[permaculture] TESTS & EQUIPMENT required for a functional SUSTAINABLE AG LAB? | Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

Lawrence London lfljvenaura at gmail.com
Wed Mar 6 19:48:12 EST 2013


Cross-biome metagenomic analyses of soil microbial communities and their
functional attributes
http://www.pnas.org/content/early/2012/12/13/1215210110.abstract

Cross-biome metagenomic analyses of soil microbial communities and their
functional attributes

   1. Noah Fierer<http://www.pnas.org/search?author1=Noah+Fierer&sortspec=date&submit=Submit>
   a<http://www.pnas.org/content/early/2012/12/13/1215210110.abstract#aff-1>
   ,b<http://www.pnas.org/content/early/2012/12/13/1215210110.abstract#aff-2>
   ,1<http://www.pnas.org/content/early/2012/12/13/1215210110.abstract#corresp-1>,

   2. Jonathan W.
Leff<http://www.pnas.org/search?author1=Jonathan+W.+Leff&sortspec=date&submit=Submit>
   b<http://www.pnas.org/content/early/2012/12/13/1215210110.abstract#aff-2>,

   3. Byron J. Adams<http://www.pnas.org/search?author1=Byron+J.+Adams&sortspec=date&submit=Submit>
   c<http://www.pnas.org/content/early/2012/12/13/1215210110.abstract#aff-3>,

   4. Uffe N. Nielsen<http://www.pnas.org/search?author1=Uffe+N.+Nielsen&sortspec=date&submit=Submit>
   d<http://www.pnas.org/content/early/2012/12/13/1215210110.abstract#aff-4>,

   5. Scott Thomas
Bates<http://www.pnas.org/search?author1=Scott+Thomas+Bates&sortspec=date&submit=Submit>
   b<http://www.pnas.org/content/early/2012/12/13/1215210110.abstract#aff-2>,

   6. Christian L.
Lauber<http://www.pnas.org/search?author1=Christian+L.+Lauber&sortspec=date&submit=Submit>
   b<http://www.pnas.org/content/early/2012/12/13/1215210110.abstract#aff-2>,

   7. Sarah Owens<http://www.pnas.org/search?author1=Sarah+Owens&sortspec=date&submit=Submit>
   e<http://www.pnas.org/content/early/2012/12/13/1215210110.abstract#aff-5>
   ,f<http://www.pnas.org/content/early/2012/12/13/1215210110.abstract#aff-6>,

   8. Jack A. Gilbert<http://www.pnas.org/search?author1=Jack+A.+Gilbert&sortspec=date&submit=Submit>
   e<http://www.pnas.org/content/early/2012/12/13/1215210110.abstract#aff-5>
   ,g<http://www.pnas.org/content/early/2012/12/13/1215210110.abstract#aff-7>,

   9. Diana H. Wall<http://www.pnas.org/search?author1=Diana+H.+Wall&sortspec=date&submit=Submit>
   h<http://www.pnas.org/content/early/2012/12/13/1215210110.abstract#aff-8>,
   and
   10. J. Gregory
Caporaso<http://www.pnas.org/search?author1=J.+Gregory+Caporaso&sortspec=date&submit=Submit>
   e<http://www.pnas.org/content/early/2012/12/13/1215210110.abstract#aff-5>
   ,i<http://www.pnas.org/content/early/2012/12/13/1215210110.abstract#aff-9>

Author Affiliations<http://www.pnas.org/content/early/2012/12/13/1215210110.abstract#>

   1.

   Edited by Peter M. Vitousek, Stanford University, Stanford, CA, and
   approved November 12, 2012 (received for review September 5, 2012)

 Abstract

For centuries ecologists have studied how the diversity and functional
traits of plant and animal communities vary across biomes. In contrast, we
have only just begun exploring similar questions for soil microbial
communities despite soil microbes being the dominant engines of
biogeochemical cycles and a major pool of living biomass in terrestrial
ecosystems. We used metagenomic sequencing to compare the composition and
functional attributes of 16 soil microbial communities collected from cold
deserts, hot deserts, forests, grasslands, and tundra. Those communities
found in plant-free cold desert soils typically had the lowest levels of
functional diversity (diversity of protein-coding gene categories) and the
lowest levels of phylogenetic and taxonomic diversity. Across all soils,
functional beta diversity was strongly correlated with taxonomic and
phylogenetic beta diversity; the desert microbial communities were clearly
distinct from the nondesert communities regardless of the metric used. The
desert communities had higher relative abundances of genes associated with
osmoregulation and dormancy, but lower relative abundances of genes
associated with nutrient cycling and the catabolism of plant-derived
organic compounds. Antibiotic resistance genes were consistently threefold
less abundant in the desert soils than in the nondesert soils, suggesting
that abiotic conditions, not competitive interactions, are more important
in shaping the desert microbial communities. As the most comprehensive
survey of soil taxonomic, phylogenetic, and functional diversity to date,
this study demonstrates that metagenomic approaches can be used to build a
predictive understanding of how microbial diversity and function vary
across terrestrial biomes.

   - shotgun metagenomics<http://www.pnas.org/search?fulltext=shotgun+metagenomics&sortspec=date&submit=Submit&andorexactfulltext=phrase>
   - soil microbial
ecology<http://www.pnas.org/search?fulltext=soil+microbial+ecology&sortspec=date&submit=Submit&andorexactfulltext=phrase>
   - 16S rRNA gene
sequencing<http://www.pnas.org/search?fulltext=16S+rRNA+gene+sequencing&sortspec=date&submit=Submit&andorexactfulltext=phrase>
   - biogeography<http://www.pnas.org/search?fulltext=biogeography&sortspec=date&submit=Submit&andorexactfulltext=phrase>

 Footnotes

   - 1To whom correspondence should be addressed. E-mail:
   noah.fierer at colorado.edu.


   -

   Author contributions: N.F., B.J.A., U.N.N., and D.H.W. designed
   research; N.F. and J.G.C. performed research; U.N.N., S.O., and J.A.G.
   contributed new reagents/analytic tools; N.F., J.W.L., S.T.B., C.L.L., and
   J.G.C. analyzed data; and N.F., J.W.L., B.J.A., U.N.N., S.T.B., C.L.L.,
   S.O., J.A.G., D.H.W., and J.G.C. wrote the paper.
   -

   The authors declare no conflict of interest.
   -

   This article is a PNAS Direct Submission.
   -

   Data deposition: The data reported in this paper have been deposited in
   the Rapid Annotation using Subsystems Technology for Metagenomes database
   (MG-RAST). Accession numbers are listed in Table
S2<http://www.pnas.org/lookup/suppl/doi:10.1073/pnas.1215210110/-/DCSupplemental/pnas.201215210SI.pdf?targetid=nameddest=ST2>.

   -

   This article contains supporting information online at
   www.pnas.org/lookup/suppl/doi:10.1073/pnas.1215210110/-/DCSupplemental.

 Freely available online through the PNAS open access option.


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