Exploration of community traits as ecological markers in microbial metagenomes
Identifieur interne : 000595 ( Main/Curation ); précédent : 000594; suivant : 000596Exploration of community traits as ecological markers in microbial metagenomes
Auteurs : Albert Barberán [Espagne] ; Antoni Fernández-Guerra [Espagne] ; Brendan J. M. Bohannan [États-Unis] ; Emilio O. Casamayor [Espagne]Source :
- Molecular Ecology [ 0962-1083 ] ; 2012-04.
English descriptors
- KwdEn :
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.
Url:
DOI: 10.1111/j.1365-294X.2011.05383.x
Links toward previous steps (curation, corpus...)
- to stream Istex, to step Corpus: Pour aller vers cette notice dans l'étape Curation :000676
- to stream Istex, to step Curation: Pour aller vers cette notice dans l'étape Curation :000676
- to stream Istex, to step Checkpoint: Pour aller vers cette notice dans l'étape Curation :000114
- to stream Main, to step Merge: Pour aller vers cette notice dans l'étape Curation :000596
Links to Exploration step
ISTEX:15FCF3AF111946BE03EE7BAFBB6DB4DEAB1B762CLe document en format XML
<record><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title xml:lang="en">Exploration of community traits as ecological markers in microbial metagenomes</title>
<author><name sortKey="Barberan, Albert" sort="Barberan, Albert" uniqKey="Barberan A" first="Albert" last="Barberán">Albert Barberán</name>
</author>
<author><name sortKey="Fernandez Uerra, Antoni" sort="Fernandez Uerra, Antoni" uniqKey="Fernandez Uerra A" first="Antoni" last="Fernández-Guerra">Antoni Fernández-Guerra</name>
</author>
<author><name sortKey="Bohannan, Brendan J M" sort="Bohannan, Brendan J M" uniqKey="Bohannan B" first="Brendan J. M." last="Bohannan">Brendan J. M. Bohannan</name>
</author>
<author><name sortKey="Casamayor, Emilio O" sort="Casamayor, Emilio O" uniqKey="Casamayor E" first="Emilio O." last="Casamayor">Emilio O. Casamayor</name>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">ISTEX</idno>
<idno type="RBID">ISTEX:15FCF3AF111946BE03EE7BAFBB6DB4DEAB1B762C</idno>
<date when="2012" year="2012">2012</date>
<idno type="doi">10.1111/j.1365-294X.2011.05383.x</idno>
<idno type="url">https://api.istex.fr/document/15FCF3AF111946BE03EE7BAFBB6DB4DEAB1B762C/fulltext/pdf</idno>
<idno type="wicri:Area/Istex/Corpus">000676</idno>
<idno type="wicri:Area/Istex/Curation">000676</idno>
<idno type="wicri:Area/Istex/Checkpoint">000114</idno>
<idno type="wicri:doubleKey">0962-1083:2012:Barberan A:exploration:of:community</idno>
<idno type="wicri:Area/Main/Merge">000596</idno>
<idno type="wicri:Area/Main/Curation">000595</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title level="a" type="main" xml:lang="en">Exploration of community traits as ecological markers in microbial metagenomes</title>
<author><name sortKey="Barberan, Albert" sort="Barberan, Albert" uniqKey="Barberan A" first="Albert" last="Barberán">Albert Barberán</name>
<affiliation wicri:level="2"><country xml:lang="fr">Espagne</country>
<wicri:regionArea>Biogeodynamics & Biodiversity Group, Department of Continental Ecology, Centre d'Estudis Avançats de Blanes (CEAB‐CSIC), Accés Cala St. Francesc 14, Blanes 17300</wicri:regionArea>
<placeName><region nuts="2" type="communauté">Catalogne</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Fernandez Uerra, Antoni" sort="Fernandez Uerra, Antoni" uniqKey="Fernandez Uerra A" first="Antoni" last="Fernández-Guerra">Antoni Fernández-Guerra</name>
<affiliation wicri:level="2"><country xml:lang="fr">Espagne</country>
<wicri:regionArea>Biogeodynamics & Biodiversity Group, Department of Continental Ecology, Centre d'Estudis Avançats de Blanes (CEAB‐CSIC), Accés Cala St. Francesc 14, Blanes 17300</wicri:regionArea>
<placeName><region nuts="2" type="communauté">Catalogne</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Bohannan, Brendan J M" sort="Bohannan, Brendan J M" uniqKey="Bohannan B" first="Brendan J. M." last="Bohannan">Brendan J. M. Bohannan</name>
<affiliation wicri:level="2"><country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Biology, Center for Ecology and Evolutionary Biology, University of Oregon, 335 Pacific Hall, Eugene, OR 97403‐5289</wicri:regionArea>
<placeName><region type="state">Oregon</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Casamayor, Emilio O" sort="Casamayor, Emilio O" uniqKey="Casamayor E" first="Emilio O." last="Casamayor">Emilio O. Casamayor</name>
<affiliation wicri:level="2"><country xml:lang="fr">Espagne</country>
<wicri:regionArea>Biogeodynamics & Biodiversity Group, Department of Continental Ecology, Centre d'Estudis Avançats de Blanes (CEAB‐CSIC), Accés Cala St. Francesc 14, Blanes 17300</wicri:regionArea>
<placeName><region nuts="2" type="communauté">Catalogne</region>
</placeName>
</affiliation>
</author>
</analytic>
<monogr></monogr>
<series><title level="j">Molecular Ecology</title>
<idno type="ISSN">0962-1083</idno>
<idno type="eISSN">1365-294X</idno>
<imprint><publisher>Blackwell Publishing Ltd</publisher>
<pubPlace>Oxford, UK</pubPlace>
<date type="published" when="2012-04">2012-04</date>
<biblScope unit="volume">21</biblScope>
<biblScope unit="issue">8</biblScope>
<biblScope unit="page" from="1909">1909</biblScope>
<biblScope unit="page" to="1917">1917</biblScope>
</imprint>
<idno type="ISSN">0962-1083</idno>
</series>
<idno type="istex">15FCF3AF111946BE03EE7BAFBB6DB4DEAB1B762C</idno>
<idno type="DOI">10.1111/j.1365-294X.2011.05383.x</idno>
<idno type="ArticleID">MEC5383</idno>
</biblStruct>
</sourceDesc>
<seriesStmt><idno type="ISSN">0962-1083</idno>
</seriesStmt>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Global Ocean Sampling</term>
<term>community ecology</term>
<term>functional traits</term>
<term>metagenomics</term>
<term>microbial ecology</term>
</keywords>
</textClass>
<langUsage><language ident="en">en</language>
</langUsage>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml: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.</div>
</front>
</TEI>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Ticri/CIDE/explor/CyberinfraV1/Data/Main/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000595 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Curation/biblio.hfd -nk 000595 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Ticri/CIDE |area= CyberinfraV1 |flux= Main |étape= Curation |type= RBID |clé= ISTEX:15FCF3AF111946BE03EE7BAFBB6DB4DEAB1B762C |texte= Exploration of community traits as ecological markers in microbial metagenomes }}
![]() | This area was generated with Dilib version V0.6.25. | ![]() |