Exploration of community traits as ecological markers in microbial metagenomes
Identifieur interne : 000676 ( Istex/Corpus ); précédent : 000675; suivant : 000677Exploration of community traits as ecological markers in microbial metagenomes
Auteurs : Albert Barberán ; Antoni Fernández-Guerra ; Brendan J. M. Bohannan ; Emilio O. CasamayorSource :
- Molecular Ecology [ 0962-1083 ] ; 2012-04.
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Abstract
The rate of information collection generated by metagenomics is uncoupled with its meaningful ecological interpretation. New analytical approaches based on functional trait‐based ecology may help to bridge this gap and extend the trait approach to the community level in vast and complex environmental genetic data sets. Here, we explored a set of community traits that range from nucleotidic to genomic properties in 53 metagenomic aquatic samples from the Global Ocean Sampling (GOS) expedition. We found significant differences between the community profile derived from the commonly used 16S rRNA gene and from the functional trait set. The traits proved to be valuable ecological markers by discriminating between marine ecosystems (coastal vs. open ocean) and between oceans (Atlantic vs. Indian vs. Pacific). Intertrait relationships were also assessed, and we propose some that could be further used as habitat descriptors or indicators of artefacts during sample processing. Overall, the approach presented here may help to interpret metagenomics data to gain a full understanding of microbial community patterns in a rigorous ecological framework.
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DOI: 10.1111/j.1365-294X.2011.05383.x
Links to Exploration step
ISTEX:15FCF3AF111946BE03EE7BAFBB6DB4DEAB1B762CLe document en format XML
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BARBERÁN <i>ET AL.</i></title><title type="short">METAGENOMIC COMMUNITY TRAITS</title></titleGroup><creators><creator creatorRole="author" xml:id="cr1" affiliationRef="#a1"><personName><givenNames>ALBERT</givenNames><familyName>BARBERÁN</familyName></personName></creator><creator creatorRole="author" xml:id="cr2" affiliationRef="#a1"><personName><givenNames>ANTONI</givenNames><familyName>FERNÁNDEZ‐GUERRA</familyName></personName></creator><creator creatorRole="author" xml:id="cr3" affiliationRef="#a2"><personName><givenNames>BRENDAN J. M.</givenNames><familyName>BOHANNAN</familyName></personName></creator><creator creatorRole="author" xml:id="cr4" affiliationRef="#a1"><personName><givenNames>EMILIO O.</givenNames><familyName>CASAMAYOR</familyName></personName></creator></creators><affiliationGroup><affiliation xml:id="a1"><unparsedAffiliation>Biogeodynamics & Biodiversity Group, Department of Continental Ecology, Centre d'Estudis Avançats de Blanes (CEAB‐CSIC), Accés Cala St. Francesc 14, Blanes 17300, Spain</unparsedAffiliation></affiliation><affiliation xml:id="a2" countryCode="US"><unparsedAffiliation>Department of Biology, Center for Ecology and Evolutionary Biology, University of Oregon, 335 Pacific Hall, Eugene, OR 97403‐5289, USA</unparsedAffiliation></affiliation></affiliationGroup><keywordGroup xml:lang="en"><keyword xml:id="k1">community ecology</keyword><keyword xml:id="k2">functional traits</keyword><keyword xml:id="k3">Global Ocean Sampling</keyword><keyword xml:id="k4">metagenomics</keyword><keyword xml:id="k5">microbial ecology</keyword></keywordGroup><supportingInformation><p><b>Table S1</b> Summary of the metagenomic samples used and the community traits calculated.</p><p><b>Table S2</b> List of the 35 marker genes and their Clusters of Orthologous Groups (COG) annotation.</p><p><b>Table S3</b> All bivariate Spearman’s Rank correlations between community traits.</p><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:09621083:media:mec5383:MEC_5383_sm_TableS1"></mediaResource><caption>Supporting info item</caption></supportingInfoItem><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:09621083:media:mec5383:MEC_5383_sm_TableS2"></mediaResource><caption>Supporting info item</caption></supportingInfoItem><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:09621083:media:mec5383:MEC_5383_sm_TableS3"></mediaResource><caption>Supporting info item</caption></supportingInfoItem></supportingInformation><abstractGroup><abstract type="main" xml:lang="en"><title type="main">Abstract</title><p>The rate of information collection generated by metagenomics is uncoupled with its meaningful ecological interpretation. New analytical approaches based on functional trait‐based ecology may help to bridge this gap and extend the trait approach to the community level in vast and complex environmental genetic data sets. Here, we explored a set of community traits that range from nucleotidic to genomic properties in 53 metagenomic aquatic samples from the Global Ocean Sampling (GOS) expedition. We found significant differences between the community profile derived from the commonly used 16S rRNA gene and from the functional trait set. The traits proved to be valuable ecological markers by discriminating between marine ecosystems (coastal vs. open ocean) and between oceans (Atlantic vs. Indian vs. Pacific). Intertrait relationships were also assessed, and we propose some that could be further used as habitat descriptors or indicators of artefacts during sample processing. Overall, the approach presented here may help to interpret metagenomics data to gain a full understanding of microbial community patterns in a rigorous ecological framework.</p></abstract></abstractGroup></contentMeta></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Exploration of community traits as ecological markers in microbial metagenomes</title></titleInfo><titleInfo type="abbreviated" lang="en"><title>METAGENOMIC COMMUNITY TRAITS</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>Exploration of community traits as ecological markers in microbial metagenomes</title></titleInfo><name type="personal"><namePart type="given">ALBERT</namePart><namePart type="family">BARBERÁN</namePart><affiliation>Biogeodynamics & Biodiversity Group, Department of Continental Ecology, Centre d'Estudis Avançats de Blanes (CEAB‐CSIC), Accés Cala St. Francesc 14, Blanes 17300, Spain</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">ANTONI</namePart><namePart type="family">FERNÁNDEZ‐GUERRA</namePart><affiliation>Biogeodynamics & Biodiversity Group, Department of Continental Ecology, Centre d'Estudis Avançats de Blanes (CEAB‐CSIC), Accés Cala St. Francesc 14, Blanes 17300, Spain</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">BRENDAN J. M.</namePart><namePart type="family">BOHANNAN</namePart><affiliation>Department of Biology, Center for Ecology and Evolutionary Biology, University of Oregon, 335 Pacific Hall, Eugene, OR 97403‐5289, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">EMILIO O.</namePart><namePart type="family">CASAMAYOR</namePart><affiliation>Biogeodynamics & Biodiversity Group, Department of Continental Ecology, Centre d'Estudis Avançats de Blanes (CEAB‐CSIC), Accés Cala St. Francesc 14, Blanes 17300, Spain</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="article" displayLabel="article"></genre><originInfo><publisher>Blackwell Publishing Ltd</publisher><place><placeTerm type="text">Oxford, UK</placeTerm></place><dateIssued encoding="w3cdtf">2012-04</dateIssued><edition>Received 22 July 2011; revision received 6 October 2011; accepted 25 October 2011</edition><copyrightDate encoding="w3cdtf">2012</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><physicalDescription><internetMediaType>text/html</internetMediaType><extent unit="figures">3</extent><extent unit="tables">1</extent></physicalDescription><abstract lang="en">The rate of information collection generated by metagenomics is uncoupled with its meaningful ecological interpretation. New analytical approaches based on functional trait‐based ecology may help to bridge this gap and extend the trait approach to the community level in vast and complex environmental genetic data sets. Here, we explored a set of community traits that range from nucleotidic to genomic properties in 53 metagenomic aquatic samples from the Global Ocean Sampling (GOS) expedition. We found significant differences between the community profile derived from the commonly used 16S rRNA gene and from the functional trait set. The traits proved to be valuable ecological markers by discriminating between marine ecosystems (coastal vs. open ocean) and between oceans (Atlantic vs. Indian vs. Pacific). Intertrait relationships were also assessed, and we propose some that could be further used as habitat descriptors or indicators of artefacts during sample processing. Overall, the approach presented here may help to interpret metagenomics data to gain a full understanding of microbial community patterns in a rigorous ecological framework.</abstract><subject lang="en"><genre>keywords</genre><topic>community ecology</topic><topic>functional traits</topic><topic>Global Ocean Sampling</topic><topic>metagenomics</topic><topic>microbial ecology</topic></subject><relatedItem type="host"><titleInfo><title>Molecular Ecology</title></titleInfo><genre type="journal">journal</genre><note type="content"> Table S1 Summary of the metagenomic samples used and the community traits calculated. Table S2 List of the 35 marker genes and their Clusters of Orthologous Groups (COG) annotation. Table S3 All bivariate Spearman’s Rank correlations between community traits. Table S1 Summary of the metagenomic samples used and the community traits calculated. Table S2 List of the 35 marker genes and their Clusters of Orthologous Groups (COG) annotation. Table S3 All bivariate Spearman’s Rank correlations between community traits. Table S1 Summary of the metagenomic samples used and the community traits calculated. Table S2 List of the 35 marker genes and their Clusters of Orthologous Groups (COG) annotation. Table S3 All bivariate Spearman’s Rank correlations between community traits.Supporting Info Item: Supporting info item - Supporting info item - Supporting info item - </note><identifier type="ISSN">0962-1083</identifier><identifier type="eISSN">1365-294X</identifier><identifier type="DOI">10.1111/(ISSN)1365-294X</identifier><identifier type="PublisherID">MEC</identifier><part><date>2012</date><detail type="title"><title>ENVIRONMENTAL DNA</title></detail><detail type="volume"><caption>vol.</caption><number>21</number></detail><detail type="issue"><caption>no.</caption><number>8</number></detail><extent unit="pages"><start>1909</start><end>1917</end><total>9</total></extent></part></relatedItem><identifier type="istex">15FCF3AF111946BE03EE7BAFBB6DB4DEAB1B762C</identifier><identifier type="DOI">10.1111/j.1365-294X.2011.05383.x</identifier><identifier type="ArticleID">MEC5383</identifier><accessCondition type="use and reproduction" contentType="copyright">© 2011 Blackwell Publishing Ltd</accessCondition><recordInfo><recordContentSource>WILEY</recordContentSource><recordOrigin>Blackwell Publishing Ltd</recordOrigin></recordInfo></mods></metadata><enrichments><json:item><type>multicat</type><uri>https://api.istex.fr/document/15FCF3AF111946BE03EE7BAFBB6DB4DEAB1B762C/enrichments/multicat</uri></json:item></enrichments><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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