DOI: 10.1126/science.1146689. Microbial Population Structures in the Deep Marine Biosphere

Microbial Population Structures in the Deep Marine Biosphere

10.1126/science.1146689

Crossref journal-article

American Association for the Advancement of Science (AAAS)

Science (221)

Abstract

The analytical power of environmental DNA sequences for modeling microbial ecosystems depends on accurate assessments of population structure, including diversity (richness) and relative abundance (evenness). We investigated both aspects of population structure for microbial communities at two neighboring hydrothermal vents by examining the sequences of more than 900,000 microbial small-subunit ribosomal RNA amplicons. The two vent communities have different population structures that reflect local geochemical regimes. Descriptions of archaeal diversity were nearly exhaustive, but despite collecting an unparalleled number of sequences, statistical analyses indicated additional bacterial diversity at every taxonomic level. We predict that hundreds of thousands of sequences will be necessary to capture the vast diversity of microbial communities, and that different patterns of evenness for both high- and low-abundance taxa may be important in defining microbial ecosystem dynamics.

Bibliography

Huber, J. A., Mark Welch, D. B., Morrison, H. G., Huse, S. M., Neal, P. R., Butterfield, D. A., & Sogin, M. L. (2007). Microbial Population Structures in the Deep Marine Biosphere. Science, 318(5847), 97â100.

Authors 7

Julie A. Huber (first)
David B. Mark Welch (additional)
Hilary G. Morrison (additional)
Susan M. Huse (additional)
Phillip R. Neal (additional)
David A. Butterfield (additional)
Mitchell L. Sogin (additional)

References 25 Referenced 707

10.1038/345060a0
10.1371/journal.pbio.0050077
10.1371/journal.pbio.0050016
10.1073/pnas.0605127103
H. P. Johnson, R. W. Embley, J. Geophys. Res.95, 12689 (1990). (10.1029/JB095iB08p12689) / J. Geophys. Res. (1990)
R. W. Embley, E. T. Baker, Eos80, 213 (1999). / Eos (1999)
10.1128/AEM.68.4.1585-1594.2002
J. A. Huber, D. A. Butterfield, J. A. Baross, FEMS Microbiol. Ecol.43, 393 (2003). (10.1111/j.1574-6941.2003.tb01080.x) / FEMS Microbiol. Ecol. (2003)
D. A. Butterfieldet al., in The Subseafloor Biosphere at Mid-Ocean Ridges, W. S. D. Wilcock, E. F. DeLong, D. S. Kelley, J. A. Baross, S. C. Cary, Eds. (American Geophysical Union, Washington, DC, 2004), pp. 269â289. / The Subseafloor Biosphere at Mid-Ocean Ridges, (2004)
A. Maruyama, T. Urabe, J. Ishibashi, R. A. Feely, E. T. Baker, Cah. Biol. Mar.39, 249 (1998). / Cah. Biol. Mar. (1998)
See supporting material on Science Online.
P. D. Schloss, J. Handelsman, Appl. Environ. Microbiol.71, 1501 (2005). (10.1128/AEM.71.3.1501-1506.2005) / Appl. Environ. Microbiol. (2005)
A. Chao, Scand. J. Stat.11, 265 (1984). / Scand. J. Stat. (1984)
B. J. Campbell, A. S. Engel, M. L. Porter, K. Takai, Nat. Rev. Microbiol.4, 458 (2006). (10.1038/nrmicro1414) / Nat. Rev. Microbiol. (2006)
10.1038/30965
10.1038/nature02649
10.1128/AEM.68.3.1180-1191.2002
10.1017/S0094837300002633
10.1128/AEM.66.5.1777-1787.2000
S. M. Huse, J. A. Huber, H. G. Morrison, M. L. Sogin, D. Mark Welch, Genome Biol.8, R143 (2007). (10.1186/gb-2007-8-7-r143) / Genome Biol. (2007)
10.1016/j.tim.2006.04.007
P. D. Schloss, J. Handelsman, PLoS Comput. Biol.2, e92 (2006). (10.1371/journal.pcbi.0020092) / PLoS Comput. Biol. (2006)
R. E. Leyet al., Appl. Environ. Microbiol.72, 3685 (2006). (10.1128/AEM.72.5.3685-3695.2006) / Appl. Environ. Microbiol. (2006)
E. F. DeLong, Nat. Rev. Microbiol.5, 326 (2007). (10.1038/nrmicro1674) / Nat. Rev. Microbiol. (2007)
We thank the NOAA Pacific Marine Environmental Laboratory Vents Program the ROPOS Remotely Operated Vehicle and S. Bolton for field support and P. Schloss and L. Amaral Zettler for assistance in data analysis and primer design. Supported by NASA Astrobiology Institute Cooperative Agreement NNA04CC04A (M.L.S.) a National Research Council Research Associateship Award and L'OreÌal USA Fellowship (J.A.H.) the Alfred P. Sloan Foundation's ICoMM field project the W. M. Keck Foundation and the Joint Institute for the Study of the Atmosphere and Ocean under NOAA Cooperative Agreement NA17RJ1232 Contribution 1388. This is NOAA Pacific Marine Environmental Laboratory Contribution 3047. The new sequences reported in this paper have been deposited in the NCBI Short Read Archive under accession numbers SRA000195 and SRA000196. The zip file available for download via http from jbpc.mbl.edu/research_supplements/g454/20070822-private/supplemental.zip contains all the fasta-formatted trimmed reads used in the analyses.

Dates

Type	When
Created	17 years, 10 months ago (Oct. 4, 2007, 4:39 p.m.)
Deposited	1 year, 7 months ago (Jan. 10, 2024, 2:51 a.m.)
Indexed	51 minutes ago (Sept. 3, 2025, 6:07 a.m.)
Issued	17 years, 10 months ago (Oct. 5, 2007)
Published	17 years, 10 months ago (Oct. 5, 2007)
Published Print	17 years, 10 months ago (Oct. 5, 2007)

Funders 0

None

BibTeX

@article{Huber_2007, title={Microbial Population Structures in the Deep Marine Biosphere}, volume={318}, ISSN={1095-9203}, url={http://dx.doi.org/10.1126/science.1146689}, DOI={10.1126/science.1146689}, number={5847}, journal={Science}, publisher={American Association for the Advancement of Science (AAAS)}, author={Huber, Julie A. and Mark Welch, David B. and Morrison, Hilary G. and Huse, Susan M. and Neal, Phillip R. and Butterfield, David A. and Sogin, Mitchell L.}, year={2007}, month=oct, pages={97–100} }

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