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Microbial diversity in the deep sea and the underexplored “rare biosphere”

  1. Mitchell L. Sogin * , † ,
  2. Hilary G. Morrison *,
  3. Julie A. Huber *,
  4. David Mark Welch *,
  5. Susan M. Huse *,
  6. Phillip R. Neal *,
  7. Jesus M. Arrieta ‡ , § , and
  8. Gerhard J. Herndl ‡
  1. *Josephine Bay Paul Center, Marine Biological Laboratory at Woods Hole, 7 MBL Street, Woods Hole, MA 02543; and
  2. ‡Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands

  1. Communicated by M. S. Meselson, Harvard University, Cambridge, MA, June 20, 2006 (received for review May 5, 2006)

Abstract

The evolution of marine microbes over billions of years predicts that the composition of microbial communities should be much greater than the published estimates of a few thousand distinct kinds of microbes per liter of seawater. By adopting a massively parallel tag sequencing strategy, we show that bacterial communities of deep water masses of the North Atlantic and diffuse flow hydrothermal vents are one to two orders of magnitude more complex than previously reported for any microbial environment. A relatively small number of different populations dominate all samples, but thousands of low-abundance populations account for most of the observed phylogenetic diversity. This “rare biosphere” is very ancient and may represent a nearly inexhaustible source of genomic innovation. Members of the rare biosphere are highly divergent from each other and, at different times in earth's history, may have had a profound impact on shaping planetary processes.

Footnotes

  • †To whom correspondence should be addressed. E-mail: sogin{at}mbl.edu

  • ↵ §Present address: Instituto Mediterráneo de Estudios Avanzados, Consejo Superior de Investigaciones Cientificas-Universitat de les Illes Balears, Miquel Marques 21, E-07190 Esporles, Mallorca, Spain.

  • Author contributions: M.L.S. designed research; H.G.M., J.A.H., J.M.A., and G.J.H. performed research; H.G.M., D.M.W., S.M.H., and P.R.N. contributed new reagents/analytic tools; M.L.S., H.G.M., J.A.H., D.M.W., S.M.H., and P.R.N. analyzed data; and M.L.S., H.G.M., J.A.H., D.M.W., and G.J.H. wrote the paper.

  • Conflict of interest statement: No conflicts declared.

  • Data deposition: The sequences reported in this paper have been deposited in the GenBank database (trace archive accession nos. TI1369949070–TI1370073576).

  • Abbreviation:
    OTU,
    operational taxonomic unit

  • Freely available online through the PNAS open access option.

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