Chapter 24
Microbial Diversity in the Deep Sea and the Underexplored “Rare Biosphere”
David B. Mark Welch,
Susan M. Huse,
David B. Mark Welch
Marine Biological Laboratory at Woods Hole, Woods Hole, Massachusetts, USA
Search for more papers by this authorSusan M. Huse
Marine Biological Laboratory at Woods Hole, Woods Hole, Massachusetts, USA
Search for more papers by this authorDavid B. Mark Welch,
Susan M. Huse,
David B. Mark Welch
Marine Biological Laboratory at Woods Hole, Woods Hole, Massachusetts, USA
Search for more papers by this authorSusan M. Huse
Marine Biological Laboratory at Woods Hole, Woods Hole, Massachusetts, USA
Search for more papers by this authorBook Editor(s):Frans J. de Bruijn,
Frans J. de Bruijn
Laboratory of Plant Micro-organism Interaction, CNRS-INRA, Castanet Tolosan, France
Search for more papers by this authorSummary
This chapter contains sections titled:
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Introduction
-
Methods
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Results and Discussion
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Internet Resources
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References
INTERNET RESOURCES
- Primer sequences, the refSSU and refV6 databases, perl scripts used for SLP/PW-AN clustering, processed V6 tags, and other resources are available at http://vamps.mbl.edu. The RDP classifier is available at http://rdp.cme.msu.edu, and the Silva database of ribosomal sequences is available from www.arbsilva.de. Details of the ICoMM project can be found at http://icomm.mbl.edu.
- REFERENCES
- Acinas SG, Klepac-Ceraj V, Hunt DE, Pharino C, Ceraj I, Distel, DL. Polz, MF. 2004. Fine-scale phylogenetic architecture of a complex bacterial community. Nature 430: 551–554.
- Alain K, Querellou J, Lesongeur F, Pignet P, Crassous P, Raguenes G et al. 2002. Caminibacter hydrogeniphilus gen. nov., sp. nov., a novel thermophilic, hydrogen-oxidizing bacterium isolated from an East Pacific Rise hydrothermal vent. Int. J. Syst. Evol. Microbiol. 52: 1317–1323.
- Atlas RM, Bartha R. 1993. Microbial Ecology. Fundamentals and Applications. Redwood City, CA: Benjamin/Cummings.
- Béjà O, Suzuki MT, Koonin EV, Aravind L, Hadd A, Nguyen LP, et al. 2000. Construction and analysis of bacterial artificial chromo-some libraries from a marine microbial assemblage. Environ. Micro-biol. 2: 516–529.
- Campbell BJ, Jeanthon C, Kostka JE, Luther GW 3rd, Cary SC. 2001. Growth and phylogenetic properties of novel bacteria belonging to the epsilon subdivision of the Proteobacteria enriched from Alvinella pompejana and deep-sea hydrothermal vents. Appl. Environ. Microbiol. 67: 4566–4572.
- Chao A. 1984. Non-parametric estimation of the number of classes in a population. Scand. J. Stat. 11: 265–270.
- Chao A. 1992. Estimating the number of classes via sample coverage. J. Am. Stat. Assoc. 87: 210–217.
- Chao A, Ma MC, Yang, K. 1993. Stopping rules and estimation for recapture debugging with unequal failure rates. Biometrika 80: 193–201.
- Cole JR, Chai B, Farris RJ, Wang Q, Kulam SA, McGarrell, DM, et al. 2005. The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res. 33: D294–D296.
- Coleman ML, Sullivan MB, Martiny AC, Steglich C, Barry K, DeLong EF, Chisholm SW. 2006. Genomic islands and the ecology and evolution of Prochlorococcus. Science 311: 1768–1770.
- Curtis TP, Sloan WT, Scannell, JW. 2002. Estimating prokaryotic diversity and its limits. Proc. Natl. Acad. Sci. USA 99: 10494–10499.
- Curtis TP, Head IM, Lunn M, Woodcock S, Schloss PD, Sloan WT. 2006. What is the extent of microbial diversity? Philos. Trans. R. Soc. Lond. B 361: 2023–2037.
- DeLong EF. 1992. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA 89: 5685–5689.
- DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, Frigaard NU, et al. 2006. Community genomics among stratified microbial assemblages in the ocean’s interior. Science 311: 496–503.
- Frigaard NU, Martinez A, Mincer, TJ, DeLong, EF. 2006. Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea. Nature 439: 847–850.
- Fuhrman JA, McCallum K, Davis, AA. 1993. Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans. Appl. Environ. Microbiol. 59: 1294–1302.
- Giovannoni SJ, Britschgi TB, Moyer CL, Field KG. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345: 60–63.
- Hallam SJ, Mincer TJ, Schleper C, Preston CM, Roberts K, Richardson PM, Delong, EF. 2006. Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine crenarchaeota. PLoS Biol. 4: e95.
- Hebert PD, Cywinska A, Ball, SL, deWaard, JR. 2003. Biological identifications through DNA barcodes. Proc. Biol. Sci. 270: 313–321.
- Hewson I, Vargo GA, Fuhrman JA. 2003. Bacterial diversity in shallow oligotrophic marine benthos and overlying waters: Effects of virus infection, containment, and nutrient enrichment. Microb. Ecol. 46: 322–336.
- Hobbie JE, Daley RJ, Jasper S. 1977. Use of nuclepore filters for counting bacteria by fluorescence microscopy. Appl. Environ. Micro-biol. 33: 1225–1228.
- Huber JA, Butterfield DA, Baross JA. 2003. Bacterial diversity in a subseafloor habitat following a deep-sea volcanic eruption. FEMS Microbiol. Ecol. 43: 393–409.
- Huber JA, Johnson HP, Butterfield DA, Baross, JA. 2006. Microbial life in ridge flank crustal fluids. Environ. Microbiol. 8: 88–99.
- Huber JA, Mark Welch DB, Morrison HG, Huse SM, Neal PR, Butterfield DA, Sogin, ML. 2007. Microbial population structures in the deep marine biosphere. Science 318: 97–100.
- Hugler M, Wirsen CO, Fuchs G, Taylor CD, Sievert SM. 2005. Evidence for autotrophic CO2 fixation via the reductive tricarboxylic acid cycle by members of the epsilon subdivision of proteobacteria. J. Bacteriol. 187: 3020–3027.
- Huse S, Huber J, Morrison H, Sogin M, Mark Welch D. 2007. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol. 8: R143.
- Huse SM, Dethlefsen L, Huber JA, Mark Welch D, Relman DA, Sogin ML. 2008. Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genetics 4: e1000255.
- Huse SM, Mark Welch DB, Morrison HG, Sogin ML. 2010. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ. Microbiol. in press.
- Jeon S-O, Bunge J, Stoeck T, Barger KJ-A, Hong S-H, Epstein, SS. 2006. Synthetic statistical approach reveals a high degree of richness of microbial eukaryotes in an anoxic water column. Appl. Environ. Microbiol. 72: 6578–6583.
- Kemp PF, Aller, JY. 2003. Bacterial diversity in aquatic and other environments: What 16S rDNA libraries can tell us. GEMS Microbial. Ecol. 47: 161–177.
- Knittel K, Losekann T, Boetius A, Kort R, Amann R. 2005. Diversity and distribution of methanotrophic archaea at cold seeps. Appl. Environ. Microbiol. 71: 467–479.
- Kunin V, Engelbrektson A, Ochman H, Hugenholtz P. 2010. Wrinkles in the rare biosphere: Pyrosequencing errors lead to artificial inflation of diversity estimates. Environ. Microbiol. 12: 118–123.
- Kysela DT, Palacios C, Sogin, M. 2005. Serial analysis of V6 ribosomal sequence tags (SARST-V6): A method for efficient, high-throughput analysis of microbial community composition. Environ. Microbiol. 7: 356–364.
- Lozupone C, Knight R. 2005. UniFrac: A new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71: 8228–8235.
- Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376–380.
- Pace NR. 1997. A molecular view of microbial diversity and the biosphere. Science 276: 734–740.
- Pedrós-Alió C. 2006. Marine microbial diversity: Can it be determined? Trends Microbiol. 14: 257–263.
- Pedrós-Alió C. 2007. ECOLOGY: Dipping into the Rare Biosphere. Science 315: 192–193.
- Porter KG, Feig YS. 1980. The use of DAPI for identifying and counting aquatic microflora Limnol. Oceanogr. 25: 943–948.
- Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glockner, FO. 2007. SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35: 7188–7196.
- Quince C, Curtis TP, Sloan WT. 2008. The rational exploration of microbial diversity. ISME J. 2: 997–1006.
- Rappe MS, Giovannoni, SJ. 2003. The uncultured microbial majority. Annu. Rev. Microbiol. 57: 369–394.
- Ravenschlag K, Sahm K, Pernthaler J, Amann, R. 1999. High bacterial diversity in permanently cold marine sediments. Appl. Environ. Microbiol. 65: 3982–3989.
- Reysenbach AL, Longnecker K, Kirshtein J. 2000. Novel bacterial and archaeal lineages from an in situ growth chamber deployed at a Mid-Atlantic Ridge hydrothermal vent. Appl. Environ. Microbiol. 66: 3798–3806.
- Roux FL, Zouine M, Chakroun N, Binesse J, Saulnie, D, Bouchier C, et al. 2009. Genome sequence of Vibrio splendidus: An abundant planctonic marine species with a large genotypic diversity. Environ. Microbiol. 11: 1959–1970.
- Schloss PD, Handelsman, J. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl. Environ. Microbiol. 71: 1501–1506.
- Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. 2009. Introducing mothur: Open source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75: 7537–7541.
- Sloan WT, Woodcock S, Lunn M, Head IM, Curtis TP. 2007. Modeling taxa-abundance distributions in microbial communities using environmental sequence data. Microb. Ecol. 53: 443–455.
- Sogin ML, Morrison HG, Huber JA, Mark Welch DB, Huse SM, Neal PR, et al. 2006. Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proc. Natl. Acad. Sci. USA 103: 12115–12120.
- Takai K, Campbell BJ, Cary SC, Suzuki M, Oida H, Nunoura T, et al. 2005. Enzymatic and genetic characterization of carbon and energy metabolisms by deep-sea hydrothermal chemolithoautotrophic isolates of Epsilonproteobacteria. Appl. Environ. Microbiol. 71: 7310–7320.
- Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, et al. 2005. Comparative metagenomics of microbial communities. Science 308: 554–557.
- Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, et al. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66–74.
- Whitman WB, Coleman DC, Wiebe WJ. 1998. Prokaryotes: The unseen majority. Proc. Natl. Acad. Sci. USA 95: 6578–6583.
