Bacterial community assembly based on functional genes rather than species
Identifieur interne : 000397 ( Pmc/Corpus ); précédent : 000396; suivant : 000398Bacterial community assembly based on functional genes rather than species
Auteurs : Catherine Burke ; Peter Steinberg ; Doug Rusch ; Staffan Kjelleberg ; Torsten ThomasSource :
- Proceedings of the National Academy of Sciences of the United States of America [ 0027-8424 ] ; 2011.
Abstract
The principles underlying the assembly and structure of complex microbial communities are an issue of long-standing concern to the field of microbial ecology. We previously analyzed the community membership of bacterial communities associated with the green macroalga
Url:
DOI: 10.1073/pnas.1101591108
PubMed: 21825123
PubMed Central: 3161577
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PMC:3161577Le document en format XML
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<affiliation><nlm:aff id="aff3">The iThree Institute,<institution>University of Technology</institution>
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<author><name sortKey="Steinberg, Peter" sort="Steinberg, Peter" uniqKey="Steinberg P" first="Peter" last="Steinberg">Peter Steinberg</name>
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<affiliation><nlm:aff id="aff4"><institution>Sydney Institute of Marine Science</institution>
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<author><name sortKey="Rusch, Doug" sort="Rusch, Doug" uniqKey="Rusch D" first="Doug" last="Rusch">Doug Rusch</name>
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<author><name sortKey="Kjelleberg, Staffan" sort="Kjelleberg, Staffan" uniqKey="Kjelleberg S" first="Staffan" last="Kjelleberg">Staffan Kjelleberg</name>
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<affiliation><nlm:aff id="aff6">Singapore Centre on Environmental Life Sciences Engineering,<institution>Nanyang Technological University</institution>
,<country>Singapore</country>
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<author><name sortKey="Thomas, Torsten" sort="Thomas, Torsten" uniqKey="Thomas T" first="Torsten" last="Thomas">Torsten Thomas</name>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Bacterial community assembly based on functional genes rather than species</title>
<author><name sortKey="Burke, Catherine" sort="Burke, Catherine" uniqKey="Burke C" first="Catherine" last="Burke">Catherine Burke</name>
<affiliation><nlm:aff id="aff1">School of Biotechnology and Biomolecular Sciences,</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="aff3">The iThree Institute,<institution>University of Technology</institution>
, Ultimo, New South Wales 2007,<country>Australia</country>
;</nlm:aff>
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<author><name sortKey="Steinberg, Peter" sort="Steinberg, Peter" uniqKey="Steinberg P" first="Peter" last="Steinberg">Peter Steinberg</name>
<affiliation><nlm:aff id="aff2">School of Biological, Earth and Environmental Sciences, Centre for Marine Bio-Innovation,<institution>University of New South Wales</institution>
, Sydney, New South Wales 2052,<country>Australia</country>
;</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="aff4"><institution>Sydney Institute of Marine Science</institution>
, Mosman, New South Wales 2088,<country>Australia</country>
;</nlm:aff>
</affiliation>
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<author><name sortKey="Rusch, Doug" sort="Rusch, Doug" uniqKey="Rusch D" first="Doug" last="Rusch">Doug Rusch</name>
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, Rockville, MD 20850</nlm:aff>
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<author><name sortKey="Kjelleberg, Staffan" sort="Kjelleberg, Staffan" uniqKey="Kjelleberg S" first="Staffan" last="Kjelleberg">Staffan Kjelleberg</name>
<affiliation><nlm:aff id="aff1">School of Biotechnology and Biomolecular Sciences,</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="aff6">Singapore Centre on Environmental Life Sciences Engineering,<institution>Nanyang Technological University</institution>
,<country>Singapore</country>
</nlm:aff>
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<author><name sortKey="Thomas, Torsten" sort="Thomas, Torsten" uniqKey="Thomas T" first="Torsten" last="Thomas">Torsten Thomas</name>
<affiliation><nlm:aff id="aff1">School of Biotechnology and Biomolecular Sciences,</nlm:aff>
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<series><title level="j">Proceedings of the National Academy of Sciences of the United States of America</title>
<idno type="ISSN">0027-8424</idno>
<idno type="eISSN">1091-6490</idno>
<imprint><date when="2011">2011</date>
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<front><div type="abstract" xml:lang="en"><p>The principles underlying the assembly and structure of complex microbial communities are an issue of long-standing concern to the field of microbial ecology. We previously analyzed the community membership of bacterial communities associated with the green macroalga <italic>Ulva australis</italic>
, and proposed a competitive lottery model for colonization of the algal surface in an attempt to explain the surprising lack of similarity in species composition across different algal samples. Here we extend the previous study by investigating the link between community structure and function in these communities, using metagenomic sequence analysis. Despite the high phylogenetic variability in microbial species composition on different <italic>U. australis</italic>
(only 15% similarity between samples), similarity in functional composition was high (70%), and a core of functional genes present across all algal-associated communities was identified that were consistent with the ecology of surface- and host-associated bacteria. These functions were distributed widely across a variety of taxa or phylogenetic groups. This observation of similarity in habitat (niche) use with respect to functional genes, but not species, together with the relative ease with which bacteria share genetic material, suggests that the key level at which to address the assembly and structure of bacterial communities may not be “species” (by means of rRNA taxonomy), but rather the more functional level of genes.</p>
</div>
</front>
</TEI>
<pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Proc Natl Acad Sci U S A</journal-id>
<journal-id journal-id-type="hwp">pnas</journal-id>
<journal-id journal-id-type="pmc">pnas</journal-id>
<journal-id journal-id-type="publisher-id">PNAS</journal-id>
<journal-title-group><journal-title>Proceedings of the National Academy of Sciences of the United States of America</journal-title>
</journal-title-group>
<issn pub-type="ppub">0027-8424</issn>
<issn pub-type="epub">1091-6490</issn>
<publisher><publisher-name>National Academy of Sciences</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">21825123</article-id>
<article-id pub-id-type="pmc">3161577</article-id>
<article-id pub-id-type="publisher-id">201101591</article-id>
<article-id pub-id-type="doi">10.1073/pnas.1101591108</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Biological Sciences</subject>
<subj-group><subject>Microbiology</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group><article-title>Bacterial community assembly based on functional genes rather than species</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Burke</surname>
<given-names>Catherine</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>a</sup>
</xref>
<xref ref-type="aff" rid="aff3"><sup>b</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Steinberg</surname>
<given-names>Peter</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>c</sup>
</xref>
<xref ref-type="aff" rid="aff4"><sup>d</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Rusch</surname>
<given-names>Doug</given-names>
</name>
<xref ref-type="aff" rid="aff5"><sup>e</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Kjelleberg</surname>
<given-names>Staffan</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>a</sup>
</xref>
<xref ref-type="aff" rid="aff6"><sup>f</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Thomas</surname>
<given-names>Torsten</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>a</sup>
</xref>
<xref ref-type="corresp" rid="cor1"><sup>1</sup>
</xref>
</contrib>
<aff id="aff1"><sup>a</sup>
School of Biotechnology and Biomolecular Sciences,</aff>
<aff id="aff2"><sup>c</sup>
School of Biological, Earth and Environmental Sciences, Centre for Marine Bio-Innovation,<institution>University of New South Wales</institution>
, Sydney, New South Wales 2052,<country>Australia</country>
;</aff>
<aff id="aff3"><sup>b</sup>
The iThree Institute,<institution>University of Technology</institution>
, Ultimo, New South Wales 2007,<country>Australia</country>
;</aff>
<aff id="aff4"><sup>d</sup>
<institution>Sydney Institute of Marine Science</institution>
, Mosman, New South Wales 2088,<country>Australia</country>
;</aff>
<aff id="aff5"><sup>e</sup>
<institution>The J. Craig Venter Institute</institution>
, Rockville, MD 20850; and</aff>
<aff id="aff6"><sup>f</sup>
Singapore Centre on Environmental Life Sciences Engineering,<institution>Nanyang Technological University</institution>
,<country>Singapore</country>
</aff>
</contrib-group>
<author-notes><corresp id="cor1"><sup>1</sup>
To whom correspondence should be addressed. E-mail: <email>t.thomas@unsw.edu.au</email>
.</corresp>
<fn fn-type="edited-by"><p>Edited by W. Ford Doolittle, Dalhousie University, Halifax, Canada, and approved July 14, 2011 (received for review January 30, 2011)</p>
</fn>
<fn fn-type="con"><p>Author contributions: C.B., P.S., S.K., and T.T. designed research; C.B. and T.T. performed research; C.B., P.S., D.R., S.K., and T.T. analyzed data; and C.B., P.S., S.K., and T.T. wrote the paper.</p>
</fn>
</author-notes>
<pub-date pub-type="ppub"><day>23</day>
<month>8</month>
<year>2011</year>
</pub-date>
<pub-date pub-type="epub"><day>8</day>
<month>8</month>
<year>2011</year>
</pub-date>
<volume>108</volume>
<issue>34</issue>
<fpage>14288</fpage>
<lpage>14293</lpage>
<self-uri xlink:title="pdf" xlink:type="simple" xlink:href="pnas.201101591.pdf"></self-uri>
<abstract><p>The principles underlying the assembly and structure of complex microbial communities are an issue of long-standing concern to the field of microbial ecology. We previously analyzed the community membership of bacterial communities associated with the green macroalga <italic>Ulva australis</italic>
, and proposed a competitive lottery model for colonization of the algal surface in an attempt to explain the surprising lack of similarity in species composition across different algal samples. Here we extend the previous study by investigating the link between community structure and function in these communities, using metagenomic sequence analysis. Despite the high phylogenetic variability in microbial species composition on different <italic>U. australis</italic>
(only 15% similarity between samples), similarity in functional composition was high (70%), and a core of functional genes present across all algal-associated communities was identified that were consistent with the ecology of surface- and host-associated bacteria. These functions were distributed widely across a variety of taxa or phylogenetic groups. This observation of similarity in habitat (niche) use with respect to functional genes, but not species, together with the relative ease with which bacteria share genetic material, suggests that the key level at which to address the assembly and structure of bacterial communities may not be “species” (by means of rRNA taxonomy), but rather the more functional level of genes.</p>
</abstract>
<kwd-group><kwd>lateral gene transfer</kwd>
<kwd>biofilm</kwd>
<kwd>ecological model</kwd>
</kwd-group>
</article-meta>
</front>
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