Comparative metatranscriptomics reveals widespread community responses during phenanthrene degradation in soil
Identifieur interne : 000376 ( Istex/Corpus ); précédent : 000375; suivant : 000377Comparative metatranscriptomics reveals widespread community responses during phenanthrene degradation in soil
Auteurs : Alexandre De Menezes ; Nicholas Clipson ; Evelyn DoyleSource :
- Environmental Microbiology [ 1462-2912 ] ; 2012-09.
Abstract
Soil microbial community response to phenanthrene was evaluated by metatranscriptomics. A marked increase in transcripts involved in aromatic compound metabolism, respiration and stress responses, and concurrent decreases in virulence, carbohydrate, DNA metabolism and phosphorus metabolism transcripts was revealed. Phenanthrene addition led to a 1.8‐fold to 33‐fold increase in the abundance of dioxygenase, stress response and detoxification transcripts, whereas those of general metabolism were little affected. Heavy metal P‐type ATPases and thioredoxin transcripts were more abundant in the phenanthrene‐amended soil, and this is the first time these proteins have been associated with polycyclic aromatic hydrocarbon (PAH) stress in microorganisms. Annotation with custom databases constructed with bacterial or fungal PAH metabolism protein sequences showed that increases in PAH‐degradatory gene expression occurred for all gene groups investigated. Taxonomic determination of mRNA transcripts showed widespread changes in the bacteria, archaea and fungi, and the actinobacteria were responsible for most of the de novo expression of transcripts associated with dioxygenases, stress response and detoxification genes. This is the first report of an experimental metatranscriptomic study detailing microbial community responses to a pollutant in soil, and offers information on novel in situ effects of PAHs on soil microbes that can be explored further.
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DOI: 10.1111/j.1462-2920.2012.02781.x
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<record><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title xml:lang="en">Comparative metatranscriptomics reveals widespread community responses during phenanthrene degradation in soil</title><author><name sortKey="De Menezes, Alexandre" sort="De Menezes, Alexandre" uniqKey="De Menezes A" first="Alexandre" last="De Menezes">Alexandre De Menezes</name><affiliation><mods:affiliation>School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland</mods:affiliation></affiliation></author><author><name sortKey="Clipson, Nicholas" sort="Clipson, Nicholas" uniqKey="Clipson N" first="Nicholas" last="Clipson">Nicholas Clipson</name><affiliation><mods:affiliation>School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland</mods:affiliation></affiliation></author><author><name sortKey="Doyle, Evelyn" sort="Doyle, Evelyn" uniqKey="Doyle E" first="Evelyn" last="Doyle">Evelyn Doyle</name><affiliation><mods:affiliation>School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland</mods:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:A71EDB62A31F11FED1EB1D6DC488F24ECEF4937F</idno><date when="2012" year="2012">2012</date><idno type="doi">10.1111/j.1462-2920.2012.02781.x</idno><idno type="url">https://api.istex.fr/document/A71EDB62A31F11FED1EB1D6DC488F24ECEF4937F/fulltext/pdf</idno><idno type="wicri:Area/Istex/Corpus">000376</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a" type="main" xml:lang="en">Comparative metatranscriptomics reveals widespread community responses during phenanthrene degradation in soil</title><author><name sortKey="De Menezes, Alexandre" sort="De Menezes, Alexandre" uniqKey="De Menezes A" first="Alexandre" last="De Menezes">Alexandre De Menezes</name><affiliation><mods:affiliation>School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland</mods:affiliation></affiliation></author><author><name sortKey="Clipson, Nicholas" sort="Clipson, Nicholas" uniqKey="Clipson N" first="Nicholas" last="Clipson">Nicholas Clipson</name><affiliation><mods:affiliation>School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland</mods:affiliation></affiliation></author><author><name sortKey="Doyle, Evelyn" sort="Doyle, Evelyn" uniqKey="Doyle E" first="Evelyn" last="Doyle">Evelyn Doyle</name><affiliation><mods:affiliation>School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland</mods:affiliation></affiliation></author></analytic><monogr></monogr><series><title level="j">Environmental Microbiology</title><idno type="ISSN">1462-2912</idno><idno type="eISSN">1462-2920</idno><imprint><publisher>Blackwell Publishing Ltd</publisher><pubPlace>Oxford, UK</pubPlace><date type="published" when="2012-09">2012-09</date><biblScope unit="volume">14</biblScope><biblScope unit="issue">9</biblScope><biblScope unit="page" from="2577">2577</biblScope><biblScope unit="page" to="2588">2588</biblScope></imprint><idno type="ISSN">1462-2912</idno></series><idno type="istex">A71EDB62A31F11FED1EB1D6DC488F24ECEF4937F</idno><idno type="DOI">10.1111/j.1462-2920.2012.02781.x</idno><idno type="ArticleID">EMI2781</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">1462-2912</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Soil microbial community response to phenanthrene was evaluated by metatranscriptomics. A marked increase in transcripts involved in aromatic compound metabolism, respiration and stress responses, and concurrent decreases in virulence, carbohydrate, DNA metabolism and phosphorus metabolism transcripts was revealed. Phenanthrene addition led to a 1.8‐fold to 33‐fold increase in the abundance of dioxygenase, stress response and detoxification transcripts, whereas those of general metabolism were little affected. Heavy metal P‐type ATPases and thioredoxin transcripts were more abundant in the phenanthrene‐amended soil, and this is the first time these proteins have been associated with polycyclic aromatic hydrocarbon (PAH) stress in microorganisms. Annotation with custom databases constructed with bacterial or fungal PAH metabolism protein sequences showed that increases in PAH‐degradatory gene expression occurred for all gene groups investigated. Taxonomic determination of mRNA transcripts showed widespread changes in the bacteria, archaea and fungi, and the actinobacteria were responsible for most of the de novo expression of transcripts associated with dioxygenases, stress response and detoxification genes. This is the first report of an experimental metatranscriptomic study detailing microbial community responses to a pollutant in soil, and offers information on novel in situ effects of PAHs on soil microbes that can be explored further.</div></front></TEI><istex><corpusName>wiley</corpusName><author><json:item><name>Alexandre de Menezes</name><affiliations><json:string>School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland</json:string></affiliations></json:item><json:item><name>Nicholas Clipson</name><affiliations><json:string>School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland</json:string></affiliations></json:item><json:item><name>Evelyn Doyle</name><affiliations><json:string>School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland</json:string></affiliations></json:item></author><articleId><json:string>EMI2781</json:string></articleId><language><json:string>eng</json:string></language><originalGenre><json:string>article</json:string></originalGenre><abstract>Soil microbial community response to phenanthrene was evaluated by metatranscriptomics. A marked increase in transcripts involved in aromatic compound metabolism, respiration and stress responses, and concurrent decreases in virulence, carbohydrate, DNA metabolism and phosphorus metabolism transcripts was revealed. Phenanthrene addition led to a 1.8‐fold to 33‐fold increase in the abundance of dioxygenase, stress response and detoxification transcripts, whereas those of general metabolism were little affected. Heavy metal P‐type ATPases and thioredoxin transcripts were more abundant in the phenanthrene‐amended soil, and this is the first time these proteins have been associated with polycyclic aromatic hydrocarbon (PAH) stress in microorganisms. Annotation with custom databases constructed with bacterial or fungal PAH metabolism protein sequences showed that increases in PAH‐degradatory gene expression occurred for all gene groups investigated. Taxonomic determination of mRNA transcripts showed widespread changes in the bacteria, archaea and fungi, and the actinobacteria were responsible for most of the de novo expression of transcripts associated with dioxygenases, stress response and detoxification genes. 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(+353) 17161300; Fax (+353) 17161152.</p></note><affiliation>School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland</affiliation></author></analytic><monogr><title level="j">Environmental Microbiology</title><idno type="pISSN">1462-2912</idno><idno type="eISSN">1462-2920</idno><idno type="DOI">10.1111/(ISSN)1462-2920</idno><imprint><publisher>Blackwell Publishing Ltd</publisher><pubPlace>Oxford, UK</pubPlace><date type="published" when="2012-09"></date><biblScope unit="volume">14</biblScope><biblScope unit="issue">9</biblScope><biblScope unit="page" from="2577">2577</biblScope><biblScope unit="page" to="2588">2588</biblScope></imprint></monogr><idno type="istex">A71EDB62A31F11FED1EB1D6DC488F24ECEF4937F</idno><idno type="DOI">10.1111/j.1462-2920.2012.02781.x</idno><idno type="ArticleID">EMI2781</idno></biblStruct></sourceDesc></fileDesc><profileDesc><creation><date>2012</date></creation><langUsage><language ident="en">en</language></langUsage><abstract xml:lang="en"><p>Soil microbial community response to phenanthrene was evaluated by metatranscriptomics. A marked increase in transcripts involved in aromatic compound metabolism, respiration and stress responses, and concurrent decreases in virulence, carbohydrate, DNA metabolism and phosphorus metabolism transcripts was revealed. Phenanthrene addition led to a 1.8‐fold to 33‐fold increase in the abundance of dioxygenase, stress response and detoxification transcripts, whereas those of general metabolism were little affected. Heavy metal P‐type ATPases and thioredoxin transcripts were more abundant in the phenanthrene‐amended soil, and this is the first time these proteins have been associated with polycyclic aromatic hydrocarbon (PAH) stress in microorganisms. Annotation with custom databases constructed with bacterial or fungal PAH metabolism protein sequences showed that increases in PAH‐degradatory gene expression occurred for all gene groups investigated. Taxonomic determination of mRNA transcripts showed widespread changes in the bacteria, archaea and fungi, and the actinobacteria were responsible for most of the de novo expression of transcripts associated with dioxygenases, stress response and detoxification genes. This is the first report of an experimental metatranscriptomic study detailing microbial community responses to a pollutant in soil, and offers information on novel in situ effects of PAHs on soil microbes that can be explored further.</p></abstract></profileDesc><revisionDesc><change when="2012-09">Published</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><original>false</original><mimetype>text/plain</mimetype><extension>txt</extension><uri>https://api.istex.fr/document/A71EDB62A31F11FED1EB1D6DC488F24ECEF4937F/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 version="2.0" type="serialArticle" xml:lang="en"><header><publicationMeta level="product"><publisherInfo><publisherName>Blackwell Publishing Ltd</publisherName><publisherLoc>Oxford, UK</publisherLoc></publisherInfo><doi origin="wiley" registered="yes">10.1111/(ISSN)1462-2920</doi><issn type="print">1462-2912</issn><issn type="electronic">1462-2920</issn><idGroup><id type="product" value="EMI"></id><id type="publisherDivision" value="ST"></id></idGroup><titleGroup><title type="main" sort="ENVIRONMENTAL MICROBIOLOGY">Environmental Microbiology</title></titleGroup></publicationMeta><publicationMeta level="part" position="09109"><doi origin="wiley">10.1111/emi.2012.14.issue-9</doi><titleGroup><title type="specialIssueTitle">Microbial Communities ‐ Structure, Behaviour, Evolution</title></titleGroup><numberingGroup><numbering type="journalVolume" number="14">14</numbering><numbering type="journalIssue">9</numbering></numberingGroup><coverDate startDate="2012-09">September 2012</coverDate></publicationMeta><publicationMeta level="unit" type="article" position="26" status="forIssue"><doi origin="wiley">10.1111/j.1462-2920.2012.02781.x</doi><idGroup><id type="unit" value="EMI2781"></id></idGroup><countGroup><count type="pageTotal" number="12"></count></countGroup><titleGroup><title type="tocHeading1">Research articles</title></titleGroup><copyright>© 2012 Society for Applied Microbiology and Blackwell Publishing Ltd</copyright><eventGroup><event type="xmlConverted" agent="Converter:BPG_TO_WML3G version:3.1.6 mode:FullText" date="2012-09-04"></event><event type="publishedOnlineEarlyUnpaginated" date="2012-05-25"></event><event type="firstOnline" date="2012-05-25"></event><event type="publishedOnlineFinalForm" date="2012-09-04"></event><event type="xmlConverted" agent="Converter:WILEY_ML3G_TO_WILEY_ML3GV2 version:3.8.8" date="2014-01-24"></event><event type="xmlConverted" agent="Converter:WML3G_To_WML3G version:4.3.4 mode:FullText" date="2015-02-25"></event></eventGroup><numberingGroup><numbering type="pageFirst" number="2577">2577</numbering><numbering type="pageLast" number="2588">2588</numbering></numberingGroup><correspondenceTo> E‐mail <email>evelyn.doyle@ucd.ie</email>; Tel. (+353) 17161300; Fax (+353) 17161152. </correspondenceTo><linkGroup><link type="toTypesetVersion" href="file:EMI.EMI2781.pdf"></link></linkGroup></publicationMeta><contentMeta><unparsedEditorialHistory>Received 16 January, 2012; revised 23 March, 2012; accepted 24 April, 2012.</unparsedEditorialHistory><countGroup><count type="figureTotal" number="4"></count><count type="tableTotal" number="2"></count><count type="formulaTotal" number="0"></count><count type="referenceTotal" number="76"></count><count type="wordTotal" number="7634"></count><count type="linksPubMed" number="0"></count><count type="linksCrossRef" number="0"></count></countGroup><titleGroup><title type="main">Comparative metatranscriptomics reveals widespread community responses during phenanthrene degradation in soil</title><title type="shortAuthors">A. de Menezes, N. Clipson and E. Doyle</title><title type="short">Metatranscriptomic analysis of phenanthrene amended soil</title></titleGroup><creators><creator creatorRole="author" xml:id="cr1" affiliationRef="#a1"><personName><givenNames>Alexandre</givenNames><familyName>de Menezes</familyName></personName></creator><creator creatorRole="author" xml:id="cr2" affiliationRef="#a1"><personName><givenNames>Nicholas</givenNames><familyName>Clipson</familyName></personName></creator><creator creatorRole="author" xml:id="cr3" affiliationRef="#a1" corresponding="yes"><personName><givenNames>Evelyn</givenNames><familyName>Doyle</familyName></personName></creator></creators><affiliationGroup><affiliation xml:id="a1" countryCode="IE"><unparsedAffiliation>School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland</unparsedAffiliation></affiliation></affiliationGroup><supportingInformation><p><b>Table S1A.</b> Protein sequence GenBank accessions for sequences used in the bacterial custom database.</p><p><b>Table S1B.</b> References for PAH metabolism protein sequences used in the bacterial custom database.</p><p><b>Table S2A.</b> GenBank accessions of protein sequences used to construct fungal custom database.</p><p><b>Table S2B.</b> References for fungal PAH metabolism protein sequences used in the bacterial custom database.</p><p><b>Table S3.</b> Absolute numbers of non‐rRNA sequences classified to bacterial, archaeal and fungal classes determined by BLASTn and MEGAN analysis. Presented here are the absolute numbers of reads (non‐normalized).</p><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:14622912:media:emi2781:EMI_2781_sm_SuppInfor"></mediaResource><caption>Supporting info item</caption></supportingInfoItem></supportingInformation><abstractGroup><abstract type="main" xml:lang="en"><title type="main">Summary</title><p>Soil microbial community response to phenanthrene was evaluated by metatranscriptomics. A marked increase in transcripts involved in aromatic compound metabolism, respiration and stress responses, and concurrent decreases in virulence, carbohydrate, DNA metabolism and phosphorus metabolism transcripts was revealed. Phenanthrene addition led to a 1.8‐fold to 33‐fold increase in the abundance of dioxygenase, stress response and detoxification transcripts, whereas those of general metabolism were little affected. Heavy metal P‐type ATPases and thioredoxin transcripts were more abundant in the phenanthrene‐amended soil, and this is the first time these proteins have been associated with polycyclic aromatic hydrocarbon (PAH) stress in microorganisms. Annotation with custom databases constructed with bacterial or fungal PAH metabolism protein sequences showed that increases in PAH‐degradatory gene expression occurred for all gene groups investigated. Taxonomic determination of mRNA transcripts showed widespread changes in the bacteria, archaea and fungi, and the actinobacteria were responsible for most of the <i>de novo</i> expression of transcripts associated with dioxygenases, stress response and detoxification genes. This is the first report of an experimental metatranscriptomic study detailing microbial community responses to a pollutant in soil, and offers information on novel <i>in situ</i> effects of PAHs on soil microbes that can be explored further.</p></abstract></abstractGroup></contentMeta></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Comparative metatranscriptomics reveals widespread community responses during phenanthrene degradation in soil</title></titleInfo><titleInfo type="abbreviated" lang="en"><title>Metatranscriptomic analysis of phenanthrene amended soil</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>Comparative metatranscriptomics reveals widespread community responses during phenanthrene degradation in soil</title></titleInfo><name type="personal"><namePart type="given">Alexandre</namePart><namePart type="family">de Menezes</namePart><affiliation>School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Nicholas</namePart><namePart type="family">Clipson</namePart><affiliation>School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Evelyn</namePart><namePart type="family">Doyle</namePart><affiliation>School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland</affiliation><description>Correspondence: E‐mail ; Tel. (+353) 17161300; Fax (+353) 17161152.</description><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">2012-09</dateIssued><edition>Received 16 January, 2012; revised 23 March, 2012; accepted 24 April, 2012.</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">4</extent><extent unit="tables">2</extent><extent unit="references">76</extent><extent unit="words">7634</extent></physicalDescription><abstract lang="en">Soil microbial community response to phenanthrene was evaluated by metatranscriptomics. A marked increase in transcripts involved in aromatic compound metabolism, respiration and stress responses, and concurrent decreases in virulence, carbohydrate, DNA metabolism and phosphorus metabolism transcripts was revealed. Phenanthrene addition led to a 1.8‐fold to 33‐fold increase in the abundance of dioxygenase, stress response and detoxification transcripts, whereas those of general metabolism were little affected. Heavy metal P‐type ATPases and thioredoxin transcripts were more abundant in the phenanthrene‐amended soil, and this is the first time these proteins have been associated with polycyclic aromatic hydrocarbon (PAH) stress in microorganisms. Annotation with custom databases constructed with bacterial or fungal PAH metabolism protein sequences showed that increases in PAH‐degradatory gene expression occurred for all gene groups investigated. Taxonomic determination of mRNA transcripts showed widespread changes in the bacteria, archaea and fungi, and the actinobacteria were responsible for most of the de novo expression of transcripts associated with dioxygenases, stress response and detoxification genes. This is the first report of an experimental metatranscriptomic study detailing microbial community responses to a pollutant in soil, and offers information on novel in situ effects of PAHs on soil microbes that can be explored further.</abstract><relatedItem type="host"><titleInfo><title>Environmental Microbiology</title></titleInfo><genre type="journal">journal</genre><note type="content"> Table S1A. Protein sequence GenBank accessions for sequences used in the bacterial custom database. Table S1B. References for PAH metabolism protein sequences used in the bacterial custom database. Table S2A. GenBank accessions of protein sequences used to construct fungal custom database. Table S2B. References for fungal PAH metabolism protein sequences used in the bacterial custom database. Table S3. Absolute numbers of non‐rRNA sequences classified to bacterial, archaeal and fungal classes determined by BLASTn and MEGAN analysis. Presented here are the absolute numbers of reads (non‐normalized). Table S1A. Protein sequence GenBank accessions for sequences used in the bacterial custom database. Table S1B. References for PAH metabolism protein sequences used in the bacterial custom database. Table S2A. GenBank accessions of protein sequences used to construct fungal custom database. Table S2B. References for fungal PAH metabolism protein sequences used in the bacterial custom database. Table S3. Absolute numbers of non‐rRNA sequences classified to bacterial, archaeal and fungal classes determined by BLASTn and MEGAN analysis. Presented here are the absolute numbers of reads (non‐normalized). Table S1A. Protein sequence GenBank accessions for sequences used in the bacterial custom database. Table S1B. References for PAH metabolism protein sequences used in the bacterial custom database. Table S2A. GenBank accessions of protein sequences used to construct fungal custom database. Table S2B. References for fungal PAH metabolism protein sequences used in the bacterial custom database. Table S3. Absolute numbers of non‐rRNA sequences classified to bacterial, archaeal and fungal classes determined by BLASTn and MEGAN analysis. Presented here are the absolute numbers of reads (non‐normalized). Table S1A. Protein sequence GenBank accessions for sequences used in the bacterial custom database. Table S1B. References for PAH metabolism protein sequences used in the bacterial custom database. Table S2A. GenBank accessions of protein sequences used to construct fungal custom database. Table S2B. References for fungal PAH metabolism protein sequences used in the bacterial custom database. Table S3. Absolute numbers of non‐rRNA sequences classified to bacterial, archaeal and fungal classes determined by BLASTn and MEGAN analysis. Presented here are the absolute numbers of reads (non‐normalized). Table S1A. Protein sequence GenBank accessions for sequences used in the bacterial custom database. Table S1B. References for PAH metabolism protein sequences used in the bacterial custom database. Table S2A. GenBank accessions of protein sequences used to construct fungal custom database. Table S2B. References for fungal PAH metabolism protein sequences used in the bacterial custom database. Table S3. Absolute numbers of non‐rRNA sequences classified to bacterial, archaeal and fungal classes determined by BLASTn and MEGAN analysis. 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