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The Composition and Primary Metabolic Potential of Microbial Communities Inhabiting the Surface Water in the Equatorial Eastern Indian Ocean. BIOLOGY 2021; 10:biology10030248. [PMID: 33810062 PMCID: PMC8005183 DOI: 10.3390/biology10030248] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/09/2021] [Accepted: 03/18/2021] [Indexed: 11/29/2022]
Abstract
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. Abstract 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.
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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. Microbial tropicalization driven by a strengthening western ocean boundary current. GLOBAL CHANGE BIOLOGY 2020; 26:5613-5629. [PMID: 32715608 DOI: 10.1111/gcb.15257] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 04/22/2020] [Accepted: 06/09/2020] [Indexed: 06/11/2023]
Abstract
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 of Prochlorococcus, 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 chlorophyll a, 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.
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Affiliation(s)
- Lauren F Messer
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, Australia
| | - Martin Ostrowski
- Climate Change Cluster, University of Technology, Sydney, Sydney, Australia
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Martina A Doblin
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Katherina Petrou
- School of Life Sciences, University of Technology, Sydney, Sydney, NSW, Australia
| | - Mark E Baird
- CSIRO Oceans and Atmosphere, Hobart, Tas., Australia
| | | | | | | | - Tiffanie Nelson
- Geelong Centre for Emerging Infectious Diseases, Deakin University, Melbourne, Vic., Australia
| | - Ian Paulsen
- Climate Change Cluster, University of Technology, Sydney, Sydney, Australia
| | | | - Jed A Fuhrman
- University of Southern California, Los Angeles, CA, USA
| | - Justin R Seymour
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Mark V Brown
- School of Environmental and Life Sciences, University of Newcastle Australia, Callaghan, NSW, Australia
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Focardi A, Ostrowski M, Goossen K, Brown MV, Paulsen I. Investigating the Diversity of Marine Bacteriophage in Contrasting Water Masses Associated with the East Australian Current (EAC) System. Viruses 2020; 12:E317. [PMID: 32188136 PMCID: PMC7150976 DOI: 10.3390/v12030317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/06/2020] [Accepted: 03/11/2020] [Indexed: 12/13/2022] Open
Abstract
Virus- and bacteriophage-induced mortality can have a significant impact on marine productivity and alter the flux of nutrients in marine microbial food-webs. Viral mediated horizontal gene transfer can also influence host fitness and community composition. However, there are very few studies of marine viral diversity in the Southern Hemisphere, which hampers our ability to fully understand the complex interplay of biotic and abiotic factors that shape microbial communities. We carried out the first genetic study of bacteriophage communities within a dynamic western boundary current (WBC) system, the east Australian current (EAC). Virus DNA sequences were extracted from 63 assembled metagenomes and six metaviromes obtained from various depths at 24 different locations. More than 1700 bacteriophage genomic fragments (>9 kbps) were recovered from the assembled sequences. Bacteriophage diversity displayed distinct depth and regional patterns. There were clear differences in the bacteriophage populations associated with the EAC and Tasman Sea euphotic zones, at both the taxonomic and functional level. In contrast, bathypelagic phages were similar across the two oceanic regions. These data provide the first characterisation of viral diversity across a dynamic western boundary current, which is an emerging model for studying the response of microbial communities to climate change.
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Affiliation(s)
- Amaranta Focardi
- Department of Molecular Sciences, Macquarie University, 4 Wally’s Walk, Sydney, NSW 2109, Australia;
| | - Martin Ostrowski
- Climate Change Cluster, University of Technology Sydney, 123 Broadway, Sydney, NSW 2007, Australia;
| | - Kirianne Goossen
- CSIRO Oceans and Atmosphere, Castray Esplanade, Hobart, TAS 7001, Australia (M.V.B.)
| | - Mark V. Brown
- CSIRO Oceans and Atmosphere, Castray Esplanade, Hobart, TAS 7001, Australia (M.V.B.)
- School of Environmental and Life Sciences, University of Newcastle, University Dr, Callaghan, NSW 2308, Australia
| | - Ian Paulsen
- Department of Molecular Sciences, Macquarie University, 4 Wally’s Walk, Sydney, NSW 2109, Australia;
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4
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Modelling plankton ecosystems in the meta-omics era. Are we ready? Mar Genomics 2017; 32:1-17. [DOI: 10.1016/j.margen.2017.02.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 02/24/2017] [Accepted: 02/25/2017] [Indexed: 12/30/2022]
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Rocha AM, Yuan Q, Close DM, O’Dell KB, Fortney JL, Wu J, Hazen TC. Rapid detection of microbial cell abundance in aquatic systems. Biosens Bioelectron 2016; 85:915-923. [DOI: 10.1016/j.bios.2016.05.098] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 05/17/2016] [Accepted: 05/31/2016] [Indexed: 10/21/2022]
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Bibiloni-Isaksson J, Seymour JR, Ingleton T, van de Kamp J, Bodrossy L, Brown MV. Spatial and temporal variability of aerobic anoxygenic photoheterotrophic bacteria along the east coast of Australia. Environ Microbiol 2016; 18:4485-4500. [PMID: 27376620 DOI: 10.1111/1462-2920.13436] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 06/28/2016] [Indexed: 11/29/2022]
Abstract
Aerobic Anoxygenic Phototrophic Bacteria (AAnPB) are ecologically important microorganisms, widespread in oceanic photic zones. However, the key environmental drivers underpinning AAnPB abundance and diversity are still largely undefined. The temporal patterns in AAnPB dynamics at three oceanographic reference stations spanning at approximately 15° latitude along the Australian east coast were examined. AAnPB abundance was highly variable, with pufM gene copies ranging from 1.1 × 102 to 1.4 × 105 ml-1 and positively correlated with day length and solar radiation. pufM gene Miseq sequencing revealed that the majority of sequences were closely related to those obtained previously, suggesting that key AAnPB groups are widely distributed across similar environments globally. Temperature was a major structuring factor for AAnPB assemblages across large spatial scales, correlating positively with richness and Gammaproteobacteria (phylogroup K) abundance but negatively with Roseobacter-clade (phylogroup E) abundance, with temperatures between 16°C and 18°C identified as a potential transition zone between these groups. Network analysis revealed that discrete AAnPB populations exploit specific niches defined by varying temperature, light and nutrient conditions in the Tasman Sea system, with evidence for both niche sharing and partitioning amongst closely related operational taxonomic units.
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Affiliation(s)
- Jaime Bibiloni-Isaksson
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Sydney, Australia
| | - Justin R Seymour
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Sydney, Australia
| | - Tim Ingleton
- Department of Environment, Climate Change and Water, Waters and Coastal Science Section, Sydney South, NSW, 1232, Australia
| | - Jodie van de Kamp
- CSIRO Oceans and Atmosphere, Castray Esplanade, Hobart, TAS, 7000, Australia
| | - Levente Bodrossy
- CSIRO Oceans and Atmosphere, Castray Esplanade, Hobart, TAS, 7000, Australia
| | - Mark V Brown
- School of Biotechnology and Biomolecular Science, UNSW Australia, Sydney, 2052, Australia
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Doblin MA, Petrou K, Sinutok S, Seymour JR, Messer LF, Brown MV, Norman L, Everett JD, McInnes AS, Ralph PJ, Thompson PA, Hassler CS. Nutrient uplift in a cyclonic eddy increases diversity, primary productivity and iron demand of microbial communities relative to a western boundary current. PeerJ 2016; 4:e1973. [PMID: 27168982 PMCID: PMC4860325 DOI: 10.7717/peerj.1973] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 04/05/2016] [Indexed: 11/20/2022] Open
Abstract
The intensification of western boundary currents in the global ocean will potentially influence meso-scale eddy generation, and redistribute microbes and their associated ecological and biogeochemical functions. To understand eddy-induced changes in microbial community composition as well as how they control growth, we targeted the East Australian Current (EAC) region to sample microbes in a cyclonic (cold-core) eddy (CCE) and the adjacent EAC. Phototrophic and diazotrophic microbes were more diverse (2–10 times greater Shannon index) in the CCE relative to the EAC, and the cell size distribution in the CCE was dominated (67%) by larger micro-plankton \documentclass[12pt]{minimal}
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}{}$(\geq 20\lrm{\mu }\mathrm{m})$\end{document}≥20μm, as opposed to pico- and nano-sized cells in the EAC. Nutrient addition experiments determined that nitrogen was the principal nutrient limiting growth in the EAC, while iron was a secondary limiting nutrient in the CCE. Among the diazotrophic community, heterotrophic NifH gene sequences dominated in the EAC and were attributable to members of the gamma-, beta-, and delta-proteobacteria, while the CCE contained both phototrophic and heterotrophic diazotrophs, including Trichodesmium, UCYN-A and gamma-proteobacteria. Daily sampling of incubation bottles following nutrient amendment captured a cascade of effects at the cellular, population and community level, indicating taxon-specific differences in the speed of response of microbes to nutrient supply. Nitrogen addition to the CCE community increased picoeukaryote chlorophyll a quotas within 24 h, suggesting that nutrient uplift by eddies causes a ‘greening’ effect as well as an increase in phytoplankton biomass. After three days in both the EAC and CCE, diatoms increased in abundance with macronutrient (N, P, Si) and iron amendment, whereas haptophytes and phototrophic dinoflagellates declined. Our results indicate that cyclonic eddies increase delivery of nitrogen to the upper ocean to potentially mitigate the negative consequences of increased stratification due to ocean warming, but also increase the biological demand for iron that is necessary to sustain the growth of large-celled phototrophs and potentially support the diversity of diazotrophs over longer time-scales.
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Affiliation(s)
- Martina A Doblin
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney , Ultimo NSW , Australia
| | - Katherina Petrou
- School of Life Sciences, University of Technology Sydney , Ultimo NSW , Australia
| | - Sutinee Sinutok
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Ultimo NSW, Australia; Faculty of Environmental Management, Prince of Songkla University, Kho Hong Songkhla, Thailand
| | - Justin R Seymour
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney , Ultimo NSW , Australia
| | - Lauren F Messer
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney , Ultimo NSW , Australia
| | - Mark V Brown
- School of Biotechnology and Biomolecular Sciences, University of New South Wales , Sydney NSW , Australia
| | - Louiza Norman
- Department of Plant Sciences, University of Cambridge , Cambridge , United Kingdom
| | - Jason D Everett
- School of Biological, Earth and Environmental Sciences, University of New South Wales , Sydney NSW , Australia
| | - Allison S McInnes
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney , Ultimo NSW , Australia
| | - Peter J Ralph
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney , Ultimo NSW , Australia
| | - Peter A Thompson
- Oceans and Atmosphere Flagship, Commonwealth Scientific Industrial Research Organisation , Hobart Tas , Australia
| | - Christel S Hassler
- Institute F.-A. Forel, Earth and Environmental Sciences, University of Geneva , Geneva , Switzerland
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Siboni N, Balaraju V, Carney R, Labbate M, Seymour JR. Spatiotemporal Dynamics of Vibrio spp. within the Sydney Harbour Estuary. Front Microbiol 2016; 7:460. [PMID: 27148171 PMCID: PMC4829023 DOI: 10.3389/fmicb.2016.00460] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 03/21/2016] [Indexed: 01/22/2023] Open
Abstract
Vibrio are a genus of marine bacteria that have substantial environmental and human health importance, and there is evidence that their impact may be increasing as a consequence of changing environmental conditions. We investigated the abundance and composition of the Vibrio community within the Sydney Harbour estuary, one of the most densely populated coastal areas in Australia, and a region currently experiencing rapidly changing environmental conditions. Using quantitative PCR (qPCR) and Vibrio-specific 16S rRNA amplicon sequencing approaches we observed significant spatial and seasonal variation in the abundance and composition of the Vibrio community. Total Vibrio spp. abundance, derived from qPCR analysis, was higher during the late summer than winter and within locations with mid-range salinity (5-26 ppt). In addition we targeted three clinically important pathogens: Vibrio cholerae, V. Vulnificus, and V. parahaemolyticus. While toxigenic strains of V. cholerae were not detected in any samples, non-toxigenic strains were detected in 71% of samples, spanning a salinity range of 0-37 ppt and were observed during both late summer and winter. In contrast, pathogenic V. vulnificus was only detected in 14% of samples, with its occurrence restricted to the late summer and a salinity range of 5-26 ppt. V. parahaemolyticus was not observed at any site or time point. A Vibrio-specific 16S rRNA amplicon sequencing approach revealed clear shifts in Vibrio community composition across sites and between seasons, with several Vibrio operational taxonomic units (OTUs) displaying marked spatial patterns and seasonal trends. Shifts in the composition of the Vibrio community between seasons were primarily driven by changes in temperature, salinity and NO2, while a range of factors including pH, salinity, dissolved oxygen (DO) and NOx (Nitrogen Oxides) explained the observed spatial variation. Our evidence for the presence of a spatiotemporally dynamic Vibrio community within Sydney Harbour is notable given the high levels of human use of this waterway, and the significant increases in seawater temperature predicted for this region.
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Affiliation(s)
- Nachshon Siboni
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, UltimoNSW, Australia
| | - Varunan Balaraju
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, UltimoNSW, Australia
- School of Life Sciences, The ithree institute, University of Technology Sydney, UltimoNSW, Australia
| | - Richard Carney
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, UltimoNSW, Australia
| | - Maurizio Labbate
- School of Life Sciences, The ithree institute, University of Technology Sydney, UltimoNSW, Australia
| | - Justin R. Seymour
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, UltimoNSW, Australia
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Techtmann SM, Fortney JL, Ayers KA, Joyner DC, Linley TD, Pfiffner SM, Hazen TC. The unique chemistry of Eastern Mediterranean water masses selects for distinct microbial communities by depth. PLoS One 2015; 10:e0120605. [PMID: 25807542 PMCID: PMC4373936 DOI: 10.1371/journal.pone.0120605] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 01/24/2015] [Indexed: 11/26/2022] Open
Abstract
The waters of the Eastern Mediterranean are characterized by unique physical and chemical properties within separate water masses occupying different depths. Distinct water masses are present throughout the oceans, which drive thermohaline circulation. These water masses may contain specific microbial assemblages. The goal of this study was to examine the effect of physical and geological phenomena on the microbial community of the Eastern Mediterranean water column. Chemical measurements were combined with phospholipid fatty acid (PLFA) analysis and high-throughput 16S rRNA sequencing to characterize the microbial community in the water column at five sites. We demonstrate that the chemistry and microbial community of the water column were stratified into three distinct water masses. The salinity and nutrient concentrations vary between these water masses. Nutrient concentrations increased with depth, and salinity was highest in the intermediate water mass. Our PLFA analysis indicated different lipid classes were abundant in each water mass, suggesting that distinct groups of microbes inhabit these water masses. 16S rRNA gene sequencing confirmed the presence of distinct microbial communities in each water mass. Taxa involved in autotrophic nitrogen cycling were enriched in the intermediate water mass suggesting that microbes in this water mass may be important to the nitrogen cycle of the Eastern Mediterranean. The Eastern Mediterranean also contains numerous active hydrocarbon seeps. We sampled above the North Alex Mud Volcano, in order to test the effect of these geological features on the microbial community in the adjacent water column. The community in the waters overlaying the mud volcano was distinct from other communities collected at similar depths and was enriched in known hydrocarbon degrading taxa. Our results demonstrate that physical phenomena such stratification as well as geological phenomena such as mud volcanoes strongly affect microbial community structure in the Eastern Mediterranean water column.
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Affiliation(s)
- Stephen M. Techtmann
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, United States of America
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Julian L. Fortney
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, United States of America
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Kati A. Ayers
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, United States of America
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Dominique C. Joyner
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, United States of America
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Thomas D. Linley
- Ocean Lab, University of Aberdeen, Newburgh, Aberdeenshire, United Kingdom
| | - Susan M. Pfiffner
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, United States of America
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Terry C. Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, United States of America
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, United States of America
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, Tennessee, United States of America
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
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10
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Li J, Li N, Li F, Zou T, Yu S, Wang Y, Qin S, Wang G. Spatial diversity of bacterioplankton communities in surface water of northern South China Sea. PLoS One 2014; 9:e113014. [PMID: 25402458 PMCID: PMC4234503 DOI: 10.1371/journal.pone.0113014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 10/21/2014] [Indexed: 11/23/2022] Open
Abstract
The South China Sea is one of the largest marginal seas, with relatively frequent passage of eddies and featuring distinct spatial variation in the western tropical Pacific Ocean. Here, we report a phylogenetic study of bacterial community structures in surface seawater of the northern South China Sea (nSCS). Samples collected from 31 sites across large environmental gradients were used to construct clone libraries and yielded 2,443 sequences grouped into 170 OTUs. Phylogenetic analysis revealed 23 bacterial classes with major components α-, β- and γ-Proteobacteria, as well as Cyanobacteria. At class and genus taxon levels, community structure of coastal waters was distinctively different from that of deep-sea waters and displayed a higher diversity index. Redundancy analyses revealed that bacterial community structures displayed a significant correlation with the water depth of individual sampling sites. Members of α-Proteobacteria were the principal component contributing to the differences of the clone libraries. Furthermore, the bacterial communities exhibited heterogeneity within zones of upwelling and anticyclonic eddies. Our results suggested that surface bacterial communities in nSCS had two-level patterns of spatial distribution structured by ecological types (coastal VS. oceanic zones) and mesoscale physical processes, and also provided evidence for bacterial phylogenetic phyla shaped by ecological preferences.
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Affiliation(s)
- Jialin Li
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Nan Li
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Fuchao Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Tao Zou
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Shuxian Yu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Yinchu Wang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Song Qin
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- * E-mail: (SQ); (GW)
| | - Guangyi Wang
- Tianjin University Center for Marine Environmental Ecology, School of Environmental Sciences and Engineering, Tianjin University, Tianjin, China
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
- * E-mail: (SQ); (GW)
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11
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Tout J, Jeffries TC, Webster NS, Stocker R, Ralph PJ, Seymour JR. Variability in microbial community composition and function between different niches within a coral reef. MICROBIAL ECOLOGY 2014; 67:540-552. [PMID: 24477921 DOI: 10.1007/s00248-013-0362-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 12/26/2013] [Indexed: 06/03/2023]
Abstract
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.
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Affiliation(s)
- Jessica Tout
- Plant Functional Biology and Climate Change Cluster, University of Technology, Sydney, NSW, Australia,
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12
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Brown MV, Ostrowski M, Grzymski JJ, Lauro FM. A trait based perspective on the biogeography of common and abundant marine bacterioplankton clades. Mar Genomics 2014; 15:17-28. [PMID: 24662471 DOI: 10.1016/j.margen.2014.03.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 03/08/2014] [Accepted: 03/08/2014] [Indexed: 11/26/2022]
Abstract
Marine microbial communities provide much of the energy upon which all higher trophic levels depend, particularly in open-ocean and oligotrophic systems, and play a pivotal role in biogeochemical cycling. How and why species are distributed in the global oceans, and whether net ecosystem function can be accurately predicted from community composition are fundamental questions for marine scientists. Many of the most abundant clades of marine bacteria, including the Prochlorococcus, Synechococcus, SAR11, SAR86 and Roseobacter, have a very broad, if not a cosmopolitan distribution. However this is not reflected in an underlying genetic identity. Rather, widespread distribution in these organisms is achieved by the existence of closely related but discrete ecotypes that display niche adaptations. Closely related ecotypes display specific nutritional or energy generating mechanisms and are adapted to different physical parameters including temperature, salinity, and hydrostatic pressure. Furthermore, biotic phenomena such as selective grazing and viral loss contribute to the success or failure of ecotypes allowing some to compete effectively in particular marine provinces but not in others. An additional layer of complexity is added by ocean currents and hydrodynamic specificity of water body masses that bound microbial dispersal and immigration. These vary in space and time with respect to intensity and direction, making the definition of large biogeographic provinces problematic. A deterministic theory aimed at understanding how all these factors shape microbial life in the oceans can only proceed through analysis of microbial traits, rather than pure phylogenetic assessments. Trait based approaches seek mechanistic explanations for the observed temporal and spatial patterns. This review will present successful recent advances in phylogenetic and trait based biogeographic analyses in some of the most abundant marine taxa.
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Affiliation(s)
- Mark V Brown
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia; Evolution and Ecology Research Center, University of New South Wales, Sydney, Australia
| | - Martin Ostrowski
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
| | - Joseph J Grzymski
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, USA
| | - Federico M Lauro
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia; Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore.
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