Hostname: page-component-7c8c6479df-hgkh8 Total loading time: 0 Render date: 2024-03-28T13:32:37.429Z Has data issue: false hasContentIssue false

Biodiversity of the bacterioplankton in the surface waters around Southern Thule in the Southern Ocean

Published online by Cambridge University Press:  19 May 2008

David A. Pearce*
Affiliation:
British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge CB3 OET, UK

Abstract

Seven independent clone libraries were constructed to study the biodiversity of the bacterioplankton in the surface waters around Southern Thule, South Sandwich Islands, in order to identify the species present, to determine the sample effort required to estimate the total diversity, and to determine whether the surface waters around Southern Thule represented a highly specialized local anomaly or a subset of the marine meta-community. In total, 672 clones generated 629 useable sequences. These 629 clones matched 278 different sequences deposited in the 16S rDNA sequence databases. The majority of the clones were related to marine microorganisms, many of which had been previously detected in permanently cold Arctic and Antarctic marine environments. Each clone library generated an average of 35.8 new sequence matches. 346 clones covered two-thirds of the total estimated diversity, while 438 clones covered three-quarters of the total estimated diversity. Above this number, the coverage tended to stabilize and a relatively large number of additional clones were required to improve coverage significantly, increasing at the rate of about one new sequence match per 100 new clones. Comparing the different clone libraries, eight matches occurred in each of the seven libraries, whilst fifty-five occurred in only one, suggesting that there might be a relatively small number of common dominant ubiquitous species, with a much larger underlying diversity or ‘seed bank’ from which this dominant diversity is drawn. This study suggests that the dominant bacterioplankton in the surface waters around Southern Thule represent a subset of the marine meta-community, whilst sub-dominant diversity appears to be a highly specialized local anomaly.

Type
Research Article
Copyright
Copyright © Antarctic Science Ltd 2008

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Abell, G.C.J. & Bowman, J.P. 2005. Ecological and biogeographic relationships of class Flavobacteria in the Southern Ocean. FEMS Microbiology Ecology, 51, 265277.CrossRefGoogle ScholarPubMed
Altschul, S.F., Madden, T., Schäffer, A.A., Zhang, J., Zhang, Z.W. & Miller, W. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25, 33893402.CrossRefGoogle ScholarPubMed
Bano, N., Ruffin, S., Ransom, B. & Hollibaugh, J.T. 2004. Phylogenetic composition of Arctic Ocean archaeal assemblages and comparison with Antarctic assemblages. Applied and Environmental Microbiology, 70, 781789.CrossRefGoogle ScholarPubMed
Borneman, J. & Triplett, E.W. 1997. Molecular microbial diversity in soils from eastern Amazonia - evidence for unusual microorganisms and microbial population shifts associated with deforestation. Applied and Environmental Microbiology, 63, 26472653.CrossRefGoogle ScholarPubMed
Bowman, J.P., Mccammon, S.A., Brown, M.V., Nichols, D.S. & Mcmeekin, T.A. 1997. Diversity and association of psychrophilic bacteria in Antarctic sea ice. Applied and Environmental Microbiology, 63, 30683078.CrossRefGoogle ScholarPubMed
Bowman, J.P., Rea, S.M., Mccammon, S.A. & Mcmeekin, T.A. 2000. Diversity and community structure within anoxic sediment from marine salinity meromictic lakes and a coastal meromictic marine basin, Vestfold Hilds, Eastern Antarctica. Environmental Microbiology, 2, 227237.CrossRefGoogle Scholar
Brown, M.V. & Bowman, J.P. 2001. A molecular phylogenetic survey of sea-ice microbial communities (SIMCO). FEMS Microbiology Ecology, 35, 267275.CrossRefGoogle ScholarPubMed
Chao, A. 1984. Non-parametric estimation of the number of classes in a population. Scandinavian Journal of Statistics, 11, 265270.Google Scholar
Curtis, T.P., Sloan, W. & Scannell, J. 2002. Estimating prokaryotic diversity and its limits. Proceedings of the National Academy of Sciences of the United States, 99, 10 494–10 499.CrossRefGoogle ScholarPubMed
Curtis, T.P. & Sloan, W.T. 2004. Prokaryotic diversity and its limits: microbial community structure in nature and implications for microbial ecology. Current Opinion in Microbiology, 7, 221226.CrossRefGoogle ScholarPubMed
Delong, E.F. 1998. Archaeal means and extremes. Science, 280, 542543.CrossRefGoogle ScholarPubMed
Dunbar, J., Barns, S.M., Ticknor, L.O. & Kuske, C.R. 2002. Empirical and theoretical bacterial biodiversity in four Arizona soils. Applied and Environmental Microbiology, 68, 30353045.CrossRefGoogle ScholarPubMed
Field, K.G., Gordon, D., Wright, T., Rappé, M., Urback, E., Vergin, K. & Giovannoni, S.J. 1997. Diversity and depth-specific distribution of SAR11 cluster rRNA genes from marine planktonic bacteria. Applied and Environmental Microbiology, 63, 6370.CrossRefGoogle ScholarPubMed
Finlay, B.J. 2002. Global dispersal of free-living microbial eukaryote species. Science, 296, 10611063.CrossRefGoogle ScholarPubMed
Fuhrman, J.A., Mccallum, K. & Davis, A.A. 1992. Novel major archaebacterial group from marine plankton. Nature, 356, 148149.CrossRefGoogle ScholarPubMed
Fuhrman, J.A. & Davis, A.A. 1997. Widespread archaea and novel bacteria from the deep sea as shown by 16S rRNA gene sequences. Marine Ecology Progress Series, 150, 275285.CrossRefGoogle Scholar
Fuhrman, J.A. & Campbell, L. 1998. Microbial diversity. Nature, 393, 410411.CrossRefGoogle Scholar
Fuhrman, J.A., Comeau, D.E., Hagstrom, A. & Chan, A.M. 1988. Extraction from natural planktonic microorganisms of DNA suitable for molecular biological studies. Applied and Environmental Microbiology, 54, 14261429.CrossRefGoogle ScholarPubMed
Gast, R.J., Moran, D.M., Beaudoin, D.J., Blythe, J.M., Dennett, M.R. & Caron, D.A. 2006. Abundance of a novel dinoflagellate phylotype in the Ross Sea, Antarctica. Journal of Phycology, 42, 233242.CrossRefGoogle Scholar
Gentile, G., Giuliano, L., D'auria, G., Smedile, F., Azzaro, M., Dedomenico, M. & Yakimov, M.M. 2006. Study of bacterial communities in Antarctic coastal waters by a combination of 16S rRNA and 16S rDNA sequencing. Environmental Microbiology, 8, 21502161.CrossRefGoogle ScholarPubMed
Glöckner, F.O., Zaichikov, E., Belkova, N., Denissova, L., Pernthaler, J., Pernthaler, A. & Amann, R. 2000. Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of Actinobacteria. Applied and Environmental Microbiology, 66, 50535065.CrossRefGoogle ScholarPubMed
Good, I.J. 1953. The population frequencies of species and the estimation of the population parameters. Biometrica, 40, 237264.CrossRefGoogle Scholar
Hagström, Å., Pommier, T., Rohwer, F., Simu, K., Stolte, W., Svensson, D. & Zweifel, U.L. 2002. Use of 16S ribosomal DNA for delineation of marine bacterioplankton species. Applied and Environmental Microbiology, 68, 36283633.CrossRefGoogle ScholarPubMed
Hahn, M.W. 2003. Isolation of novel ultramicrobacteria classified as Actinobacteria from five freshwater habitats in Europe and Asia. Applied and Environmental Microbiology, 69, 14421451.CrossRefGoogle ScholarPubMed
Hughes, J.B., Hellmann, J.J., Ricketts, T.H. & Bohannan, B.J.M. 2001. Counting the uncountable: statistical approaches to estimating microbial diversity. Applied and Environmental Microbiology, 67, 43994406.CrossRefGoogle ScholarPubMed
Labrenz, M., Tindall, B.J., Lawson, P.A., Collins, M.D., Schumann, P. & Hirsch, P. 2000. Staleya guttiformis gen. nov., sp. nov. and Sulfibacter brevis sp. nov., α-3-Proteobacteria from hypersaline, heliothermal and meromictic Antarctic Ekho Lake. International Journal of Systematic and Evolutionary Microbiology, 50, 303313.CrossRefGoogle ScholarPubMed
Lau, K.W.K., Ng, C.Y.M., Ren, J., Lau, S.C.L., Qian, P.-Y., Wong, P.-K., Lau, T.C. & Wu, M. 2005. Owenweeksia hongkongensis gen. nov., sp. nov., a novel marine bacterium of the phylum ‘Bacteroidetes’. International Journal of Systematic and Evolutionary Microbiology, 55, 10511057.CrossRefGoogle Scholar
Lee, S.-M. & Chao, A. 1994. Estimating population size via sample coverage for closed capture-recapture models. Biometrics, 50, 8897.CrossRefGoogle ScholarPubMed
Le Quéré, C., Rödenbeck, C., Buitenhuis, E.T., Conway, T.J., Langensfelds, R., Gomez, A., Labuschangne, C., Ramonet, M., Nakazawa, T., Metzl, N., Gillett, N.P. & Heimann, M. 2007. Saturations of the Southern Ocean CO2 sink due to recent climate change. Science, 316, 17351738.CrossRefGoogle ScholarPubMed
López-Garcia, P., Rodríguez-Valera, F., Pedrós-Alió, C. & Moreira, D. 2001. Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton. Nature, 409, 603607.CrossRefGoogle ScholarPubMed
Lunn, M., Sloan, W.T. & Curtis, T.P. 2004. Estimating bacterial diversity from clone libraries with flat rank abundance distributions. Environmental Microbiology, 6, 10811086.CrossRefGoogle ScholarPubMed
Massana, R., Delong, E.F. & Pedrós-Alió, C. 2000. A few cosmopolitan phylotypes dominate planktonic archaeal assemblages in widely different oceanic provinces. Applied and Environmental Microbiology, 66, 17771787.CrossRefGoogle ScholarPubMed
Matsuzaki, M., Kubota, K., Satoh, T., Kunugi, N., Ban, S. & Imura, S. 2006. Dimethyl sulfoxide-respiring bacteria in Suribati Ike, a hypersaline lake, in Antarctica and the marine environment. Polar Bioscience, 20, 7381.Google Scholar
Pearce, D.A., Cockell, C.S., Lindström, E.S. & Tranvik, L.J. 2007. First evidence for a bipolar distribution of dominant freshwater lake bacterioplankton. Antarctic Science, 19, 245252.CrossRefGoogle Scholar
Pommier, T., Canbäck, B., Riemann, K., Boström, H., Simu, K., Lundberg, P., Tunlid, A. & Hagström, Å. 2007. Global patterns of diversity and community structure in marine bacterioplankton. Molecular Ecology, 16, 867880.CrossRefGoogle ScholarPubMed
Simpson, E.H. 1949. Measurement of diversity. Nature, 163, 688.CrossRefGoogle Scholar
Staley, J.T. & Gosink, J.J. 1999. Poles apart: biodiversity and biogeography of sea ice bacteria. Annual Review of Microbiology, 53, 189215.CrossRefGoogle ScholarPubMed
Stingl, U., Tripp, H.J. & Giovannoni, S.J. 2007. Improvements of high-throughput culturing yielded novel SAR11 strains and other abundant marine bacteria from the Oregon coast and the Bermuda Atlantic Time Series study site. The ISME Journal, 1, 361371.CrossRefGoogle ScholarPubMed
Telford, R.J., Vandvik, V. & Birks, H.J.B. 2006. Dispersal limitations matter for microbial morphospecies. Science, 312, 1015.CrossRefGoogle ScholarPubMed
Torsvik, V., Øvreas, L. & Thingstad, T.F. 2002. Prokaryotic diversity - magnitude, dynamics, and controlling factors. Science, 296, 1061066.CrossRefGoogle ScholarPubMed
Venter, J.C., Remmington, K., Heidelberg, J.F., Halpern, A.L., Ruscch, D., Eisen, J.A., Wu, D., Paulsen, I., Nelson, K.E., Nelson, W., Fouts, D.E., Levy, S., Knap, A.H., Lomas, M.W., Nealson, K., White, O., Peterson, J., Hoffman, J., Parsons, R., Baden-Tillson, H., Pfannkoch, C., Rogers, Y.-H. & Smith, H.O. 2004. Environmental genome shotgun sequencing of the Sargasso sea. Science, 304, 6674.CrossRefGoogle ScholarPubMed
Webster, N.S. & Bourne, D. 2007. Bacterial community structure associated with the Antarctic soft coral, Alcyonium antarcticum. FEMS Microbiology Ecology, 59, 8194.CrossRefGoogle ScholarPubMed
Whitaker, R.J., Grogen, D.W. & Taylor, J.W. 2003. Geographic barriers isolate endemic populations of hyperthermophilic Archaea. Science, 301, 976978.CrossRefGoogle ScholarPubMed
Whitman, W.B., Coleman, D.C. & Wiebe, W.J. 1998. Prokaryotes: the unseen majority. Proceedings of the National Academy of Science of the United States of America, 95, 65786583.CrossRefGoogle ScholarPubMed
Zwart, G., Hiorns, D.W., Methé, B.A., Van Agterveld, M.D., Huisman, R., Nold, S.C., Zehr, J.P. & Laanbroek, H.J. 1998. Nearly identical 16S rRNA sequences recovered from lakes in North America and Europe indicate the existence of clades of globally distributed freshwater bacteria. Systematic and Applied Microbiology, 21, 546556.CrossRefGoogle ScholarPubMed