Qingdao, Peoples R China.
RP Yang, GP (corresponding author), Ocean Univ China, Coll Chem & Chem Engn, Frontiers Sci Ctr Deep Ocean Multispheres & Earth, Key Lab Marine Chem Theory & Technol, Qingdao, Peoples R China.; Yang, GP (corresponding author), Qingdao Natl Lab Marine Sci & Technol, Lab Marine Ecol & Environm Sci, Qingdao, Peoples R China.
EM gpyang@mail.ouc.edu.cn
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NR 96
TC 8
Z9 8
PD APR
PY 2023
VL 128
IS 4
AR e2022JC019030
DI 10.1029/2022JC019030
UT WOS:000973050300001
DA 2025-07-30
ER

PT J
AU Allen, LZ
   McCrow, JP
   Ininbergs, K
   Dupont, CL
   Badger, JH
   Hoffman, JM
   Ekman, M
   Allen, AE
   Bergman, B
   Venter, JC
AF Allen, Lisa Zeigler
   McCrow, John P.
   Ininbergs, Karolina
   Dupont, Christopher L.
   Badger, Jonathan H.
   Hoffman, Jeffery M.
   Ekman, Martin
   Allen, Andrew E.
   Bergman, Birgitta
   Venter, J. Craig
TI The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and
   RNA Viruses
SO MSYSTEMS
DT Article
AB Metagenomic and metatranscriptomic data were generated from size-fractionated samples from 11 sites within the Baltic Sea and adjacent marine waters of Kattegat and freshwater Lake Tornetrask in order to investigate the diversity, distribution, and transcriptional activity of virioplankton. Such a transect, spanning a salinity gradient from freshwater to the open sea, facilitated a broad genome-enabled investigation of natural as well as impacted aspects of Baltic Sea viral communities. Taxonomic signatures representative of phages within the widely distributed order Caudovirales were identified with enrichments in lesser-known families such as Podoviridae and Siphoviridae. The distribution of phage reported to infect diverse and ubiquitous heterotrophic bacteria (SAR11 clades) and cyanobacteria (Synechococcus sp.) displayed population-level shifts in diversity. Samples from higher-salinity conditions (>14 practical salinity units [PSU]) had increased abundances of viruses for picoeukaryotes, i.e., Ostreococcus. These data, combined with host diversity estimates, suggest viral modulation of diversity on the whole-community scale, as well as in specific prokaryotic and eukaryotic lineages. RNA libraries revealed single-stranded DNA (ssDNA) and RNA viral populations throughout the Baltic Sea, with ssDNA phage highly represented in Lake Tornetrask. Further, our data suggest relatively high transcriptional activity of fish viruses within diverse families known to have broad host ranges, such as Nodoviridae (RNA), Iridoviridae (DNA), and predicted zoonotic viruses that can cause ecological and economic damage as well as impact human health.
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C1 [Allen, Lisa Zeigler; McCrow, John P.; Dupont, Christopher L.; Badger, Jonathan H.; Hoffman, Jeffery M.; Allen, Andrew E.; Venter, J. Craig] J Craig Venter Inst, Microbial & Environm Genom, San Diego, CA 92037 USA.
   [Allen, Andrew E.] Scripps Inst Oceanog, La Jolla, CA USA.
   [Ininbergs, Karolina; Ekman, Martin; Bergman, Birgitta] Stockholm Univ, Sci Life Lab, Dept Ecol Environm & Plant Sci, Solna, Sweden.
   [Badger, Jonathan H.] NCI, Natl Canc Inst, Bethesda, MD 20892 USA.
RP Allen, LZ (corresponding author), J Craig Venter Inst, Microbial & Environm Genom, San Diego, CA 92037 USA.
EM lzeigler@jcvi.org
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TC 55
Z9 60
PD JAN-FEB
PY 2017
VL 2
IS 1
AR e00125-16
DI 10.1128/mSystems.00125-16
UT WOS:000408193500005
DA 2025-07-30
ER

PT J
AU Nelson, CE
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AF Nelson, Craig E.
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DT Article
AB Coral reefs are highly productive ecosystems bathed in unproductive, low-nutrient oceanic waters, where microbially dominated food webs are supported largely by bacterioplankton recycling of dissolved compounds. Despite evidence that benthic reef organisms efficiently scavenge particulate organic matter and inorganic nutrients from advected oceanic waters, our understanding of the role of bacterioplankton and dissolved organic matter (DOM) in the interaction between reefs and the surrounding ocean remains limited. In this study, we present the results of a 4-year study conducted in a well-characterized coral reef ecosystem (Paopao Bay, Moorea, French Polynesia) where changes in bacterioplankton abundance and dissolved organic carbon (DOC) concentrations were quantified and bacterial community structure variation was examined along spatial gradients of the reef: ocean interface. Our results illustrate that the reef is consistently depleted in concentrations of both DOC and bacterioplankton relative to offshore waters (averaging 79 mu mol l(-1) DOC and 5.5 x 10(8) cells l(-1) offshore and 68 lmol l(-1) DOC and 3.1 x 10(8) cells l(-1) over the reef, respectively) across a 4-year time period. In addition, using a suite of culture-independent measures of bacterial community structure, we found consistent differentiation of reef bacterioplankton communities from those offshore or in a nearby embayment across all taxonomic levels. Reef habitats were enriched in Gamma-, Delta-, and Betaproteobacteria, Bacteriodetes, Actinobacteria and Firmicutes. Specific bacterial phylotypes, including members of the SAR11, SAR116, Flavobacteria, and Synechococcus clades, exhibited clear gradients in relative abundance among nearshore habitats. Our observations indicate that this reef system removes oceanic DOC and exerts selective pressures on bacterioplankton community structure on timescales approximating reef water residence times, observations which are notable both because fringing reefs do not exhibit long residence times (unlike those characteristic of atoll lagoons) and because oceanic DOC is generally recalcitrant to degradation by ambient microbial assemblages. Our findings thus have interesting implications for the role of oceanic DOM and bacterioplankton in the ecology and metabolism of reef ecosystems. The ISME Journal (2011) 5, 1374-1387; doi:10.1038/ismej.2011.12; published online 10 March 2011
C1 [Nelson, Craig E.; Alldredge, Alice L.; Carlson, Craig A.] Univ Calif Santa Barbara, Inst Marine Sci, Santa Barbara, CA 93106 USA.
   [Alldredge, Alice L.; Carlson, Craig A.] Univ Calif Santa Barbara, Dept Ecol Evolut & Marine Biol, Santa Barbara, CA 93106 USA.
   [McCliment, Elizabeth A.; Amaral-Zettler, Linda A.] Marine Biol Lab, Josephine Bay Paul Ctr Comparat Mol Biol & Evolut, Woods Hole, MA 02543 USA.
   [Amaral-Zettler, Linda A.] Brown Univ, Dept Geol Sci, Providence, RI 02912 USA.
RP Nelson, CE (corresponding author), Univ Calif Santa Barbara, Inst Marine Sci, Santa Barbara, CA 93106 USA.
EM cr_nelson@lifesci.ucsb.edu
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NR 93
TC 108
Z9 120
PD AUG
PY 2011
VL 5
IS 8
BP 1374
EP 1387
DI 10.1038/ismej.2011.12
UT WOS:000295782200013
DA 2025-07-30
ER

PT J
AU Li, JT
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   Su, L
   Wang, H
   Gao, JQ
   Bai, SJ
AF Li, Jiangtao
   Yang, Jingyu
   Sun, Mingxue
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   Wang, Hu
   Gao, Jianqi
   Bai, Shijie
TI Distribution and Succession of Microbial Communities Along the Dispersal
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DT Article
AB The distribution and succession of microbial communities along the dispersion path of hydrothermal plumes has not been well investigated. In this study, we collected several types of samples from the Longqi hydrothermal field located on the Southwest Indian Ridge, including hydrothermal plumes at different stages of formation, a suite of water column samples across the non-buoyant hydrothermal plumes above this field, and a background seawater column approximately 350 km away from the hydrothermal field. Using CH4 concentration anomalies, three non-buoyant plume samples between 2,535 and 2,735 m were identified within the water column. Microbial community compositions within these plumes and background seawater samples were examined based on the 16S rRNA genes and revealed significant variations and successions in community composition between different portions of the hydrothermal plumes. Near the vent orifice, representing the initial stage of plume formation, microbial populations were characterized by abundant and diverse putative vent-associated communities including (hyper)thermophiles such as Aquificaceae and Hydrogenothermaceae within the phylum Aquificae, and some epsilonproteobacterial chemolithoautotrophs such as Sulfurovum, Sulfurimonas, and Caminibacter. By contrast, in the rising buoyant plumes and adjacent seawaters, most vent-associated microbial taxa were still present but made only minor contributions to community composition. Some microbial taxa that are common in seawater columns such as alphaproteobacterial Sphingomonadaceae and SAR11 clade, deltaproteobacterial SAR324 clade, and gammaproteobacterial Pseudomonas, together with Sulfurimonas and SUP05 clade, became predominant. Members within the Sulfurimonas and SUP05 clade flourished with considerable abundance in the non-buoyant plumes, although these plumes were mainly composed of alphaproteobacterial Rhodobacteraceae, gammaproteobacterial Alteromonadaceae and Saccharospirilaceae putatively derived from the surrounding ambient seawater. We also analyzed archaeal components in the initial discharge and rising buoyant plume stages, with both primarily consisting of thaumarchaeal Nitrosopumilales and euryarchaeal Marine Group II. Our results indicated that being characteristic microbial lineages within the hydrothermal plumes of the Southwest Indian Ridge, both Sulfurimonas and SUP05 clade display a common and abundant distribution across the plume path. However, out of these clades, Sulfurimonas is more abundant and widespread.
C1 [Li, Jiangtao; Yang, Jingyu; Sun, Mingxue; Su, Lei; Wang, Hu; Gao, Jianqi] Tongji Univ, State Key Lab Marine Geol, Shanghai, Peoples R China.
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RP Bai, SJ (corresponding author), Chinese Acad Sci, Inst Deep Sea Sci & Engn, Sanya, Peoples R China.
EM baishijie@idsse.ac.cn
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TC 12
Z9 14
PD NOV 5
PY 2020
VL 7
AR 581381
DI 10.3389/fmars.2020.581381
UT WOS:000591538300001
DA 2025-07-30
ER

PT J
AU Coutinho, FH
   Rosselli, R
   Rodríguez-Valera, F
AF Hernandes Coutinho, Felipe
   Rosselli, Riccardo
   Rodriguez-Valera, Francisco
TI Trends of Microdiversity Reveal Depth-Dependent Evolutionary Strategies
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SO MSYSTEMS
DT Article
AB The evolutionary interactions between viruses and their prokaryotic hosts remain a little-known aspect of microbial evolution. Most studies on this topic were carried out in pure cultures that challenge one virus with one bacterial clone at a time, which is very removed from real-life situations. Few studies have addressed trends of microdiversity in marine viral communities throughout depth gradients. We analyzed metagenomes from both the cellular and viral fractions of Mediterranean seawater samples spanning the epipelagic to the bathypelagic zones at depths of 15, 45, 60, and 2,000 m during the summer stratification of the water column. We evaluated microdiversity patterns by measuring the accumulation of synonymous and nonsynonymous mutations in viral genes. Our results demonstrated clear depth-dependent trends in the frequency of polymorphic sites and nonsynonymous mutations among genes encoding metabolic, structural, and replication proteins. These differences were linked to changes in energy availability, host and viral densities, and the proportions of actively replicating viruses. We propose the hypothesis that in the energy-rich, high-host-density, euphotic depths, selection acts to favor diversity of the host recognition machinery to increase host range, while in energy-depleted aphotic waters, selection acts on viral replication fitness, enhancing diversity in auxiliary metabolic genes.
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C1 [Hernandes Coutinho, Felipe; Rosselli, Riccardo; Rodriguez-Valera, Francisco] Univ Miguel Hernandez, Dept Prod Vegetal & Microbiol, Evolutionary Genom Grp, Campus San Juan, Alicante, Spain.
   [Rodriguez-Valera, Francisco] Moscow Inst Phys & Technol, Dolgoprudnyi, Russia.
RP Coutinho, FH (corresponding author), Univ Miguel Hernandez, Dept Prod Vegetal & Microbiol, Evolutionary Genom Grp, Campus San Juan, Alicante, Spain.
EM fhernandes@umh.es
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NR 54
TC 26
Z9 27
PD NOV-DEC
PY 2019
VL 4
IS 6
AR e00554-19
DI 10.1128/mSystems.00554-19
UT WOS:000500495300003
DA 2025-07-30
ER

PT J
AU Muck, S
   De Corte, D
   Clifford, EL
   Bayer, B
   Herndl, GJ
   Sintes, E
AF Muck, Simone
   De Corte, Daniele
   Clifford, Elisabeth L.
   Bayer, Barbara
   Herndl, Gerhard J.
   Sintes, Eva
TI Niche Differentiation of Aerobic and Anaerobic Ammonia Oxidizers in a
   High Latitude Deep Oxygen Minimum Zone
SO FRONTIERS IN MICROBIOLOGY
DT Article
AB To elucidate the potential for nitrification and denitrification processes in a high latitude deep oxygen minimum zone (OMZ) we determined the abundance and community composition of the main microbial players in the aerobic and anaerobic (anammox) ammonium oxidation and denitrification processes in the Gulf of Alaska throughout the water column. Within the dominant bacterial groups, Flavobacterales, Rhodobacterales, Actinomarinales, and SAR86 were more abundant in epipelagic waters and decreased with depth, whereas SAR11, SAR324, Marinimicrobia, and Thiomicrospirales increased their contribution to the bacterial community with depth. Nitrosopumilaceae also increased with depth and dominated the OMZ and bathypelagic archaeal communities. Euryarchaeota Marine Group II exhibited an opposite depth pattern to Nitrosopumilaceae, whereas Marine Group III and Woesearchaeota were more abundant in the bathypelagic realm. Candidatus Brocadia contributed 70-100% of the anammox bacterial community throughout the water column. Archaeal ammonia oxidizers (AOA) dominated the microbial community involved in the nitrogen cycle. Two AOA ecotypes, the high ammonia (HAC) and low ammonia (LAC)-AOA, characterized by distinct genes for aerobic ammonia oxidation (amoA) and for denitrification (nirK), exhibited a distinct distribution pattern related to depth and ammonia concentrations. HAC-AOA dominated in epipelagic (80.5 +/- 28.3% of total AOA) oxygenated and ammonia-rich waters, and LAC-AOA dominated in the OMZ (90.9 +/- 5.1%) and bathypelagic waters (85.5 +/- 13.5%), characterized by lower oxygen and ammonia concentrations. Bacterial denitrifiers (3.7 +/- 6.9 bacterial nirK gene mL(-1)) and anaerobic ammonia oxidizers (78 +/- 322 anammox 16S rRNA genes L-1) were low in abundance under the oxygen conditions in the Gulf of Alaska throughout the water column. The widespread distribution of bacterial denitrifiers and anaerobic ammonia oxidizers in low abundances reveals a reservoir of genetic and metabolic potential ready to colonize the environment under the predicted increase of OMZs in the ocean. Taken together, our results reinforce the niche partitioning of archaeal ammonia oxidizers based on their distinct metabolic characteristics resulting in the dominance of LAC-AOA in a high latitude deep OMZ. Considering the different ecological roles and functions of the two archaeal ecotypes, the expansion of the zones dominated by the LAC-ecotype might have implications for the nitrogen cycle in the future ocean.
C1 [Muck, Simone; Clifford, Elisabeth L.; Bayer, Barbara; Herndl, Gerhard J.; Sintes, Eva] Univ Vienna, Dept Limnol & Biooceanog, Ctr Funct Ecol, Vienna, Austria.
   [Muck, Simone; Herndl, Gerhard J.] Univ Utrecht, NIOZ, Dept Marine Microbiol & Biogeochem, Royal Netherlands Inst Sea Res, Den Burg, Netherlands.
   [De Corte, Daniele] Japan Agcy Marine Earth Sci & Technol JAMSTEC, Res & Dev Ctr Marine Biosci, Yokosuka, Kanagawa, Japan.
   [Sintes, Eva] Ctr Oceanog Baleares, Ecosyst Oceanog Grp GRECO, Inst Espanol Oceanog, Palma De Mallorca, Spain.
RP Sintes, E (corresponding author), Univ Vienna, Dept Limnol & Biooceanog, Ctr Funct Ecol, Vienna, Austria.; Sintes, E (corresponding author), Ctr Oceanog Baleares, Ecosyst Oceanog Grp GRECO, Inst Espanol Oceanog, Palma De Mallorca, Spain.
EM eva.sintes@ieo.es
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NR 157
TC 37
Z9 38
PD SEP 13
PY 2019
VL 10
AR 2141
DI 10.3389/fmicb.2019.02141
UT WOS:000485654200002
DA 2025-07-30
ER

PT J
AU Valdés, V
   Carlotti, F
   Escribano, R
   Donoso, K
   Pagano, M
   Molina, V
   Fernandez, C
AF Valdes, Valentina
   Carlotti, Francois
   Escribano, Ruben
   Donoso, Katty
   Pagano, Marc
   Molina, Veronica
   Fernandez, Camila
TI Nitrogen and phosphorus recycling mediated by copepods and response of
   bacterioplankton community from three contrasting areas in the western
   tropical South Pacific (20 °S)
SO BIOGEOSCIENCES
DT Article
AB Zooplankton play a key role in the regeneration of nitrogen and phosphorus in the ocean through grazing and metabolism. This study investigates the role of the organic and inorganic nitrogen and phosphorus compounds released by copepods on biogeochemical processes and on the microbial community composition during the OUTPACE cruise (18 February-3 April 2015) at three longduration stations (LD). Two LD stations were located in the Melanesian Archipelago region (MA; LD A and LD B) and one in the South Pacific Gyre (SG; LD C), which represent oligotrophic and ultra-oligotrophic regions respectively. At each station, on-board microcosm experiments were performed with locally sampled organisms, comprising a mix of epipelagic copepods fed with their natural food and then incubated along with wild microbial assemblages. In the presence of copepods, ammonium and dissolved organic nitrogen showed a significant increase compared to a control in two situations: in ammonium concentration (rate: 0.29 mu mol L-1 h(-1) after 4 h of incubation) in LD C and in dissolved organic nitrogen concentration (rate: 2.13 mu mol L-1 h(-1) after 0.5 h of incubation) in LD A. In addition, during the three experiments, an enhanced remineralization (ammonification and nitrification) was observed when adding copepods compared to the controls. A shift in the composition of the active bacterial community was observed for the experiments in LD A and LD B, which were mainly characterized by an increase in Alteromonadales and SAR11, respectively, and linked with changes in nutrient concentrations. In the experiment performed in LD C, both groups increased but at different periods of incubation. Alteromonadales increased between 1 and 2 h after the beginning of the experiment, and SAR 11 at the end of incubation. Our results in near in situ conditions show that copepods can be a source of organic and inorganic compounds for bacterial communities, which respond to excretion pulses at different timescales, depending on the initial environmental conditions and on their community composition. These processes can significantly contribute to nutrient recycling and regenerated production in the photic zone of ultra-oligotrophic and oligotrophic oceanic regions.
C1 [Valdes, Valentina] Univ Concepcion, Fac Ciencias Nat & Oceanog, Dept Oceanog, Programa Doctorado Oceanog, Concepcion, Chile.
   [Valdes, Valentina; Fernandez, Camila] UPMC Univ Paris 06, Sorbonne Univ, Lab Oceanog Microbienne LOMIC, Observ Oceanol Banyuls Mer, F-66650 Banyuls Sur Mer, France.
   [Carlotti, Francois; Donoso, Katty; Pagano, Marc] Univ Toulon & Var, Aix Marseille Univ, CNRS, IRD,OSU PYTHEAS,MIO,UM110, F-13288 Marseille 09, France.
   [Escribano, Ruben] Univ Concepcion, Dept Oceanog, Concepcion, Chile.
   [Escribano, Ruben] Univ Concepcion, Inst Milenio Oceanog, Concepcion, Chile.
   [Molina, Veronica] Univ Playa Ancha, Dept Biol, Fac Ciencias Nat & Exactas, Valparaiso, Chile.
   [Molina, Veronica] Univ Playa Ancha, Fac Ciencias Nat & Exactas, Programa Biodiversidad, Valparaiso, Chile.
   [Fernandez, Camila] Univ Concepcion, FONDAP INCAR Ctr 15110027, Concepcion, Chile.
   [Fernandez, Camila] Univ Concepcion, Dept Oceanog, COPAS Austral Program, PFB 31, Concepcion, Chile.
   [Fernandez, Camila] Ctr FONDAP, Invest Dinam Ecosistemas Marinos Altas Latitudes, Valdivia, Chile.
RP Valdés, V (corresponding author), Univ Concepcion, Fac Ciencias Nat & Oceanog, Dept Oceanog, Programa Doctorado Oceanog, Concepcion, Chile.; Valdés, V (corresponding author), UPMC Univ Paris 06, Sorbonne Univ, Lab Oceanog Microbienne LOMIC, Observ Oceanol Banyuls Mer, F-66650 Banyuls Sur Mer, France.
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NR 60
TC 13
Z9 13
PD OCT 15
PY 2018
VL 15
IS 20
BP 6019
EP 6032
DI 10.5194/bg-15-6019-2018
UT WOS:000447403800002
DA 2025-07-30
ER

PT J
AU Giebel, HA
   Arnosti, C
   Badewien, TH
   Bakenhus, I
   Balmonte, JP
   Billerbeck, S
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AF Giebel, Helge-Ansgar
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   Milke, Felix
   Voss, Daniela
   Wienhausen, Gerrit
   Wietz, Matthias
   Winkler, Holger
   Wolterink, Mathias
   Simon, Meinhard
TI Microbial Growth and Organic Matter Cycling in the Pacific Ocean Along a
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SO FRONTIERS IN MARINE SCIENCE
DT Article
AB The Pacific Ocean constitutes about half of the global oceans and thus microbial processes in this ocean have a large impact on global elemental cycles. Despite several intensely studied regions large areas are still greatly understudied regarding microbial activities, organic matter cycling and biogeography. Refined information about these features is most important to better understand the significance of this ocean for global biogeochemical and elemental cycles. Therefore we investigated a suite of microbial and geochemical variables along a transect from the subantarctic to the subarctic Pacific in the upper 200 m of the water column. The aim was to quantify rates of organic matter processing, identify potential controlling factors and prokaryotic key players. The assessed variables included abundance of heterotrophic prokaryotes and cyanobacteria, heterotrophic prokaryotic production (HPP), turnover rate constants of amino acids, glucose, and acetate, leucine aminopeptidase and beta-glucosidase activities, and the composition of the bacterial community by fluorescence in situ hybridization (FISH). The additional quantification of nitrate, dissolved amino acids and carbohydrates, chlorophyll a, particulate organic carbon and nitrogen (POC, PON) provided a rich environmental context. The oligotrophic gyres exhibited the lowest prokaryotic abundances, rates of HPP and substrate turnover. Low nucleic acid prokaryotes dominated in these gyres, whereas in temperate and subpolar regions further north and south, high nucleic acid prokaryotes dominated. Turnover rate constants of glucose and acetate, as well as leucine aminopeptidase activity, increased from (sub)tropical toward the subpolar regions. In contrast, HPP and bulk growth rates were highest near the equatorial upwelling and lowest in the central gyres and subpolar regions. The SAR11 clade, the Roseobacter group and Flavobacteria constituted the majority of the prokaryotic communities. Vertical profiles of the biogeochemical and microbial variables markedly differed among the different regions and showed close covariations of the microbial variables and chlorophyll a, POC and PON. The results show that hydrographic, microbial, and biogeochemical properties exhibited distinct patterns reflecting the biogeographic provinces along the transect. The microbial variables assessed contribute to a better and refined understanding of the scales of microbial organic matter processing in large areas of the epipelagic Pacific beyond its well-studied regions.
C1 [Giebel, Helge-Ansgar; Badewien, Thomas H.; Bakenhus, Insa; Billerbeck, Sara; Dlugosch, Leon; Henkel, Rohan; Kuerzel, Birgit; Meyerjuergens, Jens; Milke, Felix; Voss, Daniela; Wienhausen, Gerrit; Wietz, Matthias; Winkler, Holger; Wolterink, Mathias; Simon, Meinhard] Carl von Ossietzky Univ Oldenburg, Inst Chem & Biol Marine Environm, Oldenburg, Germany.
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   [Balmonte, John Paul] Univ Southern Denmark, Dept Biol, HADAL & NordCEE, Odense, Denmark.
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RP Simon, M (corresponding author), Carl von Ossietzky Univ Oldenburg, Inst Chem & Biol Marine Environm, Oldenburg, Germany.; Simon, M (corresponding author), Univ Oldenburg HIFMB, Helmholtz Inst Funct Marine Biodivers, Oldenburg, Germany.
EM m.simon@icbm.de
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NR 78
TC 10
Z9 10
PD DEC 13
PY 2021
VL 8
AR 764383
DI 10.3389/fmars.2021.764383
UT WOS:000735587400001
DA 2025-07-30
ER

PT J
AU Isaac, A
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB The complex interactions between bacterioplankton and phytoplankton have prompted numerous studies that investigate phytoplankton microbiomes with the aim of characterizing beneficial or opportunistic taxa and elucidating core bacterial members. Oftentimes, this knowledge is garnered through 16S rRNA gene profiling of microbiomes from phytoplankton isolated across spatial and temporal scales, yet these studies do not offer insight into microbiome assembly and structuring. In this study, we aimed to identify taxa central to structuring and establishing the microbiome of the ubiquitous diatom Asterionellopsis glacialis. We introduced a diverse environmental bacterial community to A. glacialis in nutrient-rich or nutrient-poor media in a continuous dilution culture setup and profiled the bacterial community over 7 days. 16S rRNA amplicon sequencing showed that cyanobacteria (Coleofasciculaceae) and Rhodobacteraceae dominate the microbiome early on and maintain a persistent association throughout the experiment. Differential abundance, co-abundance networks, and differential association analyses revealed that specific members of the family Rhodobacteraceae, particularly Sulfitobacter amplicon sequence variants, become integral members in microbiome assembly. In the presence of the diatom, Sulfitobacter species and other Rhodobacteraceae developed positive associations with taxa that are typically in high abundance in marine ecosystems (Pelagibacter and Synechococcus), leading to restructuring of the microbiome compared to diatom-free controls. These positive associations developed predominantly under oligotrophic conditions, highlighting the importance of investigating phytoplankton microbiomes in as close to natural conditions as possible to avoid biases that develop under routine laboratory conditions. These findings offer further insight into phytoplankton-bacteria interactions and illustrate the importance of Rhodobacteraceae, not merely as phytoplankton symbionts but as key taxa involved in microbiome assembly. IMPORTANCE Most, if not all, microeukaryotic organisms harbor an associated microbial community, termed the microbiome. The microscale interactions that occur between these partners have global-scale consequences, influencing marine primary productivity, carbon cycling, and harmful algal blooms to name but a few. Over the last decade, there has been a growing interest in the study of phytoplankton microbiomes, particularly within the context of bloom dynamics. However, long-standing questions remain regarding the process of phytoplankton microbiome assembly. The significance of our research is to tease apart the mechanism of microbiome assembly with a particular focus on identifying bacterial taxa, which may not merely be symbionts but architects of the phytoplankton microbiome. Our results strengthen the understanding of the ecological mechanisms that underpin phytoplankton-bacteria interactions in order to accurately predict marine ecosystem responses to environmental perturbations.
C1 [Isaac, Ashley; Mohamed, Amin R.; Amin, Shady A.] New York Univ Abu Dhabi, Biol Program, Marine Microbi Lab, Abu Dhabi, U Arab Emirates.
   [Isaac, Ashley] Max Planck Inst Marine Microbiol, Dept Mol Ecol, Bremen, Germany.
   [Amin, Shady A.] New York Univ Abu Dhabi, Ctr Genom & Syst Biol, Abu Dhabi, U Arab Emirates.
   [Amin, Shady A.] New York Univ Abu Dhabi, Mubadala ACCESS Ctr, Abu Dhabi, U Arab Emirates.
RP Amin, SA (corresponding author), New York Univ Abu Dhabi, Biol Program, Marine Microbi Lab, Abu Dhabi, U Arab Emirates.; Amin, SA (corresponding author), New York Univ Abu Dhabi, Ctr Genom & Syst Biol, Abu Dhabi, U Arab Emirates.; Amin, SA (corresponding author), New York Univ Abu Dhabi, Mubadala ACCESS Ctr, Abu Dhabi, U Arab Emirates.
EM samin@nyu.edu
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NR 99
TC 5
Z9 5
PD JUN 18
PY 2024
VL 90
IS 6
DI 10.1128/aem.00570-24
EA MAY 2024
UT WOS:001234672300004
DA 2025-07-30
ER

PT J
AU Wang, FQ
   Bartosik, D
   Sidhu, C
   Siebers, R
   Lu, DC
   Trautwein-Schult, A
   Becher, D
   Huettel, B
   Rick, J
   Kirstein, IV
   Wiltshire, KH
   Schweder, T
   Fuchs, BM
   Bengtsson, MM
   Teeling, H
   Amann, RI
AF Wang, Feng-Qing
   Bartosik, Daniel
   Sidhu, Chandni
   Siebers, Robin
   Lu, De-Chen
   Trautwein-Schult, Anke
   Becher, Doerte
   Huettel, Bruno
   Rick, Johannes
   Kirstein, Inga V.
   Wiltshire, Karen H.
   Schweder, Thomas
   Fuchs, Bernhard M.
   Bengtsson, Mia M.
   Teeling, Hanno
   Amann, Rudolf I.
TI Particle-attached bacteria act as gatekeepers in the decomposition of
   complex phytoplankton polysaccharides
SO MICROBIOME
DT Article
AB Background Marine microalgae (phytoplankton) mediate almost half of the worldwide photosynthetic carbon dioxide fixation and therefore play a pivotal role in global carbon cycling, most prominently during massive phytoplankton blooms. Phytoplankton biomass consists of considerable proportions of polysaccharides, substantial parts of which are rapidly remineralized by heterotrophic bacteria. We analyzed the diversity, activity, and functional potential of such polysaccharide-degrading bacteria in different size fractions during a diverse spring phytoplankton bloom at Helgoland Roads (southern North Sea) at high temporal resolution using microscopic, physicochemical, biodiversity, metagenome, and metaproteome analyses. Results Prominent active 0.2-3 mu m free-living clades comprised Aurantivirga, "Formosa", Cd. Prosiliicoccus, NS4, NS5, Amylibacter, Planktomarina, SAR11 Ia, SAR92, and SAR86, whereas BD1-7, Stappiaceae, Nitrincolaceae, Methylophagaceae, Sulfitobacter, NS9, Polaribacter, Lentimonas, CL500-3, Algibacter, and Glaciecola dominated 3-10 mu m and > 10 mu m particles. Particle-attached bacteria were more diverse and exhibited more dynamic adaptive shifts over time in terms of taxonomic composition and repertoires of encoded polysaccharide-targeting enzymes. In total, 305 species-level metagenome-assembled genomes were obtained, including 152 particle-attached bacteria, 100 of which were novel for the sampling site with 76 representing new species. Compared to free-living bacteria, they featured on average larger metagenome-assembled genomes with higher proportions of polysaccharide utilization loci. The latter were predicted to target a broader spectrum of polysaccharide substrates, ranging from readily soluble, simple structured storage polysaccharides (e.g., laminarin, alpha-glucans) to less soluble, complex structural, or secreted polysaccharides (e.g., xylans, cellulose, pectins). In particular, the potential to target poorly soluble or complex polysaccharides was more widespread among abundant and active particle-attached bacteria. Conclusions Particle-attached bacteria represented only 1% of all bloom-associated bacteria, yet our data suggest that many abundant active clades played a pivotal gatekeeping role in the solubilization and subsequent degradation of numerous important classes of algal glycans. The high diversity of polysaccharide niches among the most active particle-attached clades therefore is a determining factor for the proportion of algal polysaccharides that can be rapidly remineralized during generally short-lived phytoplankton bloom events.
C1 [Wang, Feng-Qing; Sidhu, Chandni; Lu, De-Chen; Fuchs, Bernhard M.; Teeling, Hanno; Amann, Rudolf I.] Max Planck Inst Marine Microbiol, Celsiusstr 1, D-28359 Bremen, Germany.
   [Bartosik, Daniel; Schweder, Thomas] Univ Greifswald, Inst Pharm, Felix Hausdorff Str 3, D-17489 Greifswald, Germany.
   [Bartosik, Daniel; Schweder, Thomas] Inst Marine Biotechnol, Walther Rathenau Str 49a, D-17489 Greifswald, Germany.
   [Siebers, Robin; Trautwein-Schult, Anke; Becher, Doerte; Bengtsson, Mia M.] Univ Greifswald, Inst Microbiol, Felix Hausdorff Str 8, D-17489 Greifswald, Germany.
   [Lu, De-Chen] Shandong Univ, Marine Coll, Weihai 264209, Peoples R China.
   [Huettel, Bruno] Max Planck Genome Ctr Cologne, Carl von Linne Weg 10, D-50829 Cologne, Germany.
   [Rick, Johannes; Kirstein, Inga V.; Wiltshire, Karen H.] Alfred Wegener Inst Polar & Marine Res, Biol Anstalt Helgoland, D-27483 Helgoland, Germany.
RP Teeling, H; Amann, RI (corresponding author), Max Planck Inst Marine Microbiol, Celsiusstr 1, D-28359 Bremen, Germany.; Bengtsson, MM (corresponding author), Univ Greifswald, Inst Microbiol, Felix Hausdorff Str 8, D-17489 Greifswald, Germany.
EM mia.bengtsson@uni-greifswald.de; hteeling@mpi-bremen.de;
   ramann@mpi-bremen.de
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NR 132
TC 29
Z9 29
PD FEB 20
PY 2024
VL 12
IS 1
AR 32
DI 10.1186/s40168-024-01757-5
UT WOS:001166748500002
HC Y
HP N
DA 2025-07-30
ER

PT J
AU Tarnecki, AM
   Levi, NJ
   Resley, M
   Main, K
AF Tarnecki, Andrea M.
   Levi, Noah J.
   Resley, Matthew
   Main, Kevan
TI Effect of copper sulfate on the external microbiota of adult common
   snook (Centropomus undecimalis)
SO ANIMAL MICROBIOME
DT Article
AB Background The environment exerts a strong influence on the fish external microbiota, with lower diversity and increased abundances of opportunistic bacterial groups characterizing cultured fish compared to their wild counterparts. Deviation from a healthy external microbiota structure has been associated with increased susceptibility to bacterial pathogens. Treatment of wild-caught broodstock with copper sulfate for the removal of external parasites is a common aquaculture practice. Despite the microbiota's importance to fish health, the effects of copper sulfate on mucosal bacterial communities and their ability to recover following this chemical treatment have not been examined. The skin microbiota of adult common snook was characterized from wild individuals (Wild), and wild-caught fish maintained in recirculating aquaculture systems (RAS) immediately following a month-long copper sulfate treatment (Captive-1), and then two-weeks (Captive-2) and 2 years (Captive-3) after cessation of copper treatment. Results The skin microbiota of wild fish were characterized by high diversity and taxa including Synechocococcus, SAR11, and a member of the Roseobacter clade. Bacterial diversity decreased in Captive individuals during the 2-year sampling period. Captive fish harbored greater abundances of Firmicutes, which may reflect glycan differences between aquaculture and natural feeds. Bacterial taxa with copper resistance mechanisms and indicative of metal contamination were enriched in Captive-1 and Captive-2 fish. Vibrionaceae were dominant in Captive fish, particularly immediately and 2 weeks following copper treatment. Based on our observations and previous literature, our results suggest putatively beneficial taxa amass over time in captivity. Within 2 years, Captive individuals harbored Bacillus which contains numerous probiotic candidates and the complex carbon degraders of the family Saprospiraceae. Predicted butanoate metabolism exceeded that of Wild fish, and its reported roles in immunity and energy provision suggest a prebiotic effect for fishes. Conclusions The mucosal microbiota contains bacterial taxa that may act as bioindicators of environmental pollution. Increases in mutualistic groups indicate a return to a beneficial skin microbiota following copper sulfate treatment. Our data also suggests that vastly different taxa, influenced by environmental conditions, can be associated with adult fish without noticeable health impairment, perhaps due to establishment of various mutualists to maintain fish mucosal health.
C1 [Tarnecki, Andrea M.] Mote Marine Lab, Marine Immunol Program, 1600 Ken Thompson Pkwy, Sarasota, FL 34236 USA.
   [Levi, Noah J.] Wabash Coll, Dept Biol, 301 West Wabash Ave, Crawfordsville, IN 47933 USA.
   [Levi, Noah J.] Univ Miami, Med Scientist Training Program, Miller Sch Med, 1600 NW 10th Ave, Miami, FL 33101 USA.
   [Resley, Matthew; Main, Kevan] Mote Aquaculture Res Pk, Directorate Fisheries & Aquaculture, 874 WR Mote Way, Sarasota, FL 34240 USA.
RP Tarnecki, AM (corresponding author), Mote Marine Lab, Marine Immunol Program, 1600 Ken Thompson Pkwy, Sarasota, FL 34236 USA.
EM atarnecki@mote.rg
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NR 79
TC 11
Z9 11
PD MAR 2
PY 2021
VL 3
IS 1
AR 21
DI 10.1186/s42523-021-00085-5
UT WOS:000704670300001
DA 2025-07-30
ER

PT J
AU Kim, SJ
   Kim, JG
   Lee, SH
   Park, SJ
   Gwak, JH
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AF Kim, So-Jeong
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   Hahn, Yoonsoo
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   Madsen, Eugene L.
   Rodriguez-Valera, Francisco
   Hyun, Jung-Ho
   Rhee, Sung-Keun
TI Genomic and metatranscriptomic analyses of carbon remineralization in an
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SO MICROBIOME
DT Article
AB Polynyas in the Southern Ocean are regions of intense primary production, mainly by Phaeocystis antarctica. Carbon fixed by phytoplankton in the water column is transferred to higher trophic levels, and finally, to the deep ocean. However, in the Amundsen Sea, most of this organic carbon does not reach the sediment but is degraded in the water column due to high bacterial heterotrophic activity.
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C1 [Kim, So-Jeong] Korea Inst Geosci & Mineral Resources, Geol Environm Res Div, Daejeon 34132, South Korea.
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RP Rhee, SK (corresponding author), Chungbuk Natl Univ, Dept Microbiol, Cheongju 28644, South Korea.
EM rhees@chungbuk.ac.kr
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NR 82
TC 13
Z9 13
PD FEB 20
PY 2019
VL 7
AR 29
DI 10.1186/s40168-019-0643-4
UT WOS:000459563300001
DA 2025-07-30
ER

PT J
AU Ding, CL
   Wu, C
   Guo, CC
   Gui, J
   Wei, YQ
   Sun, J
AF Ding, Changling
   Wu, Chao
   Guo, Congcong
   Gui, Jiang
   Wei, Yuqiu
   Sun, Jun
TI The Composition and Primary Metabolic Potential of Microbial Communities
   Inhabiting the Surface Water in the Equatorial Eastern Indian Ocean
SO BIOLOGY-BASEL
DT Article
AB Simple Summary
   Marine microbes are regarded as the most diverse organisms in the biosphere and drive biogeochemical cycles through their metabolism. It is essential to understand the structure and metabolic function of microbial communities. The Indian Ocean is the third largest ocean in the world, and it possesses unique hydrographical properties. So far, assessments of microbial diversity and metabolism need to be improved in the Indian Ocean. Therefore, we carried out a series of investigations in the equatorial eastern Indian Ocean in order to clarify the local microbial communities and detect the genetic potential for microbial functions. The obtained results suggested Cyanobacteria was the dominant microbial group, and predicted the Calvin cycle and the assimilatory nitrate and nitrite reduction played important role in the pathway of carbon fixation and nitrogen metabolism respectively. This study provides insights into microbial community structures as well as the metabolic potential that may be active in the local environment, and lays the groundwork for understanding the roles of microbes in energy and resource cycling in this habitat.
   Currently, there is scant information about the biodiversity and functional diversity of microbes in the eastern Indian Ocean (EIO). Here, we used a combination of high-throughput sequencing of 16S rRNA genes and a metagenomic approach to investigate the microbial population structure and its metabolic function in the equatorial EIO. Our results show that Cyanobacterial Prochlorococcus made up the majority of the population. Interestingly, there were fewer contributions from clades SAR11 (Alphaproteobacteria) and SAR86 (Gammaproteobacteria) to microbial communities than contributions from Prochlorococcus. Based on functional gene analysis, functional genes rbcL, narB, and nasA were relatively abundant among the relevant genes. The abundance of Prochlorococcus implies its typically ecological adaptation in the local ecosystem. The microbial metabolic potential shows that in addition to the main carbon fixation pathway Calvin cycle, the rTCA cycle and the 3-HP/4-HB cycle have potential alternative carbon fixation contributions to local ecosystems. For the nitrogen cycle, the assimilatory nitrate and nitrite reduction pathway is potentially the crucial form of nitrogen utilization; unexpectedly, nitrogen fixation activity was relatively weak. This study extends our knowledge of the roles of microbes in energy and resource cycling in the EIO and provides a foundation for revealing profound biogeochemical processes driven by the microbial community in the ocean.
C1 [Ding, Changling] Tianjin Univ Sci & Technol, Coll Biotechnol, Tianjin 300457, Peoples R China.
   [Ding, Changling; Wu, Chao; Guo, Congcong; Gui, Jiang; Wei, Yuqiu; Sun, Jun] Tianjin Univ Sci & Technol, Res Ctr Indian Ocean Ecosyst, Tianjin 300457, Peoples R China.
   [Guo, Congcong; Wei, Yuqiu] Shandong Univ, Inst Marine Sci & Technol, Qingdao 266237, Peoples R China.
   [Sun, Jun] China Univ Geosci Wuhan, Coll Marine Sci & Technol, Wuhan 430074, Peoples R China.
RP Sun, J (corresponding author), Tianjin Univ Sci & Technol, Res Ctr Indian Ocean Ecosyst, Tianjin 300457, Peoples R China.; Sun, J (corresponding author), China Univ Geosci Wuhan, Coll Marine Sci & Technol, Wuhan 430074, Peoples R China.
EM docean@mail.tust.edu.cn; wuchao@tust.edu.cn; smart_guo@mail.sdu.edu.cn;
   gui18825008@mail.tust.edu.cn; 201720544@mail.sdu.edu.cn;
   phytoplankton@163.com
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NR 72
TC 15
Z9 15
PD MAR
PY 2021
VL 10
IS 3
AR 248
DI 10.3390/biology10030248
UT WOS:000633323200001
DA 2025-07-30
ER

PT J
AU Johnston, AWB
   Todd, JD
   Curson, AR
   Lei, S
   Nikolaidou-Katsaridou, N
   Gelfand, MS
   Rodionov, DA
AF Johnston, Andrew W. B.
   Todd, Jonathan D.
   Curson, Andrew R.
   Lei, Sun
   Nikolaidou-Katsaridou, Nefeli
   Gelfand, Mikhail S.
   Rodionov, Dmitry A.
TI Living without Fur:: the subtlety and complexity of iron-responsive gene
   regulation in the symbiotic bacterium Rhizobium and other
   α-proteobacteria
SO BIOMETALS
DT Article; Proceedings Paper
CT 5th International Biometals Symposium (Biometals 2006)
CY JUL 30-AUG 06, 2006
CL Welches, OR
AB The alpha-proteobacteria include several important genera, including the symbiotic N-2-fixing "rhizobia", the plant pathogen Agrobacterium, the mammalian pathogens Brucella, Bartonella as well as many others that are of environmental or other interest-including Rhodobacter, Caulobacter and the hugely abundant marine genus Pelagibacter. Only a few species-mainly different members of the rhizobia-have been analyzed directly for their ability to use and to respond to iron. These studies, however, have shown that at least some of the "alphas" differ fundamentally in the ways in which they regulate their genes in response to Fe availability. In this paper, we build on our own work on Rhizobium leguminosarum (the symbiont of peas, beans and clovers) and on Bradyrhizobium japonicum, which nodulates soybeans and which has been studied in Buffalo and Zurich. In the former species, the predominant Fe-responsive regulator is not Fur, but RirA, a member of the Rrf2 protein family and which likely has an FeS cluster cofactor. In addition, there are several R. leguminosarum genes that are expressed at higher levels in Fe-replete conditions and at least some of these are regulated by Irr, a member of the Fur superfamily and which has the unusual property of being degraded by the presence of heme. In silico analyses of the genome sequences of other bacteria indicate that Irr occurs in all members of the Rhizobiales and the Rhodobacterales and that RirA is found in all but one branch of these two lineages, the exception being the clade that includes B. japonicum. Nearly all the Rhizobiales and the Rhodobacterales contain a gene whose product resembles bona fide Fur. However, direct genetic studies show that in most of the Rhizobiales and in the Rhodobacterales it is a "Mur" (a manganese responsive repressor of a small number of genes involved in Mn uptake) or, in Bradyrhizobium, it recognizes the operator sequences of only a few genes that are involved in Fe metabolism. We propose that the Rhizobiales and the Rhodobacterales have relegated Fur to a far more minor role than in (say) E. coli and that they employ Irr and, in the Rhizobiales, RirA as their global Fe-responsive transcriptional regulators. In contrast to the direct interaction between Fe2+ and conventional Fur, we suggest that these bacteria sense Fe more indirectly as functions of the intracellular concentrations of FeS clusters and of heme. Thus, their "iron-omes" may be more accurately linked to the real-time needs for the metal and not just to its absolute concentration in the environment.
C1 Univ E Anglia, Sch Biol Sci, Norwich NR4 7TJ, Norfolk, England.
   Russian Acad Sci, Inst Informat Transmiss Problems, Moscow 127994, Russia.
   Moscow MV Lomonosov State Univ, Dept Bioengn & Bioinformat, Moscow 119992, Russia.
   Burnham Inst Med Res, La Jolla, CA 92037 USA.
RP Johnston, AWB (corresponding author), Univ E Anglia, Sch Biol Sci, Norwich NR4 7TJ, Norfolk, England.
EM a.johnston@uea.ac.uk
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NR 37
TC 80
Z9 101
PD JUN
PY 2007
VL 20
IS 3-4
BP 501
EP 511
DI 10.1007/s10534-007-9085-8
UT WOS:000246610700022
DA 2025-07-30
ER

PT J
AU Cifuentes-Anticevic, J
   Alcamán-Arias, ME
   Alarcón-Schumacher, T
   Tamayo-Leiva, J
   Pedrós-Alió, C
   Farías, L
   Díez, B
AF Cifuentes-Anticevic, Jeronimo
   Alcaman-Arias, Maria E.
   Alarcon-Schumacher, Tomas
   Tamayo-Leiva, Javier
   Pedros-Alio, Carlos
   Farias, Laura
   Diez, Beatriz
TI Proteorhodopsin Phototrophy in Antarctic Coastal Waters
SO MSPHERE
DT Article
AB Microbial proton-pumping rhodopsins are considered the simplest strategy among phototrophs to conserve energy from light. Proteorhodopsins are the most studied rhodopsins thus far because of their ubiquitous presence in the ocean, except in Antarctica, where they remain understudied. We analyzed proteorhodopsin abundance and transcriptional activity in the Western Antarctic coastal seawaters. Combining quantitative PCR (qPCR) and metagenomics, the relative abundance of proteorhodopsin-bearing bacteria accounted on average for 17, 3.5, and 29.7% of the bacterial community in Chile Bay (South Shetland Islands) during 2014, 2016, and 2017 summer-autumn, respectively. The abundance of proteorhodopsin-bearing bacteria changed in relation to environmental conditions such as chlorophyll a and temperature. Alphaproteobacteria, Gammaproteobacteria, and Flavobacteriia were the main bacteria that transcribed the proteorhodopsin gene during day and night. Although green light-absorbing proteorhodopsin genes were more abundant than blue-absorbing ones, the latter were transcribed more intensely, resulting in .50% of the proteorhodopsin transcripts during the day and night. Flavobacteriia were the most abundant proteorhodopsin-bearing bacteria in the metagenomes; however, Alphaproteobacteria and Gammaproteobacteria were more represented in the metatranscriptomes, with qPCR quantification suggesting the dominance of the active SAR11 clade. Our results show that proteorhodopsin-bearing bacteria are prevalent in Antarctic coastal waters in late austral summer and early autumn, and their ecological relevance needs to be elucidated to better understand how sunlight energy is used in this marine ecosystem.
   IMPORTANCE Proteorhodopsin-bearing microorganisms in the Southern Ocean have been overlooked since their discovery in 2000. The present study identify taxonomy and quantify the relative abundance of proteorhodopsin-bearing bacteria and proteorhodopsin gene transcription in the West Antarctic Peninsula's coastal waters. This information is crucial to understand better how sunlight enters this marine environment through alternative ways unrelated to chlorophyll-based strategies. The relative abundance of proteorhodopsin-bearing bacteria seems to be related to environmental parameters (e.g., chlorophyll a, temperature) that change yearly at the coastal water of the West Antarctic Peninsula during the austral late summers and early autumns. Proteorhodopsin-bearing bacteria from Antarctic coastal waters are potentially able to exploit both the green and blue spectrum of sunlight and are a prevalent group during the summer in this polar environment.
C1 [Cifuentes-Anticevic, Jeronimo; Tamayo-Leiva, Javier; Diez, Beatriz] Pontificia Univ Catolica Chile, Dept Mol Genet & Microbiol, Santiago, Chile.
   [Alcaman-Arias, Maria E.; Farias, Laura] Univ Concepcion, Dept Oceanog, Concepcion, Chile.
   [Alcaman-Arias, Maria E.; Farias, Laura; Diez, Beatriz] Ctr Climate & Resilience Res CR 2, Santiago, Chile.
   [Alcaman-Arias, Maria E.] Univ Espiritu Santo, Escuela Med, Samborondon, Ecuador.
   [Alarcon-Schumacher, Tomas] Max Planck Inst Marine Microbiol, Bremen, Germany.
   [Pedros-Alio, Carlos] Ctr Nacl Biotecnol CSIC, Dept Biol Sistemas, Madrid, Spain.
   [Diez, Beatriz] Ctr Genome Regulat CRG, Santiago, Chile.
RP Díez, B (corresponding author), Pontificia Univ Catolica Chile, Dept Mol Genet & Microbiol, Santiago, Chile.; Díez, B (corresponding author), Ctr Climate & Resilience Res CR 2, Santiago, Chile.; Díez, B (corresponding author), Ctr Genome Regulat CRG, Santiago, Chile.
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NR 83
TC 3
Z9 4
PD JUL-AUG
PY 2021
VL 6
IS 4
AR e00525-21
DI 10.1128/mSphere.00525-21
UT WOS:000753900100005
DA 2025-07-30
ER

PT J
AU Fuchsman, CA
   Devol, AH
   Saunders, JK
   McKay, C
   Rocap, G
AF Fuchsman, Clara A.
   Devol, Allan H.
   Saunders, Jaclyn K.
   McKay, Cedar
   Rocap, Gabrielle
TI Niche Partitioning of the N Cycling Microbial Community of an Offshore
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SO FRONTIERS IN MICROBIOLOGY
DT Article
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C1 [Fuchsman, Clara A.; Devol, Allan H.; Saunders, Jaclyn K.; McKay, Cedar; Rocap, Gabrielle] Univ Washington, Sch Oceanog, Seattle, WA 98195 USA.
RP Fuchsman, CA; Rocap, G (corresponding author), Univ Washington, Sch Oceanog, Seattle, WA 98195 USA.
EM cfuchsm1@u.washington.edu; rocap@u.washington.edu
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NR 85
TC 66
Z9 70
PD DEC 5
PY 2017
VL 8
AR 2384
DI 10.3389/fmicb.2017.02384
UT WOS:000417045800001
DA 2025-07-30
ER

PT J
AU Patin, NV
   Goodwin, KD
AF Patin, N. V.
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TI Long-Read Sequencing Improves Recovery of Picoeukaryotic Genomes and
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SO MSYSTEMS
DT Article
AB Ocean microbes provide critical ecosystem services, but most remain uncultivated. Their communities can be studied through shotgun metagenomic sequencing and bioinformatic analyses, including binning draft microbial genomes.
   Long-read sequencing offers the potential to improve metagenome assemblies and provide more robust assessments of microbial community composition and function than short-read sequencing. We applied Pacific Biosciences (PacBio) CCS (circular consensus sequencing) HiFi shotgun sequencing to 14 marine water column samples and compared the results with those for short-read metagenomes from the corresponding environmental DNA samples. We found that long-read metagenomes varied widely in quality and biological information. The community compositions of the corresponding long- and short-read metagenomes were frequently dissimilar, suggesting higher stochasticity and/or bias associated with PacBio sequencing. Long reads provided few improvements to the assembly qualities, gene annotations, and prokaryotic metagenome-assembled genome (MAG) binning results. However, only long reads produced high-quality eukaryotic MAGs and contigs containing complete zooplankton marker gene sequences. These results suggest that high-quality long-read metagenomes can improve marine community composition analyses and provide important insight into eukaryotic phyto- and zooplankton genetics, but the benefits may be outweighed by the inconsistent data quality.IMPORTANCE Ocean microbes provide critical ecosystem services, but most remain uncultivated. Their communities can be studied through shotgun metagenomic sequencing and bioinformatic analyses, including binning draft microbial genomes. However, most sequencing to date has been done using short-read technology, which rarely yields genome sequences of key microbes like SAR11. Long-read sequencing can improve metagenome assemblies but is hampered by technological shortcomings and high costs. In this study, we compared long- and short-read sequencing of marine metagenomes. We found a wide range of long-read metagenome qualities and minimal improvements to microbiome analyses. However, long reads generated draft genomes of eukaryotic algal species and provided full-length marker gene sequences of zooplankton species, including krill and copepods. These results suggest that long-read sequencing can provide greater genetic insight into the wide diversity of eukaryotic phyto- and zooplankton that interact as part of and with the marine microbiome.
C1 [Patin, N. V.; Goodwin, K. D.] NOAA, Ocean Chem & Ecosyst Div, Atlantic Oceanog & Meteorol Lab, Miami, FL 33149 USA.
   [Patin, N. V.] Univ Miami, Cooperat Inst Marine & Atmospher Studies, Rosenstiel Sch Marine Atmospher & Earth Sci, Miami, FL 33149 USA.
   [Patin, N. V.; Goodwin, K. D.] NOAA, Southwest Fisheries Sci Ctr, Natl Marine Fisheries Serv, La Jolla, CA 92037 USA.
RP Patin, NV (corresponding author), NOAA, Ocean Chem & Ecosyst Div, Atlantic Oceanog & Meteorol Lab, Miami, FL 33149 USA.; Patin, NV (corresponding author), Univ Miami, Cooperat Inst Marine & Atmospher Studies, Rosenstiel Sch Marine Atmospher & Earth Sci, Miami, FL 33149 USA.; Patin, NV (corresponding author), NOAA, Southwest Fisheries Sci Ctr, Natl Marine Fisheries Serv, La Jolla, CA 92037 USA.
EM nastassia.patin@noaa.gov
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DA 2025-07-30
ER

PT J
AU Silva, BSD
   Coutinho, FH
   Gregoracci, GB
   Leomil, L
   de Oliveira, LS
   Fróes, A
   Tschoeke, D
   Soares, AC
   Cabral, AS
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   Krusche, AV
   Yager, PL
   de Rezende, CE
   Thompson, CC
   Thompson, FL
AF Silva, Bruno S. de O.
   Coutinho, Felipe H.
   Gregoracci, Gustavo B.
   Leomil, Luciana
   de Oliveira, Louisi S.
   Froes, Adriana
   Tschoeke, Diogo
   Soares, Ana Carolina
   Cabral, Anderson S.
   Ward, Nicholas D.
   Richey, Jeffrey E.
   Krusche, Alex V.
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   de Rezende, Carlos Eduardo
   Thompson, Cristiane C.
   Thompson, Fabiano L.
TI Virioplankton Assemblage Structure in the Lower River and Ocean
   Continuum of the Amazon
SO MSPHERE
DT Article
AB The Amazon River watershed and its associated plume comprise a vast continental and oceanic area. The microbial activities along this continuum contribute substantially to global carbon and nutrient cycling, and yet there is a dearth of information on the diversity, abundance, and possible roles of viruses in this globally important river. The aim of this study was to elucidate the diversity and structure of virus assemblages of the Amazon River-ocean continuum. Environmental viral DNA sequences were obtained for 12 locations along the river's lower reach (n = 5) and plume (n = 7). Sequence assembly yielded 29,358 scaffolds, encoding 82,546 viral proteins, with 15 new complete viral genomes. Despite the spatial connectivity mediated by the river, virome analyses and physical-chemical water parameters clearly distinguished river and plume ecosystems. Bacteriophages were ubiquitous in the continuum and were more abundant in the transition region. Eukaryotic viruses occurred mostly in the river, while the plume had more viruses of autotrophic organisms (Prochlorococcus, Synechococcus) and heterotrophic bacteria (Pelagibacter). The viral families Microviridae and Myoviridae were the most abundant and occurred throughout the continuum. The major functions of the genes in the continuum involved viral structures and life cycles, and viruses from plume locations and Tapajos River showed the highest levels of functional diversity. The distribution patterns of the viral assemblages were defined not only by the occurrence of possible hosts but also by water physical and chemical parameters, especially salinity. The findings presented here help to improve understanding of the possible roles of viruses in the organic matter cycle along the river-ocean continuum.
   IMPORTANCE The Amazon River forms a vast plume in the Atlantic Ocean that can extend for more than 1,000 km. Microbial communities promote a globally relevant carbon sink system in the plume. Despite the importance of viruses for the global carbon cycle, the diversity and the possible roles of viruses in the Amazon are poorly understood. The present work assesses, for the first time, the abundance and diversity of viruses simultaneously in the river and ocean in order to elucidate their possible roles. DNA sequence assembly yielded 29,358 scaffolds, encoding 82,546 viral proteins, with 15 new complete viral genomes from the 12 river and ocean locations. Viral diversity was clearly distinguished by river and ocean. Bacteriophages were the most abundant and occurred throughout the continuum. Viruses that infect eukaryotes were more abundant in the river, whereas phages appeared to have strong control over the host prokaryotic populations in the plume.
C1 [Silva, Bruno S. de O.; Coutinho, Felipe H.; Leomil, Luciana; de Oliveira, Louisi S.; Froes, Adriana; Tschoeke, Diogo; Soares, Ana Carolina; Thompson, Cristiane C.; Thompson, Fabiano L.] Fed Univ Rio de Janeiro UFRJ, Inst Biol, Lab Microbiol, Rio De Janeiro, RJ, Brazil.
   [Leomil, Luciana; de Oliveira, Louisi S.; Froes, Adriana; Tschoeke, Diogo; Thompson, Cristiane C.; Thompson, Fabiano L.] Fed Univ Rio de Janeiro UFRJ, COPPE Technol Management Ctr CT2, Lab Adv Prod Management Syst SAGE, Rio De Janeiro, RJ, Brazil.
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RP Thompson, FL (corresponding author), Fed Univ Rio de Janeiro UFRJ, Inst Biol, Lab Microbiol, Rio De Janeiro, RJ, Brazil.; Thompson, FL (corresponding author), Fed Univ Rio de Janeiro UFRJ, COPPE Technol Management Ctr CT2, Lab Adv Prod Management Syst SAGE, Rio De Janeiro, RJ, Brazil.
EM fabianothompson1@gmail.com
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PT J
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   Chen, HH
AF Pan, Ying
   Tao, Ye
   Yang, Xian
   Du, Siyi
   Ding, Hongguang
   Li, Jiaxin
   Jia, Hanwen
   Chen, Huaihai
TI Underlying mechanisms of spatial distribution of prokaryotic community
   in surface seawater from Arctic Ocean to the Sea of Japan
SO MICROBIOLOGY SPECTRUM
DT Article
AB Microorganisms play critical roles in marine ecosystems, so understanding the factors shaping microbial communities across various oceanic regions is essential for predicting ecosystem resilience and biogeochemical cycles. This study investigated the marine prokaryotic communities across 22 stations spanning the Arctic Ocean, the Chukchi Sea, the Bering Sea, and the Sea of Japan, with an emphasis on how environmental factors shape these communities. Results showed that the microbial alpha diversity generally declines with increasing latitude, though Arctic Ocean stations exhibited higher Chao 1 indices compared to the Bering Sea. Beta diversity analyses revealed that temperature and salinity were key factors associated with community composition variation across latitudes. Proteobacteria and Cyanobacteria were the dominant phyla showing opposite distribution trends across sampling stations. Cold-adapted oligotrophs such as Planktomarina and the SAR11 clade thrived in Arctic waters, while Sphingomonas, known for pollutant degradation, was more abundant in the Sea of Japan. Temperature was positively correlated to the relative abundance of Sphingomonas. At broad spatial scales, stochastic processes dominated community assembly of microbial phylogenetic diversity, while in specific regions like the Arctic Ocean, deterministic homogeneous selection appeared to shape microbial communities; and temperature showed a pronounced influence on phylogenetic turnover across all samples. Co-occurrence networks identified several key taxa, such as Polaribacter_1, Candidatus_Aquiluna, and NS5_marine_group. Overall, the study underscores temperature's role in shaping microbial community diversity, composition, and assembly processes across latitudinal gradients, highlighting unique community adaptations to extreme environments.IMPORTANCEMicrobes are the invisible engines of ocean health, recycling nutrients and sustaining marine life. This research helps us understand how climate factors like temperature shape these microscopic communities, which differ starkly between icy Arctic waters and warmer seas. As oceans warm due to climate change, microbial populations and their critical roles in cleaning pollutants or supporting food webs could shift dramatically. The study suggests Arctic microbes are uniquely adapted to cold, low-nutrient conditions, making them vulnerable to warming. By linking temperature to microbial diversity, this work provides clues to predict how marine ecosystems might respond to climate shifts, informing efforts to protect ocean biodiversity and processes vital to Earth's carbon and nutrient cycles.
C1 [Pan, Ying; Tao, Ye; Yang, Xian; Du, Siyi; Ding, Hongguang; Li, Jiaxin; Jia, Hanwen; Chen, Huaihai] Sun Yat Sen Univ, Sch Ecol, State Key Lab Biocontrol, Shenzhen Campus, Shenzhen, Guangdong, Peoples R China.
RP Chen, HH (corresponding author), Sun Yat Sen Univ, Sch Ecol, State Key Lab Biocontrol, Shenzhen Campus, Shenzhen, Guangdong, Peoples R China.
EM chenhh68@mail.sysu.edu.cn
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NR 60
TC 0
Z9 0
PD JUL 1
PY 2025
VL 13
IS 7
DI 10.1128/spectrum.00517-25
EA MAY 2025
UT WOS:001499026800001
DA 2025-07-30
ER

PT J
AU Tominaga, K
   Ogawa-Haruki, N
   Nishimura, Y
   Watai, H
   Yamamoto, K
   Ogata, H
   Yoshida, T
AF Tominaga, Kento
   Ogawa-Haruki, Nana
   Nishimura, Yosuke
   Watai, Hiroyasu
   Yamamoto, Keigo
   Ogata, Hiroyuki
   Yoshida, Takashi
TI Prevalence of Viral Frequency-Dependent Infection in Coastal Marine
   Prokaryotes Revealed Using Monthly Time Series Virome Analysis
SO MSYSTEMS
DT Article
AB There is little room for doubt that viral infection is prevalent among abundant marine prokaryotes regardless of their taxa or growth strategy. However, comprehensive evaluations of viral infections in natural prokaryotic communities are still technically difficult.
   Viruses infecting marine prokaryotes have a large impact on the diversity and dynamics of their hosts. Model systems suggest that viral infection is frequency dependent and constrained by the virus-host encounter rate. However, it is unclear whether frequency-dependent infection is pervasive among the abundant prokaryotic populations with different temporal dynamics. To address this question, we performed a comparison of prokaryotic and viral communities using 16S rRNA amplicon and virome sequencing based on samples collected monthly for 2 years at a Japanese coastal site, Osaka Bay. Concurrent seasonal shifts observed in prokaryotic and viral community dynamics indicated that the abundance of viruses correlated with that of their predicted host phyla (or classes). Cooccurrence network analysis between abundant prokaryotes and viruses revealed 6,423 cooccurring pairs, suggesting a tight coupling of host and viral abundances and their "one-to-many" correspondence. Although stable dominant species, such as SAR11, showed few cooccurring viruses, a fast succession of their viruses suggests that viruses infecting these populations changed continuously. Our results suggest that frequency-dependent viral infection prevails in coastal marine prokaryotes regardless of host taxa and temporal dynamics.IMPORTANCE There is little room for doubt that viral infection is prevalent among abundant marine prokaryotes regardless of their taxa or growth strategy. However, comprehensive evaluations of viral infections in natural prokaryotic communities are still technically difficult. In this study, we examined viral infection in abundant prokaryotes by monitoring the monthly dynamics of prokaryotic and viral communities at a eutrophic coastal site, Osaka Bay. We compared the community dynamics of viruses with those of their putative hosts based on genome-based in silico host prediction. We observed frequent cooccurrence among the predicted virus-host pairs, suggesting that viral infection is prevalent in abundant prokaryotes regardless of their taxa or temporal dynamics. This likely indicates that frequent lysis of the abundant prokaryotes via viral infection has a considerable contribution to the biogeochemical cycling and maintenance of prokaryotic community diversity.
C1 [Tominaga, Kento; Ogawa-Haruki, Nana; Watai, Hiroyasu; Yoshida, Takashi] Kyoto Univ, Grad Sch Agr, Kyoto, Japan.
   [Tominaga, Kento] Univ Tokyo, Grad Sch Frontier Sci, Tokyo, Japan.
   [Nishimura, Yosuke] Japan Agcy Marine Earth Sci & Technol JAMSTEC, Yokosuka, Kanagawa, Japan.
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   [Ogata, Hiroyuki] Kyoto Univ, Inst Chem Res, Kyoto, Japan.
RP Yoshida, T (corresponding author), Kyoto Univ, Grad Sch Agr, Kyoto, Japan.; Ogata, H (corresponding author), Kyoto Univ, Inst Chem Res, Kyoto, Japan.
EM ogata@kuicr.kyoto-u.ac.jp; yoshida.takashi.7a@kyoto-u.ac.jp
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NR 103
TC 7
Z9 7
PD FEB 23
PY 2023
VL 8
IS 1
DI 10.1128/msystems.00931-22
EA FEB 2023
UT WOS:000924096900001
DA 2025-07-30
ER

PT J
AU Joglar, V
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AF Joglar, Vanessa
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TI Microbial Plankton Community Structure and Function Responses to Vitamin
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB B vitamins are essential cofactors for practically all living organisms on Earth and are produced by a selection of microorganisms. An imbalance between high demand and limited production, in concert with abiotic processes, may explain the low availability of these vitamins in marine systems. Natural microbial communities from surface shelf water in the productive area off northwestern Spain were enclosed in mesocosms in winter, spring, and summer 2016. In order to explore the impact of B-vitamin availability on microbial community composition (16S and 18S rRNA gene sequence analysis) and bacterial function (metatranscriptomics analysis) in different seasons, enrichment experiments were conducted with seawater from the mesocosms. Our findings revealed that significant increases in phytoplankton or prokaryote biomass associated with vitamin B-12 and/or B-1 amendments were not accompanied by significant changes in community composition, suggesting that most of the microbial taxa benefited from the external B-vitamin supply. Metatranscriptome analysis suggested that many bacteria were potential consumers of vitamins B-12 and B-1, although the relative abundance of reads related to synthesis was ca. 3.6-fold higher than that related to uptake. Alteromonadales and Oceanospirillales accounted for important portions of vitamin B-1 and B-12 synthesis gene transcription, despite accounting for only minor portions of the bacterial community. Flavobacteriales appeared to be involved mostly in vitamin B-12 and B-1 uptake, and Pelagibacterales expressed genes involved in vitamin B-1 uptake. Interestingly, the relative expression of vitamin B-12 and B-1 synthesis genes among bacteria strongly increased upon inorganic nutrient amendment. Collectively, these findings suggest that upwelling events intermittently occurring during spring and summer in productive ecosystems may ensure an adequate production of these cofactors to sustain high levels of phytoplankton growth and biomass.
   IMPORTANCE B vitamins are essential growth factors for practically all living organisms on Earth that are produced by a selection of microorganisms. An imbalance between high demand and limited production may explain the low concentration of these compounds in marine systems. In order to explore the impact of B-vitamin availability on bacteria and algae in the coastal waters off northwestern Spain, six experiments were conducted with natural surface water enclosed in winter, spring, and summer. Our findings revealed that increases in phytoplankton or bacterial growth associated with B-12 and/or B-1 amendments were not accompanied by significant changes in community composition, suggesting that most microorganisms benefited from the B-vitamin supply. Our analyses confirmed the role of many bacteria as consumers of vitamins B-12 and B-1, although the relative abundance of genes related to synthesis was ca. 3.6-fold higher than that related to uptake. Interestingly, prokaryote expression of B-12 and B-1 synthesis genes strongly increased when inorganic nutrients were added. Collectively, these findings suggest that upwelling of cold and nutrient-rich waters occurring during spring and summer in this coastal area may ensure an adequate production of B vitamins to sustain high levels of algae growth and biomass.
C1 [Joglar, Vanessa; Martinez-Garcia, Sandra; Fuentes-Lema, Antonio; Perez-Lorenzo, Maria; Fernandez, Emilio; Teira, Eva] Univ Vigo, Ctr Invest Marina Univ Vigo, Dept Ecol & Biol Anim, Vigo, Spain.
   [Pontiller, Benjamin; Lundin, Daniel; Pinhassi, Jarone] Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, Kalmar, Sweden.
   [Pontiller, Benjamin] GEOMAR Helmholtz Ctr Ocean Res, Kiel, Germany.
RP Joglar, V (corresponding author), Univ Vigo, Ctr Invest Marina Univ Vigo, Dept Ecol & Biol Anim, Vigo, Spain.
EM vjoglar@uvigo.es
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NR 103
TC 16
Z9 19
PD NOV
PY 2021
VL 87
IS 22
AR e01525-21
DI 10.1128/AEM.01525-21
UT WOS:000713169300021
DA 2025-07-30
ER

PT J
AU Fecskeová, LK
   Piwosz, K
   Santic, D
   Sestanovic, S
   Tomas, AV
   Hanusová, M
   Solic, M
   Koblízek, M
AF Fecskeova, Livia K.
   Piwosz, Kasia
   Santic, Danijela
   Sestanovic, Stefanija
   Tomas, Ana Vrdoljak
   Hanusova, Martina
   Solic, Mladen
   Koblizek, Michal
TI Lineage-Specific Growth Curves Document Large Differences in Response of
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SO MSYSTEMS
DT Article
AB Marine bacterioplankton represent a diverse assembly of species differing largely in their abundance, physiology, metabolic activity, and role in microbial food webs. To analyze their sensitivity to bottom-up and top-down controls, we performed a manipulation experiment where grazers were removed, with or without the addition of phosphate. Using amplicon-reads normalization by internal standard (ARNIS), we reconstructed growth curves for almost 300 individual phylotypes. Grazer removal caused a rapid growth of most bacterial groups, which grew at rates of 0.6 to 3.5 day(-1), with the highest rates (>4 day(-1)) recorded among Rhodobacteraceae, Oceanospirillales, Alteromonadaceae, and Arcobacteraceae. Based on their growth response, the phylotypes were divided into three basic groups. Most of the phylotypes responded positively to both grazer removal as well as phosphate addition. The second group (containing, e.g., Rhodobacterales and Rhizobiales) responded to the grazer removal but not to the phosphate addition. Finally, some clades, such as SAR11 and Flavobacteriaceae, responded only to phosphate amendment but not to grazer removal. Our results show large differences in bacterial responses to experimental manipulations at the phylotype level and document different life strategies of marine bacterioplankton. In addition, growth curves of 130 phylogroups of aerobic anoxygenic phototrophs were reconstructed based on changes of the functional pufM gene. The use of functional genes together with rRNA genes may significantly expand the scientific potential of the ARNIS technique.
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C1 [Fecskeova, Livia K.; Piwosz, Kasia; Hanusova, Martina; Koblizek, Michal] Czech Acad Sci, Ctr Algatech, Inst Microbiol, Trebon, Czech Republic.
   [Piwosz, Kasia] Natl Marine Fisheries Res Inst, Gdynia, Poland.
   [Santic, Danijela; Sestanovic, Stefanija; Tomas, Ana Vrdoljak; Solic, Mladen] Inst Oceanog & Fisheries, Lab Marine Microbiol, Split, Croatia.
RP Koblízek, M (corresponding author), Czech Acad Sci, Ctr Algatech, Inst Microbiol, Trebon, Czech Republic.
EM koblizek@alga.cz
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NR 70
TC 16
Z9 17
PD SEP-OCT
PY 2021
VL 6
IS 5
AR e00934-21
DI 10.1128/mSystems.00934-21
UT WOS:000711939400014
DA 2025-07-30
ER

PT J
AU Zhang, SW
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TI Community Dynamics of Free-Living and Particle-Attached Bacteria over
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Shifts in the bacterioplankton community composition during phytoplankton blooms have been studied extensively; however, investigations on protozoan blooms are rare. This study first evaluated the impact of perturbations caused by sequential protozoan blooms of the heterotrophic dinoflagellate Noctiluca scintillans and the mixotrophic ciliate Mesodinium rubrum on the structuring of these two bacterial communities.
   During a series of blooms of Noctiluca scintillans and Mesodinium rubrum, we applied high-throughput sequencing of the 16S rRNA gene to investigate the population dynamics of free-living (FL) and particle-attached (PA) bacteria in an attempt to evaluate the influence of protozoan bloom-induced disturbances on the structuring of these two communities. Our findings revealed that the FL and PA bacterial community compositions (BCCs) displayed distinct profiles during sequential blooms, and the PA flora responded more dynamically to these pulse perturbations. The dominant bacterial groups (e.g., Flavobacteriaceae, Rhodobacteraceae, Vibrionaceae, and SAR11 subclade I) in these two communities displayed different levels of connectivity with the bloom-causative species and environmental factors. In addition, more FL bacterial groups were associated with M. rubrum, while more PA bacterial groups were related to N. scintillans. Potential endocytic bacteria of N. scintillans, particularly Vibrionaceae and Rickettsiaceae, opportunistically thrived at the peak of the bloom, suggesting that they could be important players influencing the dynamics and biogeochemical cycling of the blooms. Overall, disparities in the substrate preferences and thermal niches of various bacterial taxa as well as the short duration of the blooms (1 to 3 days) contributed to the diverse responses of the FL and PA bacterial communities to these protozoan blooms. Our research provides insight into the responses of FL and PA bacterial communities to blooms caused by protozoa like N. scintillans and M. rubrum and highlights the ecological significance of certain keystone bacterial groups during this kind of cosmopolitan protozoan bloom. IMPORTANCE Shifts in the bacterioplankton community composition during phytoplankton blooms have been studied extensively; however, investigations on protozoan blooms are rare. This study first evaluated the impact of perturbations caused by sequential protozoan blooms of the heterotrophic dinoflagellate Noctiluca scintillans and the mixotrophic ciliate Mesodinium rubrum on the structuring of these two bacterial communities. Our findings shed light on the responses of these two bacterial communities to such cosmopolitan protozoan blooms and highlight the possible ecological significance of certain keystone bacterial groups during these blooms. This research prepares the way for more focused studies that will help in understanding the roles that bacteria play during protozoan blooms and their impact on environmental health.
C1 [Zhang, Shuwen] South China Normal Univ, Sch Life Sci, Guangzhou Key Lab Subtrop Biodivers & Biomonitori, Guangdong Prov Key Lab Hlth & Safe Aquaculture, Guangzhou, Peoples R China.
   [Liu, Hongbin] Hong Kong Univ Sci & Technol, Div Life Sci, Clear Water Bay, Hong Kong, Peoples R China.
   [Liu, Hongbin] Hong Kong Univ Sci & Technol, Dept Ocean Sci, Clear Water Bay, Hong Kong, Peoples R China.
   [Xia, Xiaomin] Chinese Acad Sci, South China Sea Inst Oceanol, Key Lab Trop Marine Bioresources & Ecol, Guangdong Prov Key Lab Appl Marine Biol, Guangzhou, Peoples R China.
RP Zhang, SW (corresponding author), South China Normal Univ, Sch Life Sci, Guangzhou Key Lab Subtrop Biodivers & Biomonitori, Guangdong Prov Key Lab Hlth & Safe Aquaculture, Guangzhou, Peoples R China.; Xia, XM (corresponding author), Chinese Acad Sci, South China Sea Inst Oceanol, Key Lab Trop Marine Bioresources & Ecol, Guangdong Prov Key Lab Appl Marine Biol, Guangzhou, Peoples R China.
EM shuwen@m.scnu.edu.cn; xiaxiaomin@scsio.ac.cn
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NR 86
TC 4
Z9 4
PD NOV 22
PY 2022
VL 88
IS 22
DI 10.1128/aem.01323-22
EA NOV 2022
UT WOS:000888314900001
DA 2025-07-30
ER

PT J
AU Linney, MD
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   Romano, AE
   Luo, E
   DeLong, EF
   Karl, DM
AF Linney, Morgan D.
   Eppley, John M.
   Romano, Anna E.
   Luo, Elaine
   DeLong, Edward F.
   Karl, David M.
TI Microbial Sources of Exocellular DNA in the Ocean
SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB With advances in metagenomic sequencing, the microbial composition of diverse environmental systems has been investigated, providing new perspectives on potential ecological dynamics and dimensions for experimental investigations. Here, we characterized exocellular free DNA via metagenomics, using a newly developed method that separates free DNA from cells, viruses, and vesicles, and facilitated the independent characterization of each fraction.
   Exocellular DNA is operationally defined as the fraction of the total DNA pool that passes through a membrane filter (0.1 mu m). It is composed of DNA-containing vesicles, viruses, and free DNA and is ubiquitous in all aquatic systems, although the sources, sinks, and ecological consequences are largely unknown. Using a method that provides separation of these three fractions, we compared open ocean depth profiles of DNA associated with each fraction. Pelagibacter-like DNA dominated the vesicle fractions for all samples examined over a depth range of 75 to 500 m. Viral DNA consisted predominantly of myovirus-like and podovirus-like DNA and contained the highest proportion of unannotated sequences. Euphotic zone free DNA (75 to 125 m) contained primarily bacterial and viral sequences, with bacteria dominating samples from the mesopelagic zone (500 to 1,000 m). A high proportion of mesopelagic zone free DNA sequences appeared to originate from surface waters, including a large amount of DNA contributed by high-light Prochlorococcus ecotypes. Throughout the water column, but especially in the mesopelagic zone, the composition of free DNA sequences was not always reflective of cooccurring microbial communities that inhabit the same sampling depth. These results reveal the composition of free DNA in different regions of the water column (euphotic and mesopelagic zones), with implications for dissolved organic matter cycling and export (by way of sinking particles and/or migratory zooplankton) as a delivery mechanism. IMPORTANCE With advances in metagenomic sequencing, the microbial composition of diverse environmental systems has been investigated, providing new perspectives on potential ecological dynamics and dimensions for experimental investigations. Here, we characterized exocellular free DNA via metagenomics, using a newly developed method that separates free DNA from cells, viruses, and vesicles, and facilitated the independent characterization of each fraction. The fate of this free DNA has both ecological consequences as a nutrient (N and P) source and potential evolutionary consequences as a source of genetic transformation. Here, we document different microbial sources of free DNA at the surface (0 to 200 m) versus depths of 250 to 1,000 m, suggesting that distinct free DNA production mechanisms may be present throughout the oligotrophic water column. Examining microbial processes through the lens of exocellular DNA provides insights into the production of labile dissolved organic matter (i.e., free DNA) at the surface (likely by viral lysis) and processes that influence the fate of sinking, surface-derived organic matter.
C1 [Linney, Morgan D.; Eppley, John M.; Romano, Anna E.; Luo, Elaine; DeLong, Edward F.; Karl, David M.] Univ Hawaii Manoa, Daniel K Inouye Ctr Microbial Oceanog Res & Educ, Dept Oceanog, Honolulu, HI 96822 USA.
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RP Linney, MD (corresponding author), Univ Hawaii Manoa, Daniel K Inouye Ctr Microbial Oceanog Res & Educ, Dept Oceanog, Honolulu, HI 96822 USA.; Linney, MD (corresponding author), MIT, Dept Civil & Environm Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA.
EM linney@mit.edu
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NR 70
TC 7
Z9 7
PD APR 12
PY 2022
VL 88
IS 7
AR e02093-21
DI 10.1128/aem.02093-21
UT WOS:000782461400034
DA 2025-07-30
ER

PT B
AU Okafor, N
AF Okafor, Nduka
BA Okafor, N
BF Okafor, N
TI Ecology of Microorganisms in Saline Waters (Seas and Oceans)
SO ENVIRONMENTAL MICROBIOLOGY OF AQUATIC AND WASTE SYSTEMS
DT Article; Book Chapter
AB The waters of the seas and oceans of the world contain large amounts of solutes; mainly, salt of about 3.5 g/L, occupy about 71% of the earth's surface and have an average depth of 3.8 km. The photic zone of seas and oceans, about 200 m deep, is the region permeated by sunlight where photosynthesis can take place. It has the greatest biodiversity, and all food for the marine population arises from the photic zone; such food includes marine snow which consists of globules of mucopolyssacharides containing dead and living microorganisms floating downward toward the deep ocean. Marine organisms are adapted to the unique conditions found in the marine open sea (pelagic zone) environment: high salinity (3.5 g/L), low temperature (about 4 degrees C), and high barometric pressure of up to 500 bar depending on the depth. Thermophilic organisms grow near the occasional hot thermal vents where hot magma spews out onto the ocean floor.
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C1 Clemson Univ, Dept Biol Sci, Clemson, SC 29634 USA.
RP Okafor, N (corresponding author), Clemson Univ, Dept Biol Sci, Clemson, SC 29634 USA.
EM nokafor@g.clemson.edu; nokafor@g.clemson.edu
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NR 23
TC 0
Z9 0
PY 2011
BP 123
EP 148
DI 10.1007/978-94-007-1460-1_6
D2 10.1007/978-94-007-1460-1
UT WOS:000293760400006
DA 2025-07-30
ER

PT J
AU Ren, LJ
   Song, XY
   Wu, CF
   Li, G
   Zhang, XF
   Xia, XM
   Xiang, CH
   Han, BP
   Jeppesen, E
   Wu, QLL
AF Ren, Lijuan
   Song, Xingyu
   Wu, Chuangfeng
   Li, Gang
   Zhang, Xiufeng
   Xia, Xiaomin
   Xiang, Chenhui
   Han, Bo-Ping
   Jeppesen, Erik
   Wu, Qinglong L.
TI Biogeographical and Biodiversity Patterns of Marine Planktonic Bacteria
   Spanning from the South China Sea across the Gulf of Bengal to the
   Northern Arabian Sea
SO MICROBIOLOGY SPECTRUM
DT Article
AB Understanding the biogeographical and biodiversity patterns of bacterial communities is essential in unraveling their responses to future environmental changes. However, the relationships between marine planktonic bacterial biodiversity and seawater chlorophyll a are largely understudied. Here, we used high-throughput sequencing to study the biodiversity patterns of marine planktonic bacteria across a broad chlorophyll a gradient spanning from the South China Sea across the Gulf of Bengal to the northern Arabian Sea. We found that the biogeographical patterns of marine planktonic bacteria complied with the scenario of homogeneous selection, with chlorophyll a concentration being the key environmental selecting variable of bacteria taxa. The relative abundance of Prochlorococcus, the SAR11 clade, the SAR116 clade, and the SAR86 clade significantly decreased in habitats with high chlorophyll a concentrations (>0.5 mu g/L). Free-living bacteria (FLB) and particle-associated bacteria (PAB) displayed contrasting alpha diversity and chlorophyll a relationships with a positive linear correlation for FLB but a negative correlation for PAB. We further found that PAB had a narrower niche breadth of chlorophyll a than did FLB, with far fewer bacterial taxa being favored at higher chlorophyll a concentrations. Higher chlorophyll a concentrations were linked to the enhanced stochastic drift and reduced beta diversity of PAB but to the weakened homogeneous selection, enhanced dispersal limitation, and increased beta diversity of FLB. Taken together, our findings might broaden our knowledge about the biogeography of marine planktonic bacteria and advance the understanding of bacterial roles in predicting ecosystem functioning under future environmental changes that are derived from eutrophication.IMPORTANCE One of the long-standing interests of biogeography is to explore diversity patterns and uncover their underlying mechanisms. Despite intensive studies on the responses of eukaryotic communities to chlorophyll a concentrations, we know little about how changes in seawater chlorophyll a concentrations affect free-living bacteria (FLB) and particle-associated bacteria (PAB) diversity patterns in natural systems. Our biogeography study demonstrated that marine FLB and PAB displayed contrasting diversity and chlorophyll a relationships and exhibited completely different assembly mechanisms. Our findings broaden our knowledge about the biogeographical and biodiversity patterns of marine planktonic bacteria in nature systems and suggest that PAB and FLB should be considered independently in predicting marine ecosystem functioning under future frequent eutrophication.
   One of the long-standing interests of biogeography is to explore diversity patterns and uncover their underlying mechanisms. Despite intensive studies on the responses of eukaryotic communities to chlorophyll a concentrations, we know little about how changes in seawater chlorophyll a concentrations affect free-living bacteria (FLB) and particle-associated bacteria (PAB) diversity patterns in natural systems.
C1 [Ren, Lijuan; Wu, Chuangfeng; Zhang, Xiufeng; Han, Bo-Ping] Jinan Univ, Dept Ecol, Guangzhou, Peoples R China.
   [Ren, Lijuan; Wu, Chuangfeng; Zhang, Xiufeng; Han, Bo-Ping] Jinan Univ, Inst Hydrobiol, Guangzhou, Peoples R China.
   [Ren, Lijuan; Song, Xingyu; Li, Gang; Xia, Xiaomin; Xiang, Chenhui] Chinese Acad Sci, South China Sea Inst Oceanol, Key Lab Trop Marine Bioresources & Ecol, Guangzhou, Peoples R China.
   [Ren, Lijuan; Song, Xingyu; Li, Gang; Xia, Xiaomin; Xiang, Chenhui] Chinese Acad Sci, South China Sea Inst Oceanol, Key Lab Sci & Technol Operat Oceanog, Guangzhou, Peoples R China.
   [Jeppesen, Erik] Univ Chinese Acad Sci, Sino Danish Ctr Educ & Res, Beijing, Peoples R China.
   [Jeppesen, Erik] Aarhus Univ, Dept Biosci, Silkeborg, Denmark.
   [Jeppesen, Erik] Middle East Tech Univ, Dept Biol Sci, Limnol Lab, Ankara, Turkiye.
   [Jeppesen, Erik] Middle East Tech Univ, Ctr Ecosyst Res & Implementat, Ankara, Turkiye.
   [Wu, Qinglong L.] Southern Marine Sci & Engn Guangdong Lab Guangzho, Ctr Evolut & Conservat Biol, Guangzhou, Peoples R China.
   [Wu, Qinglong L.] Chinese Acad Sci, Nanjing Inst Geog & Limnol, State Key Lab Lake Sci & Environm, Nanjing, Peoples R China.
RP Ren, LJ (corresponding author), Jinan Univ, Dept Ecol, Guangzhou, Peoples R China.; Ren, LJ (corresponding author), Jinan Univ, Inst Hydrobiol, Guangzhou, Peoples R China.; Ren, LJ (corresponding author), Chinese Acad Sci, South China Sea Inst Oceanol, Key Lab Trop Marine Bioresources & Ecol, Guangzhou, Peoples R China.; Ren, LJ (corresponding author), Chinese Acad Sci, South China Sea Inst Oceanol, Key Lab Sci & Technol Operat Oceanog, Guangzhou, Peoples R China.
EM lijuanren@jnu.edu.cn
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NR 86
TC 5
Z9 5
PD JUN
PY 2023
VL 11
IS 3
DI 10.1128/spectrum.00398-23
EA APR 2023
UT WOS:000976550700001
DA 2025-07-30
ER

PT J
AU Bennke, CM
   Reintjes, G
   Schattenhofer, M
   Ellrott, A
   Wulf, J
   Zeder, M
   Fuchs, BM
AF Bennke, Christin M.
   Reintjes, Greta
   Schattenhofer, Martha
   Ellrott, Andreas
   Wulf, Joerg
   Zeder, Michael
   Fuchs, Bernhard M.
TI Modification of a High-Throughput Automatic Microbial Cell Enumeration
   System for Shipboard Analyses
SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB In the age of ever-increasing "-omics" studies, the accurate and statistically robust determination of microbial cell numbers within often-complex samples remains a key task in microbial ecology. Microscopic quantification is still the only method to enumerate specific subgroups of microbial clades within complex communities by, for example, fluorescence in situ hybridization (FISH). In this study, we improved an existing automatic image acquisition and cell enumeration system and adapted it for usage at high seas on board an oceanographic research ship. The system was evaluated by testing settings such as minimal pixel area and image exposure times ashore under stable laboratory conditions before being brought on board and tested under various wind and wave conditions. The system was robust enough to produce high-quality images even with ship heaves of up to 3m and pitch and roll angles of up to 6.3 degrees. On board the research ship, on average, 25% of the images acquired from plankton samples on filter membranes could be used for cell enumeration. Automated enumeration was highly correlated with manual counts (r(2)>0.9). Even the smallest of microbial cells in the open ocean, members of the alphaproteobacterial SAR11 clade, could be confidently detected and enumerated. The automated image acquisition and cell enumeration system developed here enables an accurate and reproducible determination of microbial cell counts in planktonic samples and allows insight into the abundance and distribution of specific microorganisms already on board within a few hours.
   IMPORTANCE
   In this research article, we report on a new system and software pipeline, which allows for an easy and quick image acquisition and the subsequent enumeration of cells in the acquired images. We put this pipeline through vigorous testing and compared it to manual microscopy counts of microbial cells on membrane filters. Furthermore, we tested this system at sea on board a marine research vessel and counted bacteria on board within a few hours after the retrieval of water samples. The imaging and counting system described here has been successfully applied to a number of laboratory-based studies and allowed the quantification of thousands of samples and FISH preparations (see, e.g., H. Teeling, B. M. Fuchs, D. Becher, C. Klockow, A. Gardebrecht, C. M. Bennke, M. Kassabgy, S. Huang, A. J. Mann, J. Waldmann, M. Weber, A. Klindworth, A. Otto, J. Lange, J. Bernhardt, C. Reinsch, M. Hecker, J. Peplies, F. D. Bockelmann, U. Callies, G. Gerdts, A. Wichels, K. H. Wiltshire, F. O. Glockner, T. Schweder, and R. Amann, Science 336:608-611, 2012, http://dx.doi.org/10.1126/science.1218344). We adjusted the standard image acquisition software to withstand ship movements. This system will allow for more targeted sampling of the microbial community, leading to a better understanding of the role of microorganisms in the global oceans.
C1 [Bennke, Christin M.; Reintjes, Greta; Schattenhofer, Martha; Ellrott, Andreas; Wulf, Joerg; Zeder, Michael; Fuchs, Bernhard M.] Max Planck Inst Marine Microbiol, Dept Mol Ecol, Bremen, Germany.
   [Schattenhofer, Martha] Uppsala Univ, Dept Ecol Genet, Limnol, Uppsala, Sweden.
   [Zeder, Michael] Technobiol GmbH, Buchrain, Switzerland.
RP Fuchs, BM (corresponding author), Max Planck Inst Marine Microbiol, Dept Mol Ecol, Bremen, Germany.
EM bfuchs@mpi-bremen.de
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NR 33
TC 33
Z9 35
PD JUN
PY 2016
VL 82
IS 11
BP 3289
EP 3296
DI 10.1128/AEM.03931-15
UT WOS:000376159400014
DA 2025-07-30
ER

PT J
AU O'Brien, J
   Focardi, A
   Deschaseaux, ESM
   Petrou, K
   Ostrowski, M
   Beckley, LE
   Seymour, JR
AF O'Brien, James
   Focardi, Amaranta
   Deschaseaux, Elisabeth S. M.
   Petrou, Katherina
   Ostrowski, Martin
   Beckley, Lynnath E.
   Seymour, Justin R.
TI Microbial dimethylsulfoniopropionate (DMSP) cycling in the
   ultraoligotrophic eastern Indian Ocean
SO DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY
DT Article
AB Dimethylsulfoniopropionate (DMSP) is an important source of dissolved organic matter for the marine food web and its cycling is a key step in ocean-atmosphere fluxes involved in the global sulfur cycle. To date, the abundance and biogeography of the genes encoding bacterial DMSP cycling in the eastern Indian Ocean (EIO) is virtually unknown. Moreover, DMSP measurements from the IO are sparse compared to other major oceans. In May-June 2019, we characterized dissolved DMSP (DMSPd) concentrations and the abundance of representative bacterial DMSP cycling genes along the 110 degrees E transect line as part of a voyage that contributed to Australia's involvement in the second International Indian Ocean Expedition. During the multidisciplinary voyage, surface water samples were collected from 19 stations spanning temperate to tropical waters of the EIO (39.5 degrees S to 11.5 degrees S, 110 degrees E). Somewhat surprisingly, a trend of greater DMSPd was measured in ultraoligotrophic (<0.02 mu mol L-1 of nitrate/nitrite), low latitude waters compared to relatively nutrient-rich high latitudes, which contradicts global DMSPd patterns of high concentrations at high latitudes. Additionally, the average DMSPd concentration in EIO samples (17.2 +/- 18.64 nM) was an order of magnitude greater than concentrations previously reported at similar latitudes in the Pacific and Atlantic Oceans, which suggests DMSPd is a readily available food source for microbes in a region that is often considered an ocean desert. The abundances of the bacterial DMSP production gene (dsyB), the DMSP lyase gene (dddP) and phylogenetically diverse DMSP demethylation genes (dmdA subclade A/1, D/all and E/2) were reported for the first time in the EIO region, demonstrating significant shifts in all genes with latitude. The SAR11 dmdA (D/all) gene was the dominant DMSP degradation gene across the transect (3.4 +/- 0.94% of bacteria) and was notably positively correlated to DMSPd, demonstrating a tight coupling between the variables across the 30 degrees transect. Our results also showed greater DMSPd and relative abundance of genes encoding both DMSP degradation pathways (dddP, dmdA A/1 and D/all) within a Leeuwin Current meander when compared to adjacent stations outside of the meander, providing evidence that mesoscale perturbations from the Leeuwin Current can greatly influence the EIO sulfur cycle. Overall, our data indicates that reduced sulfur in the form of DMSP is an abundant and readily available food source for some microbial metabolisms within the ultraoligotrophic surface waters of the EIO.
C1 [O'Brien, James; Focardi, Amaranta; Ostrowski, Martin; Seymour, Justin R.] Univ Technol Sydney, Ocean Microbiol Grp, Climate Change Cluster, POB 123, Broadway, NSW 2007, Australia.
   [Deschaseaux, Elisabeth S. M.] Southern Cross Univ, Ctr Coastal Biogeochem, Sch Environm Sci & Engn, Lismore, NSW 2480, Australia.
   [Petrou, Katherina] Univ Technol Sydney, Sch Life Sci, POB 123, Broadway, NSW 2007, Australia.
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RP O'Brien, J; Seymour, JR (corresponding author), Univ Technol Sydney, Ocean Microbiol Grp, Climate Change Cluster, POB 123, Broadway, NSW 2007, Australia.
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NR 87
TC 7
Z9 7
PD DEC
PY 2022
VL 206
AR 105195
DI 10.1016/j.dsr2.2022.105195
EA OCT 2022
UT WOS:000875404800001
DA 2025-07-30
ER

PT J
AU Wang, LR
   Chen, S
   Vergin, KL
   Giovannoni, SJ
   Chan, SW
   DeMott, MS
   Taghizadeh, K
   Cordero, OX
   Cutler, M
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   Alm, EJ
   Polz, MF
   Pinhassi, J
   Deng, ZX
   Dedon, PC
AF Wang, Lianrong
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   Vergin, Kevin L.
   Giovannoni, Stephen J.
   Chan, Simon W.
   DeMott, Michael S.
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   Cordero, Otto X.
   Cutler, Michael
   Timberlake, Sonia
   Alm, Eric J.
   Polz, Martin F.
   Pinhassi, Jarone
   Deng, Zixin
   Dedon, Peter C.
TI DNA phosphorothioation is widespread and quantized in bacterial genomes
SO PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
   AMERICA
DT Article
AB Phosphorothioate (PT) modification of DNA, with sulfur replacing a nonbridging phosphate oxygen, was recently discovered as a product of the dnd genes found in bacteria and archaea. Given our limited understanding of the biological function of PT modifications, including sequence context, genomic frequencies, and relationships to the diversity of dnd gene clusters, we under-took a quantitative study of PT modifications in prokaryotic genomes using a liquid chromatography-coupled tandem quadrupole mass spectrometry approach. The results revealed a diversity of unique PT sequence contexts and three discrete genomic frequencies in a wide range of bacteria. Metagenomic analyses of PT modifications revealed unique ecological distributions, and a phylogenetic comparison of dnd genes and PT sequence contexts strongly supports the horizontal transfer of dnd genes. These results are consistent with the involvement of PT modifications in a type of restriction-modification system with wide distribution in prokaryotes.
C1 [Wang, Lianrong; Chen, Shi; Deng, Zixin] Shanghai Jiao Tong Univ, Lab Microbial Metab, Shanghai 200030, Peoples R China.
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RP Chen, S (corresponding author), Shanghai Jiao Tong Univ, Lab Microbial Metab, Shanghai 200030, Peoples R China.
EM shichen@whu.edu.cn; pcdedon@mit.edu
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NR 37
TC 133
Z9 156
PD FEB 15
PY 2011
VL 108
IS 7
BP 2963
EP 2968
DI 10.1073/pnas.1017261108
UT WOS:000287377000063
DA 2025-07-30
ER

PT J
AU Giovannoni, SJ
AF Giovannoni, Stephen J.
TI Vitamins in the sea
SO PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
   AMERICA
DT Editorial Material
C1 Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
RP Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
EM steve.giovannoni@oregonstate.edu
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NR 19
TC 36
Z9 41
PD AUG 28
PY 2012
VL 109
IS 35
BP 13888
EP 13889
DI 10.1073/pnas.1211722109
UT WOS:000308565300014
DA 2025-07-30
ER

PT J
AU Kirchman, DL
AF Kirchman, David L.
TI A marine virus as foe and friend
SO NATURE MICROBIOLOGY
DT Editorial Material
AB A virus has been found inserted into the genome of the most abundant bacteria in the oceans. Even though the virus can kill its host, the genes carried by the prophage may help these bacteria flourish around the world.
C1 [Kirchman, David L.] Univ Delaware, Sch Marine Sci & Policy, Lewes, DE 19958 USA.
RP Kirchman, DL (corresponding author), Univ Delaware, Sch Marine Sci & Policy, Lewes, DE 19958 USA.
EM kirchman@udel.edu
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NR 9
TC 0
Z9 0
PD AUG
PY 2020
VL 5
IS 8
BP 982
EP 983
DI 10.1038/s41564-020-0764-3
UT WOS:000552017200004
DA 2025-07-30
ER

PT J
AU Gómez-Consarnau, L
   González, JM
   Coll-Lladó, M
   Gourdon, P
   Pascher, T
   Neutze, R
   Pedrós-Alió, C
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AF Gomez-Consarnau, Laura
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   Coll-Llado, Montserrat
   Gourdon, Pontus
   Pascher, Torbjoern
   Neutze, Richard
   Pedros-Alio, Carlos
   Pinhassi, Jarone
TI Light stimulates growth of proteorhodopsin-containing marine
   Flavobacteria
SO NATURE
DT Article
AB Proteorhodopsins are bacterial light-dependent proton pumps. Their discovery within genomic material from uncultivated marine bacterioplankton caused considerable excitement because it indicated a potential phototrophic function within these organisms, which had previously been considered strictly chemotrophic(1). Subsequent studies established that sequences encoding proteorhodopsin are broadly distributed throughout the world's oceans(2-5). Nevertheless, the role of proteorhodopsins in native marine bacteria is still unknown(6). Here we show, from an analysis of the complete genomes of three marine Flavobacteria, that cultivated bacteria in the phylum Bacteroidetes, one of the principal components of marine bacterioplankton, contain proteorhodopsin. Moreover, growth experiments in both natural and artificial seawater ( low in labile organic matter, which is typical of the world's oceans) establish that exposure to light results in a marked increase in the cell yield of one such bacterium (Dokdonia sp. strain MED134) when compared with cells grown in darkness. Thus, our results show that the phototrophy conferred by proteorhodopsin can provide critical amounts of energy, not only for respiration and maintenance but also for active growth of marine bacterioplankton in their natural environment.
C1 Univ Kalmar, Dept Biol & Environm Sci, SE-39182 KAlmar, Sweden.
   Univ La Laguna, Dept Microbiol & Cell Biol, ES-38206 Tenerife, Spain.
   CSIC, CMIMA, Inst Ciencies Mar, ES-08003 Barcelona, Spain.
   Chalmers, Dept Biol & Chem Engn, SE-41296 Gothenburg, Sweden.
   Lund Univ, Kemictr, SE-22100 Lund, Sweden.
   Univ Gothenburg, Dept Chem Biochem & Biophys, SE-40530 Gothenburg, Sweden.
RP Pinhassi, J (corresponding author), Univ Kalmar, Dept Biol & Environm Sci, SE-39182 KAlmar, Sweden.
EM jarone.pinhassi@hik.se
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NR 26
TC 292
Z9 323
PD JAN 11
PY 2007
VL 445
IS 7124
BP 210
EP 213
DI 10.1038/nature05381
UT WOS:000243384300052
DA 2025-07-30
ER

PT J
AU Burr, DJ
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   Ryan, KG
AF Burr, David J.
   Martin, Andrew
   Maas, Elizabeth W.
   Ryan, Ken G.
TI In situ light responses of the proteorhodopsin-bearing Antarctic
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DT Article
AB Proteorhodopsin (PR) is a wide-spread protein found in many marine prokaryotes. PR allows for the potential conversion of solar energy to ATP, possibly assisting in cellular growth and survival during periods of high environmental stress. PR utilises either blue or green light through a single amino acid substitution. We incubated the PR-bearing bacterium Psychroflexus torquis 50 cm deep within Antarctic sea ice for 13 days, exposing cultures to diurnal fluctuations in light and temperature. Enhanced growth occurred most prominently in cultures incubated under irradiance levels of similar to 50 mu mol photons m(-2) s(-1), suggesting PR provides a strong selective advantage. In addition, cultures grown under blue light yielded over 5.5 times more live cells per photon compared to greenlight incubations. Because P. torquis expresses an apparently 'green-shifted' PR gene variant, this finding infers that the spectral tuning of PR is more complex than previously thought. This study supports the theory that PR provides additional energy to bacteria under sub-optimal conditions, and raises several points of interest to be addressed by future research.
C1 [Burr, David J.; Martin, Andrew; Ryan, Ken G.] Victoria Univ Wellington, Sch Biol Sci, POB 600, Wellington 6140, New Zealand.
   [Burr, David J.; Maas, Elizabeth W.] Natl Inst Water & Atmospher Res NIWA, Wellington, New Zealand.
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RP Ryan, KG (corresponding author), Victoria Univ Wellington, Sch Biol Sci, POB 600, Wellington 6140, New Zealand.
EM ken.ryan@vuw.ac.nz
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DA 2025-07-30
ER

PT J
AU Zhu, WJ
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AF Zhu, Wenjun
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TI Isolation of proteorhodopsin-bearing bacterium JL-3 from fresh water and
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DT Article
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C1 [Zhu, Wenjun; Lan, Yanli; Lou, Xiangdi; Han, Ning; Ran, Tingting; Xu, Dongqing; Wang, Wei-Wu] Nanjing Agr Univ, Key Lab Microbiol Engn Agr Environm, Minist Agr, Dept Microbiol,Coll Life Sci, Nanjing 210095, Jiangsu, Peoples R China.
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RP Wang, WW (corresponding author), Nanjing Agr Univ, Key Lab Microbiol Engn Agr Environm, Minist Agr, Dept Microbiol,Coll Life Sci, Nanjing 210095, Jiangsu, Peoples R China.
EM www.ang@njau.edu.cn
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TC 7
Z9 7
PD JUL
PY 2013
VL 344
IS 1
BP 10
EP 17
DI 10.1111/1574-6968.12144
UT WOS:000320387800002
DA 2025-07-30
ER

PT J
AU Moncadas, LS
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AF Moncadas, Lucas Serra
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   Andrei, Adrian-Stefan
TI Freshwater genome-reduced bacteria exhibit pervasive episodes of
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DT Article
AB The emergence of bacterial species is rooted in their inherent potential for continuous evolution and adaptation to an ever-changing ecological landscape. The adaptive capacity of most species frequently resides within the repertoire of genes encoding the secreted proteome (SP), as it serves as a primary interface used to regulate survival/reproduction strategies. Here, by applying evolutionary genomics approaches to metagenomics data, we show that abundant freshwater bacteria exhibit biphasic adaptation states linked to the eco-evolutionary processes governing their genome sizes. While species with average to large genomes adhere to the dominant paradigm of evolution through niche adaptation by reducing the evolutionary pressure on their SPs (via the augmentation of functionally redundant genes that buffer mutational fitness loss) and increasing the phylogenetic distance of recombination events, most of the genome-reduced species exhibit a nonconforming state. In contrast, their SPs reflect a combination of low functional redundancy and high selection pressure, resulting in significantly higher levels of conservation and invariance. Our findings indicate that although niche adaptation is the principal mechanism driving speciation, freshwater genome-reduced bacteria often experience extended periods of adaptive stasis. Understanding the adaptive state of microbial species will lead to a better comprehension of their spatiotemporal dynamics, biogeography, and resilience to global change.
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C1 [Moncadas, Lucas Serra; Hofer, Cyrill; Pernthaler, Jakob; Andrei, Adrian-Stefan] Univ Zurich, Dept Plant & Microbial Biol, Limnol Stn, Kilchberg, Switzerland.
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RP Andrei, AS (corresponding author), Univ Zurich, Dept Plant & Microbial Biol, Limnol Stn, Kilchberg, Switzerland.
EM stefan.andrei@limnol.uzh.ch
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TC 3
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PD APR 23
PY 2024
VL 15
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DA 2025-07-30
ER

PT J
AU Kopprio, GA
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AF Kopprio, German A.
   Le Huu Cuong
   Nguyen Dinh Luyen
   Tran Mai Duc
   Tran Hong Ha
   Le Mai Huong
   Gaerdes, Astrid
TI Carrageenophyte-attached and planktonic bacterial communities in two
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SO ECOLOGICAL INDICATORS
DT Article
AB The composition of the bacterial community of carrageenophyte-attached and planktonic bacteria was studied in two bays of Vietnam with contrasting anthropogenic inputs to assess their role as ecological indicators. Clear differences (similar to 73% dissimilarity) between carrageenophyte-attached bacteria and bacterioplankton were detected in terms of genus composition: mainly Agaribacter, Ruegeria, Alteromonas, the Pir4 lineage and Vibrio for the carrageenophytes and Candidatus Actinomarina, HIMB 11, NS groups and SAR Glades for the bacterioplankton. The copiotrophic nature, potential for complex-polymer degradation, and ability to form and defend biofilms were common features inferred for the carrageenophyte-attached microbiome. Significant differences between the bays were detected in the concentration of most inorganic nutrients. More eutrophic conditions and presumptive wastewater pollution in Cam Ranh (CR) bay were primarily indicated by the dominance of Rubripirellula, Leptobacterium, Hypnocyclicus and Porphyrobacter and their correlations with phosphate. In terms of bacterioplankton, the influence of intensive aquaculture in CR bay was suggested by the dominance of the N55 and N54 marine groups, the SUP05 cluster, Flavobacteriaceae unclassified and SAR 11 Glade III as well as their strong correlations with ammonium and phosphate. The link between silicate and other inorganic nutrients suggests freshwater input in CR bay. Arenicellaceae unclassified and Formosa were also potential indicators of eutrophication. Operational taxonomic units (OTUs) of Marinagarivorans, Cobetia, Vibrio, Alteromonas and Pseudoalteromonas were typical of the carrageenophytes showing ice-ice disease symptoms. Vibrio and Alteromonas were also common among healthy macroalgae, and differences at the OTU level suggested potential succession of species from the healthy to the diseased state. The probable beneficial roles of some bacteria, such as Ruegeria, Cutibacterium and unidentified members of the family Rhizobiaceae, were discussed. This study provides pioneering insights into the bacterial community composition of carrageenophytes and highlights their ecological value as strong indicators of the sources of organic matter, anthropogenic impacts and health status of marine systems.
C1 [Kopprio, German A.; Gaerdes, Astrid] Leibniz Ctr Trop Marine Res, Fahrenheitstr 6, D-28359 Bremen, Germany.
   [Le Huu Cuong; Nguyen Dinh Luyen; Le Mai Huong] Vietnam Acad Sci & Technol, Inst Nat Prod Chem, 18 Hoang Quoc Viet, Hanoi, Vietnam.
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RP Kopprio, GA (corresponding author), Leibniz Inst Freshwater Ecol & Inland Fisheries, Chem Analyt & Biogeochem, Muggelseedamm 301, D-12587 Berlin, Germany.
EM kopprio@igb-berlin.de
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PY 2021
VL 121
AR 107067
DI 10.1016/j.ecolind.2020.107067
UT WOS:000604896100006
DA 2025-07-30
ER

PT J
AU Gómez-Consarnau, L
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AF Gomez-Consarnau, Laura
   Akram, Neelam
   Lindell, Kristoffer
   Pedersen, Anders
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   Milton, Debra L.
   Gonzalez, Jose M.
   Pinhassi, Jarone
TI Proteorhodopsin Phototrophy Promotes Survival of Marine Bacteria during
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SO PLOS BIOLOGY
DT Article
AB Proteorhodopsins are globally abundant photoproteins found in bacteria in the photic zone of the ocean. Although their function as proton pumps with energy-yielding potential has been demonstrated, the ecological role of proteorhodopsins remains largely unexplored. Here, we report the presence and function of proteorhodopsin in a member of the widespread genus Vibrio, uncovered through whole-genome analysis. Phylogenetic analysis suggests that the Vibrio strain AND4 obtained proteorhodopsin through lateral gene transfer, which could have modified the ecology of this marine bacterium. We demonstrate an increased long-term survival of AND4 when starved in seawater exposed to light rather than held in darkness. Furthermore, mutational analysis provides the first direct evidence, to our knowledge, linking the proteorhodopsin gene and its biological function in marine bacteria. Thus, proteorhodopsin phototrophy confers a fitness advantage to marine bacteria, representing a novel mechanism for bacterioplankton to endure frequent periods of resource deprivation at the ocean's surface.
C1 [Gomez-Consarnau, Laura; Akram, Neelam; Pinhassi, Jarone] Linnaeus Univ, Sch Nat Sci, Kalmar, Sweden.
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RP Gómez-Consarnau, L (corresponding author), Linnaeus Univ, Sch Nat Sci, Kalmar, Sweden.
EM jarone.pinhassi@lnu.se
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PD APR
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VL 8
IS 4
AR e1000358
DI 10.1371/journal.pbio.1000358
UT WOS:000278125500011
DA 2025-07-30
ER

PT J
AU DeLong, EF
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AF DeLong, Edward F.
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DT Editorial Material
C1 [DeLong, Edward F.] MIT, Dept Civil & Environm Engn, Cambridge, MA 02139 USA.
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EM Delong@mit.edu; beja@tx.technion.ac.il
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PY 2010
VL 8
IS 4
AR e1000359
DI 10.1371/journal.pbio.1000359
UT WOS:000278125500012
DA 2025-07-30
ER

PT J
AU Cui, Y
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   Kim, Y
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AF Cui, Yingshun
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DT Article
AB To investigate the interactions between bacterial species in relation to the biotic and abiotic environmental fluctuations, free-living (FL), nanoparticle-associated (NP), and microparticle-associated (MP) bacterial community compositions (BCCs) were analyzed. A total of 267 samples were collected from July to December 2016 in the dynamic and shallow southern coastal water of Korea. The variations in BCC mostly depended on planktonic size fraction. Network analysis revealed water depth-dependent co-occurrence patterns of coastal bacterial communities. Higher interspecies connectivity was observed within FL bacteria than NP/MP bacteria, suggesting that FL bacteria with a streamlined genome may need other bacterial metabolites for survival, while the NP/MP copiotrophs may have the self-supporting capacity to produce the vital nutrients. The analysis of topological roles of individual OTUs in the network revealed that several groups of metabolically versatile bacteria (the marine Roseobacters, Flavobacteriales, Desulfobacterales, and SAR406 clade) acted as module hubs in different water depth. In conclusion, interspecies interactions dominated in FL bacteria, compared to NP and MP bacteria; modular structures of bacterial communities and keystone species strongly depended on the water depth-derived environmental factors. Furthermore, the multifunctional, versatile FL bacteria could play pivotal roles in dynamic shallow coastal ecosystems.
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RP Ahn, CY; Oh, HM (corresponding author), KRIBB, Cell Factory Res Ctr, Daejeon, South Korea.; Ahn, CY; Oh, HM (corresponding author), Korea Univ Sci & Technol UST, KRIBB Sch Biotechnol, Dept Environm Biotechnol, Daejeon, South Korea.
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NR 70
TC 40
Z9 45
PD JUN 24
PY 2019
VL 9
AR 9176
DI 10.1038/s41598-019-45512-5
UT WOS:000472597400079
DA 2025-07-30
ER

PT J
AU Alfreider, A
   Vogt, C
   Babel, W
AF Alfreider, A
   Vogt, C
   Babel, W
TI Microbial diversity in an in situ reactor system treating
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SO SYSTEMATIC AND APPLIED MICROBIOLOGY
DT Article
AB A molecular approach based on the construction of 16S ribosomal DNA clone libraries was used to investigate the microbial diversity of an underground in situ reactor system filled with the original aquifer sediments. After chemical steady state was reached in the monochlorobenzene concentration between the original inflowing groundwater and the reactor outflow, samples from different reactor locations and from inflowing and outflowing groundwater were taken for DNA extraction. Small-subunit rRNA genes were PCR-amplified with primers specific for Bacteria, subsequently cloned and screened for variation by restriction fragment length polymorphism (RFLP). A total of 87 bacterial 16S rDNA genes were sequenced and subjected to phylogeneric analysis. The original groundwater was found to be dominated by a bacterial consortium affiliated with various members of the class of Proteobacteria, by phylotypes not affiliated with currently recognized bacterial phyla, and also by sporulating and non-sporulating sulfate-reducing bacteria. The most occurring clone types obtained from the sediment samples of the reactor were related to the beta-Proteobacteria, dominated by sequences almost identical to the widespread bacterium Alcaligenes faecalis, to low G+C gram-positive bacteria and to Acidithiobacillus ferrooxidans (formerly Thiobacillus ferrooxidans) within the gamma subclass of Proteobacteria in the upper reactor sector. Although bacterial phylotypes originating from the groundwater outflow of the reactors also grouped within different subdivisions of Proteobacteria and low G+C gram-positive bacteria, most of the 16S rDNA sequences were not associated with the sequence types observed in the reactor samples. Our results suggest that the different environments were inhabited by distinct microbial communities in respect to their taxonomic diversity, particular pronounced between sediment attached microbial communities from the reactor samples and free-living bacteria from the groundwater in- and outflow.
C1 UFZ Helmholtz Ctr Environm Res, Sekt Umweltmikrobiol, D-04318 Leipzig, Germany.
RP UFZ Helmholtz Ctr Environm Res, Sekt Umweltmikrobiol, D-04318 Leipzig, Germany.
EM alfreid@umb.ufz.de
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NR 35
TC 84
Z9 89
PD AUG
PY 2002
VL 25
IS 2
BP 232
EP 240
DI 10.1078/0723-2020-00111
UT WOS:000178458000010
DA 2025-07-30
ER

PT J
AU Koh, EY
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AF Koh, Eileen Y.
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TI Proteorhodopsin-Bearing Bacteria in Antarctic Sea Ice
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DT Article
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C1 [Koh, Eileen Y.; Cowie, Rebecca O. M.; Davy, Simon K.; Ryan, Ken G.] Victoria Univ Wellington, Sch Biol Sci, Wellington 6140, New Zealand.
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RP Koh, EY (corresponding author), Victoria Univ Wellington, Sch Biol Sci, POB 600, Wellington 6140, New Zealand.
EM koh_eileen@yahoo.com
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NR 64
TC 57
Z9 67
PD SEP
PY 2010
VL 76
IS 17
BP 5918
EP 5925
DI 10.1128/AEM.00562-10
UT WOS:000281288000031
DA 2025-07-30
ER

PT J
AU Zakem, EJ
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   Weissman, JL
   Raut, Y
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AF Zakem, Emily J.
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TI Functional biogeography of marine microbial heterotrophs
SO SCIENCE
DT Article
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RP Zakem, EJ (corresponding author), Carnegie Inst Sci, Dept Global Ecol, Stanford, CA 94305 USA.
EM ezakem@carnegiescience.edu
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NR 96
TC 0
Z9 0
PD MAY 22
PY 2025
VL 388
IS 6749
AR eado5323
DI 10.1126/science.ado5323
UT WOS:001494011800018
DA 2025-07-30
ER

PT J
AU Bandekar, M
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AF Bandekar, Mandar
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TI Comparative analysis of microbiome inhabiting oxygenated and
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SO MARINE ENVIRONMENTAL RESEARCH
DT Article
AB We examine how oxygen levels and the choice of 16S ribosomal RNA (rRNA) tags impact marine bacterial communities using Next-Generation amplicon sequencing. Analyzing V3 and V6 regions, we assess microbial composition in both Oxygen minimum zones (OMZ) and non-OMZ (NOMZ) areas in the Arabian Sea (AS) and the Central Indian Ocean basin (CIOB) respectively. Operational taxonomic units (OTUs) at 97% similarity showed slightly higher richness and diversity with V6 compared to V3. Vertical diversity patterns were consistent across both regions. NOMZ showed greater richness and diversity than OMZ. AS and CIOB exhibited significant differences in bacterial community, diversity, and relative abundance at the order and family levels. Alteromonadaceae dominated the OMZ, while Pelagibacteraceae dominated the NOMZ. Synechococcaceae were found exclusively at 250 m in OMZ. Bacteria putatively involved in nitrification, denitrification, and sulfurylation were detected at both sites. Dissolved oxygen significantly influenced microbial diversity at both sites, while seasonal environmental parameters affected diversity consistently, with no observed temporal variation.
C1 [Bandekar, Mandar; Akkanen, Jarkko] Univ Eastern Finland, Dept Environm & Biol Sci, Joensuu, Kuopio, Finland.
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RP Bandekar, M (corresponding author), Univ Eastern Finland, Dept Environm & Biol Sci, Joensuu, Kuopio, Finland.
EM mandar.bandekar@uef.fi
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NR 81
TC 1
Z9 1
PD JUL
PY 2024
VL 199
AR 106615
DI 10.1016/j.marenvres.2024.106615
EA JUN 2024
UT WOS:001266499900001
DA 2025-07-30
ER

PT J
AU Franklin, MP
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AF Franklin, MP
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DT Article
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C1 Univ Warwick, Dept Biol Sci, Coventry CV4 7AL, W Midlands, England.
   Newcastle Univ, Sch Marine Sci & Technol, Ocean Res Grp, Newcastle Upon Tyne NE1 7RU, Tyne & Wear, England.
   Plymouth Marine Lab, Plymouth, Devon, England.
RP Univ Warwick, Dept Biol Sci, Coventry CV4 7AL, W Midlands, England.
EM j.c.murrell@warwick.ac.uk
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UT WOS:000228266600012
DA 2025-07-30
ER

PT J
AU Gray, MW
AF Gray, Michael W.
TI The Pre-Endosymbiont Hypothesis: A New Perspective on the Origin and
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SO COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY
DT Article
AB Mitochondrial DNA (mtDNA) is unquestionably the remnant of an alpha-proteobacterial genome, yet only similar to 10%-20% of mitochondrial proteins are demonstrably alpha-proteobacterial in origin (the "alpha-proteobacterial component," or APC). The evolutionary ancestry of the non-alpha-proteobacterial component (NPC) is obscure and not adequately accounted for in current models of mitochondrial origin. I propose that in the host cell that accommodated an alpha-proteobacterial endosymbiont, much of the NPC was already present, in the form of a membrane-bound metabolic organelle (the premitochondrion) that compartmentalized many of the non-energy-generating functions of the contemporary mitochondrion. I suggest that this organelle also possessed a protein import system and various ion and small-molecule transporters. In such a scenario, an alpha-proteobacterial endosymbiont could have been converted relatively directly and rapidly into an energy-generating organelle that incorporated the extant metabolic functions of the premitochondrion. This model (the "pre-endosymbiont hypothesis") effectively represents a synthesis of previous, contending mitochondrial origin hypotheses, with the bulk of the mitochondrial proteome (much of the NPC) having an endogenous origin and the minority component (the APC) having a xenogenous origin.
C1 Dalhousie Univ, Ctr Comparat Genom & Evolutionary Bioinformat, Dept Biochem & Mol Biol, Halifax, NS B3M 4R2, Canada.
RP Gray, MW (corresponding author), Dalhousie Univ, Ctr Comparat Genom & Evolutionary Bioinformat, Dept Biochem & Mol Biol, Halifax, NS B3M 4R2, Canada.
EM m.w.gray@dal.ca
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AR a016097
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DA 2025-07-30
ER

PT S
AU Gilbert, JA
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AF Gilbert, Jack A.
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BE Carlson, CA
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TI Microbial Metagenomics: Beyond the Genome
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SE Annual Review of Marine Science
DT Review; Book Chapter
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C1 [Gilbert, Jack A.] Plymouth Marine Lab, Plymouth PL1 3DH, Devon, England.
   [Gilbert, Jack A.] Argonne Natl Lab, Argonne, IL 60439 USA.
   [Gilbert, Jack A.] Univ Chicago, Dept Ecol & Evolut, Chicago, IL 60637 USA.
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RP Gilbert, JA (corresponding author), Plymouth Marine Lab, Citadel Hill, Plymouth PL1 3DH, Devon, England.
EM gilbertjack@gmail.com; cdupont@jcvi.org
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NR 133
TC 242
Z9 295
PY 2011
VL 3
BP 347
EP 371
DI 10.1146/annurev-marine-120709-142811
UT WOS:000286638700013
DA 2025-07-30
ER

PT J
AU Hiraoka, S
   Sumida, T
   Hirai, M
   Toyoda, A
   Kawagucci, S
   Yokokawa, T
   Nunoura, T
AF Hiraoka, Satoshi
   Sumida, Tomomi
   Hirai, Miho
   Toyoda, Atsushi
   Kawagucci, Shinsuke
   Yokokawa, Taichi
   Nunoura, Takuro
TI Diverse DNA modification in marine prokaryotic and viral communities
SO NUCLEIC ACIDS RESEARCH
DT Article
AB DNA chemical modifications, including methylation, are widespread and play important roles in prokaryotes and viruses. However, current knowledge of these modification systems is severely biased towards a limited number of culturable prokaryotes, despite the fact that a vast majority of microorganisms have not yet been cultured. Here, using single-molecule real-time sequencing, we conducted culture-independent 'metaepigenomic' analyses (an integrated analysis of metagenomics and epigenomics) of marine microbial communities. A total of 233 and 163 metagenomic-assembled genomes (MAGs) were constructed from diverse prokaryotes and viruses, respectively, and 220 modified motifs and 276 DNA methyltransferases (MTases) were identified. Most of the MTase genes were not genetically linked with the endonuclease genes predicted to be involved in defense mechanisms against extracellular DNA. The MTase-motif correspondence found in the MAGs revealed 10 novel pairs, 5 of which showed novel specificities and experimentally confirmed the catalytic specificities of the MTases. We revealed novel alternative specificities in MTases that are highly conserved in Alphaproteobacteria, which may enhance our understanding of the co-evolutionary history of the methylation systems and the genomes. Our findings highlight diverse unexplored DNA modifications that potentially affect the ecology and evolution of prokaryotes and viruses in nature.
C1 [Hiraoka, Satoshi; Sumida, Tomomi; Nunoura, Takuro] Japan Agcy Marine Earth Sci & Technol JAMSTEC, Res Inst Marine Resources Utilizat, Res Ctr Biosci & Nanosci CeBN, Yokosuka, Kanagawa 2370061, Japan.
   [Hirai, Miho; Kawagucci, Shinsuke; Yokokawa, Taichi] Japan Agcy Marine Earth Sci & Technol JAMSTEC, Inst Extra Cutting Edge Sci & Technol Avant Garde, Yokosuka, Kanagawa 2370061, Japan.
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   [Kawagucci, Shinsuke] Japan Agcy Marine Earth Sci & Technol JAMSTEC, Res Inst Global Change RIGC, Marine Biodivers & Environm Assessment Res Ctr Bi, Yokosuka, Kanagawa 2370061, Japan.
RP Hiraoka, S (corresponding author), Japan Agcy Marine Earth Sci & Technol JAMSTEC, Res Inst Marine Resources Utilizat, Res Ctr Biosci & Nanosci CeBN, Yokosuka, Kanagawa 2370061, Japan.
EM hiraokas@jamstec.go.jp
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NR 104
TC 10
Z9 11
PD FEB 22
PY 2022
VL 50
IS 3
BP 1531
EP 1550
DI 10.1093/nar/gkab1292
UT WOS:000767881000027
DA 2025-07-30
ER

PT J
AU Coutinho, FH
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AF Coutinho, Felipe Hernandes
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DT Review
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RP Thompson, FL (corresponding author), Univ Fed Rio de Janeiro UFRJ, Inst Biol, Lab Microbiol, Rio De Janeiro, Brazil.; Thompson, FL (corresponding author), Fed Univ Fed Rio de Janeiro UFRJ, SAGE COPPE, Ctr Technol CT2, Rio De Janeiro, Brazil.
EM fabiano.thompson@biologia.ufrj.br
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NR 106
TC 48
Z9 59
PD NOV
PY 2018
VL 26
IS 11
BP 955
EP 965
DI 10.1016/j.tim.2018.05.015
UT WOS:000447272100009
DA 2025-07-30
ER

PT J
AU Wemheuer, B
   Güllert, S
   Billerbeck, S
   Giebel, HA
   Voget, S
   Simon, M
   Daniel, R
AF Wemheuer, Bernd
   Guellert, Simon
   Billerbeck, Sara
   Giebel, Helge-Ansgar
   Voget, Sonja
   Simon, Meinhard
   Daniel, Rolf
TI Impact of a phytoplankton bloom on the diversity of the active bacterial
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SO FEMS MICROBIOLOGY ECOLOGY
DT Article
AB Despite their importance for ecosystem functioning, little is known about the composition of active marine bacterioplankton communities. Hence, this study was focused on assessing the diversity of these communities in the southern North Sea and examining the impact of a phytoplankton spring bloom on the ambient bacterioplankton community. Community composition in and outside the bloom was assessed in 14 samples by pyrosequencing-based analysis of 16S rRNA gene amplicons generated from environmental RNA. The data set comprised of 211769 16S rRNA gene sequences. Proteobacteria were the predominant phylogenetic group with Alphaproteobacteria and Gammaproteobacteria as the most abundant classes. Actinobacteria and Bacteroidetes were identified in minor abundances. Active bacterial communities were dominated by few lineages such as the Roseobacter RCA cluster and the SAR92 clade. Community structures of three selected samples were also assessed by direct sequencing of cDNA generated from rRNA-depleted environmental RNA. Generated data sets comprised of 988202 sequences. Taxonomic assignment of the reads confirmed the predominance of Proteobacteria. The examined phytoplankton spring bloom affected the bacterioplankton community structures significantly. Bacterial richness was reduced in the bloom area, and the abundance of certain bacterial groups was affected by bloom presence. The SAR92 clade and the Roseobacter RCA cluster were significantly more abundant and active in the bloom. Functions affected by the bloom include photosynthesis, protein metabolism, and DNA metabolism.
C1 [Wemheuer, Bernd; Guellert, Simon; Voget, Sonja; Daniel, Rolf] Univ Gottingen, Inst Microbiol & Genet, Dept Genom & Appl Microbiol, D-37077 Gottingen, Germany.
   [Wemheuer, Bernd; Guellert, Simon; Voget, Sonja; Daniel, Rolf] Univ Gottingen, Inst Microbiol & Genet, Gottingen Genom Lab, D-37077 Gottingen, Germany.
   [Billerbeck, Sara; Giebel, Helge-Ansgar; Simon, Meinhard] Carl von Ossietzky Univ Oldenburg, Inst Chem & Biol Marine Environm ICBM, D-26111 Oldenburg, Germany.
RP Daniel, R (corresponding author), Univ Gottingen, Inst Microbiol & Genet, Dept Genom & Appl Microbiol, Grisebachstr 8, D-37077 Gottingen, Germany.
EM rdaniel@gwdg.de
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PD FEB
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VL 87
IS 2
BP 378
EP 389
DI 10.1111/1574-6941.12230
UT WOS:000331262700007
DA 2025-07-30
ER

PT J
AU DeLong, EE
AF DeLong, EE
TI Microbial community genomics in the ocean
SO NATURE REVIEWS MICROBIOLOGY
DT Review
AB Marine microbial communities were among the first microbial communities to be studied using cultivation-independent genomic approaches. Ocean-going genomic studies are now providing a more comprehensive description of the organisms and processes that shape microbial community structure, function and dynamics in the sea. Through the lens of microbial community genomics, a more comprehensive view of uncultivated microbial species, gene and biochemical pathway distributions, and naturally occurring genomic variability is being brought into sharper focus. Besides providing new perspectives on oceanic microbial communities, these new studies are now poised to reveal the fundamental principles that drive microbial ecological and evolutionary processes.
C1 MIT, Div Biol Engn, Cambridge, MA 02139 USA.
   MIT, Dept Civil & Environm Engn, Cambridge, MA 02139 USA.
RP MIT, Div Biol Engn, Room 48-427,77 Massachusetts Ave, Cambridge, MA 02139 USA.
EM delong@mit.edu
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PY 2005
VL 3
IS 6
BP 459
EP 469
DI 10.1038/nrmicro1158
UT WOS:000229435100011
DA 2025-07-30
ER

PT J
AU Hagström, Å
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DT Article
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   San Diego State Univ, Dept Biol, San Diego, CA 92182 USA.
EM ake.hagstrom@hik.se
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BP 3628
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DA 2025-07-30
ER

PT J
AU Crump, BC
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AF Crump, BC
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DT Article
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ER

PT J
AU Teeling, H
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DT Article
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C1 [Teeling, Hanno; Fuchs, Bernhard M.; Bennke, Christin M.; Krueger, Karen; Chafee, Meghan; Kappelmann, Lennart; Reintjes, Greta; Waldmann, Jost; Quast, Christian; Gloeckner, Frank Oliver; Amann, Rudolf I.] Max Planck Inst Marine Microbiol, Bremen, Germany.
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RP Teeling, H; Fuchs, BM; Amann, RI (corresponding author), Max Planck Inst Marine Microbiol, Bremen, Germany.
EM hteeling@mpi-bremen.de; bfuchs@mpi-bremen.de; ramann@mpi-bremen.de
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ER

PT J
AU Thingstad, TF
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AF Thingstad, T. Frede
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C1 [Thingstad, T. Frede; Pree, Bernadette; Giske, Jar; Vage, Selina] Univ Bergen, Dept Biol, Hjort Ctr Marine Ecosyst Dynam, N-5020 Bergen, Norway.
RP Thingstad, TF (corresponding author), Univ Bergen, Dept Biol, Hjort Ctr Marine Ecosyst Dynam, POB 7803, N-5020 Bergen, Norway.
EM frede.thingstad@uib.no
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NR 53
TC 19
Z9 20
PD APR 20
PY 2015
VL 6
AR 320
DI 10.3389/fmicb.2015.00320
UT WOS:000354788500002
DA 2025-07-30
ER

PT J
AU Ferrera, I
   Sebastian, M
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AF Ferrera, Isabel
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   Acinas, Silvia G.
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TI Prokaryotic functional gene diversity in the sunlit ocean: Stumbling in
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SO CURRENT OPINION IN MICROBIOLOGY
DT Review
AB Prokaryotes are extremely abundant in the ocean where they drive biogeochemical cycles. The recent development and application of -omics techniques has provided an astonishing amount of information revealing the existence of a vast diversity of functional genes and a large heterogeneity within each gene. The big challenge for microbial ecologists is now to understand the ecological relevance of this variability for ecosystem functioning, a question that remains largely understudied. This brief review highlights some of the latest advances in the study of the diversity of biogeochemically relevant functional genes in the sunlit ocean.
C1 [Ferrera, Isabel; Sebastian, Marta; Acinas, Silvia G.; Gasol, Josep M.] CSIC, Dept Biol Marina & Oceanog, Inst Ciencies Mar, E-08003 Barcelona, Catalunya, Spain.
RP Ferrera, I (corresponding author), CSIC, Dept Biol Marina & Oceanog, Inst Ciencies Mar, Pg Maritim Barceloneta 37-49, E-08003 Barcelona, Catalunya, Spain.
EM iferrera@icm.csic.es
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NR 59
TC 21
Z9 22
PD JUN
PY 2015
VL 25
BP 33
EP 39
DI 10.1016/j.mib.2015.03.007
UT WOS:000360510900007
DA 2025-07-30
ER

PT J
AU Aguirre, M
   Abad, D
   Albaina, A
   Gutiérrez-Muto, M
   Langa, J
   Goñi-Urriza, M
   Orruño, M
   Arana, I
   Estonba, A
   Zarraonaindia, I
AF Aguirre, Mikel
   Abad, David
   Albaina, Aitor
   Gutierrez-Muto, Mikel
   Langa, Jorge
   Goni-Urriza, Marisol
   Orruno, Maite
   Arana, Ines
   Estonba, Andone
   Zarraonaindia, Iratxe
TI Ecological status of Urdaibai Biosphere reserve based on bacterial
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SO MARINE AND FRESHWATER RESEARCH
DT Article
AB Context. The influence of anthropogenic pressures on plankton communities in well-flushed estuaries has been overlooked. Owing to this ecosystem's short water-residence time, they are foreseen to be mainly composed of microorganisms from neritic-oceanic sources, more resilient to anthropogenic impacts.Aims. This study characterises the bacterioplankton of Urdaibai, a small-drainage estuary located at a UNESCO biosphere reserve, to unravel its annual dynamic and ecological status.Methods. Amplicon sequencing was used to assess the euhaline bacterioplankton shifts and microgAMBI index depicted the ecological status of the estuary.Key results. A differentiated community was identified in upstream waters throughout the year. In addition, organisms commonly associated with faecal waste were detected. The ecological status of the estuary was poor or moderate along the annual cycle, but surprisingly worsened during winter.Conclusions. The above suggests that the bacterial community dynamic in this well-fluxed small-drainage estuary is more complex than anticipated. Importantly, the analysis of pollution-indicative bacteria proved that the water policy of this estuary needs to be further evaluated.Implications. The completion of an efficient sewage treatment system for this protected and touristic estuary is strongly recommended. Incorporating bacterial information to its current monitoring system will constitute a useful and valuable tool.
C1 [Aguirre, Mikel; Abad, David; Gutierrez-Muto, Mikel; Langa, Jorge; Estonba, Andone; Zarraonaindia, Iratxe] Univ Basque Country, UPV EHU, Fac Sci & Technol, Dept Genet Phys Anthropol & Anim Physiol, Leioa, Bizkaia, Spain.
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   [Abad, David] Agr Tech Inst Castilla & Leon ITACyL, Mol Biol & Microbiol Lab, Valladolid, Spain.
   [Albaina, Aitor] Univ Basque Country, UPV EHU, Fac Sci & Technol, Dept Zool & Anim Cell Biol, Leioa, Bizkaia, Spain.
   [Goni-Urriza, Marisol] Univ Pau & Pays Adour, Inst Sci Analyt & Physicochim Environm & Mat, CNRS, Pau, France.
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RP Zarraonaindia, I (corresponding author), Univ Basque Country, UPV EHU, Fac Sci & Technol, Dept Genet Phys Anthropol & Anim Physiol, Leioa, Bizkaia, Spain.
EM iratxe.zarraonaindia@ehu.eus
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TC 0
Z9 0
PY 2023
VL 74
IS 8
BP 651
EP 664
DI 10.1071/MF22072
EA MAY 2023
UT WOS:000982174500001
DA 2025-07-30
ER

PT J
AU Castledine, M
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AF Castledine, Meaghan
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DT Article
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RP Castledine, M (corresponding author), Univ Exeter, Environm & Sustainabil Inst, Cornwall TR10 9FE, England.
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NR 94
TC 17
Z9 17
PD OCT
PY 2024
VL 32
IS 10
BP 957
EP 969
DI 10.1016/j.tim.2024.02.014
EA OCT 2024
UT WOS:001368335000001
DA 2025-07-30
ER

PT J
AU Swan, BK
   Tupper, B
   Sczyrba, A
   Lauro, FM
   Martinez-Garcia, M
   González, JM
   Luo, HW
   Wright, JJ
   Landry, ZC
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   Thompson, BP
   Poulton, NJ
   Schwientek, P
   Acinas, SG
   Giovannoni, SJ
   Moran, MA
   Hallam, SJ
   Cavicchioli, R
   Woyke, T
   Stepanauskas, R
AF Swan, Brandon K.
   Tupper, Ben
   Sczyrba, Alexander
   Lauro, Federico M.
   Martinez-Garcia, Manuel
   Gonzalez, Jose M.
   Luo, Haiwei
   Wright, Jody J.
   Landry, Zachary C.
   Hanson, Niels W.
   Thompson, Brian P.
   Poulton, Nicole J.
   Schwientek, Patrick
   Acinas, Silvia G.
   Giovannoni, Stephen J.
   Moran, Mary Ann
   Hallam, Steven J.
   Cavicchioli, Ricardo
   Woyke, Tanja
   Stepanauskas, Ramunas
TI Prevalent genome streamlining and latitudinal divergence of planktonic
   bacteria in the surface ocean
SO PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
   AMERICA
DT Article
AB Planktonic bacteria dominate surface ocean biomass and influence global biogeochemical processes, but remain poorly characterized owing to difficulties in cultivation. Using large-scale single cell genomics, we obtained insight into the genome content and biogeography of many bacterial lineages inhabiting the surface ocean. We found that, compared with existing cultures, natural bacterioplankton have smaller genomes, fewer gene duplications, and are depleted in guanine and cytosine, noncoding nucleotides, and genes encoding transcription, signal transduction, and noncytoplasmic proteins. These findings provide strong evidence that genome streamlining and oligotrophy are prevalent features among diverse, free-living bacterioplankton, whereas existing laboratory cultures consist primarily of copiotrophs. The apparent ubiquity of metabolic specialization and mixotrophy, as predicted from single cell genomes, also may contribute to the difficulty in bacterioplankton cultivation. Using metagenome fragment recruitment against single cell genomes, we show that the global distribution of surface ocean bacterioplankton correlates with temperature and latitude and is not limited by dispersal at the time scales required for nucleotide substitution to exceed the current operational definition of bacterial species. Single cell genomes with highly similar small subunit rRNA gene sequences exhibited significant genomic and biogeographic variability, highlighting challenges in the interpretation of individual gene surveys and metagenome assemblies in environmental microbiology. Our study demonstrates the utility of single cell genomics for gaining an improved understanding of the composition and dynamics of natural microbial assemblages.
C1 [Swan, Brandon K.; Tupper, Ben; Thompson, Brian P.; Poulton, Nicole J.; Stepanauskas, Ramunas] Bigelow Lab Ocean Sci, East Boothbay, ME 04544 USA.
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RP Stepanauskas, R (corresponding author), Bigelow Lab Ocean Sci, East Boothbay, ME 04544 USA.
EM rstepanauskas@bigelow.org
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PD JUL 9
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IS 28
BP 11463
EP 11468
DI 10.1073/pnas.1304246110
UT WOS:000321827000063
DA 2025-07-30
ER

PT J
AU Joint, I
   Mühling, M
   Querellou, J
AF Joint, Ian
   Muehling, Martin
   Querellou, Joel
TI Culturing marine bacteria - an essential prerequisite for biodiscovery
SO MICROBIAL BIOTECHNOLOGY
DT Review
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C1 [Joint, Ian] Plymouth Marine Lab, Plymouth PL1 3DH, Devon, England.
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RP Joint, I (corresponding author), Plymouth Marine Lab, Prospect Pl, Plymouth PL1 3DH, Devon, England.
EM irj@pml.ac.uk
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SI SI
BP 564
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UT WOS:000289739300009
DA 2025-07-30
ER

PT J
AU Papale, M
   Rappazzo, AC
   Mikkonen, A
   Rizzo, C
   Moscheo, F
   Conte, A
   Michaud, L
   Lo Giudice, A
AF Papale, Maria
   Rappazzo, Alessandro Ciro
   Mikkonen, Anu
   Rizzo, Carmen
   Moscheo, Federica
   Conte, Antonella
   Michaud, Luigi
   Lo Giudice, Angelina
TI Bacterial Diversity in a Dynamic and Extreme Sub-Arctic Watercourse
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SO WATER
DT Article
AB Microbial communities promptly respond to the environmental perturbations, especially in the Arctic and sub-Arctic systems that are highly impacted by climate change, and fluctuations in the diversity level of microbial assemblages could give insights on their expected response. 16S rRNA gene amplicon sequencing was applied to describe the bacterial community composition in water and sediment through the sub-Arctic Pasvik River. Our results showed that river water and sediment harbored distinct communities in terms of diversity and composition at genus level. The distribution of the bacterial communities was mainly affected by both salinity and temperature in sediment samples, and by oxygen in water samples. Glacial meltwaters and runoff waters from melting ice probably influenced the composition of the bacterial community at upper and middle river sites. Interestingly, marine-derived bacteria consistently accounted for a small proportion of the total sequences and were also more prominent in the inner part of the river. Results evidenced that particular conditions occurring at sampling sites (such as algal blooms, heavy metal contamination and anaerobiosis) may select species at local scale from a shared bacterial pool, thus favoring certain bacterial taxa. Conversely, the few phylotypes specifically detected in some sites are probably due to localized external inputs introducing allochthonous microbial groups.
C1 [Papale, Maria; Rappazzo, Alessandro Ciro; Lo Giudice, Angelina] Natl Res Council CNR ISP, Inst Polar Sci, I-98122 Messina, Italy.
   [Mikkonen, Anu] Univ Jyvaskyla, Nanosci Ctr, Dept Biol & Environm Sci, Jyvaskyla 40014, Finland.
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   [Moscheo, Federica; Conte, Antonella; Michaud, Luigi] Univ Messina, Dept Chem Biol Pharmaceut & Environm Sci, I-98122 Messina, Italy.
RP Lo Giudice, A (corresponding author), Natl Res Council CNR ISP, Inst Polar Sci, I-98122 Messina, Italy.
EM maria.papale@isp.cnr.it; rappale@libero.com; anu.mikkonen@helsinki.fi;
   carmen.rizzo@szn.it; fede-mo@live.it; conte.antonella@outlook.com;
   lmichaud@unime.it; angelina.logiudice@cnr.it
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NR 56
TC 13
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PD NOV
PY 2020
VL 12
IS 11
AR 3098
DI 10.3390/w12113098
UT WOS:000594236600001
DA 2025-07-30
ER

PT J
AU Liu, L
   Chen, Q
   Chen, JX
   Chen, NW
   Zhong, KX
   Zheng, Q
AF Liu, Lu
   Chen, Qi
   Chen, Jiaxin
   Chen, Nengwang
   Zhong, Kevin Xu
   Zheng, Qiang
TI Role of virus-mediated lysis in spatiotemporal dynamics of prokaryotic
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SO LIMNOLOGY AND OCEANOGRAPHY
DT Article
AB Viral lysis accounts for approximately 50% of prokaryotic mortality, significantly influencing the diversity, composition, and succession of prokaryotic communities. Despite its importance, the specific influence of viral lysis on seasonal dynamics within aquatic ecosystems remains poorly understood. In this study, we investigated the seasonal dynamics of prokaryotes in the river-estuary-coastal ecosystem surrounding Xiamen Island and explored the environmental factors and virus-mediated cell lysis driving microbial seasonal successions across spatiotemporal scales. A taxon-specific cell lysis was applied to evaluate the contribution of viral lysis to seasonal variations in prokaryotes. Our findings revealed distinct spatiotemporal successions within the prokaryotic community structure, where temporal-related factors, spatial-related factors, and virus-mediated cell lysis contribute comparably to the seasonal variation of prokaryotes. The viral lysis controls on prokaryotic structures were determined by a significant negative correlation between the total microbial community and the cell lysis index (CLI) from amplicon sequence variant (ASV) to order levels. Viral lytic shaping on prokaryotic communities was more pronounced in the estuary-coastal compared to the river region, with similar seasonal variations noted. Specific ASVs, such as ASV3 (Nitrosopumilales), ASV2 (Synechococcales), ASV16 (Nitrosopumilales), and ASV17 (Oceanospirillales) were significantly correlated with CLI, highlighting the pivotal role of viral lysis in their seasonal succession. This study highlights the intricate interplay between microbial populations and viral lysis across spatiotemporal scales, enhancing our understanding of how top-down (virus-mediated cell lysis) and bottom-up (environmental factors) controls drive the seasonal variations in prokaryotic communities.
C1 [Liu, Lu; Chen, Qi; Chen, Jiaxin; Zheng, Qiang] Xiamen Univ, Inst Marine Microbes & Ecospheres, Coll Ocean & Earth Sci, State Key Lab Marine Environm Sci, Xiamen, Peoples R China.
   [Liu, Lu; Chen, Qi; Chen, Jiaxin; Zheng, Qiang] Xiamen Univ, Fujian Key Lab Marine Carbon Sequestrat, Xiamen, Peoples R China.
   [Chen, Qi] Oregon State Univ, Dept Microbiol, Corvallis, OR USA.
   [Chen, Nengwang] Xiamen Univ, Coll Environm & Ecol, Fujian Prov Key Lab Coastal Ecol & Environm Studie, Xiamen, Peoples R China.
   [Zhong, Kevin Xu] Univ British Columbia, Dept Earth Ocean & Atmospher Sci, Vancouver, BC, Canada.
RP Zheng, Q (corresponding author), Xiamen Univ, Inst Marine Microbes & Ecospheres, Coll Ocean & Earth Sci, State Key Lab Marine Environm Sci, Xiamen, Peoples R China.; Zheng, Q (corresponding author), Xiamen Univ, Fujian Key Lab Marine Carbon Sequestrat, Xiamen, Peoples R China.
EM zhengqiang@xmu.edu.cn
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BP 1518
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UT WOS:001469738500001
DA 2025-07-30
ER

PT J
AU Neuenschwander, SM
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AF Neuenschwander, Stefan M.
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DT Article
AB Actinobacteria of the acI lineage are the most abundant microbes in freshwater systems, but there are so far no pure living cultures of these organisms, possibly because of metabolic dependencies on other microbes. This, in turn, has hampered an in-depth assessment of the genomic basis for their success in the environment. Here we present genomes from 16 axenic cultures of acI Actinobacteria. The isolates were not only of minute cell size, but also among the most streamlined free-living microbes, with extremely small genome sizes (1.2-1.4 Mbp) and low genomic GC content. Genome reduction in these bacteria might have led to auxotrophy for various vitamins, amino acids and reduced sulphur sources, thus creating dependencies to co-occurring organisms (the ` Black Queen' hypothesis). Genome analyses, moreover, revealed a surprising degree of inter-and intraspecific diversity in metabolic pathways, especially of carbohydrate transport and metabolism, and mainly encoded in genomic islands. The striking genotype microdiversification of acI Actinobacteria might explain their global success in highly dynamic freshwater environments with complex seasonal patterns of allochthonous and autochthonous carbon sources. We propose a new order within Actinobacteria ('Candidatus Nanopelagicales') with two new genera ('Candidatus Nanopelagicus' and 'Candidatus Planktophila') and nine new species.
C1 [Neuenschwander, Stefan M.; Pernthaler, Jakob; Salcher, Michaela M.] Univ Zurich, Inst Microbial & Plant Biol, Limnol Stn, Zurich, Switzerland.
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RP Salcher, MM (corresponding author), Univ Zurich, Inst Plant & Microbial Biol, Limnol Stn, Seestr 187, CH-8802 Zurich, Switzerland.
EM michaelasalcher@gmail.com
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ER

PT J
AU Hill, PG
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AF Hill, Polly G.
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SO LIMNOLOGY AND OCEANOGRAPHY
DT Article
AB Bacterioplankton are the primary consumers of dissolved organic matter in the ocean, thus the quantification of bacterioplankton production (BP) is essential to our understanding of carbon cycling in the largest ecosystems on Earth. We compared BP, measured as the rate of C-14-leucine or H-3-leucine uptake at close to saturating concentration (20 nmol L-1), with ambient uptake measured from dilution bioassays. We hypothesized that saturation with leucine would lead to its respiration as a carbon source, thereby not truly representing ambient BP. Seawater was collected from the photic zone throughout the Atlantic Ocean. Respiration as a proportion of total consumption (uptake + respiration) of close to ambient (0.4 nmol L-1) and close to saturating (20 nmol L-1) C-14-leucine concentrations were compared. Saturating H-3-leucine additions overestimated ambient leucine uptake at low rates (200% +/- 100% ambient) and underestimated uptake at high rates (90% + 20% ambient). The proportion of total leucine uptake that was respired was threefold higher for 20 nmol L-1 C-14-leucine additions than 0.4 nmol L-1 C-14-leucine additions (15% +/- 8% and 5% +/- 4%, respectively). Consequently, microbial efficiency of leucine assimilation-an indicator of bacterioplankton growth efficiency-was significantly higher and more stable at close to ambient C-14-leucine additions than at saturating concentrations (95% +/- 4% and 85% +/- 8%, respectively). Thus, saturation of oligotrophic open Atlantic Ocean bacterioplankton with leucine, or other molecules indicative of microbial metabolism, leads to the measurement of a response to a nutrient addition, rather than an ambient measurement.
C1 [Hill, Polly G.; Zubkov, Mikhail V.] Natl Oceanog Ctr, Southampton, Hants, England.
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RP Zubkov, MV (corresponding author), Natl Oceanog Ctr, European Way, Southampton, Hants, England.
EM mvz@noc.ac.uk
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PT J
AU Ismail, N
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AF Ismail, Nasra
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DT Article
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C1 [Ismail, Nasra; Almutairi, Awatef] Kuwait Univ, Dept Biol Sci, Fac Sci, Safat, Kuwait.
RP Almutairi, A (corresponding author), Kuwait Univ, Dept Biol Sci, Fac Sci, Safat, Kuwait.
EM a.almutairi@ku.edu.kw
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NR 120
TC 6
Z9 6
PD APR 19
PY 2022
VL 9
AR 838101
DI 10.3389/fmars.2022.838101
UT WOS:000793313400001
DA 2025-07-30
ER

PT J
AU Våge, S
   Pree, B
   Thingstad, TF
AF Vage, Selina
   Pree, Bernadette
   Thingstad, T. Frede
TI Linking internal and external bacterial community control gives
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
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C1 [Vage, Selina] Univ Bergen, Dept Biol, N-5020 Bergen, Norway.
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RP Våge, S (corresponding author), Univ Bergen, Dept Biol, N-5020 Bergen, Norway.
EM selina.vage@uib.no
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NR 68
TC 9
Z9 9
PD NOV
PY 2016
VL 18
IS 11
SI SI
BP 3932
EP 3948
DI 10.1111/1462-2920.13391
UT WOS:000388614800025
DA 2025-07-30
ER

PT J
AU Traving, SJ
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AF Traving, Sachia J.
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   Pena, Angelica
   Krzywinski, Martin
   Robert, Marie
   Hallam, Steven J.
TI Prokaryotic responses to a warm temperature anomaly in northeast
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SO COMMUNICATIONS BIOLOGY
DT Article
AB Recent studies on marine heat waves describe water temperature anomalies causing changes in food web structure, bloom dynamics, biodiversity loss, and increased plant and animal mortality. However, little information is available on how water temperature anomalies impact prokaryotes (bacteria and archaea) inhabiting ocean waters. This is a nontrivial omission given their integral roles in driving major biogeochemical fluxes that influence ocean productivity and the climate system. Here we present a time-resolved study on the impact of a large-scale warm water surface anomaly in the northeast subarctic Pacific Ocean, colloquially known as the Blob, on prokaryotic community compositions. Multivariate statistical analyses identified significant depth- and season-dependent trends that were accentuated during the Blob. Moreover, network and indicator analyses identified shifts in specific prokaryotic assemblages from typically particle-associated before the Blob to taxa considered free-living and chemoautotrophic during the Blob, with potential implications for primary production and organic carbon conversion and export.
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C1 [Traving, Sachia J.; Kieft, Brandon; Ho, Grace Y.; Hallam, Steven J.] Univ British Columbia, Dept Microbiol & Immunol, Vancouver, BC V6T 1Z1, Canada.
   [Kellogg, Colleen T. E.] Hakai Inst, Heriot Bay, BC V0P 1H0, Canada.
   [Ross, Tetjana; Pena, Angelica; Robert, Marie] Inst Ocean Sci Fisheries & Ocean Canada, Sidney, BC, Canada.
   [McLaughlin, Ryan; Hallam, Steven J.] Univ British Columbia, Grad Program Bioinformat, Vancouver, BC V6T 1Z4, Canada.
   [Krzywinski, Martin] BC Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4S6, Canada.
   [Hallam, Steven J.] Univ British Columbia, Genome Sci & Technol Program, 2329 West Mall, Vancouver, BC V6T 1Z4, Canada.
   [Hallam, Steven J.] Univ British Columbia, Life Sci Inst, Vancouver, BC V6T 1Z3, Canada.
   [Hallam, Steven J.] Univ British Columbia, ECOSCOPE Training Program, Vancouver, BC V6T 1Z3, Canada.
   [Traving, Sachia J.] Univ Southern Denmark, HADAL & Nordcee, Dept Biol, Campusvej 55, DK-5230 Odense M, Denmark.
   [Ho, Grace Y.] Max Planck Inst Marine Microbiol, Celsiusstr 1, D-28359 Bremen, Germany.
RP Hallam, SJ (corresponding author), Univ British Columbia, Dept Microbiol & Immunol, Vancouver, BC V6T 1Z1, Canada.; Hallam, SJ (corresponding author), Univ British Columbia, Grad Program Bioinformat, Vancouver, BC V6T 1Z4, Canada.; Hallam, SJ (corresponding author), Univ British Columbia, Genome Sci & Technol Program, 2329 West Mall, Vancouver, BC V6T 1Z4, Canada.; Hallam, SJ (corresponding author), Univ British Columbia, Life Sci Inst, Vancouver, BC V6T 1Z3, Canada.; Hallam, SJ (corresponding author), Univ British Columbia, ECOSCOPE Training Program, Vancouver, BC V6T 1Z3, Canada.
EM shallam@mail.ubc.ca
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NR 124
TC 19
Z9 20
PD OCT 22
PY 2021
VL 4
IS 1
AR 1217
DI 10.1038/s42003-021-02731-9
UT WOS:000710158900004
DA 2025-07-30
ER

PT J
AU Grossart, HP
   Massana, R
   McMahon, KD
   Walsh, DA
AF Grossart, Hans-Peter
   Massana, Ramon
   McMahon, Katherine D.
   Walsh, David A.
TI Linking metagenomics to aquatic microbial ecology and biogeochemical
   cycles
SO LIMNOLOGY AND OCEANOGRAPHY
DT Article
AB Microbial communities are essential components of aquatic ecosystems through their contribution to food web dynamics and biogeochemical processes. Aquatic microbial diversity is immense and a general challenge is to understand how metabolism and interactions of single organisms shape microbial community dynamics and ecosystem-scale biogeochemical transformations. Metagenomic approaches have developed rapidly, and proven to be powerful in linking microbial community dynamics to biogeochemical processes. In this review, we provide an overview of metagenomic approaches, followed by a discussion on some recent insights they have provided, including those in this special issue. These include the discovery of new taxa and metabolisms in aquatic microbiomes, insights into community assembly and functional ecology as well as evolutionary processes shaping microbial genomes and microbiomes, and the influence of human activities on aquatic microbiomes. Given that metagenomics can now be considered a mature technology where data generation and descriptive analyses are relatively routine and informative, we then discuss metagenomic-enabled research avenues to further link microbial dynamics to biogeochemical processes. These include the integration of metagenomics into well-designed ecological experiments, the use of metagenomics to inform and validate metabolic and biogeochemical models, and the pressing need for ecologically relevant model organisms and simple microbial systems to better interpret the taxonomic and functional information integrated in metagenomes. These research avenues will contribute to a more mechanistic and predictive understanding of links between microbial dynamics and biogeochemical cycles. Owing to rapid climate change and human impacts on aquatic ecosystems, the urgency of such an understanding has never been greater.
C1 [Grossart, Hans-Peter] Leibniz Inst Freshwater Ecol & Inland Fisheries, Berlin, Germany.
   [Grossart, Hans-Peter] Potsdam Univ, Potsdam, Germany.
   [Massana, Ramon] CSIC, Inst Ciencies Mar, Barcelona, Catalonia, Spain.
   [McMahon, Katherine D.] Univ Wisconsin, Dept Civil & Environm Engn & Bacteriol, Madison, WI USA.
   [Walsh, David A.] Concordia Univ, Dept Biol, Montreal, PQ, Canada.
RP Walsh, DA (corresponding author), Concordia Univ, Dept Biol, Montreal, PQ, Canada.
EM david.walsh@concordia.ca
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NR 183
TC 107
Z9 113
PD JAN
PY 2020
VL 65
SU 1
SI SI
BP S2
EP S20
DI 10.1002/lno.11382
EA NOV 2019
UT WOS:000497259700001
DA 2025-07-30
ER

PT J
AU Jameson, BD
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AF Jameson, Brett D.
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SO COMMUNICATIONS BIOLOGY
DT Article
AB The mechanisms by which large-scale microbial community function emerges from complex ecological interactions between individual taxa and functional groups remain obscure. We leveraged network analyses of 16S rRNA amplicon sequences obtained over a seven-month timeseries in seasonally anoxic Saanich Inlet (Vancouver Island, Canada) to investigate relationships between microbial community structure and water column N2O cycling. Taxa separately broadly into three discrete subnetworks with contrasting environmental distributions. Oxycline subnetworks were structured around keystone aerobic heterotrophs that correlated with nitrification rates and N2O supersaturations, linking N2O production and accumulation to taxa involved in organic matter remineralization. Keystone taxa implicated in anaerobic carbon, nitrogen, and sulfur cycling in anoxic environments clustered together in a low-oxygen subnetwork that correlated positively with nitrification N2O yields and N2O production from denitrification. Close coupling between N2O producers and consumers in the anoxic basin is indicated by strong correlations between the low-oxygen subnetwork, PICRUSt2-predicted nitrous oxide reductase (nosZ) gene abundances, and N2O undersaturation. This study implicates keystone taxa affiliated with common ODZ groups as a potential control on water column N2O cycling and provides a theoretical basis for further investigations into marine microbial interaction networks.
   Network analysis of 16S rRNA-sequencing data collected over six months in the Sannich Inlet on Vancouver Island, Canada, suggests keystone microbial taxa that might contribute to water column N2O production and accumulation.
C1 [Jameson, Brett D.; Stevens, Catherine J.; Kim Juniper, S.] Univ Victoria, Sch Earth & Ocean Sci, POB 1700 Stn CSC, Victoria, BC V8W 2Y2, Canada.
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RP Jameson, BD (corresponding author), Univ Victoria, Sch Earth & Ocean Sci, POB 1700 Stn CSC, Victoria, BC V8W 2Y2, Canada.
EM bjameson@uvic.ca
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TC 3
Z9 3
PD FEB 23
PY 2023
VL 6
IS 1
AR 212
DI 10.1038/s42003-023-04597-5
UT WOS:000955679400008
DA 2025-07-30
ER

PT J
AU Bertagnolli, AD
   Stewart, FJ
AF Bertagnolli, Anthony D.
   Stewart, Frank J.
TI Microbial niches in marine oxygen minimum zones
SO NATURE REVIEWS MICROBIOLOGY
DT Review
AB In the ocean's major oxygen minimum zones (OMZs), oxygen is effectively absent from sea water and life is dominated by microorganisms that use chemicals other than oxygen for respiration. Recent studies that combine advanced genomic and chemical detection methods are delineating the different metabolic niches that microorganisms can occupy in OMZs. Understanding these niches, the microorganisms that inhabit them, and their influence on marine biogeochemical cycles is crucial as OMZs expand with increasing seawater temperatures.
C1 [Bertagnolli, Anthony D.; Stewart, Frank J.] Georgia Inst Technol, Sch Biol Sci, Atlanta, GA 30332 USA.
RP Stewart, FJ (corresponding author), Georgia Inst Technol, Sch Biol Sci, Atlanta, GA 30332 USA.
EM frank.stewart@biology.gatech.edu
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PY 2018
VL 16
IS 12
BP 723
EP 729
DI 10.1038/s41579-018-0087-z
UT WOS:000452616500007
DA 2025-07-30
ER

PT J
AU Khandeparker, L
   Kale, D
   Hede, N
   Anil, AC
AF Khandeparker, Lidita
   Kale, Dipesh
   Hede, Niyati
   Anil, Arga Chandrashekar
TI Application of functional metagenomics in the evaluation of microbial
   community dynamics in the Arabian Sea: Implications of environmental
   settings
SO JOURNAL OF ENVIRONMENTAL MANAGEMENT
DT Article
AB Ocean microbial communities form the base of marine food webs, facilitating energy transfer and nutrient cycling, thereby supporting higher trophic levels. We investigated their composition and functional profiles across depths (surface waters 0, 29, and 63 m and bottom waters 100, 150, and 200 m) in the central-eastern Arabian Sea (CEAS) using next-generation sequencing. It was hypothesized that the composition and functional diversity of these communities would be influenced by depth and environmental parameters. Our research showed that microbial communities vary with depth and are shaped by environmental factors like irradiance, temperature, dissolved oxygen, suspended particulate matter, chlorophyll a , and ammonia concentrations. Cyanobacteria ( Prochlorococcus sp) and Mamiellaceae, belonging to picoeukaryotes, exhibited distinct depth- specific distributions up to subsurface chlorophyll maxima (SCM) at 63 m. On the other hand, a community shift in the microbial communities comprising Firmicutes, Bacteroidetes, and Actinobacteria phyla was observed at the deeper water depths. The profiling of functional genes pointed out the expression of carbon fixation by photosynthetic organisms at the surface (0, 29, and 63 m), which shifted to prokaryotic carbon fixation in deeper waters (0, 150, and 200 m). Microcosm experiments (mixing of surface water with water from the SCM) carried out simulating disturbances such as climate change forced mixing (cyclones), revealed shifts in microbial structure and function. It was observed that within 48 h, the carbon fixation activity changed from photosynthetic organisms to prokaryotes and indicated an increase in stress-related biosynthetic pathways such as expression of quorum sensing, biosynthesis of antibiotics, lipopolysaccharides, and secondary metabolites. These findings have implications for predictive modelling of food web dynamics and fisheries management in the context of climate change.
C1 [Khandeparker, Lidita; Kale, Dipesh; Hede, Niyati; Anil, Arga Chandrashekar] Natl Inst Oceanog, CSIR, Panaji 403004, Goa, India.
RP Khandeparker, L (corresponding author), Natl Inst Oceanog, CSIR, Panaji 403004, Goa, India.
EM klidita@nio.res.in
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NR 128
TC 1
Z9 1
PD JAN
PY 2025
VL 373
AR 123449
DI 10.1016/j.jenvman.2024.123449
EA NOV 2024
UT WOS:001370989400001
DA 2025-07-30
ER

PT J
AU Fu, YY
   Keats, KF
   Rivkin, RB
   Lang, AS
AF Fu, Yunyun
   Keats, Kimberley F.
   Rivkin, Richard B.
   Lang, Andrew S.
TI Water mass and depth determine the distribution and diversity of
   Rhodobacterales in an Arctic marine system
SO FEMS MICROBIOLOGY ECOLOGY
DT Article
AB Marine Rhodobacterales are recognized as a widespread, abundant, and metabolically versatile bacterial group in the world's oceans. They also show a nearly universal conservation of the genes for production of gene transfer agents (GTAs), virus-like particles that mediate genetic exchange between cells. It is not yet clear what factors determine the distribution of the various taxonomic subgroups of this order. To address this question, we analyzed the Rhodobacterales communities in 10 seawater samples from northern Baffin Bay collected during September 2008. A conserved gene from the GTA gene cluster was used to characterize the Rhodobacterales community structure. A total of 320 clones from 10 clone libraries were sequenced, and 22 operational taxonomic units representing putative species and 13 clusters representing putative genera were identified. A cluster related to Octadecabacter comprised 59% of total clones from the northern Baffin Bay. Phylogenetic analysis of the clones showed that the Rhodobacterales communities had distinct compositions in the different water masses that were sampled. A change in community structure related to depth was also observed. Therefore, in northern Baffin Bay where two ocean currents meet and mix, the Rhodobacterales community structures were primarily determined by water mass and depth.
C1 [Fu, Yunyun; Lang, Andrew S.] Mem Univ Newfoundland, Dept Biol, St John, NF A1B 3X9, Canada.
   [Keats, Kimberley F.; Rivkin, Richard B.] Mem Univ Newfoundland, Dept Ocean Sci, Ctr Ocean Sci, St John, NF A1B 3X9, Canada.
RP Lang, AS (corresponding author), Mem Univ Newfoundland, Dept Biol, St John, NF A1B 3X9, Canada.
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NR 77
TC 20
Z9 24
PD JUN
PY 2013
VL 84
IS 3
BP 564
EP 576
DI 10.1111/1574-6941.12085
UT WOS:000318932300011
DA 2025-07-30
ER

PT J
AU Halsey, KH
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AF Halsey, Kimberly H.
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DT Article
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RP Halsey, KH (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
EM halseyk@science.oregonstate.edu
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NR 56
TC 65
Z9 68
PD MAR
PY 2012
VL 14
IS 3
BP 630
EP 640
DI 10.1111/j.1462-2920.2011.02605.x
UT WOS:000302539900007
DA 2025-07-30
ER

PT J
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AF Brown, Mark V.
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DT Article
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Z9 22
PD FEB 2
PY 2007
VL 46
IS 2
BP 107
EP 115
DI 10.3354/ame046107
UT WOS:000244426800001
DA 2025-07-30
ER

PT J
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RP Kalmar Univ, S-39182 Kalmar, Sweden.
EM ake.hagstrom@hik.se
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VL 41
IS 1
BP 79
EP 89
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UT WOS:000233696000008
DA 2025-07-30
ER

PT J
AU Pajares, S
AF Pajares, Silvia
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DT Article
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RP Pajares, S (corresponding author), Univ Nacl Autonoma Mexico, Inst Ciencias Mar & Limnol, Unidad Acad Ecol & Biodiversidad Acuat, Mexico City 04510, DF, Mexico.
EM spajares@cmarl.unam.mx
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DA 2025-07-30
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PT J
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DA 2025-07-30
ER

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C1 [Li, Weiwei; Zhang, Fenfen; Ye, Qi; Wu, Dan; Deng, Bing; Du, Jinzhou] East China Normal Univ, State Key Lab Estuarine & Coastal Res, 3663 North Zhongshan Rd, Shanghai 200062, Peoples R China.
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RP Zhang, FF (corresponding author), East China Normal Univ, State Key Lab Estuarine & Coastal Res, 3663 North Zhongshan Rd, Shanghai 200062, Peoples R China.
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NR 75
TC 67
Z9 80
PD APR
PY 2017
VL 172
BP 496
EP 504
DI 10.1016/j.chemosphere.2017.01.008
UT WOS:000394065200056
DA 2025-07-30
ER

PT J
AU Malmstrom, RR
   Coe, A
   Kettler, GC
   Martiny, AC
   Frias-Lopez, J
   Zinser, ER
   Chisholm, SW
AF Malmstrom, Rex R.
   Coe, Allison
   Kettler, Gregory C.
   Martiny, Adam C.
   Frias-Lopez, Jorge
   Zinser, Erik R.
   Chisholm, Sallie W.
TI Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and
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SO ISME JOURNAL
DT Article
AB To better understand the temporal and spatial dynamics of Prochlorococcus populations, and how these populations co-vary with the physical environment, we followed monthly changes in the abundance of five ecotypes-two high-light adapted and three low-light adapted-over a 5-year period in coordination with the Bermuda Atlantic Time Series (BATS) and Hawaii Ocean Time-series (HOT) programs. Ecotype abundance displayed weak seasonal fluctuations at HOT and strong seasonal fluctuations at BATS. Furthermore, stable 'layered' depth distributions, where different Prochlorococcus ecotypes reached maximum abundance at different depths, were maintained consistently for 5 years at HOT. Layered distributions were also observed at BATS, although winter deep mixing events disrupted these patterns each year and produced large variations in ecotype abundance. Interestingly, the layered ecotype distributions were regularly reestablished each year after deep mixing subsided at BATS. In addition, Prochlorococcus ecotypes each responded differently to the strong seasonal changes in light, temperature and mixing at BATS, resulting in a reproducible annual succession of ecotype blooms. Patterns of ecotype abundance, in combination with physiological assays of cultured isolates, confirmed that the low-light adapted eNATL could be distinguished from other low-light adapted ecotypes based on its ability to withstand temporary exposure to high-intensity light, a characteristic stress of the surface mixed layer. Finally, total Prochlorococcus and Synechococcus dynamics were compared with similar time series data collected a decade earlier at each location. The two data sets were remarkably similar-testimony to the resilience of these complex dynamic systems on decadal time scales. The ISME Journal (2010) 4, 1252-1264; doi: 10.1038/ismej.2010.60; published online 13 May 2010
C1 [Malmstrom, Rex R.; Coe, Allison; Martiny, Adam C.; Frias-Lopez, Jorge; Zinser, Erik R.; Chisholm, Sallie W.] MIT, Dept Civil & Environm Engn, Cambridge, MA 02139 USA.
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RP Chisholm, SW (corresponding author), MIT, Dept Civil & Environm Engn, 15 Vassar St, Cambridge, MA 02139 USA.
EM chisholm@mit.edu
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PY 2010
VL 4
IS 10
BP 1252
EP 1264
DI 10.1038/ismej.2010.60
UT WOS:000282250400004
DA 2025-07-30
ER

PT J
AU Xu, PH
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AF Xu, Peihang
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SO FRONTIERS IN MARINE SCIENCE
DT Article
AB Microbial plankton is essential for ocean biogeochemistry. As part of the prokaryotic phototrophic microbial community, both oxygenic phototrophs (OP) and anoxygenic phototrophs (AP) are widely distributed in the ocean and may play a significant role in carbon flow and oxygen production. However, comparative studies of microbial OP and AP have received very little attention, even though their different roles might be important in various marine environments, especially in oxygen minimum zones (OMZ). We explored the spatial distribution of the microbial community in the Baltic Sea, including an OMZ region, with a particular focus on the distribution and activity of OP and AP. We used 16S rRNA amplicon sequencing in combination with a qPCR-based quantification of photosynthesis marker genes. We found that specific bacterial groups dominated surface and intermediate depths, the OMZ, and deep waters, respectively. Salinity, temperature, oxygen, and depth were significant factors explaining the microbial community composition and distribution. A high diversity of OP and AP was observed, including OP-Chlorophyta, Diatoms, Cyanobacteria and Cryptomonads, and AP-Proteobacteria and Chloroflexota. OP were more abundant at most stations compared to AP. OP showed high photosynthetic activity and more photosynthesis activity in higher temperature and upper waters, while AP photosynthesis cannot be detected in most stations. Both, cyanobacterial and eukaryotic OP preferred to live in higher temperature and upper waters, but Cyanobacteria also preferred to live in oxic water while the whole OP community showed preference to live in higher salinity area. However, AP did not show any significant hydrochemical preference but prefer to live with OP community. The Baltic Sea is exposed to multiple climate change related stressors, such as warming, decreasing salinity, and deoxygenation. This study contributes to understanding and interpretation of how microbial community, especially phototrophic groups, might shift in their distribution and activity in a changing ocean like the Baltic Sea.
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RP Xu, PH (corresponding author), Univ Southern Denmark, Dept Biol, Nordcee, Odense, Denmark.
EM peihang@biology.sdu.dk
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NR 96
TC 3
Z9 4
PD JAN 6
PY 2022
VL 8
AR 773210
DI 10.3389/fmars.2021.773210
UT WOS:000745844200001
DA 2025-07-30
ER

PT J
AU Sosa, OA
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   Repeta, DJ
   DeLong, EF
AF Sosa, Oscar A.
   Gifford, Scott M.
   Repeta, Daniel J.
   DeLong, Edward F.
TI High molecular weight dissolved organic matter enrichment selects for
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SO ISME JOURNAL
DT Article
AB The role of bacterioplankton in the cycling of marine dissolved organic matter (DOM) is central to the carbon and energy balance in the ocean, yet there are few model organisms available to investigate the genes, metabolic pathways, and biochemical mechanisms involved in the degradation of this globally important carbon pool. To obtain microbial isolates capable of degrading semi-labile DOM for growth, we conducted dilution to extinction cultivation experiments using seawater enriched with high molecular weight (HMW) DOM. In total, 93 isolates were obtained. Amendments using HMW DOM to increase the dissolved organic carbon concentration 4x (280 mu M) or 10x (700 mu M) the ocean surface water concentrations yielded positive growth in 4-6% of replicate dilutions, whereas <1% scored positive for growth in non-DOM-amended controls. The majority (71%) of isolates displayed a distinct increase in cell yields when grown in increasing concentrations of HMW DOM. Whole-genome sequencing was used to screen the culture collection for purity and to determine the phylogenetic identity of the isolates. Eleven percent of the isolates belonged to the gammaproteobacteria including Alteromonadales (the SAR92 clade) and Vibrio. Surprisingly, 85% of isolates belonged to the methylotrophic OM43 clade of betaproteobacteria, bacteria thought to metabolically specialize in degrading C1 compounds. Growth of these isolates on methanol confirmed their methylotrophic phenotype. Our results indicate that dilution to extinction cultivation enrichede with natural sources of organic substrates has a potential to reveal the previously unsuspected relationships between naturally occurring organic nutrients and the microorganisms that consume them.
C1 [Sosa, Oscar A.; DeLong, Edward F.] Univ Hawaii, Ctr Microbial Oceanog Res & Educ, Honolulu, HI 96822 USA.
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   [Repeta, Daniel J.] Woods Hole Oceanog Inst, Dept Marine Chem & Geochem, Woods Hole, MA 02543 USA.
RP DeLong, EF (corresponding author), Univ Hawaii, Ctr Microbial Oceanog Res & Educ, Honolulu, HI 96822 USA.
EM edelong@hawaii.edu
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NR 74
TC 43
Z9 46
PD DEC
PY 2015
VL 9
IS 12
BP 2725
EP 2739
DI 10.1038/ismej.2015.68
UT WOS:000365094400015
DA 2025-07-30
ER

PT J
AU Aghababa, MP
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AF Aghababa, Mohammad Pourmahmood
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TI Exploration and demonstration of explainable machine learning models in
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SO PLOS ONE
DT Article
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C1 [Aghababa, Mohammad Pourmahmood; Andrysek, Jan] Univ Toronto, Inst Biomed Engn, Toronto, ON, Canada.
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RP Aghababa, MP (corresponding author), Univ Toronto, Inst Biomed Engn, Toronto, ON, Canada.; Aghababa, MP (corresponding author), Holland Bloorview Kids Rehabil Hosp, Bloorview Res Inst, Toronto, ON, Canada.
EM m.p.aghababa@gmail.com
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TC 1
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DA 2025-07-30
ER

PT J
AU Suominen, S
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SO LIMNOLOGY AND OCEANOGRAPHY
DT Article
AB Large quantities of carbon are stored in marine dissolved organic matter (DOM), and its recycling has a major effect on the carbon cycle. Microbes are responsible for turnover of DOM. Little is known about how the complex pool of DOM shapes microbial communities and vice versa, especially in anoxic systems. In this study, we characterized the DOM pool with high-resolution Fourier transform ion cyclotron resonance mass spectrometry and analyzed the microbial community composition with 16S rRNA gene amplicon sequencing across a redox gradient in the Black Sea. The chemical stratification of the water column was clearly reflected in the microbial community, with different putative autotrophic taxa abundant across redox zones. The nitrate maximum was characterized by a high abundance of Thaumarchaeota, the suboxic zone by Gammaproteobacteria Chromatiales, while Epsilonbacteraeota Campylobacterales were abundant at the onset of the sulfidic zone. Compared to the variance in the microbial community, the molecular composition of DOM was relatively uniform across the sampled depths. However, underlying differences in the oxidation state of the DOM molecular formulas showed distinct changes that were linked to the redox zones, possibly connecting autotrophic metabolisms to changes in the DOM composition. In addition, known heterotrophs like Planctomycetes Phycisphaerae and Chloroflexi Anaerolineales were linked to more oxidized molecular forms of DOM, and not to the identified redox zones, suggesting that these fermentative organisms are reliant on newly formed carbon molecules. Our study suggests that the metabolism of autotrophic microbes influences the composition of DOM across the Black Sea water column.
C1 [Suominen, Saara; Damste, Jaap S. Sinninghe; Villanueva, Laura] NIOZ Royal Netherlands Inst Sea Res, Dept Marine Microbiol & Biogeochem, Texel, Netherlands.
   [Gomez-Saez, Gonzalo, V; Dittmar, Thorsten] Carl von Ossietzky Univ Oldenburg, Inst Chem & Biol Marine Environm ICBM, Res Grp Marine Geochem ICBM MPI Bridging Grp, Oldenburg, Germany.
   [Dittmar, Thorsten] Carl von Ossietzky Univ Oldenburg, Helmholtz Inst Funct Marine Biodivers HIFMB, Oldenburg, Germany.
   [Damste, Jaap S. Sinninghe; Villanueva, Laura] Univ Utrecht, Fac Geosci, Dept Earth Sci, Utrecht, Netherlands.
RP Villanueva, L (corresponding author), NIOZ Royal Netherlands Inst Sea Res, Dept Marine Microbiol & Biogeochem, Texel, Netherlands.; Villanueva, L (corresponding author), Univ Utrecht, Fac Geosci, Dept Earth Sci, Utrecht, Netherlands.
EM laura.villanueva@nioz.nl
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NR 101
TC 9
Z9 10
PD FEB
PY 2022
VL 67
IS 2
BP 329
EP 347
DI 10.1002/lno.11995
EA DEC 2021
UT WOS:000734100300001
DA 2025-07-30
ER

PT J
AU Hu, C
   Chen, XW
   Yu, LQ
   Xu, DP
   Jiao, NZ
AF Hu, Chen
   Chen, Xiaowei
   Yu, Liuqian
   Xu, Dapeng
   Jiao, Nianzhi
TI Elevated Contribution of Low Nucleic Acid Prokaryotes and Viral Lysis to
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SO FRONTIERS IN MICROBIOLOGY
DT Article
AB Prokaryotes represent the largest living biomass reservoir in aquatic environments and play a crucial role in the global ocean. However, the factors that shape the abundance and potential growth rate of the ecologically distinct prokaryotic subgroups [i.e., high nucleic acid (HNA) and low nucleic acid (LNA) cells] along varying trophic conditions in the ocean remain poorly understood. This study conducted a series of modified dilution experiments to investigate how the abundance and potential growth rate of HNA and LNA prokaryotes and their regulating factors (i.e., protozoan grazing and viral lysis) change along a cross-shore nutrient gradient in the northern South China Sea. The results showed that the abundance of both HNA and LNA cells was significantly positively correlated with the abundance of heterotrophic nanoflagellates and viruses, whereas only HNA abundance exhibited a significant positive correlation with nutrient level. With a decreasing nutrient concentration, the potential growth rate of the HNA subgroup declined significantly, while that of the LNA subgroup was significantly enhanced, leading to an elevated relative potential growth rate of the LNA to HNA subgroup under decreasing nutrient levels. Furthermore, our data revealed different regulatory roles of protozoan grazing and viral lysis on the HNA and LNA subgroups, with HNA suffering higher mortality pressure from grazing than from lysis in contrast to LNA, which experienced equivalent pressures. As the nutrient levels declined, the relative contribution of lysis to the mortality of the HNA subgroup increased significantly, in contrast to the insignificant change in that of the LNA subgroup. Our results indicated the elevated role of LNA cells in the prokaryotic community and the enhanced viral lysis pressure on the total prokaryotes under oligotrophic conditions. This implies a weakened efficiency of carbon cycling within the microbial loop and enhanced viral lysis to shunt more carbon and energy flow in the future ocean, in which oligotrophication will be strengthened due to global warming.
C1 [Hu, Chen; Chen, Xiaowei; Xu, Dapeng; Jiao, Nianzhi] Xiamen Univ, Inst Marine Microbes & Ecospheres, Coll Ocean & Earth Sci, State Key Lab Marine Environm Sci, Xiamen, Peoples R China.
   [Hu, Chen; Chen, Xiaowei; Xu, Dapeng; Jiao, Nianzhi] Xiamen Univ, Fujian Key Lab Marine Carbon Sequestrat, Xiamen, Peoples R China.
   [Yu, Liuqian] Hong Kong Univ Sci & Technol, Dept Ocean Sci, Hong Kong, Peoples R China.
RP Xu, DP; Jiao, NZ (corresponding author), Xiamen Univ, Inst Marine Microbes & Ecospheres, Coll Ocean & Earth Sci, State Key Lab Marine Environm Sci, Xiamen, Peoples R China.; Xu, DP; Jiao, NZ (corresponding author), Xiamen Univ, Fujian Key Lab Marine Carbon Sequestrat, Xiamen, Peoples R China.
EM dapengxu@xmu.edu.cn; jiao@xmu.edu.cn
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NR 72
TC 12
Z9 13
PD DEC 15
PY 2020
VL 11
AR 612053
DI 10.3389/fmicb.2020.612053
UT WOS:000603027000001
DA 2025-07-30
ER

PT J
AU Rhodes, LD
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AF Rhodes, Linda D.
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TI Nearshore microbial communities of the Pacific Northwest coasts of
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SO FRONTIERS IN MARINE SCIENCE
DT Article
AB A survey of marine pelagic coastal microbial communities was conducted over a large geographic latitude range, from Cape Mendocino in northern California USA to Queen Charlotte Sound in British Columbia Canada, during the spring to summer transition. DNA metabarcoding and flow cytometry were used to characterize microbial communities. Physical and chemical oceanography indicated moderate conditions during the survey with no widespread upwelling, marine heat wave, or other extreme conditions. However, four locations displayed features approaching acidified conditions: Heceta Head, Newport, Copalis Beach, and Cape Flattery. Although bacterial and archaeal communities at the Juan de Fuca canyon and northward had high similarity, those south of the Juan de Fuca canyon were well differentiated from each other. In contrast, eukaryotic microbial communities exhibited stronger geographic differentiation than bacterial and archaeal communities across the extent of the survey. Seawater parameters that were best predictors of bacterial and archaeal community structure were temperature, pH, and dissolved inorganic nutrients (nitrate, phosphate, silicate), while those that were best predictors of eukaryotic microbial community structure were salinity, dissolved oxygen, total alkalinity, and dissolved inorganic nutrients (nitrite, silicate). Although five bacterial and archaeal indicators for potentially corrosive waters were identified (Colwellia, Nitrosopumilus, Nitrosopelagicus, Sup05 cluster, Sva0996 marine group), no eukaryotic microbial indicators were found. Potentially pathogenic taxa detected in the survey included four disease-causing bacteria for mammals, finfish, and/or shellfish (Coxiella, Flavobacterium, Francisella, Tenacibaculum), sixteen genera of microalgae capable of producing biotoxins, and fifteen parasitic species. This study demonstrates the value of coordinating microbial sampling and analysis with broad-scale oceanographic surveys to generate insights into community structures of these important pelagic trophic levels.
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   [Gallego Simon, Ramon] Univ Autonoma Madrid, Biol Dept Univ, Unidad Genet, Madrid, Spain.
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RP Rhodes, LD (corresponding author), Natl Ocean & Atmospher Adm NOAA Fisheries, Northwest Fisheries Sci Ctr, Seattle, WA 98115 USA.
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NR 146
TC 1
Z9 1
PD SEP 5
PY 2024
VL 11
AR 1430930
DI 10.3389/fmars.2024.1430930
UT WOS:001315327800001
DA 2025-07-30
ER

PT J
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DT Article
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NR 38
TC 68
Z9 70
PD JAN
PY 2002
VL 4
IS 1
BP 42
EP 50
DI 10.1046/j.1462-2920.2002.00255.x
UT WOS:000174890800018
DA 2025-07-30
ER

PT J
AU Poole, AM
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AF Poole, Anthony M.
   Gribaldo, Simonetta
TI Eukaryotic Origins: How and When Was the Mitochondrion Acquired?
SO COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY
DT Article
AB Comparative genomics has revealed that the last eukaryotic common ancestor possessed the hallmark cellular architecture of modern eukaryotes. However, the remarkable success of such analyses has created a dilemma. If key eukaryotic features are ancestral to this group, then establishing the relative timing of their origins becomes difficult. In discussions of eukaryote origins, special significance has been placed on the timing of mitochondrial acquisition. In one view, mitochondrial acquisition was the trigger for eukaryogenesis. Others argue that development of phagocytosis was a prerequisite to acquisition. Results from comparative genomics and molecular phylogeny are often invoked to support one or the other scenario. We show here that the associations between specific cell biological models of eukaryogenesis and evolutionary genomic data are not as strong as many suppose. Disentangling these eliminates many of the arguments that polarize current debate.
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RP Poole, AM (corresponding author), Univ Canterbury, Sch Biol Sci, Christchurch 8140, New Zealand.
EM anthony.poole@canterbury.ac.nz; simonetta.gribaldo@pasteur.fr
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NR 83
TC 69
Z9 71
PD DEC
PY 2014
VL 6
IS 12
AR a015990
DI 10.1101/cshperspect.a015990
UT WOS:000346449100008
DA 2025-07-30
ER

PT J
AU Thrash, JC
AF Thrash, J. Cameron
TI Towards culturing the microbe of your choice
SO ENVIRONMENTAL MICROBIOLOGY REPORTS
DT Editorial Material
C1 [Thrash, J. Cameron] Univ Southern Calif, Dept Biol Sci, Los Angeles, CA 90089 USA.
RP Thrash, JC (corresponding author), Univ Southern Calif, Dept Biol Sci, Los Angeles, CA 90089 USA.
EM joz.ennn@gmail.com
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NR 86
TC 9
Z9 10
PD FEB
PY 2021
VL 13
IS 1
BP 36
EP 41
DI 10.1111/1758-2229.12898
EA OCT 2020
UT WOS:000583194100001
DA 2025-07-30
ER

PT J
AU Zhong, X
   Jacquet, S
AF Zhong, Xu
   Jacquet, Stephan
TI Differing assemblage composition and dynamics in T4-like myophages of
   two neighbouring sub-alpine lakes
SO FRESHWATER BIOLOGY
DT Article
AB 1. Bacteriophages play an important role in plankton population dynamics and biogeochemical cycling, but their community dynamics and diversity are still poorly known, especially in fresh waters.
   2. We conducted a 1-year investigation of the T4-like bacteriophages in the surface waters of two Western European peri-alpine lakes (lakes Annecy and Bourget), using fingerprinting and cloning-sequencing approaches targeting the major capsid protein g23 gene.
   3. Our results suggest that T4-like bacteriophages are diverse (we found several new sequences) and differed substantially between the two lakes. Further, these phages displayed seasonal patterns with marked shifts in community composition.
   4. Examining the dynamics of some individual constituents (e. g. DGGE bands), we found that (i) the majority of these myoviruses were rare (mean relative abundance <1%) and only a few were abundant (mean relative abundance >5%); (ii) the dominance of the most abundant DGGE bands changed throughout the year and their dynamics were very different between the two lakes; (iii) only a few bands (e. g. <20%) were detectable throughout the year and their proportion was higher in the oligomesotrophic Lake Bourget.
   5. Our results suggest a highly dynamic T4-like myoviral assemblage. T4-like-viruses seem to conform to a standard model of community organisation and a common type of species abundance curve, with mainly rare organisms that occasionally may become abundant (termed a 'seed bank' for virus assemblages).
C1 [Zhong, Xu; Jacquet, Stephan] INRA, UMR CARRTEL, Thonon Les Bains, France.
RP Jacquet, S (corresponding author), INRA, Stn Hydrobiol, UMR CARRTEL, F-74203 Thonon Les Bains, France.
EM sjacquet@thonon.inra.fr
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NR 75
TC 15
Z9 17
PD AUG
PY 2014
VL 59
IS 8
BP 1577
EP 1595
DI 10.1111/fwb.12365
UT WOS:000339385100002
DA 2025-07-30
ER

PT J
AU Aalto, NJ
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   Krsmanovic, S
   Campbell, K
   Bernstein, HC
AF Aalto, Nerea J.
   Schweitzer, Hannah D.
   Krsmanovic, Stina
   Campbell, Karley
   Bernstein, Hans C.
TI Diversity and Selection of Surface Marine Microbiomes in the
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SO FRONTIERS IN MICROBIOLOGY
DT Article
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C1 [Aalto, Nerea J.; Schweitzer, Hannah D.; Krsmanovic, Stina; Campbell, Karley; Bernstein, Hans C.] UiT Arctic Univ Norway, Fac Biosci Fisheries & Econ, Tromso, Norway.
   [Aalto, Nerea J.; Schweitzer, Hannah D.; Bernstein, Hans C.] UiT Arctic Univ Norway, Arctic Ctr Sustainable Energy, Tromso, Norway.
RP Bernstein, HC (corresponding author), UiT Arctic Univ Norway, Fac Biosci Fisheries & Econ, Tromso, Norway.; Bernstein, HC (corresponding author), UiT Arctic Univ Norway, Arctic Ctr Sustainable Energy, Tromso, Norway.
EM hans.c.bernstein@uit.no
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NR 91
TC 14
Z9 14
PD JUL 14
PY 2022
VL 13
AR 892634
DI 10.3389/fmicb.2022.892634
UT WOS:000886959500001
DA 2025-07-30
ER

PT J
AU Urbach, E
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AF Urbach, E
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SO LIMNOLOGY AND OCEANOGRAPHY
DT Article
AB The bacterioplankton assemblage in Crater Lake, Oregon (U.S.A.), is different from communities found in other oxygenated lakes, as demonstrated by four small subunit ribosomal ribonucleic acid (SSU rRNA) gene clone libraries and oligonucleotide probe hybridization to RNA from lake water. Populations in the euphotic zone of this deep (589 m), oligotrophic caldera lake are dominated by two phylogenetic clusters of currently uncultivated bacteria: CL120-10, a newly identified cluster in the verrucomicrobiales, and ACK4 actinomycetes, known as a minor constituent of bacterioplankton in other lakes. Deep-water populations at 300 and 500 m are dominated by a different pair of uncultivated taxa: CL500-11, a novel cluster in the green nonsulfur bacteria, and group I marine crenarchaeota. beta -Proteobacteria, dominant in most other freshwater environments, are relatively rare in Crater Lake (less than or equal to 16% of nonchloroplast bacterial rRNA at all depths). Other taxa identified in Crater Lake libraries include a newly identified candidate bacterial division, ABY1, and a newly identified subcluster, CL0-1, within candidate division OP10. Probe analyses confirmed vertical stratification of several microbial groups, similar to patterns observed in open-ocean systems. Additional similarities between Crater Lake and ocean microbial populations include aphotic zone dominance of group I marine crenarchaeota and green nonsulfur bacteria. Comparison of Crater Lake to other lakes studied by rRNA methods suggests that selective factors structuring Crater Lake bacterioplankton populations may include low concentrations of available trace metals and dissolved organic matter, chemistry of infiltrating hydrothermal waters, and irradiation by high levels of ultraviolet light.
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   Oregon State Univ, Forest Sci Lab, USGS Forest & Rangeland Ecosyst Sci Ctr, Corvallis, OR 97331 USA.
RP Urbach, E (corresponding author), Univ Tennessee, Dept Microbiol, Knoxville, TN 37996 USA.
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TC 177
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BP 557
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PT J
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DT Article
AB Marine picoplankton are central mediators of many oceanic biogeochemical processes, but much of their biology and ecology remains ill defined. One approach to better defining these environmentally significant microbes involves the acquisition of genomic data that can provide information about genome content, metabolic capabilities, and population variability in picoplankton assemblages. Previously, we constructed and phylogenetically screened a Bacterial Artificial Chromosome (BAC) library from surface water picoplankton of Monterey Bay. To further describe niche partitioning, metabolic variability, and population structure in coastal picoplankton populations, we constructed and compared several picoplankton BAC libraries recovered from different depths in Monterey Bay. To facilitate library screening, a rapid technique was developed (ITS-LH-PCR) to identify and quantify ribosomal RNA (rRNA) gene-containing BAC clones in BAC libraries. The approach exploited natural length variations in the internal transcribed spacer (ITS) located between SSU and LSU rRNA genes, as well as the presence and location of tRNA-alanine coding genes within the ITS. The correspondence between ITS-LH-PCR fragment sizes and 16S rRNA gene phylogenies facilitated rapid identification of rRNA genes in BAC clones without requiring direct DNA sequencing. Using this approach, 35 phylogenetic groups (previously identified by cultivation or PCR-based rRNA gene surveys) were detected and quantified among the BAC clones. Since the probability of recovering chimeric rRNA gene sequences in large insert BAC clones was low, we used these sequences to identify potentially chimeric sequences from previous PCR amplified clones deposited in public databases. Full-length SSU rRNA gene sequences from picoplankton BAC libraries, cultivated bacterioplankton, and nonchimeric RNA genes were then used to refine phylogenetic analyses of planktonic marine gamma Proteobacteria, Roseobacter, and Rhodospirillales species.
C1 Univ Maryland, Chesapeake Biol Lab, Ctr Environm Sci, Solomons, MD 20688 USA.
   Monterey Bay Aquarium Res Inst, Moss Landing, CA 95039 USA.
RP MIT, Dept Civil & Environm Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA.
EM delong@mit.edu
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NR 50
TC 96
Z9 107
PD DEC
PY 2004
VL 48
IS 4
BP 473
EP 488
DI 10.1007/s00248-004-0213-5
UT WOS:000226829500004
DA 2025-07-30
ER

PT J
AU Brum, JR
   Sullivan, MB
AF Brum, Jennifer R.
   Sullivan, Matthew B.
TI Rising to the challenge: accelerated pace of discovery transforms marine
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SO NATURE REVIEWS MICROBIOLOGY
DT Review
AB Marine viruses have important roles in microbial mortality, gene transfer, metabolic reprogramming and biogeochemical cycling. In this Review, we discuss recent technological advances in marine virology including the use of near-quantitative, reproducible metagenomics for large-scale investigation of viral communities and the emergence of gene-based viral ecology. We also describe the reprogramming of microbially driven processes by viral metabolic genes, the identification of novel viruses using cultivation-dependent and cultivation-independent tools, and the potential for modelling studies to provide a framework for studying virus-host interactions. These transformative advances have set a rapid pace in exploring and predicting how marine viruses manipulate and respond to their environment.
C1 [Brum, Jennifer R.; Sullivan, Matthew B.] Univ Arizona, Dept Ecol & Evolutionary Biol, Tucson, AZ 85721 USA.
RP Sullivan, MB (corresponding author), Univ Arizona, Dept Ecol & Evolutionary Biol, Tucson, AZ 85721 USA.
EM mbsulli@gmail.com
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NR 129
TC 237
Z9 266
PD MAR
PY 2015
VL 13
IS 3
BP 147
EP 159
DI 10.1038/nrmicro3404
UT WOS:000349844300010
DA 2025-07-30
ER

PT J
AU Singh, SK
   Kotakonda, A
   Kapardar, RK
   Kankipati, HK
   Rao, PS
   Sankaranarayanan, PM
   Vetaikorumagan, SR
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   Nagappa, R
   Shivaji, S
AF Singh, Sanjay K.
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   Rao, Pasupuleti Sreenivasa
   Sankaranarayanan, Pratibha Mambatta
   Vetaikorumagan, Sundareswaran R.
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   Nagappa, Ramaiah
   Shivaji, Sisinthy
TI Response of bacterioplankton to iron fertilization of the Southern
   Ocean, Antarctica
SO FRONTIERS IN MICROBIOLOGY
DT Article
AB Ocean iron fertilization is an approach to increase CO2 sequestration. The Ingo-German iron fertilization experiment "LOHAFEX" was carried out in the Southern Ocean surrounding Antarctica in 2009 to monitor changes in bacterial community structure following iron fertilization-induced phytoplankton bloom of the seawater from different depths. 16S rRNA gene libraries were constructed using metagenomic DNA from seawater prior to and after iron fertilization and the clones were sequenced for identification of the major bacterial groups present and for phylogenetic analyses. A total of 4439 clones of 16S rRNA genes from ten 16S rRNA gene libraries were sequenced. More than 97.35% of the sequences represented four bacterial lineages i.e. Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and Firmicutes and confirmed their role in scavenging of phytoplankton blooms induced following iron fertilization. The present study demonstrates the response of Firmicutes due to Iron fertilization which was not observed in previous southern ocean Iron fertilization studies. In addition, this study identifies three unique phylogenetic clusters LOHAFEX Cluster 1 (affiliated to Bacteroidetes), 2, and 3 (affiliated to Firmicutes) which were not detected in any of the earlier studies on iron fertilization. The relative abundance of these clusters in response to iron fertilization was different. The increase in abundance of LOHAFEX Cluster 2 and Papillibacter sp. another dominant Firmicutes may imply a role in phytoplankton degradation. Disappearance of LOHAFEX Cluster 3 and other bacterial genera after iron fertilization may imply conditions not conducive for their survival. It is hypothesized that heterotrophic bacterial abundance in the Southern Ocean would depend on their ability to utilize algal exudates, decaying algal biomass and other nutrients thus resulting in a dynamic bacterial succession of distinct genera.
C1 [Singh, Sanjay K.; Kotakonda, Arunasri; Kapardar, Raj K.; Kankipati, Hara Kishore; Rao, Pasupuleti Sreenivasa; Sankaranarayanan, Pratibha Mambatta; Vetaikorumagan, Sundareswaran R.; Gundlapally, Sathyanarayana Reddy; Shivaji, Sisinthy] CSIR, Ctr Cellular & Mol Biol, Hyderabad 500007, Andhra Pradesh, India.
   [Nagappa, Ramaiah] CSIR, Natl Inst Oceanog, Hyderabad 500007, Andhra Pradesh, India.
RP Shivaji, S (corresponding author), CSIR, Ctr Cellular & Mol Biol, Uppal Rd, Hyderabad 500007, Andhra Pradesh, India.
EM shivas@ccmb.res.in
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NR 64
TC 18
Z9 18
PD AUG 26
PY 2015
VL 6
AR 863
DI 10.3389/fmicb.2015.00863
UT WOS:000360339500001
DA 2025-07-30
ER

PT J
AU Arandia-Gorostidi, N
   González, JM
   Huete-Stauffer, TM
   Ansari, MI
   Morán, XAG
   Alonso-Sáez, L
AF Arandia-Gorostidi, Nestor
   Gonzalez, Jose M.
   Huete-Stauffer, Tamara M.
   Ansari, Mohd, I
   Moran, Xose Anxelu G.
   Alonso-Saez, Laura
TI Light supports cell-integrity and growth rates of taxonomically diverse
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB Despite the widespread distribution of proteorhodopsin (PR)-containing bacteria in the oceans, the use of light-derived energy to promote bacterial growth has only been shown in a few bacterial isolates, and there is a paucity of data describing the metabolic effects of light on environmental photoheterotrophic taxa. Here, we assessed the effects of light on the taxonomic composition, cell integrity and growth responses of microbial communities in monthly incubations between spring and autumn under different environmental conditions. The photoheterotrophs expressing PRin situwere dominated byPelagibacteralesand SAR116 in July and November, while members ofEuryarchaeota,GammaproteobacteriaandBacteroidetesdominated the PR expression in spring. Cell-membrane integrity decreased under dark conditions throughout most of the assessment, with maximal effects in summer, under low-nutrient conditions. A positive effect of light on growth was observed in one incubation (out of nine), coinciding with a declining phytoplankton bloom. Light-enhanced growth was found inGammaproteobacteria(Alteromonadales) andBacteroidetes(PolaribacterandTenacibaculum). Unexpectedly, somePelagibacteralesalso exhibited higher growth rates under light conditions. We propose that the energy harvested by PRs helps to maintain cell viability in dominant coastal photoheterotrophic oligotrophs while promoting the growth of some widespread taxa benefiting from the decline of phytoplankton blooms.
C1 [Arandia-Gorostidi, Nestor; Huete-Stauffer, Tamara M.; Alonso-Saez, Laura] Ctr Oceanog Ajon Xixon, Inst Espanol Oceanog, Gijon Xixon, Asturias, Spain.
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   [Gonzalez, Jose M.] Univ La Laguna, Dept Microbiol, San Cristobal la Laguna, Spain.
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   [Alonso-Saez, Laura] Basque Res & Technol Alliance BRTA, AZTI, Marine Res, Sukarrieta 48395, Bizkaia, Spain.
RP Arandia-Gorostidi, N; Alonso-Sáez, L (corresponding author), Ctr Oceanog Ajon Xixon, Inst Espanol Oceanog, Gijon Xixon, Asturias, Spain.; Arandia-Gorostidi, N (corresponding author), Stanford Univ, Dept Earth Syst Sci, Stanford, CA 94305 USA.; Alonso-Sáez, L (corresponding author), Basque Res & Technol Alliance BRTA, AZTI, Marine Res, Sukarrieta 48395, Bizkaia, Spain.
EM n.arandia86@gmail.com; lalonso@azti.es
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NR 71
TC 7
Z9 7
PD SEP
PY 2020
VL 22
IS 9
BP 3823
EP 3837
DI 10.1111/1462-2920.15158
EA AUG 2020
UT WOS:000554482300001
DA 2025-07-30
ER

PT J
AU Buchanan, PJ
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AF Buchanan, Pearse J.
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TI Oxygen intrusions sustain aerobic nitrite-oxidizing bacteria in anoxic
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SO SCIENCE
DT Article
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RP Buchanan, PJ (corresponding author), Carnegie Inst Sci, Dept Global Ecol, Stanford, CA 94305 USA.; Buchanan, PJ (corresponding author), CSIRO Environm, Hobart, Australia.
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ER

PT J
AU Alonso, C
AF Alonso, Cecilia
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SO SYSTEMATIC AND APPLIED MICROBIOLOGY
DT Review
AB The combination of microautoradiography and fluorescence in situ hybridization (MAR-FISH) is a powerful technique for tracking the incorporation of radiolabelled compounds by specific bacterial populations at a single cell resolution. It has been widely applied in aquatic microbial ecology as a tool to unveil key ecophysiological features, shedding light on relevant ecological issues such as bacterial biomass production, the role of different bacterioplankton groups in the global carbon and sulphur cycle, and, at the same time, providing insights into the life styles and niche differentiation of cosmopolitan members of the aquatic microbial communities. Despite its great potential, its application has remained restricted to a few laboratories around the world, in part due to its reputation as a "difficult technique". Therefore, the objective of this minireview is to highlight the impact of MAR-FISH application on aquatic microbial ecology, and also to provide basic concepts, as well as practical tips, for processing MAR-FISH preparations, thus aiming to contribute to a more widespread application of this powerful method. (c) 2012 Elsevier GmbH. All rights reserved.
C1 CURE Univ Republ, Rocha, Uruguay.
RP Alonso, C (corresponding author), CURE Univ Republ, Rocha, Uruguay.
EM ceci.babilonia@gmail.com
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BP 503
EP 512
DI 10.1016/j.syapm.2012.02.005
UT WOS:000314015000004
DA 2025-07-30
ER

PT J
AU Orsi, WD
   Smith, JM
   Liu, ST
   Liu, ZF
   Sakamoto, CM
   Wilken, S
   Poirier, C
   Richards, TA
   Keeling, PJ
   Worden, AZ
   Santoro, AE
AF Orsi, William D.
   Smith, Jason M.
   Liu, Shuting
   Liu, Zhanfei
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   Wilken, Susanne
   Poirier, Camille
   Richards, Thomas A.
   Keeling, Patrick J.
   Worden, Alexandra Z.
   Santoro, Alyson E.
TI Diverse, uncultivated bacteria and archaea underlying the cycling of
   dissolved protein in the ocean
SO ISME JOURNAL
DT Article
AB Dissolved organic nitrogen (DON) supports a significant amount of heterotrophic production in the ocean. Yet, to date, the identity and diversity of microbial groups that transform DON are not well understood. To better understand the organisms responsible for transforming high molecular weight (HMW)-DON in the upper ocean, isotopically labeled protein extract from Micromonas pusilla, a eukaryotic member of the resident phytoplankton community, was added as substrate to euphotic zone water from the central California Current system. Carbon and nitrogen remineralization rates from the added proteins ranged from 0.002 to 0.35 mol C l(-1) per day and 0.03 to 0.27nmol N l(-1) per day. DNA stable-isotope probing (DNA-SIP) coupled with high-throughput sequencing of 16S rRNA genes linked the activity of 77 uncultivated free-living and particle-associated bacterial and archaeal taxa to the utilization of Micromonas protein extract. The high-throughput DNA-SIP method was sensitive in detecting isotopic assimilation by individual operational taxonomic units (OTUs), as substrate assimilation was observed after only 24 h. Many uncultivated free-living microbial taxa are newly implicated in the cycling of dissolved proteins affiliated with the Verrucomicrobia, Planctomycetes, Actinobacteria and Marine Group II (MGII) Euryarchaeota. In addition, a particle-associated community actively cycling DON was discovered, dominated by uncultivated organisms affiliated with MGII, Flavobacteria, Planctomycetes, Verrucomicrobia and Bdellovibrionaceae. The number of taxa assimilating protein correlated with genomic representation of TonB-dependent receptor (TBDR)-encoding genes, suggesting a possible role of TBDR in utilization of dissolved proteins by marine microbes. Our results significantly expand the known microbial diversity mediating the cycling of dissolved proteins in the ocean.
C1 [Orsi, William D.; Santoro, Alyson E.] Univ Maryland, Ctr Environm Sci, Horn Point Lab, Cambridge, MD 21613 USA.
   [Smith, Jason M.; Sakamoto, Carole M.; Wilken, Susanne; Poirier, Camille; Worden, Alexandra Z.] Monterey Bay Aquarium Res Inst, Moss Landing, CA USA.
   [Liu, Shuting; Liu, Zhanfei] Univ Texas Austin, Dept Marine Sci, Port Aransas, TX USA.
   [Richards, Thomas A.] Univ Exeter, Dept Biosci, Exeter, Devon, England.
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   [Keeling, Patrick J.] Univ British Columbia, Dept Bot, Vancouver, BC, Canada.
RP Santoro, AE (corresponding author), Univ Maryland, Ctr Environm Sci, Horn Point Lab, Cambridge, MD 21613 USA.; Orsi, WD (corresponding author), Univ Munich, Dept Earth & Environm Sci, Munich, Germany.
EM w.orsi@lrz.uni-muenchen.de; asantoro@umces.edu
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VL 10
IS 9
BP 2158
EP 2173
DI 10.1038/ismej.2016.20
UT WOS:000386664600008
DA 2025-07-30
ER

PT J
AU Hu, W
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AF Hu, Wei
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   Bartlam, Mark
   Wang, Yingying
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DT Review
AB Low nucleic acid content (LNA) bacteria are ubiquitous and estimated to constitute 20%-90% of the total bacterial community in marine and freshwater environment. LNA bacteria with unique physiological characteristics, including small cell size and small genomes, can pass through 0.45-mu m filtration. The researchers came up with different terminologies for low nucleic acid content bacteria based on different research backgrounds, such as: filterable bacteria, oligotrophic bacteria, and low-DNA bacteria. LNA bacteria have an extremely high level of genetic diversity and play an important role in material circulation in oligotrophic environment. However, the majority of LNA bacteria in the environment remain uncultivated. Thus, an important challenge now is to isolate more LNA bacteria from oligotrophic environments and gain insights into their unique metabolic mechanisms and ecological functions. Here, we reviewed LNA bacteria in aquatic environments, focusing on their characteristics, community structure and diversity, functions, and cultivation strategies. Exciting future prospects for LNA bacteria are also discussed.
C1 [Hu, Wei; Zhang, Hui; Lin, Xiaowen; Liu, Ruidan; Wang, Yingying] Nankai Univ, Nankai Int Adv Res Inst Shenzhen Futian, Coll Environm Sci & Engn, Key Lab Pollut Proc & Environm Criteria Minist Edu, Tianjin, Peoples R China.
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RP Wang, YY (corresponding author), Nankai Univ, Nankai Int Adv Res Inst Shenzhen Futian, Coll Environm Sci & Engn, Key Lab Pollut Proc & Environm Criteria Minist Edu, Tianjin, Peoples R China.
EM wangyy@nankai.edu.cn
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TC 10
Z9 11
PD JUN 15
PY 2022
VL 13
AR 900669
DI 10.3389/fmicb.2022.900669
UT WOS:000817983600001
DA 2025-07-30
ER

PT J
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AF Brown, Mark V.
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C1 [Brown, Mark V.; Lauro, Federico M.] Univ New S Wales, Sch Biotechnol & Biomol Sci, Sydney, NSW, Australia.
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RP Lauro, FM (corresponding author), Univ New S Wales, Sch Biotechnol & Biomol Sci, Sydney, NSW, Australia.
EM flauro@unsw.edu.au
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NR 137
TC 64
Z9 73
PD JUN
PY 2014
VL 15
BP 17
EP 28
DI 10.1016/j.margen.2014.03.002
UT WOS:000338606500007
DA 2025-07-30
ER

PT J
AU Kim, S
   Park, MS
   Song, J
   Kang, I
   Cho, JC
AF Kim, Suhyun
   Park, Miri S.
   Song, Jaeho
   Kang, Ilnam
   Cho, Jang-Cheon
TI High-throughput cultivation based on dilution-to-extinction with
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SO JOURNAL OF MICROBIOLOGY
DT Article
AB Multi-omics approaches, including metagenomics and single-cell amplified genomics, have revolutionized our understanding of the hidden diversity and function of microbes in nature. Even in the omics age, cultivation is an essential discipline in microbial ecology since microbial cultures are necessary to assess the validity of an in silico prediction about the microbial metabolism and to isolate viruses infecting bacteria and archaea. However, the ecophysiological characteristics of predominant freshwater bacterial lineages remain largely unknown due to the scarcity of cultured representatives. In an ongoing effort to cultivate the uncultured majority of freshwater bacteria, the most abundant freshwater Actinobacteria acI clade has recently been cultivated from Lake Soyang through catalase-supplemented high-throughput cultivation based on dilution-to-extinction. This method involves physical isolation of target microbes from mixed populations, culture media simulating natural habitats, and removal of toxic compounds. In this protocol, we describe detailed procedures for isolating freshwater oligotrophic microbes, as well as the essence of the dilution-to-extinction culturing. As a case study employing the catalase-supplemented dilution-to-extinction protocol, we also report a cultivation trial using a water sample collected from Lake Soyang. Of the 480 cultivation wells inoculated with a single lake-water sample, 75 new acI strains belonging to 8 acI tribes (acI-A1, A2, A4, A5, A6, A7, B1, B4, C1, and C2) were cultivated, and each representative strain per subclade could be revived from glycerol stocks. These cultivation results demonstrate that the protocol described in this study is efficient in isolating freshwater bacterioplankton harboring streamlined genomes.
C1 [Kim, Suhyun; Park, Miri S.; Song, Jaeho; Kang, Ilnam; Cho, Jang-Cheon] Inha Univ, Dept Biol Sci, Incheon 22212, South Korea.
RP Cho, JC (corresponding author), Inha Univ, Dept Biol Sci, Incheon 22212, South Korea.
EM chojc@inha.ac.kr
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TC 12
Z9 16
PD NOV
PY 2020
VL 58
IS 11
BP 893
EP 905
DI 10.1007/s12275-020-0452-2
UT WOS:000583050500001
DA 2025-07-30
ER

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NR 62
TC 0
Z9 0
PY 2007
BP 393
EP 398
UT WOS:000278001100032
DA 2025-07-30
ER

PT J
AU Zaballos, M
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AF Zaballos, Milagros
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DT Article
AB The bacterial and archaeal assemblages at two offshore sites located in polar (Greenland Sea; depth: 50 and 2000 m) and Mediterranean (Ionian Sea; depth 50 and 3000 m) waters were studied by PCR amplification and sequencing of the last 450-500 bp of the 16S rRNA gene. A total of 1621 sequences, together with alignable 16S rRNA gene fragments from the Sargasso Sea metagenome database, were analysed to ascertain variations associated with geographical location and depth. The Ionian 50 m sample appeared to be the most diverse and also had remarkable differences in terms of the prokaryotic groups retrieved; surprisingly, however, many similarities were found at the level of large-scale diversity between the Sargasso database fragments and the Greenland 50 m sample. Most sequences with more than 97% sequence similarity, a value often taken as indicative of species delimitation, were only found at a single location/depth; nevertheless, a few examples of cosmopolitan sequences were found in all samples. Depth was also an important factor and, although both deep-water samples had overall similarities, there were important differences that could be due to the warmer waters at depth of the Mediterranean Sea.
C1 Univ Miguel Hernandez, Div Microbiol, Alicante 03550, Spain.
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   Univ Bergen, Dept Biol, Bergen, Norway.
RP Rodríguez-Valera, F (corresponding author), Univ Miguel Hernandez, Div Microbiol, Campus San Juan, Alicante 03550, Spain.
EM frvalera@umh.es
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NR 58
TC 65
Z9 71
PD JUN
PY 2006
VL 56
IS 3
BP 389
EP 405
DI 10.1111/j.1574-6941.2006.00060.x
UT WOS:000237517300007
DA 2025-07-30
ER

PT J
AU Elifantz, H
   Malmstrom, RR
   Cottrell, MT
   Kirchman, DL
AF Elifantz, H
   Malmstrom, RR
   Cottrell, MT
   Kirchman, DL
TI Assimilation of polysaccharides and glucose by major bacterial groups in
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB The contribution of major bacterial groups to the assimilation of extracellular polymeric substances (EPS) and glucose in the Delaware Estuary was assessed using microautoradiography and fluorescence in situ hybridization. Bacterial groups contributed to EPS and glucose assimilation in part according to their distribution in the estuary. Abundance of the phylogenetic groups explained 35% and 55% of the variation in EPS and glucose assimilation, respectively. Actinobacteria contributed 70% to glucose assimilation in freshwater, while Alphaproteobacteria assimilated 60% of this compound in saline water. In contrast, various bacterial groups dominated the assimilation of EPS. Actinobacteria and Betaproteobacteria contributed the most in the freshwater section, whereas Cytophaga-like bacteria and Alpha- and Gammaproteobacteria participated in EPS assimilation in the lower part of the estuary. In addition, we examined the fraction of bacteria in each group that assimilated glucose or EPS. Overall, the fraction of bacteria in all groups that assimilated glucose was higher than the fraction that assimilated EPS (15 to 30% versus 5 to 20%, respectively). We found no correlation between the relative abundance of a group in the estuary and the fraction of bacteria actively assimilating glucose or EPS; the more active groups were often less abundant. Our results imply that the bacterial community in the Delaware Estuary is not controlled solely by "bottom-up" factors such as dissolved organic matter.
C1 Univ Delaware, Coll Marine Studies, Lewes, DE 19958 USA.
RP Univ Delaware, Coll Marine Studies, Lewes, DE 19958 USA.
EM Kirchman@cms.udel.edu
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NR 46
TC 116
Z9 126
PD DEC
PY 2005
VL 71
IS 12
BP 7799
EP 7805
DI 10.1128/AEM.71.12.7799-7805.2005
UT WOS:000234417600020
DA 2025-07-30
ER

PT J
AU de la Higuera, I
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AF de la Higuera, Ignacio
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TI Viruses in astrobiology
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DT Review
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C1 [de la Higuera, Ignacio] Portland State Univ, Ctr Life Extreme Environm, Dept Biol, Portland, OR 97207 USA.
   [Lazaro, Ester] CSIC INTA, Ctr Astrobiol CAB, Torrejon De Ardoz, Spain.
RP Lázaro, E (corresponding author), CSIC INTA, Ctr Astrobiol CAB, Torrejon De Ardoz, Spain.
EM lazarole@cab.inta-csic.es
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NR 302
TC 8
Z9 8
PD OCT 26
PY 2022
VL 13
AR 1032918
DI 10.3389/fmicb.2022.1032918
UT WOS:000882389400001
DA 2025-07-30
ER

PT J
AU Pérez, MT
   Rofner, C
   Sommaruga, R
AF Perez, Maria Teresa
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   Sommaruga, Ruben
TI Dissolved organic monomer partitioning among bacterial groups in two
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SO ENVIRONMENTAL MICROBIOLOGY REPORTS
DT Article
AB Understanding how resource partitioning works among taxa is crucial in explaining coexistence and competition within a community. Here, we assessed resource partitioning among freshwater bacterial groups from two oligotrophic lakes using four types of organic substrates as compound models. Substrate uptake patterns were examined by microautoradiography combined with catalysed reporter deposition fluorescent in situ hybridization. Four large taxonomic groups were found in the lakes, but Actinobacteria (AcI lineage) and Betaproteobacteria (R-BTcluster) dominated the bacterial assemblage. Monomers containing nitrogen and/or phosphorus were preferred over the ones containing only carbon. All groups were able to incorporate amino acids, adenosine triphosphate and glucose. However, acetate was only taken up by approximate to 10-12% of bacteria, and its uptake was not detected in Cytophaga-Flavobacteria. Apart from acetate, the contribution of a particular bacterial group to the uptake of a substrate was proportional to its relative abundance. In both lakes, we detected substrate partitioning between AcIActinobacteria, which was overrepresented in glucose and acetate utilization, and R-BT Betaproteobacteria, which dominated amino acid uptake. Our results strongly point to physiological niche separation of those bacterial groups in alpine lakes.
C1 [Perez, Maria Teresa; Rofner, Carina; Sommaruga, Ruben] Univ Innsbruck, Inst Ecol, Lake & Glacier Res Grp, A-6020 Innsbruck, Austria.
RP Pérez, MT (corresponding author), Univ Innsbruck, Inst Ecol, Lake & Glacier Res Grp, Tech Str 25, A-6020 Innsbruck, Austria.
EM maria.perez@uibk.ac.at
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NR 44
TC 13
Z9 15
PD APR
PY 2015
VL 7
IS 2
BP 265
EP 272
DI 10.1111/1758-2229.12240
UT WOS:000351407300013
DA 2025-07-30
ER

PT J
AU Hoefman, S
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   De Vos, P
   Boon, N
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AF Hoefman, Sven
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SO MICROBIAL BIOTECHNOLOGY
DT Article
AB Methane-oxidizing bacteria (MOB) have a large potential as a microbial sink for the greenhouse gas methane as well as for biotechnological purposes. However, their application in biotechnology has so far been hampered, in part due to the relative slow growth rate of the available strains. To enable the availability of novel strains, this study compares the isolation of MOB by conventional dilution plating with miniaturized extinction culturing, both performed after an initial enrichment step. The extinction approach rendered 22 MOB isolates from four environmental samples, while no MOB could be isolated by plating. In most cases, extinction culturing immediately yielded MOB monocultures making laborious purification redundant. Both type I (Methylomonas spp.) and type II (Methylosinus sp.) MOB were isolated. The isolated methanotrophic diversity represented at least 11 different strains and several novel species based on 16S rRNA gene sequence dissimilarity. These strains possessed the particulate (100%) and soluble (64%) methane monooxygenase gene. Also, 73% of the strains could be linked to a highly active fast-growing mixed MOB community. In conclusion, miniaturized extinction culturing was more efficient in rapidly isolating numerous MOB requiring little effort and fewer materials, compared with the more widely applied plating procedure. This miniaturized approach allowed straightforward isolation and could be very useful for subsequent screening of desired characteristics, in view of their future biotechnological potential.
C1 [Hoefman, Sven; De Vos, Paul; Heylen, Kim] Univ Ghent, Dept Biochem & Microbiol, Lab Microbiol, B-9000 Ghent, Belgium.
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RP Heylen, K (corresponding author), Univ Ghent, Dept Biochem & Microbiol, Lab Microbiol, KL Ledeganckstr 35, B-9000 Ghent, Belgium.
EM kim.heylen@ugent.be
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TC 29
Z9 30
PD MAY
PY 2012
VL 5
IS 3
SI SI
BP 368
EP 378
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UT WOS:000302858900006
DA 2025-07-30
ER

PT J
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C1 Univ Vienna, Dept Microbial Ecol, A-1090 Vienna, Austria.
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RP Univ Vienna, Dept Microbial Ecol, Althanstr 14, A-1090 Vienna, Austria.
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NR 60
TC 143
Z9 172
PD FEB
PY 2006
VL 17
IS 1
BP 83
EP 91
DI 10.1016/j.copbio.2005.12.006
UT WOS:000235775200013
DA 2025-07-30
ER

PT J
AU Gómez-Consarnau, L
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   Pinhassi, J
AF Gomez-Consarnau, Laura
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   Pinhassi, Jarone
TI Structuring of bacterioplankton communities by specific dissolved
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SO ENVIRONMENTAL MICROBIOLOGY
DT Article
AB The main role of microorganisms in the cycling of the bulk dissolved organic carbon pool in the ocean is well established. Nevertheless, it remains unclear if particular bacteria preferentially utilize specific carbon compounds and whether such compounds have the potential to shape bacterial community composition. Enrichment experiments in the Mediterranean Sea, Baltic Sea and the North Sea (Skagerrak) showed that different low-molecular-weight organic compounds, with a proven importance for the growth of marine bacteria (e.g. amino acids, glucose, dimethylsulphoniopropionate, acetate or pyruvate), in most cases differentially stimulated bacterial growth. Denaturing gradient gel electrophoresis fingerprints and 16S rRNA gene sequencing revealed that some bacterial phylotypes that became abundant were highly specific to enrichment with specific carbon compounds (e.g. Acinetobacter sp. B1-A3 with acetate or Psychromonas sp. B3-U1 with glucose). In contrast, other phylotypes increased in relative abundance in response to enrichment with several, or all, of the investigated carbon compounds (e.g. Neptuniibacter sp. M2-A4 with acetate, pyruvate and dimethylsulphoniopropionate, and Thalassobacter sp. M3-A3 with pyruvate and amino acids). Furthermore, different carbon compounds triggered the development of unique combinations of dominant phylotypes in several of the experiments. These results suggest that bacteria differ substantially in their abilities to utilize specific carbon compounds, with some bacteria being specialists and others having a more generalist strategy. Thus, changes in the supply or composition of the dissolved organic carbon pool can act as selective forces structuring bacterioplankton communities.
C1 [Gomez-Consarnau, Laura; Lindh, Markus V.; Pinhassi, Jarone] Linnaeus Univ, Sch Nat Sci, Kalmar, Sweden.
   [Gasol, Josep M.] CSIC, Inst Ciencies Mar, Barcelona, Catalonia, Spain.
RP Pinhassi, J (corresponding author), Linnaeus Univ, Sch Nat Sci, Kalmar, Sweden.
EM jarone.pinhassi@lnu.se
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NR 62
TC 115
Z9 129
PD SEP
PY 2012
VL 14
IS 9
SI SI
BP 2361
EP 2378
DI 10.1111/j.1462-2920.2012.02804.x
UT WOS:000308300600010
DA 2025-07-30
ER

PT J
AU Vergin, KL
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AF Vergin, Kevin L.
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DT Article
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C1 [Vergin, Kevin L.; Done, Brad; Giovannoni, Stephen J.] Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
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RP Giovannoni, SJ (corresponding author), Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA.
EM steve.giovannoni@oregonstate.edu
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NR 72
TC 82
Z9 92
PY 2013
VL 71
IS 1
BP 1
EP U129
DI 10.3354/ame01661
UT WOS:000327552900001
DA 2025-07-30
ER

PT J
AU Castillo, DJ
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   Bezuidt, OK
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AF Castillo, Diego J.
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TI Microbial ecology of the Southern Ocean
SO FEMS MICROBIOLOGY ECOLOGY
DT Review
AB The Southern Ocean (SO) distributes climate signals and nutrients worldwide, playing a pivotal role in global carbon sequestration. Microbial communities are essential mediators of primary productivity and carbon sequestration, yet we lack a comprehensive understanding of microbial diversity and functionality in the SO. Here, we examine contemporary studies in this unique polar system, focusing on prokaryotic communities and their relationships with other trophic levels (i.e. phytoplankton and viruses). Strong seasonal variations and the characteristic features of this ocean are directly linked to community composition and ecosystem functions. Specifically, we discuss characteristics of SO microbial communities and emphasise differences from the Arctic Ocean microbiome. We highlight the importance of abundant bacteria in recycling photosynthetically derived organic matter. These heterotrophs appear to control carbon flux to higher trophic levels when light and iron availability favour primary production in spring and summer. Conversely, during winter, evidence suggests that chemolithoautotrophs contribute to prokaryotic production in Antarctic waters. We conclude by reviewing the effects of climate change on marine microbiota in the SO.
C1 [Castillo, Diego J.; Dithugoe, Choaro D.; Bezuidt, Oliver K.; Makhalanyane, Thulani P.] Univ Pretoria, Dept Biochem Genet & Microbiol, Microbiome Res Grp, ZA-0028 Pretoria, South Africa.
   [Castillo, Diego J.; Dithugoe, Choaro D.; Bezuidt, Oliver K.; Makhalanyane, Thulani P.] Univ Pretoria, Dept Sci, ZA-0028 Pretoria, South Africa.
   [Castillo, Diego J.; Dithugoe, Choaro D.; Bezuidt, Oliver K.; Makhalanyane, Thulani P.] Univ Pretoria, Innovat South African Res Chair Marine Microbiom, Dept Biochem Genet & Microbiol, ZA-0028 Pretoria, South Africa.
RP Makhalanyane, TP (corresponding author), Univ Pretoria, Dept Biochem Genet & Microbiol, Microbiome Res Grp, ZA-0028 Pretoria, South Africa.; Makhalanyane, TP (corresponding author), Univ Pretoria, Dept Sci, ZA-0028 Pretoria, South Africa.; Makhalanyane, TP (corresponding author), Univ Pretoria, Innovat South African Res Chair Marine Microbiom, Dept Biochem Genet & Microbiol, ZA-0028 Pretoria, South Africa.
EM thulani.makhalanyane@up.ac.za
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NR 197
TC 13
Z9 13
PD OCT 26
PY 2022
VL 98
IS 11
AR fiac123
DI 10.1093/femsec/fiac123
EA OCT 2022
UT WOS:000874067600001
DA 2025-07-30
ER

PT S
AU Kujawinski, EB
AF Kujawinski, Elizabeth B.
BE Carlson, CA
   Giovannoni, SJ
TI The Impact of Microbial Metabolism on Marine Dissolved Organic Matter
SO ANNUAL REVIEW OF MARINE SCIENCE, VOL 3
SE Annual Review of Marine Science
DT Review; Book Chapter
AB Microbes mediate global biogeochemical cycles through their metabolism, and all metabolic processes begin with the interaction between the microbial cell wall or membrane and the external environment. For all heterotrophs and many autotrophs, critical growth substrates and factors are present within the dilute and heterogeneous mixture of compounds that constitutes dissolved organic matter (DOM). In short, the microbe molecule interaction is one of the fundamental reactions within the global carbon cycle. Here, I summarize recent findings from studies that examine DOM microbe interactions from either the DOM perspective (organic geochemistry) or the microbe perspective (microbial ecology). Gaps in our knowledge are highlighted and future integrative research directions are proposed.
C1 Woods Hole Oceanog Inst, Dept Marine Chem & Geochem, Woods Hole, MA 02543 USA.
RP Kujawinski, EB (corresponding author), Woods Hole Oceanog Inst, Dept Marine Chem & Geochem, Woods Hole, MA 02543 USA.
EM ekujawinski@whoi.edu
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NR 136
TC 239
Z9 266
PY 2011
VL 3
BP 567
EP 599
DI 10.1146/annurev-marine-120308-081003
UT WOS:000286638700021
DA 2025-07-30
ER

PT J
AU Mehrshad, M
   Amoozegar, MA
   Ghai, R
   Fazeli, SAS
   Rodriguez-Valera, F
AF Mehrshad, Maliheh
   Amoozegar, Mohammad Ali
   Ghai, Rohit
   Fazeli, Seyed Abolhassan Shahzadeh
   Rodriguez-Valera, Francisco
TI Genome Reconstruction from Metagenomic Data Sets Reveals Novel Microbes
   in the Brackish Waters of the Caspian Sea
SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB We present here the findings from a study of the microbiome of the southern basin of the Caspian Sea, the largest water body on Earth disconnected from any ocean and a brackish inland sea. By high-throughput metagenomics, we were able to reconstruct the genomes of representative microbes. The gross community structure (at the phylum level) was different from the structure of typical marine and freshwater communities in temperate open oceans, with the Caspian Sea having freshwater-like amounts of Actinobacteria and Alphaproteobacteria, while Gammaproteobacteria and Betaproteobacteria were present at intermediate levels. We assembled the genomes of several groups and provide detailed descriptions of partial genomes from Actinobacteria, Thaumarchaea, and Alphaproteobacteria. Most belonged to hitherto unknown groups, although they were related to either marine or freshwater groups. The phylogenetic placement of the Caspian genomes indicates that the organisms have multiple and separate phylogenetic origins and that they are related to organisms with both freshwater and marine lineages. Comparative recruitment from global aquatic metagenomes indicated that most Caspian microbes are endemic. However, some Caspian genomes were recruited significantly from either marine water (a member of the Alphaproteobacteria) or freshwater (a member of the Actinobacteria). Reciprocally, some genomes of other origins, such as the marine thaumarchaeon "Candidatus Nitrosopelagicus" or the actinobacterium "Candidatus Actinomarina," were recruited from the Caspian Sea, indicating some degree of overlap with the microbiota of other water bodies. Some of these microbes seem to have a remarkably widespread geographic and environmental distribution.
C1 [Mehrshad, Maliheh; Amoozegar, Mohammad Ali] Univ Tehran, Fac Biol, Dept Microbiol, Extremophiles Lab, Tehran, Iran.
   [Mehrshad, Maliheh; Amoozegar, Mohammad Ali] Univ Tehran, Ctr Excellence Phylogeny Living Organisms, Coll Sci, Tehran, Iran.
   [Ghai, Rohit; Rodriguez-Valera, Francisco] Univ Miguel Hernandez, Evolutionary Genom Grp, Alacant, Spain.
   [Fazeli, Seyed Abolhassan Shahzadeh] ACECR, Iranian Biol Resource Ctr IBRC, Microorganisms Bank, Tehran, Iran.
   [Fazeli, Seyed Abolhassan Shahzadeh] Univ Sci & Culture, Fac Basic Sci & Adv Technol Biol, Dept Mol & Cellular Biol, Tehran, Iran.
   [Ghai, Rohit] Acad Sci Czech Republic, Inst Hydrobiol, Ctr Biol, Vvi, Ceske Budejovice, Czech Republic.
RP Amoozegar, MA (corresponding author), Univ Tehran, Fac Biol, Dept Microbiol, Extremophiles Lab, Tehran, Iran.; Amoozegar, MA (corresponding author), Univ Tehran, Ctr Excellence Phylogeny Living Organisms, Coll Sci, Tehran, Iran.
EM amoozegar@ut.ac.ir
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NR 102
TC 36
Z9 37
PD MAR
PY 2016
VL 82
IS 5
BP 1599
EP 1612
DI 10.1128/AEM.03381-15
UT WOS:000373338800024
DA 2025-07-30
ER

PT J
AU Parikka, KJ
   Le Romancer, M
   Wauters, N
   Jacquet, S
AF Parikka, Kaarle J.
   Le Romancer, Marc
   Wauters, Nina
   Jacquet, Stephan
TI Deciphering the virus-to-prokaryote ratio (VPR): insights into
   virus-host relationships in a variety of ecosystems
SO BIOLOGICAL REVIEWS
DT Review
AB The discovery of the numerical importance of viruses in a variety of (aquatic) ecosystems has changed our perception of their importance in microbial processes. Bacteria and Archaea undoubtedly represent the most abundant cellular life forms on Earth and past estimates of viral numbers (represented mainly by viruses infecting prokaryotes) have indicated abundances at least one order of magnitude higher than that of their cellular hosts. Such dominance has been reflected most often by the virus-to-prokaryote ratio (VPR), proposed as a proxy for the relationship between viral and prokaryotic communities. VPR values have been discussed in the literature to express viral numerical dominance (or absence of it) over their cellular hosts, but the ecological meaning and interpretation of this ratio has remained somewhat nebulous or contradictory. We gathered data from 210 publications (and additional unpublished data) on viral ecology with the aim of exploring VPR. The results are presented in three parts: the first consists of an overview of the minimal, maximal and calculated average VPR values in an extensive variety of different environments. Results indicate that VPR values fluctuate over six orders of magnitude, with variations observed within each ecosystem. The second part investigates the relationship between VPR and other indices, in order to assess whether VPR can provide insights into virus-host relationships. A positive relationship was found between VPR and viral abundance (VA), frequency of visibly infected cells (FVIC), burst size (BS), frequency of lysogenic cells (FLC) and chlorophyll a (Chl a) concentration. An inverse relationship was detected between VPR and prokaryotic abundance (PA) (in sediments), prokaryotic production (PP) and virus-host contact rates (VCR) as well as salinity and temperature. No significant relationship was found between VPR and viral production (VP), fraction of mortality from viral lysis (FMVL), viral decay rate (VDR), viral turnover (VT) or depth. Finally, we summarize our results by proposing two scenarios in two contrasting environments, based on current theories on viral ecology as well as the present results. We conclude that since VPR fluctuates in every habitat for different reasons, as it is linked to a multitude of factors related to virus-host dynamics, extreme caution should be used when inferring relationships between viruses and their hosts. Furthermore, we posit that the VPR is only useful in specific, controlled conditions, e. g. for the monitoring of fluctuations in viral and host abundance over time.
C1 [Parikka, Kaarle J.; Le Romancer, Marc] Inst Univ Europeen Mer, Lab Microbiol Extreme Environm, F-29280 Plouzane, France.
   [Parikka, Kaarle J.] Queen Astrid Mil Hosp, Belgian Dept Def, LabMCT, B-1120 Brussels, Belgium.
   [Wauters, Nina] Univ Libre Bruxelles, Biol Evolut & Ecol, B-1050 Brussels, Belgium.
   [Jacquet, Stephan] INRA CARRTEL, F-74200 Thonon Les Bains, France.
RP Jacquet, S (corresponding author), INRA CARRTEL, F-74200 Thonon Les Bains, France.
EM sjacquet@thonon.inra.fr
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NR 183
TC 96
Z9 107
PD MAY
PY 2017
VL 92
IS 2
BP 1081
EP 1100
DI 10.1111/brv.12271
UT WOS:000398567200025
DA 2025-07-30
ER

PT J
AU Hamasaki, K
   Taniguchi, A
   Tada, Y
   Long, RA
   Azam, F
AF Hamasaki, Koji
   Taniguchi, Akito
   Tada, Yuya
   Long, Richard A.
   Azam, Farooq
TI Actively growing bacteria in the Inland Sea of Japan, identified by
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SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY
DT Article
AB A fundamental question in microbial oceanography concerns the relationship between prokaryote diversity and biogeochemical function in an ecosystem context. We combined bromodeoxymidine (BrdU) magnetic bead immunocapture and PCR-denaturing gradient gel electrophoresis (BUMP-DGGE) to examine phylotype-specific growth in natural marine assemblages. We also examined a broad range of marine bacterial isolates to determine their abilities to incorporate BrdU in order to test the validity of the method for application to diverse marine assemblages. We found that 27 of 29 isolates belonging to different taxa could incorporate BrdU. BUMP-DGGE analysis revealed phylogenetic affiliations of DNA-synthesizing, presumably actively growing bacteria across a eutrophic to mesotrophic transect in the Inland Sea of Japan. We found that the BrdU-incorporating (growing) communities were substantially different from the total communities. The majority (34/56) of phylotypes incorporated BrdU and were presumably growing, and these phylotypes comprised 10 alphaproteobacteria, 1 betaproteobacterium, 11 gammaproteobacteria, 11 Cytophaga-Flavobacterium-Bateroides group bacteria, and 1 unclassified bacterium. All BrdU-responsive alphaproteobacteria were members of the Rhodobacterales, suggesting that such bacteria were dominant in the growing alphaproteobacterial populations in our samples. The BrdU-responsive gammaproteobacteria belonged to the Oceanospirillales, the SAR86 cluster, the Pseudomonadales, the Alteromonadales, and the Vibrionales. Thus, contemporaneous cooccurrence of diverse actively growing bacterial taxa was a consistent pattern in our biogeochemically varied study area.
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   Texas A&M Univ, Coll Geosci, Dept Oceanog, College Stn, TX 77843 USA.
   Univ Calif San Diego, Scripps Inst Oceanog, MBRD, La Jolla, CA 92037 USA.
RP Hamasaki, K (corresponding author), Univ Tokyo, Ocean Res Inst, Dept Marine Ecosyst Dynam, Nakano Ku, 1-15-1 Minamidai, Tokyo 1648639, Japan.
EM hamasaki@ori.u-tokyo.ac.jp
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BP 2787
EP 2798
DI 10.1128/AEM.02111-06
UT WOS:000246238500003
DA 2025-07-30
ER

PT J
AU Pachiadaki, MG
   Brown, JM
   Brown, J
   Bezuidt, O
   Berube, PM
   Biller, SJ
   Poulton, NJ
   Burkart, MD
   La Clair, JJ
   Chisholm, SW
   Stepanauskas, R
AF Pachiadaki, Maria G.
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   Brown, Joseph
   Bezuidt, Oliver
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TI Charting the Complexity of the Marine Microbiome through Single-Cell
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SO CELL
DT Article
AB Marine bacteria and archaea play key roles in global biogeochemistry. To improve our understanding of this complex microbiome, we employed single-cell genomics and a randomized, hypothesis-agnostic cell selection strategy to recover 12,715 partial genomes from the tropical and subtropical euphotic ocean. A substantial fraction of known prokaryoplankton coding potential was recovered from a single, 0.4 mL ocean sample, which indicates that genomic information disperses effectively across the globe. Yet, we found each genome to be unique, implying limited clonality within prokaryoplankton populations. Light harvesting and secondary metabolite biosynthetic pathways were numerous across lineages, highlighting the value of single-cell genomics to advance the identification of ecological roles and biotechnology potential of uncultured microbial groups. This genome collection enabled functional annotation and genus-level taxonomic assignments for >80% of individual metagenome reads from the tropical and subtropical surface ocean, thus offering a model to improve reference genome databases for complex microbiomes.
C1 [Pachiadaki, Maria G.; Brown, Julia M.; Brown, Joseph; Bezuidt, Oliver; Poulton, Nicole J.; Stepanauskas, Ramunas] Bigelow Lab Ocean Sci, East Boothbay, ME 04544 USA.
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   [Chisholm, Sallie W.] MIT, Dept Biol, Cambridge, MA 02142 USA.
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RP Stepanauskas, R (corresponding author), Bigelow Lab Ocean Sci, East Boothbay, ME 04544 USA.
EM rstepanauskas@bigelow.org
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NR 103
TC 137
Z9 148
PD DEC 12
PY 2019
VL 179
IS 7
BP 1623
EP +
DI 10.1016/j.cell.2019.11.017
UT WOS:000502546200018
DA 2025-07-30
ER

EF