Metagenomic insights into microbial metabolism affecting arsenic dispersion in Mediterranean marine sediments
Identifieur interne : 000642 ( Istex/Corpus ); précédent : 000641; suivant : 000643Metagenomic insights into microbial metabolism affecting arsenic dispersion in Mediterranean marine sediments
Auteurs : Frédéric Plewniak ; Sandrine Koechler ; Benjamin Navet ; Éric Dugat-Bony ; Olivier Bouchez ; Pierre Peyret ; Fabienne Séby ; Fabienne Battaglia-Brunet ; Philippe N. BertinSource :
- Molecular Ecology [ 0962-1083 ] ; 2013-10.
Abstract
Microorganisms dwelling in sediments have a crucial role in biogeochemical cycles and are expected to have a strong influence on the cycle of arsenic, a metalloid responsible for severe water pollution and presenting major health risks for human populations. We present here a metagenomic study of the sediment from two harbours on the Mediterranean French coast, l'Estaque and St Mandrier. The first site is highly polluted with arsenic and heavy metals, while the arsenic concentration in the second site is below toxicity levels. The goal of this study was to elucidate the potential impact of the microbial community on the chemical parameters observed in complementary geochemical studies performed on the same sites. The metagenomic sequences, along with those from four publicly available metagenomes used as control data sets, were analysed with the RAMMCAP workflow. The resulting functional profiles were compared to determine the over‐represented Gene Ontology categories in the metagenomes of interest. Categories related to arsenic resistance and dissimilatory sulphate reduction were over‐represented in l'Estaque. More importantly, despite very similar profiles, the identification of specific sequence markers for sulphate‐reducing bacteria and sulphur‐oxidizing bacteria showed that sulphate reduction was significantly more associated with l'Estaque than with St Mandrier. We propose that biotic sulphate reduction, arsenate reduction and fermentation may together explain the higher mobility of arsenic observed in l'Estaque in previous physico‐chemical studies of this site. This study also demonstrates that it is possible to draw sound conclusions from comparing complex and similar unassembled metagenomes at the functional level, even with very low sequence coverage.
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DOI: 10.1111/mec.12432
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Bertin</name><affiliation><mods:affiliation>Département Microorganismes, Génomes, Environnement, Génétique Moléculaire, Génomique et Microbiologie, UMR7156 Université de Strasbourg/CNRS, 28 rue Goethe, 67083, Strasbourg Cedex, France</mods:affiliation></affiliation></author></analytic><monogr></monogr><series><title level="j">Molecular Ecology</title><title level="j" type="abbrev">Mol Ecol</title><idno type="ISSN">0962-1083</idno><idno type="eISSN">1365-294X</idno><imprint><publisher>Blackwell Publishing Ltd</publisher><date type="published" when="2013-10">2013-10</date><biblScope unit="volume">22</biblScope><biblScope unit="issue">19</biblScope><biblScope unit="page" from="4870">4870</biblScope><biblScope unit="page" to="4883">4883</biblScope></imprint><idno type="ISSN">0962-1083</idno></series><idno type="istex">880F4AC52B91E162A84E2FF5609ED10B23955B9F</idno><idno type="DOI">10.1111/mec.12432</idno><idno type="ArticleID">MEC12432</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0962-1083</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract">Microorganisms dwelling in sediments have a crucial role in biogeochemical cycles and are expected to have a strong influence on the cycle of arsenic, a metalloid responsible for severe water pollution and presenting major health risks for human populations. We present here a metagenomic study of the sediment from two harbours on the Mediterranean French coast, l'Estaque and St Mandrier. The first site is highly polluted with arsenic and heavy metals, while the arsenic concentration in the second site is below toxicity levels. The goal of this study was to elucidate the potential impact of the microbial community on the chemical parameters observed in complementary geochemical studies performed on the same sites. The metagenomic sequences, along with those from four publicly available metagenomes used as control data sets, were analysed with the RAMMCAP workflow. The resulting functional profiles were compared to determine the over‐represented Gene Ontology categories in the metagenomes of interest. Categories related to arsenic resistance and dissimilatory sulphate reduction were over‐represented in l'Estaque. More importantly, despite very similar profiles, the identification of specific sequence markers for sulphate‐reducing bacteria and sulphur‐oxidizing bacteria showed that sulphate reduction was significantly more associated with l'Estaque than with St Mandrier. We propose that biotic sulphate reduction, arsenate reduction and fermentation may together explain the higher mobility of arsenic observed in l'Estaque in previous physico‐chemical studies of this site. This study also demonstrates that it is possible to draw sound conclusions from comparing complex and similar unassembled metagenomes at the functional level, even with very low sequence coverage.</div></front></TEI><istex><corpusName>wiley</corpusName><author><json:item><name>Frédéric Plewniak</name><affiliations><json:string>Département Microorganismes, Génomes, Environnement, Génétique Moléculaire, Génomique et Microbiologie, UMR7156 Université de Strasbourg/CNRS, 28 rue Goethe, 67083, Strasbourg Cedex, France</json:string></affiliations></json:item><json:item><name>Sandrine Koechler</name><affiliations><json:string>Département Microorganismes, Génomes, Environnement, Génétique Moléculaire, Génomique et Microbiologie, UMR7156 Université de Strasbourg/CNRS, 28 rue Goethe, 67083, Strasbourg Cedex, France</json:string></affiliations></json:item><json:item><name>Benjamin Navet</name><affiliations><json:string>Département Microorganismes, Génomes, Environnement, Génétique Moléculaire, Génomique et Microbiologie, UMR7156 Université de Strasbourg/CNRS, 28 rue Goethe, 67083, Strasbourg Cedex, France</json:string></affiliations></json:item><json:item><name>Éric Dugat‐Bony</name><affiliations><json:string>Laboratoire Microorganismes: Génome et Environnement, UMR 6023 Université Blaise Pascal Clermont‐Ferrand/CNRS, Bât de Biologie A, Les Cézeaux, 24, Avenue des Landais, BP 80026 63171, Aubière Cedex, France</json:string></affiliations></json:item><json:item><name>Olivier Bouchez</name><affiliations><json:string>Plateforme génomique (PlaGe), Génopole Toulouse‐Midi‐Pyrénées, INRA, 31326, Castanet‐Tolosan, France</json:string><json:string>INRA, UMR444 Laboratoire de Génétique Cellulaire, INRA Auzeville, 31326, Castanet‐Tolosan, France</json:string></affiliations></json:item><json:item><name>Pierre Peyret</name><affiliations><json:string>Laboratoire Microorganismes: Génome et Environnement, UMR 6023 Université Blaise Pascal Clermont‐Ferrand/CNRS, Bât de Biologie A, Les Cézeaux, 24, Avenue des Landais, BP 80026 63171, Aubière Cedex, France</json:string></affiliations></json:item><json:item><name>Fabienne Séby</name><affiliations><json:string>Ultra Traces Analyses Aquitaine (UT2A), Hélioparc Pau‐Pyrénées, 2, avenue du Président Angot, 64053, Pau Cedex 9, France</json:string></affiliations></json:item><json:item><name>Fabienne Battaglia‐Brunet</name><affiliations><json:string>BRGM, Environnement et Procédés, Unité Biogéochimie Environnementale, Avenue Claude Guillemin, 45060, Orléans, France</json:string></affiliations></json:item><json:item><name>Philippe N. Bertin</name><affiliations><json:string>Département Microorganismes, Génomes, Environnement, Génétique Moléculaire, Génomique et Microbiologie, UMR7156 Université de Strasbourg/CNRS, 28 rue Goethe, 67083, Strasbourg Cedex, France</json:string></affiliations></json:item></author><subject><json:item><lang><json:string>eng</json:string></lang><value>arsenic pollution</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>marine sediment</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>metagenomics</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>microbial metabolism</value></json:item></subject><articleId><json:string>MEC12432</json:string></articleId><language><json:string>eng</json:string></language><originalGenre><json:string>article</json:string></originalGenre><abstract>Microorganisms dwelling in sediments have a crucial role in biogeochemical cycles and are expected to have a strong influence on the cycle of arsenic, a metalloid responsible for severe water pollution and presenting major health risks for human populations. We present here a metagenomic study of the sediment from two harbours on the Mediterranean French coast, l'Estaque and St Mandrier. The first site is highly polluted with arsenic and heavy metals, while the arsenic concentration in the second site is below toxicity levels. The goal of this study was to elucidate the potential impact of the microbial community on the chemical parameters observed in complementary geochemical studies performed on the same sites. The metagenomic sequences, along with those from four publicly available metagenomes used as control data sets, were analysed with the RAMMCAP workflow. The resulting functional profiles were compared to determine the over‐represented Gene Ontology categories in the metagenomes of interest. Categories related to arsenic resistance and dissimilatory sulphate reduction were over‐represented in l'Estaque. More importantly, despite very similar profiles, the identification of specific sequence markers for sulphate‐reducing bacteria and sulphur‐oxidizing bacteria showed that sulphate reduction was significantly more associated with l'Estaque than with St Mandrier. We propose that biotic sulphate reduction, arsenate reduction and fermentation may together explain the higher mobility of arsenic observed in l'Estaque in previous physico‐chemical studies of this site. This study also demonstrates that it is possible to draw sound conclusions from comparing complex and similar unassembled metagenomes at the functional level, even with very low sequence coverage.</abstract><qualityIndicators><score>10</score><pdfVersion>1.7</pdfVersion><pdfPageSize>595.276 x 793.701 pts</pdfPageSize><refBibsNative>true</refBibsNative><keywordCount>4</keywordCount><abstractCharCount>1791</abstractCharCount><pdfWordCount>8311</pdfWordCount><pdfCharCount>52642</pdfCharCount><pdfPageCount>14</pdfPageCount><abstractWordCount>254</abstractWordCount></qualityIndicators><title>Metagenomic insights into microbial metabolism affecting arsenic dispersion in Mediterranean marine sediments</title><genre><json:string>article</json:string></genre><host><volume>22</volume><publisherId><json:string>MEC</json:string></publisherId><pages><total>14</total><last>4883</last><first>4870</first></pages><issn><json:string>0962-1083</json:string></issn><issue>19</issue><subject><json:item><value>Original Article</value></json:item></subject><genre><json:string>journal</json:string></genre><language><json:string>unknown</json:string></language><eissn><json:string>1365-294X</json:string></eissn><title>Molecular Ecology</title><doi><json:string>10.1111/(ISSN)1365-294X</json:string></doi></host><publicationDate>2013</publicationDate><copyrightDate>2013</copyrightDate><doi><json:string>10.1111/mec.12432</json:string></doi><id>880F4AC52B91E162A84E2FF5609ED10B23955B9F</id><score>0.11161533</score><fulltext><json:item><original>true</original><mimetype>application/pdf</mimetype><extension>pdf</extension><uri>https://api.istex.fr/document/880F4AC52B91E162A84E2FF5609ED10B23955B9F/fulltext/pdf</uri></json:item><json:item><original>false</original><mimetype>application/zip</mimetype><extension>zip</extension><uri>https://api.istex.fr/document/880F4AC52B91E162A84E2FF5609ED10B23955B9F/fulltext/zip</uri></json:item><istex:fulltextTEI uri="https://api.istex.fr/document/880F4AC52B91E162A84E2FF5609ED10B23955B9F/fulltext/tei"><teiHeader><fileDesc><titleStmt><title level="a" type="main" xml:lang="en">Metagenomic insights into microbial metabolism affecting arsenic dispersion in Mediterranean marine sediments</title></titleStmt><publicationStmt><authority>ISTEX</authority><publisher>Blackwell Publishing Ltd</publisher><availability><p>Copyright © 2013 John Wiley & Sons Ltd© 2013 John Wiley & Sons Ltd</p></availability><date>2013-07-05</date></publicationStmt><notesStmt><note>Fig. S1 ROC curve of the prediction of sulphate‐reducing bacteria (SRBs) and sulphur‐oxidizing bacteria (SOBs) reads from the correlation of their similarity profiles with the SRB and SOB reference profiles from Table .Fig. S2 Rarefaction curves for TIGRfam and Pfam hits (dashed lines) and Gene Ontology terms (plain lines) for l'Estaque and St Mandrier.Table S1 Taxonomic micro‐array results for l'Estaque and St Mandrier.Table S2 Full list of the 395 Gene Ontology Biological process entries that were significantly over‐represented (fdr q‐value ≤ 10−2) in l'Estaque, in St Mandrier and in both metagenomes.Appendix S1 Count normalization by relative average genome size: detailed description of the method used for the Effective Genome Size determination and hit counts normalization.</note><note>Agence Nationale de la Recherche - No. ANR‐2008‐CESA‐003;</note><note>Centre National de la Recherche Scientifique (CNRS) in the frame of the ‘Groupement de Recherche—Métabolisme de l'Arsenic chez les Microorganismes - No. GDR2909‐CNRS;</note><note>Université de Strasbourg (UdS)</note></notesStmt><sourceDesc><biblStruct type="inbook"><analytic><title level="a" type="main" xml:lang="en">Metagenomic insights into microbial metabolism affecting arsenic dispersion in Mediterranean marine sediments</title><author xml:id="author-1"><persName><forename type="first">Frédéric</forename><surname>Plewniak</surname></persName><note type="correspondence"><p>Correspondence: Frédéric Plewniak, Fax: (+33) 368 85 20 28; E‐mail:</p></note><affiliation>Département Microorganismes, Génomes, Environnement, Génétique Moléculaire, Génomique et Microbiologie, UMR7156 Université de Strasbourg/CNRS, 28 rue Goethe, 67083, Strasbourg Cedex, France</affiliation></author><author xml:id="author-2"><persName><forename type="first">Sandrine</forename><surname>Koechler</surname></persName><affiliation>Département Microorganismes, Génomes, Environnement, Génétique Moléculaire, Génomique et Microbiologie, UMR7156 Université de Strasbourg/CNRS, 28 rue Goethe, 67083, Strasbourg Cedex, France</affiliation></author><author xml:id="author-3"><persName><forename type="first">Benjamin</forename><surname>Navet</surname></persName><affiliation>Département Microorganismes, Génomes, Environnement, Génétique Moléculaire, Génomique et Microbiologie, UMR7156 Université de Strasbourg/CNRS, 28 rue Goethe, 67083, Strasbourg Cedex, France</affiliation></author><author xml:id="author-4"><persName><forename type="first">Éric</forename><surname>Dugat‐Bony</surname></persName><affiliation>Laboratoire Microorganismes: Génome et Environnement, UMR 6023 Université Blaise Pascal Clermont‐Ferrand/CNRS, Bât de Biologie A, Les Cézeaux, 24, Avenue des Landais, BP 80026 63171, Aubière Cedex, France</affiliation></author><author xml:id="author-5"><persName><forename type="first">Olivier</forename><surname>Bouchez</surname></persName><affiliation>Plateforme génomique (PlaGe), Génopole Toulouse‐Midi‐Pyrénées, INRA, 31326, Castanet‐Tolosan, France</affiliation><affiliation>INRA, UMR444 Laboratoire de Génétique Cellulaire, INRA Auzeville, 31326, Castanet‐Tolosan, France</affiliation></author><author xml:id="author-6"><persName><forename type="first">Pierre</forename><surname>Peyret</surname></persName><affiliation>Laboratoire Microorganismes: Génome et Environnement, UMR 6023 Université Blaise Pascal Clermont‐Ferrand/CNRS, Bât de Biologie A, Les Cézeaux, 24, Avenue des Landais, BP 80026 63171, Aubière Cedex, France</affiliation></author><author xml:id="author-7"><persName><forename type="first">Fabienne</forename><surname>Séby</surname></persName><affiliation>Ultra Traces Analyses Aquitaine (UT2A), Hélioparc Pau‐Pyrénées, 2, avenue du Président Angot, 64053, Pau Cedex 9, France</affiliation></author><author xml:id="author-8"><persName><forename type="first">Fabienne</forename><surname>Battaglia‐Brunet</surname></persName><affiliation>BRGM, Environnement et Procédés, Unité Biogéochimie Environnementale, Avenue Claude Guillemin, 45060, Orléans, France</affiliation></author><author xml:id="author-9"><persName><forename type="first">Philippe N.</forename><surname>Bertin</surname></persName><affiliation>Département Microorganismes, Génomes, Environnement, Génétique Moléculaire, Génomique et Microbiologie, UMR7156 Université de Strasbourg/CNRS, 28 rue Goethe, 67083, Strasbourg Cedex, France</affiliation></author></analytic><monogr><title level="j">Molecular Ecology</title><title level="j" type="abbrev">Mol Ecol</title><idno type="pISSN">0962-1083</idno><idno type="eISSN">1365-294X</idno><idno type="DOI">10.1111/(ISSN)1365-294X</idno><imprint><publisher>Blackwell Publishing Ltd</publisher><date type="published" when="2013-10"></date><biblScope unit="volume">22</biblScope><biblScope unit="issue">19</biblScope><biblScope unit="page" from="4870">4870</biblScope><biblScope unit="page" to="4883">4883</biblScope></imprint></monogr><idno type="istex">880F4AC52B91E162A84E2FF5609ED10B23955B9F</idno><idno type="DOI">10.1111/mec.12432</idno><idno type="ArticleID">MEC12432</idno></biblStruct></sourceDesc></fileDesc><profileDesc><creation><date>2013-07-05</date></creation><langUsage><language ident="en">en</language></langUsage><abstract><p>Microorganisms dwelling in sediments have a crucial role in biogeochemical cycles and are expected to have a strong influence on the cycle of arsenic, a metalloid responsible for severe water pollution and presenting major health risks for human populations. We present here a metagenomic study of the sediment from two harbours on the Mediterranean French coast, l'Estaque and St Mandrier. The first site is highly polluted with arsenic and heavy metals, while the arsenic concentration in the second site is below toxicity levels. The goal of this study was to elucidate the potential impact of the microbial community on the chemical parameters observed in complementary geochemical studies performed on the same sites. The metagenomic sequences, along with those from four publicly available metagenomes used as control data sets, were analysed with the RAMMCAP workflow. The resulting functional profiles were compared to determine the over‐represented Gene Ontology categories in the metagenomes of interest. Categories related to arsenic resistance and dissimilatory sulphate reduction were over‐represented in l'Estaque. More importantly, despite very similar profiles, the identification of specific sequence markers for sulphate‐reducing bacteria and sulphur‐oxidizing bacteria showed that sulphate reduction was significantly more associated with l'Estaque than with St Mandrier. We propose that biotic sulphate reduction, arsenate reduction and fermentation may together explain the higher mobility of arsenic observed in l'Estaque in previous physico‐chemical studies of this site. This study also demonstrates that it is possible to draw sound conclusions from comparing complex and similar unassembled metagenomes at the functional level, even with very low sequence coverage.</p></abstract><textClass><keywords scheme="keyword"><list><head>keywords</head><item><term>arsenic pollution</term></item><item><term>marine sediment</term></item><item><term>metagenomics</term></item><item><term>microbial metabolism</term></item></list></keywords></textClass><textClass><keywords scheme="Journal Subject"><list><head>article-category</head><item><term>Original Article</term></item></list></keywords></textClass></profileDesc><revisionDesc><change when="2013-04-03">Received</change><change when="2013-06-25">Registration</change><change when="2013-07-05">Created</change><change when="2013-10">Published</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><original>false</original><mimetype>text/plain</mimetype><extension>txt</extension><uri>https://api.istex.fr/document/880F4AC52B91E162A84E2FF5609ED10B23955B9F/fulltext/txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="Wiley, elements deleted: body"><istex:xmlDeclaration>version="1.0" encoding="UTF-8" standalone="yes"</istex:xmlDeclaration><istex:document><component type="serialArticle" version="2.0" xml:id="mec12432" xml:lang="en"><header><publicationMeta level="product"><doi origin="wiley" registered="yes">10.1111/(ISSN)1365-294X</doi><issn type="print">0962-1083</issn><issn type="electronic">1365-294X</issn><idGroup><id type="product" value="MEC"></id></idGroup><titleGroup><title sort="MOLECULAR ECOLOGY" type="main">Molecular Ecology</title><title type="short">Mol Ecol</title></titleGroup></publicationMeta><publicationMeta level="part" position="10119"><doi origin="wiley">10.1111/mec.2013.22.issue-19</doi><copyright ownership="publisher">Copyright © 2013 John Wiley & Sons Ltd</copyright><numberingGroup><numbering type="journalVolume" number="22">22</numbering><numbering type="journalIssue">19</numbering></numberingGroup><coverDate startDate="2013-10">October 2013</coverDate></publicationMeta><publicationMeta level="unit" position="40" status="forIssue" type="article"><doi>10.1111/mec.12432</doi><idGroup><id type="unit" value="MEC12432"></id></idGroup><countGroup><count number="14" type="pageTotal"></count></countGroup><titleGroup><title type="articleCategory">Original Article</title><title type="tocHeading1">ORIGINAL ARTICLES</title><title type="tocHeading2">Ecological Genomics</title></titleGroup><copyright ownership="publisher">© 2013 John Wiley & Sons Ltd</copyright><eventGroup><event date="2013-04-03" type="manuscriptReceived"></event><event date="2013-06-13" type="manuscriptRevised"></event><event date="2013-06-25" type="manuscriptAccepted"></event><event agent="SPS" date="2013-07-05" type="xmlCreated"></event><event agent="SPS" date="2013-11-22" type="xmlCorrected"></event><event type="xmlConverted" agent="Converter:WILEY_ML3G_TO_WILEY_ML3GV2 version:3.2.6 mode:FullText" date="2013-11-25"></event><event type="publishedOnlineEarlyUnpaginated" date="2013-09-03"></event><event type="publishedOnlineFinalForm" date="2013-09-23"></event><event type="firstOnline" date="2013-09-03"></event><event type="xmlConverted" agent="Converter:WML3G_To_WML3G version:4.6.4 mode:FullText" date="2015-10-04"></event></eventGroup><numberingGroup><numbering type="pageFirst">4870</numbering><numbering type="pageLast">4883</numbering></numberingGroup><correspondenceTo>Correspondence: Frédéric Plewniak, Fax: (+33) 368 85 20 28; E‐mail: <email>f.plewniak@unistra.fr</email></correspondenceTo><linkGroup><link type="toTypesetVersion" href="file:MEC.MEC12432.pdf"></link></linkGroup></publicationMeta><contentMeta><titleGroup><title type="main">Metagenomic insights into microbial metabolism affecting arsenic dispersion in <fc>M</fc>editerranean marine sediments</title><title type="shortAuthors">F. Plewniak <i>et al</i>.</title></titleGroup><creators><creator affiliationRef="#mec12432-aff-0001" corresponding="yes" creatorRole="author" xml:id="mec12432-cr-0001"><personName><givenNames>Frédéric</givenNames> <familyName>Plewniak</familyName></personName></creator><creator affiliationRef="#mec12432-aff-0001" creatorRole="author" xml:id="mec12432-cr-0002"><personName><givenNames>Sandrine</givenNames> <familyName>Koechler</familyName></personName></creator><creator affiliationRef="#mec12432-aff-0001" creatorRole="author" xml:id="mec12432-cr-0003"><personName><givenNames>Benjamin</givenNames> <familyName>Navet</familyName></personName></creator><creator affiliationRef="#mec12432-aff-0002" creatorRole="author" xml:id="mec12432-cr-0004"><personName><givenNames>Éric</givenNames> <familyName>Dugat‐Bony</familyName></personName></creator><creator affiliationRef="#mec12432-aff-0003 #mec12432-aff-0004" creatorRole="author" xml:id="mec12432-cr-0005"><personName><givenNames>Olivier</givenNames> <familyName>Bouchez</familyName></personName></creator><creator affiliationRef="#mec12432-aff-0002" creatorRole="author" xml:id="mec12432-cr-0006"><personName><givenNames>Pierre</givenNames> <familyName>Peyret</familyName></personName></creator><creator affiliationRef="#mec12432-aff-0005" creatorRole="author" xml:id="mec12432-cr-0007"><personName><givenNames>Fabienne</givenNames> <familyName>Séby</familyName></personName></creator><creator affiliationRef="#mec12432-aff-0006" creatorRole="author" xml:id="mec12432-cr-0008"><personName><givenNames>Fabienne</givenNames> <familyName>Battaglia‐Brunet</familyName></personName></creator><creator affiliationRef="#mec12432-aff-0001" creatorRole="author" xml:id="mec12432-cr-0009"><personName><givenNames>Philippe N.</givenNames> <familyName>Bertin</familyName></personName></creator></creators><affiliationGroup><affiliation countryCode="FR" type="organization" xml:id="mec12432-aff-0001"><orgDiv>Département Microorganismes, Génomes, Environnement</orgDiv> <orgDiv>Génétique Moléculaire, Génomique et Microbiologie</orgDiv> <orgName>UMR7156 Université de Strasbourg/CNRS</orgName> <address><street>28 rue Goethe</street> <postCode>67083</postCode> <city>Strasbourg Cedex</city> <country>France</country></address></affiliation><affiliation countryCode="FR" type="organization" xml:id="mec12432-aff-0002"><orgDiv>Laboratoire Microorganismes: Génome et Environnement</orgDiv> <orgName>UMR 6023 Université Blaise Pascal Clermont‐Ferrand/CNRS</orgName> <address><street>Bât de Biologie A, Les Cézeaux, 24, Avenue des Landais</street> <postCode>BP 80026 63171</postCode> <city>Aubière Cedex</city> <country>France</country></address></affiliation><affiliation countryCode="FR" type="organization" xml:id="mec12432-aff-0003"><orgDiv>Plateforme génomique (PlaGe)</orgDiv> <orgName>Génopole Toulouse‐Midi‐Pyrénées</orgName> <orgName>INRA</orgName> <address><postCode>31326</postCode> <city>Castanet‐Tolosan</city> <country>France</country></address></affiliation><affiliation countryCode="FR" type="organization" xml:id="mec12432-aff-0004"><orgDiv>INRA</orgDiv> <orgName>UMR444 Laboratoire de Génétique Cellulaire</orgName> <orgName>INRA Auzeville</orgName> <address><postCode>31326</postCode> <city>Castanet‐Tolosan</city> <country>France</country></address></affiliation><affiliation countryCode="FR" type="organization" xml:id="mec12432-aff-0005"><orgDiv>Ultra Traces Analyses Aquitaine (UT2A)</orgDiv> <orgName>Hélioparc Pau‐Pyrénées</orgName> <address><street>2, avenue du Président Angot</street> <postCode>64053</postCode> <city>Pau Cedex 9</city> <country>France</country></address></affiliation><affiliation countryCode="FR" type="organization" xml:id="mec12432-aff-0006"><orgDiv>BRGM</orgDiv> <orgDiv>Environnement et Procédés</orgDiv> <orgName>Unité Biogéochimie Environnementale</orgName> <address><street>Avenue Claude Guillemin</street> <postCode>45060</postCode> <city>Orléans</city> <country>France</country></address></affiliation></affiliationGroup><keywordGroup type="author"><keyword xml:id="mec12432-kwd-0001">arsenic pollution</keyword><keyword xml:id="mec12432-kwd-0002">marine sediment</keyword><keyword xml:id="mec12432-kwd-0003">metagenomics</keyword><keyword xml:id="mec12432-kwd-0004">microbial metabolism</keyword></keywordGroup><fundingInfo><fundingAgency>Agence Nationale de la Recherche</fundingAgency><fundingNumber>ANR‐2008‐CESA‐003</fundingNumber></fundingInfo><fundingInfo><fundingAgency>Centre National de la Recherche Scientifique (CNRS) in the frame of the ‘Groupement de Recherche—Métabolisme de l'Arsenic chez les Microorganismes</fundingAgency><fundingNumber>GDR2909‐CNRS</fundingNumber></fundingInfo><fundingInfo><fundingAgency>Université de Strasbourg (UdS)</fundingAgency></fundingInfo><supportingInformation><supportingInfoItem><mediaResource alt="supporting" mimeType="application/PDF" href="urn-x:wiley:09621083:media:mec12432:mec12432-sup-0001-FigS1"></mediaResource><caption><b>Fig. S1 </b><fc>ROC</fc> curve of the prediction of sulphate‐reducing bacteria (<fc>SRB</fc>s) and sulphur‐oxidizing bacteria (<fc>SOB</fc>s) reads from the correlation of their similarity profiles with the <fc>SRB</fc> and <fc>SOB</fc> reference profiles from <fc>T</fc>able <link href="#mec12432-tbl-0001"></link>.</caption></supportingInfoItem><supportingInfoItem><mediaResource alt="supporting" mimeType="application/PDF" href="urn-x:wiley:09621083:media:mec12432:mec12432-sup-0003-FigS2"></mediaResource><caption><b>Fig. S2</b> Rarefaction curves for <fc>TIGR</fc>fam and <fc>P</fc>fam hits (dashed lines) and <fc>G</fc>ene <fc>O</fc>ntology terms (plain lines) for l'<fc>E</fc>staque and <fc>S</fc>t <fc>M</fc>andrier.</caption></supportingInfoItem><supportingInfoItem><mediaResource alt="supporting" mimeType="application/msexcel" href="urn-x:wiley:09621083:media:mec12432:mec12432-sup-0002-TableS1"></mediaResource><caption><b>Table S1</b> Taxonomic micro‐array results for l'<fc>E</fc>staque and <fc>S</fc>t <fc>M</fc>andrier.</caption></supportingInfoItem><supportingInfoItem><mediaResource alt="supporting" mimeType="application/msexcel" href="urn-x:wiley:09621083:media:mec12432:mec12432-sup-0004-TableS2"></mediaResource><caption><b>Table S2</b> Full list of the 395 <fc>G</fc>ene <fc>O</fc>ntology Biological process entries that were significantly over‐represented (fdr <i>q</i>‐value ≤ 10<sup>−2</sup>) in l'<fc>E</fc>staque, in <fc>S</fc>t <fc>M</fc>andrier and in both metagenomes.</caption></supportingInfoItem><supportingInfoItem><mediaResource alt="supporting" mimeType="application/PDF" href="urn-x:wiley:09621083:media:mec12432:mec12432-sup-0005-AppendixS1"></mediaResource><caption><b>Appendix S1</b> Count normalization by relative average genome size: detailed description of the method used for the Effective Genome Size determination and hit counts normalization.</caption></supportingInfoItem></supportingInformation><abstractGroup><abstract type="main" xml:id="mec12432-abs-0001"><title type="main">Abstract</title><p>Microorganisms dwelling in sediments have a crucial role in biogeochemical cycles and are expected to have a strong influence on the cycle of arsenic, a metalloid responsible for severe water pollution and presenting major health risks for human populations. We present here a metagenomic study of the sediment from two harbours on the <fc>M</fc>editerranean <fc>F</fc>rench coast, l'<fc>E</fc>staque and <fc>S</fc>t <fc>M</fc>andrier. The first site is highly polluted with arsenic and heavy metals, while the arsenic concentration in the second site is below toxicity levels. The goal of this study was to elucidate the potential impact of the microbial community on the chemical parameters observed in complementary geochemical studies performed on the same sites. The metagenomic sequences, along with those from four publicly available metagenomes used as control data sets, were analysed with the <fc>RAMMCAP</fc> workflow. The resulting functional profiles were compared to determine the over‐represented <fc>G</fc>ene <fc>O</fc>ntology categories in the metagenomes of interest. Categories related to arsenic resistance and dissimilatory sulphate reduction were over‐represented in l'<fc>E</fc>staque. More importantly, despite very similar profiles, the identification of specific sequence markers for sulphate‐reducing bacteria and sulphur‐oxidizing bacteria showed that sulphate reduction was significantly more associated with l'<fc>E</fc>staque than with <fc>S</fc>t <fc>M</fc>andrier. We propose that biotic sulphate reduction, arsenate reduction and fermentation may together explain the higher mobility of arsenic observed in l'<fc>E</fc>staque in previous physico‐chemical studies of this site. This study also demonstrates that it is possible to draw sound conclusions from comparing complex and similar unassembled metagenomes at the functional level, even with very low sequence coverage.</p></abstract></abstractGroup></contentMeta></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Metagenomic insights into microbial metabolism affecting arsenic dispersion in Mediterranean marine sediments</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>Metagenomic insights into microbial metabolism affecting arsenic dispersion in Mediterranean marine sediments</title></titleInfo><name type="personal"><namePart type="given">Frédéric</namePart><namePart type="family">Plewniak</namePart><affiliation>Département Microorganismes, Génomes, Environnement, Génétique Moléculaire, Génomique et Microbiologie, UMR7156 Université de Strasbourg/CNRS, 28 rue Goethe, 67083, Strasbourg Cedex, France</affiliation><description>Correspondence: Frédéric Plewniak, Fax: (+33) 368 85 20 28; E‐mail: </description><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Sandrine</namePart><namePart type="family">Koechler</namePart><affiliation>Département Microorganismes, Génomes, Environnement, Génétique Moléculaire, Génomique et Microbiologie, UMR7156 Université de Strasbourg/CNRS, 28 rue Goethe, 67083, Strasbourg Cedex, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Benjamin</namePart><namePart type="family">Navet</namePart><affiliation>Département Microorganismes, Génomes, Environnement, Génétique Moléculaire, Génomique et Microbiologie, UMR7156 Université de Strasbourg/CNRS, 28 rue Goethe, 67083, Strasbourg Cedex, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Éric</namePart><namePart type="family">Dugat‐Bony</namePart><affiliation>Laboratoire Microorganismes: Génome et Environnement, UMR 6023 Université Blaise Pascal Clermont‐Ferrand/CNRS, Bât de Biologie A, Les Cézeaux, 24, Avenue des Landais, BP 80026 63171, Aubière Cedex, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Olivier</namePart><namePart type="family">Bouchez</namePart><affiliation>Plateforme génomique (PlaGe), Génopole Toulouse‐Midi‐Pyrénées, INRA, 31326, Castanet‐Tolosan, France</affiliation><affiliation>INRA, UMR444 Laboratoire de Génétique Cellulaire, INRA Auzeville, 31326, Castanet‐Tolosan, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Pierre</namePart><namePart type="family">Peyret</namePart><affiliation>Laboratoire Microorganismes: Génome et Environnement, UMR 6023 Université Blaise Pascal Clermont‐Ferrand/CNRS, Bât de Biologie A, Les Cézeaux, 24, Avenue des Landais, BP 80026 63171, Aubière Cedex, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Fabienne</namePart><namePart type="family">Séby</namePart><affiliation>Ultra Traces Analyses Aquitaine (UT2A), Hélioparc Pau‐Pyrénées, 2, avenue du Président Angot, 64053, Pau Cedex 9, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Fabienne</namePart><namePart type="family">Battaglia‐Brunet</namePart><affiliation>BRGM, Environnement et Procédés, Unité Biogéochimie Environnementale, Avenue Claude Guillemin, 45060, Orléans, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Philippe N.</namePart><namePart type="family">Bertin</namePart><affiliation>Département Microorganismes, Génomes, Environnement, Génétique Moléculaire, Génomique et Microbiologie, UMR7156 Université de Strasbourg/CNRS, 28 rue Goethe, 67083, Strasbourg Cedex, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="article" displayLabel="article"></genre><originInfo><publisher>Blackwell Publishing Ltd</publisher><dateIssued encoding="w3cdtf">2013-10</dateIssued><dateCreated encoding="w3cdtf">2013-07-05</dateCreated><dateCaptured encoding="w3cdtf">2013-04-03</dateCaptured><dateValid encoding="w3cdtf">2013-06-25</dateValid><copyrightDate encoding="w3cdtf">2013</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><physicalDescription><internetMediaType>text/html</internetMediaType></physicalDescription><abstract>Microorganisms dwelling in sediments have a crucial role in biogeochemical cycles and are expected to have a strong influence on the cycle of arsenic, a metalloid responsible for severe water pollution and presenting major health risks for human populations. We present here a metagenomic study of the sediment from two harbours on the Mediterranean French coast, l'Estaque and St Mandrier. The first site is highly polluted with arsenic and heavy metals, while the arsenic concentration in the second site is below toxicity levels. The goal of this study was to elucidate the potential impact of the microbial community on the chemical parameters observed in complementary geochemical studies performed on the same sites. The metagenomic sequences, along with those from four publicly available metagenomes used as control data sets, were analysed with the RAMMCAP workflow. The resulting functional profiles were compared to determine the over‐represented Gene Ontology categories in the metagenomes of interest. Categories related to arsenic resistance and dissimilatory sulphate reduction were over‐represented in l'Estaque. More importantly, despite very similar profiles, the identification of specific sequence markers for sulphate‐reducing bacteria and sulphur‐oxidizing bacteria showed that sulphate reduction was significantly more associated with l'Estaque than with St Mandrier. We propose that biotic sulphate reduction, arsenate reduction and fermentation may together explain the higher mobility of arsenic observed in l'Estaque in previous physico‐chemical studies of this site. This study also demonstrates that it is possible to draw sound conclusions from comparing complex and similar unassembled metagenomes at the functional level, even with very low sequence coverage.</abstract><note type="additional physical form">Fig. S1 ROC curve of the prediction of sulphate‐reducing bacteria (SRBs) and sulphur‐oxidizing bacteria (SOBs) reads from the correlation of their similarity profiles with the SRB and SOB reference profiles from Table .Fig. S2 Rarefaction curves for TIGRfam and Pfam hits (dashed lines) and Gene Ontology terms (plain lines) for l'Estaque and St Mandrier.Table S1 Taxonomic micro‐array results for l'Estaque and St Mandrier.Table S2 Full list of the 395 Gene Ontology Biological process entries that were significantly over‐represented (fdr q‐value ≤ 10−2) in l'Estaque, in St Mandrier and in both metagenomes.Appendix S1 Count normalization by relative average genome size: detailed description of the method used for the Effective Genome Size determination and hit counts normalization.</note><note type="funding">Agence Nationale de la Recherche - No. ANR‐2008‐CESA‐003; </note><note type="funding">Centre National de la Recherche Scientifique (CNRS) in the frame of the ‘Groupement de Recherche—Métabolisme de l'Arsenic chez les Microorganismes - No. GDR2909‐CNRS; </note><note type="funding">Université de Strasbourg (UdS)</note><subject><genre>keywords</genre><topic>arsenic pollution</topic><topic>marine sediment</topic><topic>metagenomics</topic><topic>microbial metabolism</topic></subject><relatedItem type="host"><titleInfo><title>Molecular Ecology</title></titleInfo><titleInfo type="abbreviated"><title>Mol Ecol</title></titleInfo><genre type="journal">journal</genre><subject><genre>article-category</genre><topic>Original Article</topic></subject><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>2013</date><detail type="volume"><caption>vol.</caption><number>22</number></detail><detail type="issue"><caption>no.</caption><number>19</number></detail><extent unit="pages"><start>4870</start><end>4883</end><total>14</total></extent></part></relatedItem><identifier type="istex">880F4AC52B91E162A84E2FF5609ED10B23955B9F</identifier><identifier type="DOI">10.1111/mec.12432</identifier><identifier type="ArticleID">MEC12432</identifier><accessCondition type="use and reproduction" contentType="copyright">Copyright © 2013 John Wiley & Sons Ltd© 2013 John Wiley & Sons Ltd</accessCondition><recordInfo><recordContentSource>WILEY</recordContentSource></recordInfo></mods></metadata><enrichments><json:item><type>multicat</type><uri>https://api.istex.fr/document/880F4AC52B91E162A84E2FF5609ED10B23955B9F/enrichments/multicat</uri></json:item></enrichments><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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