Bioinformatic Approaches Reveal Metagenomic Characterization of Soil Microbial Community
Identifieur interne : 000229 ( Pmc/Checkpoint ); précédent : 000228; suivant : 000230Bioinformatic Approaches Reveal Metagenomic Characterization of Soil Microbial Community
Auteurs : Zhuofei Xu ; Martin Asser Hansen ; Lars H. Hansen ; Samuel Jacquiod ; S Ren J. S RensenSource :
- PLoS ONE [ 1932-6203 ] ; 2014.
Abstract
As is well known, soil is a complex ecosystem harboring the most prokaryotic biodiversity on the Earth. In recent years, the advent of high-throughput sequencing techniques has greatly facilitated the progress of soil ecological studies. However, how to effectively understand the underlying biological features of large-scale sequencing data is a new challenge. In the present study, we used 33 publicly available metagenomes from diverse soil sites (i.e. grassland, forest soil, desert, Arctic soil, and mangrove sediment) and integrated some state-of-the-art computational tools to explore the phylogenetic and functional characterizations of the microbial communities in soil. Microbial composition and metabolic potential in soils were comprehensively illustrated at the metagenomic level. A spectrum of metagenomic biomarkers containing 46 taxa and 33 metabolic modules were detected to be significantly differential that could be used as indicators to distinguish at least one of five soil communities. The co-occurrence associations between complex microbial compositions and functions were inferred by network-based approaches. Our results together with the established bioinformatic pipelines should provide a foundation for future research into the relation between soil biodiversity and ecosystem function.
Url:
DOI: 10.1371/journal.pone.0093445
PubMed: 24691166
PubMed Central: 3972102
Affiliations:
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<front><div type="abstract" xml:lang="en"><p>As is well known, soil is a complex ecosystem harboring the most prokaryotic biodiversity on the Earth. In recent years, the advent of high-throughput sequencing techniques has greatly facilitated the progress of soil ecological studies. However, how to effectively understand the underlying biological features of large-scale sequencing data is a new challenge. In the present study, we used 33 publicly available metagenomes from diverse soil sites (i.e. grassland, forest soil, desert, Arctic soil, and mangrove sediment) and integrated some state-of-the-art computational tools to explore the phylogenetic and functional characterizations of the microbial communities in soil. Microbial composition and metabolic potential in soils were comprehensively illustrated at the metagenomic level. A spectrum of metagenomic biomarkers containing 46 taxa and 33 metabolic modules were detected to be significantly differential that could be used as indicators to distinguish at least one of five soil communities. The co-occurrence associations between complex microbial compositions and functions were inferred by network-based approaches. Our results together with the established bioinformatic pipelines should provide a foundation for future research into the relation between soil biodiversity and ecosystem function.</p>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id>
<journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id>
<journal-id journal-id-type="publisher-id">plos</journal-id>
<journal-id journal-id-type="pmc">plosone</journal-id>
<journal-title-group><journal-title>PLoS ONE</journal-title>
</journal-title-group>
<issn pub-type="epub">1932-6203</issn>
<publisher><publisher-name>Public Library of Science</publisher-name>
<publisher-loc>San Francisco, USA</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">24691166</article-id>
<article-id pub-id-type="pmc">3972102</article-id>
<article-id pub-id-type="publisher-id">PONE-D-13-52103</article-id>
<article-id pub-id-type="doi">10.1371/journal.pone.0093445</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
<subj-group subj-group-type="Discipline-v2"><subject>Biology and Life Sciences</subject>
<subj-group><subject>Computational Biology</subject>
<subj-group><subject>Comparative Genomics</subject>
</subj-group>
</subj-group>
<subj-group><subject>Evolutionary Biology</subject>
</subj-group>
<subj-group><subject>Genetics</subject>
<subj-group><subject>Genomics</subject>
<subj-group><subject>Functional Genomics</subject>
<subject>Metagenomics</subject>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
<subj-group subj-group-type="Discipline-v2"><subject>Ecology and Environmental Sciences</subject>
<subj-group><subject>Soil Science</subject>
<subj-group><subject>Soil Ecology</subject>
</subj-group>
</subj-group>
</subj-group>
</article-categories>
<title-group><article-title>Bioinformatic Approaches Reveal Metagenomic Characterization of Soil Microbial Community</article-title>
<alt-title alt-title-type="running-head">Characterization of Soil Metagenomes</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Xu</surname>
<given-names>Zhuofei</given-names>
</name>
<xref ref-type="aff" rid="aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Hansen</surname>
<given-names>Martin Asser</given-names>
</name>
<xref ref-type="aff" rid="aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Hansen</surname>
<given-names>Lars H.</given-names>
</name>
<xref ref-type="aff" rid="aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Jacquiod</surname>
<given-names>Samuel</given-names>
</name>
<xref ref-type="aff" rid="aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Sørensen</surname>
<given-names>Søren J.</given-names>
</name>
<xref ref-type="aff" rid="aff1"></xref>
<xref ref-type="corresp" rid="cor1"><sup>*</sup>
</xref>
</contrib>
</contrib-group>
<aff id="aff1"><addr-line>Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark</addr-line>
</aff>
<contrib-group><contrib contrib-type="editor"><name><surname>Balestrini</surname>
<given-names>Raffaella</given-names>
</name>
<role>Editor</role>
<xref ref-type="aff" rid="edit1"></xref>
</contrib>
</contrib-group>
<aff id="edit1"><addr-line>Institute for Plant Protection (IPP), CNR, Italy</addr-line>
</aff>
<author-notes><corresp id="cor1">* E-mail: <email>SJS@bio.ku.dk</email>
</corresp>
<fn fn-type="conflict"><p><bold>Competing Interests: </bold>
The authors have declared that no competing interests exist.</p>
</fn>
<fn fn-type="con"><p>Conceived and designed the experiments: ZX SJS. Performed the experiments: ZX. Analyzed the data: ZX MAH SJ. Contributed reagents/materials/analysis tools: ZX LHH SJS. Wrote the paper: ZX MAH LHH SJ SJS.</p>
</fn>
</author-notes>
<pub-date pub-type="collection"><year>2014</year>
</pub-date>
<pub-date pub-type="epub"><day>1</day>
<month>4</month>
<year>2014</year>
</pub-date>
<volume>9</volume>
<issue>4</issue>
<elocation-id>e93445</elocation-id>
<history><date date-type="received"><day>11</day>
<month>12</month>
<year>2013</year>
</date>
<date date-type="accepted"><day>28</day>
<month>2</month>
<year>2014</year>
</date>
</history>
<permissions><copyright-year>2014</copyright-year>
<copyright-holder>Xu et al</copyright-holder>
<license><license-p>This is an open-access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>
, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p>
</license>
</permissions>
<abstract><p>As is well known, soil is a complex ecosystem harboring the most prokaryotic biodiversity on the Earth. In recent years, the advent of high-throughput sequencing techniques has greatly facilitated the progress of soil ecological studies. However, how to effectively understand the underlying biological features of large-scale sequencing data is a new challenge. In the present study, we used 33 publicly available metagenomes from diverse soil sites (i.e. grassland, forest soil, desert, Arctic soil, and mangrove sediment) and integrated some state-of-the-art computational tools to explore the phylogenetic and functional characterizations of the microbial communities in soil. Microbial composition and metabolic potential in soils were comprehensively illustrated at the metagenomic level. A spectrum of metagenomic biomarkers containing 46 taxa and 33 metabolic modules were detected to be significantly differential that could be used as indicators to distinguish at least one of five soil communities. The co-occurrence associations between complex microbial compositions and functions were inferred by network-based approaches. Our results together with the established bioinformatic pipelines should provide a foundation for future research into the relation between soil biodiversity and ecosystem function.</p>
</abstract>
<funding-group><funding-statement>This work was partly funded by the EU ITN project TRAINBIODIVERSE and the Center for Environmental and Agricultural Microbiology (CREAM) funded by The Villum Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement>
</funding-group>
<counts><page-count count="11"></page-count>
</counts>
</article-meta>
</front>
</pmc>
<affiliations><list></list>
<tree><noCountry><name sortKey="Hansen, Lars H" sort="Hansen, Lars H" uniqKey="Hansen L" first="Lars H." last="Hansen">Lars H. Hansen</name>
<name sortKey="Hansen, Martin Asser" sort="Hansen, Martin Asser" uniqKey="Hansen M" first="Martin Asser" last="Hansen">Martin Asser Hansen</name>
<name sortKey="Jacquiod, Samuel" sort="Jacquiod, Samuel" uniqKey="Jacquiod S" first="Samuel" last="Jacquiod">Samuel Jacquiod</name>
<name sortKey="S Rensen, S Ren J" sort="S Rensen, S Ren J" uniqKey="S Rensen S" first="S Ren J." last="S Rensen">S Ren J. S Rensen</name>
<name sortKey="Xu, Zhuofei" sort="Xu, Zhuofei" uniqKey="Xu Z" first="Zhuofei" last="Xu">Zhuofei Xu</name>
</noCountry>
</tree>
</affiliations>
</record>
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