Metatranscriptomic signature of exogenous polyamine utilization by coastal bacterioplankton
Identifieur interne : 000508 ( Istex/Corpus ); précédent : 000507; suivant : 000509Metatranscriptomic signature of exogenous polyamine utilization by coastal bacterioplankton
Auteurs : Xiaozhen Mou ; Maria Vila-Costa ; Shulei Sun ; Weidong Zhao ; Shalabh Sharma ; Mary Ann MoranSource :
- Environmental Microbiology Reports [ 1758-2229 ] ; 2011-12.
Abstract
The polyamines putrescine (PUT) and spermidine (SPD) are ubiquitous in seawater, but mechanisms that drive the degradation of these important nitrogen sources by marine bacteria remain unclear. We employed a comparative metatranscriptomics approach to compare gene transcription patterns between coastal bacterioplankton communities with and without amendments of PUT or SPD, in an effort to understand how bacterial communities and their genes shape polyamine biogeochemistry in the ocean. Statistically different transcript categories in the PUT (25 COG groups) and SPD (23 COG groups) samples, relative to controls that received no amendment (CTRL), indicated that genes encoding the cellular translation machinery and the metabolism of organic nitrogen and carbon became enriched in the community transcriptome when polyamine availability increased. Of the three known pathways for bacterial polyamine degradation, only genes in the transamination pathway were enriched in the PUT and SPD libraries, suggesting that this route dominated polyamine degradation. Taxonomic affiliation of significantly enriched diagnostic genes in the PUT and SPD libraries pointed to roseobacter‐ and SAR11‐affiliated bacteria as the predominant taxa driving transformation in this coastal ocean, although other diverse marine bacterioplankton groups (Gammaproteobacteria, Betaproteobacteria, Actinobacteria and Bacteroidetes) also contributed to polyamine‐related gene transcription.
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DOI: 10.1111/j.1758-2229.2011.00289.x
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USA.</mods:affiliation></affiliation></author><author><name sortKey="Zhao, Weidong" sort="Zhao, Weidong" uniqKey="Zhao W" first="Weidong" last="Zhao">Weidong Zhao</name><affiliation><mods:affiliation>Northeastern Ohio Universities Colleges of Medicine and Pharmacy, Rootstown, OH 44272, USA.</mods:affiliation></affiliation></author><author><name sortKey="Sharma, Shalabh" sort="Sharma, Shalabh" uniqKey="Sharma S" first="Shalabh" last="Sharma">Shalabh Sharma</name><affiliation><mods:affiliation>Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA.</mods:affiliation></affiliation></author><author><name sortKey="Moran, Mary Ann" sort="Moran, Mary Ann" uniqKey="Moran M" first="Mary Ann" last="Moran">Mary Ann Moran</name><affiliation><mods:affiliation>Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA.</mods:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno 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of Georgia, Athens, GA 30602, USA.</mods:affiliation></affiliation></author><author><name sortKey="Sun, Shulei" sort="Sun, Shulei" uniqKey="Sun S" first="Shulei" last="Sun">Shulei Sun</name><affiliation><mods:affiliation>Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA.</mods:affiliation></affiliation></author><author><name sortKey="Zhao, Weidong" sort="Zhao, Weidong" uniqKey="Zhao W" first="Weidong" last="Zhao">Weidong Zhao</name><affiliation><mods:affiliation>Northeastern Ohio Universities Colleges of Medicine and Pharmacy, Rootstown, OH 44272, USA.</mods:affiliation></affiliation></author><author><name sortKey="Sharma, Shalabh" sort="Sharma, Shalabh" uniqKey="Sharma S" first="Shalabh" last="Sharma">Shalabh Sharma</name><affiliation><mods:affiliation>Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA.</mods:affiliation></affiliation></author><author><name sortKey="Moran, Mary Ann" sort="Moran, Mary Ann" uniqKey="Moran M" first="Mary 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We employed a comparative metatranscriptomics approach to compare gene transcription patterns between coastal bacterioplankton communities with and without amendments of PUT or SPD, in an effort to understand how bacterial communities and their genes shape polyamine biogeochemistry in the ocean. Statistically different transcript categories in the PUT (25 COG groups) and SPD (23 COG groups) samples, relative to controls that received no amendment (CTRL), indicated that genes encoding the cellular translation machinery and the metabolism of organic nitrogen and carbon became enriched in the community transcriptome when polyamine availability increased. Of the three known pathways for bacterial polyamine degradation, only genes in the transamination pathway were enriched in the PUT and SPD libraries, suggesting that this route dominated polyamine degradation. Taxonomic affiliation of significantly enriched diagnostic genes in the PUT and SPD libraries pointed to roseobacter‐ and SAR11‐affiliated bacteria as the predominant taxa driving transformation in this coastal ocean, although other diverse marine bacterioplankton groups (Gammaproteobacteria, Betaproteobacteria, Actinobacteria and Bacteroidetes) also contributed to polyamine‐related gene transcription.</div></front></TEI><istex><corpusName>wiley</corpusName><author><json:item><name>Xiaozhen Mou</name><affiliations><json:string>Department of Biological Sciences, Kent State University, Kent, OH 44242, USA.</json:string></affiliations></json:item><json:item><name>Maria Vila‐Costa</name><affiliations><json:string>Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA.</json:string></affiliations></json:item><json:item><name>Shulei Sun</name><affiliations><json:string>Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA.</json:string></affiliations></json:item><json:item><name>Weidong Zhao</name><affiliations><json:string>Northeastern Ohio Universities Colleges of Medicine and Pharmacy, Rootstown, OH 44272, USA.</json:string></affiliations></json:item><json:item><name>Shalabh Sharma</name><affiliations><json:string>Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA.</json:string></affiliations></json:item><json:item><name>Mary Ann Moran</name><affiliations><json:string>Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA.</json:string></affiliations></json:item></author><articleId><json:string>EMI4289</json:string></articleId><language><json:string>eng</json:string></language><originalGenre><json:string>shortCommunication</json:string></originalGenre><abstract>The polyamines putrescine (PUT) and spermidine (SPD) are ubiquitous in seawater, but mechanisms that drive the degradation of these important nitrogen sources by marine bacteria remain unclear. 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Taxonomic affiliation of significantly enriched diagnostic genes in the PUT and SPD libraries pointed to roseobacter‐ and SAR11‐affiliated bacteria as the predominant taxa driving transformation in this coastal ocean, although other diverse marine bacterioplankton groups (Gammaproteobacteria, Betaproteobacteria, Actinobacteria and Bacteroidetes) also contributed to polyamine‐related gene transcription.</abstract><qualityIndicators><score>7.134</score><pdfVersion>1.2</pdfVersion><pdfPageSize>595.276 x 782.362 pts</pdfPageSize><refBibsNative>true</refBibsNative><keywordCount>0</keywordCount><abstractCharCount>1469</abstractCharCount><pdfWordCount>4818</pdfWordCount><pdfCharCount>34539</pdfCharCount><pdfPageCount>9</pdfPageCount><abstractWordCount>193</abstractWordCount></qualityIndicators><title>Metatranscriptomic signature of exogenous polyamine utilization by coastal bacterioplankton</title><genre><json:string>brief-communication</json:string></genre><host><volume>3</volume><publisherId><json:string>EMI4</json:string></publisherId><pages><total>9</total><last>806</last><first>798</first></pages><issn><json:string>1758-2229</json:string></issn><issue>6</issue><genre><json:string>journal</json:string></genre><language><json:string>unknown</json:string></language><eissn><json:string>1758-2229</json:string></eissn><title>Environmental Microbiology Reports</title><doi><json:string>10.1111/(ISSN)1758-2229</json:string></doi></host><publicationDate>2011</publicationDate><copyrightDate>2011</copyrightDate><doi><json:string>10.1111/j.1758-2229.2011.00289.x</json:string></doi><id>B317ED09EF7C55D5683C5D3E9FD719D54EFCA893</id><score>0.14125362</score><fulltext><json:item><original>true</original><mimetype>application/pdf</mimetype><extension>pdf</extension><uri>https://api.istex.fr/document/B317ED09EF7C55D5683C5D3E9FD719D54EFCA893/fulltext/pdf</uri></json:item><json:item><original>false</original><mimetype>application/zip</mimetype><extension>zip</extension><uri>https://api.istex.fr/document/B317ED09EF7C55D5683C5D3E9FD719D54EFCA893/fulltext/zip</uri></json:item><istex:fulltextTEI uri="https://api.istex.fr/document/B317ED09EF7C55D5683C5D3E9FD719D54EFCA893/fulltext/tei"><teiHeader><fileDesc><titleStmt><title level="a" type="main" xml:lang="en">Metatranscriptomic signature of exogenous polyamine utilization by coastal bacterioplankton</title></titleStmt><publicationStmt><authority>ISTEX</authority><publisher>Blackwell Publishing Ltd</publisher><pubPlace>Oxford, UK</pubPlace><availability><p>© 2011 Society for Applied Microbiology and Blackwell Publishing Ltd</p></availability><date>2011</date></publicationStmt><sourceDesc><biblStruct type="inbook"><analytic><title level="a" type="main" xml:lang="en">Metatranscriptomic signature of exogenous polyamine utilization by coastal bacterioplankton</title><author xml:id="author-1"><persName><forename type="first">Xiaozhen</forename><surname>Mou</surname></persName><note type="correspondence"><p>Correspondence: E‐mail ; Tel. (+1) 330 672 3625; Fax (+1) 330 672 3713</p></note><affiliation>Department of Biological Sciences, Kent State University, Kent, OH 44242, USA.</affiliation></author><author xml:id="author-2"><persName><forename type="first">Maria</forename><surname>Vila‐Costa</surname></persName><note type="biography">Present addresses: Department of Continental Ecology‐Limnology, Centre d'Estudis Avançats de Blanes‐CSIC, Accés Cala St. Francesc, Blanes, Catalunya, Spain;</note><affiliation>Present addresses: Department of Continental Ecology‐Limnology, Centre d'Estudis Avançats de Blanes‐CSIC, Accés Cala St. Francesc, Blanes, Catalunya, Spain;</affiliation><affiliation>Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA.</affiliation></author><author xml:id="author-3"><persName><forename type="first">Shulei</forename><surname>Sun</surname></persName><note type="biography">University of California San Diego, Center for Research in Biological Systems, La Jolla, CA 92093, USA.</note><affiliation>University of California San Diego, Center for Research in Biological Systems, La Jolla, CA 92093, USA.</affiliation><affiliation>Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA.</affiliation></author><author xml:id="author-4"><persName><forename type="first">Weidong</forename><surname>Zhao</surname></persName><affiliation>Northeastern Ohio Universities Colleges of Medicine and Pharmacy, Rootstown, OH 44272, USA.</affiliation></author><author xml:id="author-5"><persName><forename type="first">Shalabh</forename><surname>Sharma</surname></persName><affiliation>Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA.</affiliation></author><author xml:id="author-6"><persName><forename type="first">Mary Ann</forename><surname>Moran</surname></persName><affiliation>Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA.</affiliation></author></analytic><monogr><title level="j">Environmental Microbiology Reports</title><idno type="pISSN">1758-2229</idno><idno type="eISSN">1758-2229</idno><idno type="DOI">10.1111/(ISSN)1758-2229</idno><imprint><publisher>Blackwell Publishing Ltd</publisher><pubPlace>Oxford, UK</pubPlace><date type="published" when="2011-12"></date><biblScope unit="volume">3</biblScope><biblScope unit="issue">6</biblScope><biblScope unit="page" from="798">798</biblScope><biblScope unit="page" to="806">806</biblScope></imprint></monogr><idno type="istex">B317ED09EF7C55D5683C5D3E9FD719D54EFCA893</idno><idno type="DOI">10.1111/j.1758-2229.2011.00289.x</idno><idno type="ArticleID">EMI4289</idno></biblStruct></sourceDesc></fileDesc><profileDesc><creation><date>2011</date></creation><langUsage><language ident="en">en</language></langUsage><abstract xml:lang="en"><p>The polyamines putrescine (PUT) and spermidine (SPD) are ubiquitous in seawater, but mechanisms that drive the degradation of these important nitrogen sources by marine bacteria remain unclear. We employed a comparative metatranscriptomics approach to compare gene transcription patterns between coastal bacterioplankton communities with and without amendments of PUT or SPD, in an effort to understand how bacterial communities and their genes shape polyamine biogeochemistry in the ocean. Statistically different transcript categories in the PUT (25 COG groups) and SPD (23 COG groups) samples, relative to controls that received no amendment (CTRL), indicated that genes encoding the cellular translation machinery and the metabolism of organic nitrogen and carbon became enriched in the community transcriptome when polyamine availability increased. Of the three known pathways for bacterial polyamine degradation, only genes in the transamination pathway were enriched in the PUT and SPD libraries, suggesting that this route dominated polyamine degradation. Taxonomic affiliation of significantly enriched diagnostic genes in the PUT and SPD libraries pointed to roseobacter‐ and SAR11‐affiliated bacteria as the predominant taxa driving transformation in this coastal ocean, although other diverse marine bacterioplankton groups (Gammaproteobacteria, Betaproteobacteria, Actinobacteria and Bacteroidetes) also contributed to polyamine‐related gene transcription.</p></abstract></profileDesc><revisionDesc><change when="2011-12">Published</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><original>false</original><mimetype>text/plain</mimetype><extension>txt</extension><uri>https://api.istex.fr/document/B317ED09EF7C55D5683C5D3E9FD719D54EFCA893/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)1758-2229</doi><issn type="print">1758-2229</issn><issn type="electronic">1758-2229</issn><idGroup><id type="product" value="EMI4"></id><id type="publisherDivision" value="ST"></id></idGroup><titleGroup><title type="main" sort="ENVIRONMENTAL MICROBIOLOGY REPORTS">Environmental Microbiology Reports</title></titleGroup></publicationMeta><publicationMeta level="part" position="12106"><doi origin="wiley">10.1111/emi4.2011.3.issue-6</doi><numberingGroup><numbering type="journalVolume" number="3">3</numbering><numbering type="journalIssue" number="6">6</numbering></numberingGroup><coverDate startDate="2011-12">December 2011</coverDate></publicationMeta><publicationMeta level="unit" type="shortCommunication" position="21" status="forIssue"><doi origin="wiley">10.1111/j.1758-2229.2011.00289.x</doi><idGroup><id type="unit" value="EMI4289"></id></idGroup><countGroup><count type="pageTotal" number="9"></count></countGroup><titleGroup><title type="tocHeading1">Brief reports</title></titleGroup><copyright>© 2011 Society for Applied Microbiology and Blackwell Publishing Ltd</copyright><eventGroup><event type="xmlConverted" agent="Converter:BPG_TO_WML3G version:3.0 mode:FullText" date="2011-11-14"></event><event type="publishedOnlineEarlyUnpaginated" date="2011-09-19"></event><event type="firstOnline" date="2011-09-19"></event><event type="publishedOnlineFinalForm" date="2011-11-14"></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:4.1.7 mode:FullText,remove_FC" date="2014-10-16"></event></eventGroup><numberingGroup><numbering type="pageFirst" number="798">798</numbering><numbering type="pageLast" number="806">806</numbering></numberingGroup><correspondenceTo> E‐mail <email>xmou@kent.edu</email>; Tel. (+1) 330 672 3625; Fax (+1) 330 672 3713 </correspondenceTo><linkGroup><link type="toTypesetVersion" href="file:EMI4.EMI4289.pdf"></link></linkGroup></publicationMeta><contentMeta><unparsedEditorialHistory>Received 28 February, 2011; accepted 2 August, 2011.</unparsedEditorialHistory><countGroup><count type="figureTotal" number="3"></count><count type="tableTotal" number="2"></count><count type="formulaTotal" number="0"></count><count type="referenceTotal" number="45"></count><count type="wordTotal" number="5545"></count><count type="linksPubMed" number="0"></count><count type="linksCrossRef" number="0"></count></countGroup><titleGroup><title type="main">Metatranscriptomic signature of exogenous polyamine utilization by coastal bacterioplankton</title><title type="shortAuthors">X. Mou <i>et al</i>.</title><title type="short">Polyamine‐transforming genes in marine bacterial communities</title></titleGroup><creators><creator creatorRole="author" xml:id="cr1" affiliationRef="#a1" corresponding="yes"><personName><givenNames>Xiaozhen</givenNames><familyName>Mou</familyName></personName></creator><creator creatorRole="author" xml:id="cr2" affiliationRef="#a2" noteRef="#fn1"><personName><givenNames>Maria</givenNames><familyName>Vila‐Costa</familyName></personName></creator><creator creatorRole="author" xml:id="cr3" affiliationRef="#a2" noteRef="#fn2"><personName><givenNames>Shulei</givenNames><familyName>Sun</familyName></personName></creator><creator creatorRole="author" xml:id="cr4" affiliationRef="#a3"><personName><givenNames>Weidong</givenNames><familyName>Zhao</familyName></personName></creator><creator creatorRole="author" xml:id="cr5" affiliationRef="#a2"><personName><givenNames>Shalabh</givenNames><familyName>Sharma</familyName></personName></creator><creator creatorRole="author" xml:id="cr6" affiliationRef="#a2"><personName><givenNames>Mary Ann</givenNames><familyName>Moran</familyName></personName></creator></creators><affiliationGroup><affiliation xml:id="a1"><unparsedAffiliation>Department of Biological Sciences, Kent State University, Kent, OH 44242, USA.</unparsedAffiliation></affiliation><affiliation xml:id="a2" countryCode="US"><unparsedAffiliation>Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA.</unparsedAffiliation></affiliation><affiliation xml:id="a3" countryCode="US"><unparsedAffiliation>Northeastern Ohio Universities Colleges of Medicine and Pharmacy, Rootstown, OH 44272, USA.</unparsedAffiliation></affiliation></affiliationGroup><supportingInformation><p><b>Fig. S1.</b> Non‐metric multidimensional scaling analysis (MDS) of the composition of PUT, SPD and CTRL libraries based on transcript sequence assignments to COG categories with normalization for size differences between metatranscriptomes.</p><p><b>Fig. S2.</b> Phylogenetic placement of <i>spuC</i> (A) and <i>kauB</i> (B) transcript sequences into reference gene trees built from the Moore Foundation Microbial Genome Sequencing Project (MMGSP) database using the pplacer program (Matsen <i>et al</i>., 2010). The output of gene alignments for reference sequences from pplacer were imported into MEGA 4 (Tamura <i>et al</i>., 2011), where bootstrapped maximum likelihood trees were built. Bootstrap values higher than 50% are indicated at the pplacer branch nodes. The scale bar indicates the amount of genetic change in terms of number of amino acid residue substitutions per site. The sequence IDs of putative genes in the experimental metatranscriptomes are in blue font. NCBI or CAMERA accession numbers of the references sequences are included in brackets following the taxonomic IDs. Out‐groups are shown in gray boxes.</p><p><b>Table S1.</b> Initial environmental and biological conditions in the microcosms.</p><p><b>Table S2.</b> Significantly depleted COG groups (marked with a negative sign) in the PUT and SPD metatranscriptomic libraries relative to CTRL.</p><p><b>Table S3.</b> Twenty‐two diagnostic polyamine genes used in tBLASTn searches of bacterioplankton metatranscriptomic libraries with a bit score cut‐off of > 40. The acetylornithine aminotransferase gene (<i>argD</i>) has a sequence similar to <i>spuC</i> but a different function unrelated to polyamine degradation<i>.</i> To distinguish between these two genes, the blast hits that met the cut‐off criteria for <i>spuC</i> but had a higher bit score against <i>argD</i> were removed from the final list of <i>spuC</i> homologues.</p><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:17582229:media:emi4289:EMI4_289_sm_Fig_S1-2_Tab_S1-3"></mediaResource><caption>Supporting info item</caption></supportingInfoItem></supportingInformation><abstractGroup><abstract type="main" xml:lang="en"><title type="main">Summary</title><p>The polyamines putrescine (PUT) and spermidine (SPD) are ubiquitous in seawater, but mechanisms that drive the degradation of these important nitrogen sources by marine bacteria remain unclear. We employed a comparative metatranscriptomics approach to compare gene transcription patterns between coastal bacterioplankton communities with and without amendments of PUT or SPD, in an effort to understand how bacterial communities and their genes shape polyamine biogeochemistry in the ocean. Statistically different transcript categories in the PUT (25 COG groups) and SPD (23 COG groups) samples, relative to controls that received no amendment (CTRL), indicated that genes encoding the cellular translation machinery and the metabolism of organic nitrogen and carbon became enriched in the community transcriptome when polyamine availability increased. Of the three known pathways for bacterial polyamine degradation, only genes in the transamination pathway were enriched in the PUT and SPD libraries, suggesting that this route dominated polyamine degradation. Taxonomic affiliation of significantly enriched diagnostic genes in the PUT and SPD libraries pointed to roseobacter‐ and SAR11‐affiliated bacteria as the predominant taxa driving transformation in this coastal ocean, although other diverse marine bacterioplankton groups (<i>Gammaproteobacteria</i>, <i>Betaproteobacteria</i>, <i>Actinobacteria</i> and <i>Bacteroidetes</i>) also contributed to polyamine‐related gene transcription.</p></abstract></abstractGroup></contentMeta><noteGroup><note xml:id="fn1"><p>Present addresses: Department of Continental Ecology‐Limnology, Centre d'Estudis Avançats de Blanes‐CSIC, Accés Cala St. Francesc, Blanes, Catalunya, Spain;</p></note><note xml:id="fn2"><p> University of California San Diego, Center for Research in Biological Systems, La Jolla, CA 92093, USA.</p></note></noteGroup></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Metatranscriptomic signature of exogenous polyamine utilization by coastal bacterioplankton</title></titleInfo><titleInfo type="abbreviated" lang="en"><title>Polyamine‐transforming genes in marine bacterial communities</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>Metatranscriptomic signature of exogenous polyamine utilization by coastal bacterioplankton</title></titleInfo><name type="personal"><namePart type="given">Xiaozhen</namePart><namePart type="family">Mou</namePart><affiliation>Department of Biological Sciences, Kent State University, Kent, OH 44242, USA.</affiliation><description>Correspondence: E‐mail ; Tel. (+1) 330 672 3625; Fax (+1) 330 672 3713</description><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Maria</namePart><namePart type="family">Vila‐Costa</namePart><affiliation>Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA.</affiliation><description>Present addresses: Department of Continental Ecology‐Limnology, Centre d'Estudis Avançats de Blanes‐CSIC, Accés Cala St. Francesc, Blanes, Catalunya, Spain;</description><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Shulei</namePart><namePart type="family">Sun</namePart><affiliation>Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA.</affiliation><description>University of California San Diego, Center for Research in Biological Systems, La Jolla, CA 92093, USA.</description><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Weidong</namePart><namePart type="family">Zhao</namePart><affiliation>Northeastern Ohio Universities Colleges of Medicine and Pharmacy, Rootstown, OH 44272, USA.</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Shalabh</namePart><namePart type="family">Sharma</namePart><affiliation>Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA.</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Mary Ann</namePart><namePart type="family">Moran</namePart><affiliation>Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA.</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="brief-communication" displayLabel="shortCommunication"></genre><originInfo><publisher>Blackwell Publishing Ltd</publisher><place><placeTerm type="text">Oxford, UK</placeTerm></place><dateIssued encoding="w3cdtf">2011-12</dateIssued><edition>Received 28 February, 2011; accepted 2 August, 2011.</edition><copyrightDate encoding="w3cdtf">2011</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">2</extent><extent unit="references">45</extent><extent unit="words">5545</extent></physicalDescription><abstract lang="en">The polyamines putrescine (PUT) and spermidine (SPD) are ubiquitous in seawater, but mechanisms that drive the degradation of these important nitrogen sources by marine bacteria remain unclear. We employed a comparative metatranscriptomics approach to compare gene transcription patterns between coastal bacterioplankton communities with and without amendments of PUT or SPD, in an effort to understand how bacterial communities and their genes shape polyamine biogeochemistry in the ocean. Statistically different transcript categories in the PUT (25 COG groups) and SPD (23 COG groups) samples, relative to controls that received no amendment (CTRL), indicated that genes encoding the cellular translation machinery and the metabolism of organic nitrogen and carbon became enriched in the community transcriptome when polyamine availability increased. Of the three known pathways for bacterial polyamine degradation, only genes in the transamination pathway were enriched in the PUT and SPD libraries, suggesting that this route dominated polyamine degradation. Taxonomic affiliation of significantly enriched diagnostic genes in the PUT and SPD libraries pointed to roseobacter‐ and SAR11‐affiliated bacteria as the predominant taxa driving transformation in this coastal ocean, although other diverse marine bacterioplankton groups (Gammaproteobacteria, Betaproteobacteria, Actinobacteria and Bacteroidetes) also contributed to polyamine‐related gene transcription.</abstract><relatedItem type="host"><titleInfo><title>Environmental Microbiology Reports</title></titleInfo><genre type="journal">journal</genre><note type="content"> Fig. S1. Non‐metric multidimensional scaling analysis (MDS) of the composition of PUT, SPD and CTRL libraries based on transcript sequence assignments to COG categories with normalization for size differences between metatranscriptomes. Fig. S2. Phylogenetic placement of spuC (A) and kauB (B) transcript sequences into reference gene trees built from the Moore Foundation Microbial Genome Sequencing Project (MMGSP) database using the pplacer program (Matsen et al., 2010). The output of gene alignments for reference sequences from pplacer were imported into MEGA 4 (Tamura et al., 2011), where bootstrapped maximum likelihood trees were built. Bootstrap values higher than 50% are indicated at the pplacer branch nodes. The scale bar indicates the amount of genetic change in terms of number of amino acid residue substitutions per site. The sequence IDs of putative genes in the experimental metatranscriptomes are in blue font. NCBI or CAMERA accession numbers of the references sequences are included in brackets following the taxonomic IDs. Out‐groups are shown in gray boxes. Table S1. Initial environmental and biological conditions in the microcosms. Table S2. Significantly depleted COG groups (marked with a negative sign) in the PUT and SPD metatranscriptomic libraries relative to CTRL. Table S3. Twenty‐two diagnostic polyamine genes used in tBLASTn searches of bacterioplankton metatranscriptomic libraries with a bit score cut‐off of > 40. The acetylornithine aminotransferase gene (argD) has a sequence similar to spuC but a different function unrelated to polyamine degradation. To distinguish between these two genes, the blast hits that met the cut‐off criteria for spuC but had a higher bit score against argD were removed from the final list of spuC homologues. Fig. S1. Non‐metric multidimensional scaling analysis (MDS) of the composition of PUT, SPD and CTRL libraries based on transcript sequence assignments to COG categories with normalization for size differences between metatranscriptomes. Fig. S2. Phylogenetic placement of spuC (A) and kauB (B) transcript sequences into reference gene trees built from the Moore Foundation Microbial Genome Sequencing Project (MMGSP) database using the pplacer program (Matsen et al., 2010). The output of gene alignments for reference sequences from pplacer were imported into MEGA 4 (Tamura et al., 2011), where bootstrapped maximum likelihood trees were built. Bootstrap values higher than 50% are indicated at the pplacer branch nodes. The scale bar indicates the amount of genetic change in terms of number of amino acid residue substitutions per site. The sequence IDs of putative genes in the experimental metatranscriptomes are in blue font. NCBI or CAMERA accession numbers of the references sequences are included in brackets following the taxonomic IDs. Out‐groups are shown in gray boxes. Table S1. Initial environmental and biological conditions in the microcosms. Table S2. Significantly depleted COG groups (marked with a negative sign) in the PUT and SPD metatranscriptomic libraries relative to CTRL. Table S3. Twenty‐two diagnostic polyamine genes used in tBLASTn searches of bacterioplankton metatranscriptomic libraries with a bit score cut‐off of > 40. The acetylornithine aminotransferase gene (argD) has a sequence similar to spuC but a different function unrelated to polyamine degradation. To distinguish between these two genes, the blast hits that met the cut‐off criteria for spuC but had a higher bit score against argD were removed from the final list of spuC homologues. Fig. S1. Non‐metric multidimensional scaling analysis (MDS) of the composition of PUT, SPD and CTRL libraries based on transcript sequence assignments to COG categories with normalization for size differences between metatranscriptomes. Fig. S2. Phylogenetic placement of spuC (A) and kauB (B) transcript sequences into reference gene trees built from the Moore Foundation Microbial Genome Sequencing Project (MMGSP) database using the pplacer program (Matsen et al., 2010). The output of gene alignments for reference sequences from pplacer were imported into MEGA 4 (Tamura et al., 2011), where bootstrapped maximum likelihood trees were built. Bootstrap values higher than 50% are indicated at the pplacer branch nodes. The scale bar indicates the amount of genetic change in terms of number of amino acid residue substitutions per site. The sequence IDs of putative genes in the experimental metatranscriptomes are in blue font. NCBI or CAMERA accession numbers of the references sequences are included in brackets following the taxonomic IDs. Out‐groups are shown in gray boxes. Table S1. Initial environmental and biological conditions in the microcosms. Table S2. Significantly depleted COG groups (marked with a negative sign) in the PUT and SPD metatranscriptomic libraries relative to CTRL. Table S3. Twenty‐two diagnostic polyamine genes used in tBLASTn searches of bacterioplankton metatranscriptomic libraries with a bit score cut‐off of > 40. The acetylornithine aminotransferase gene (argD) has a sequence similar to spuC but a different function unrelated to polyamine degradation. To distinguish between these two genes, the blast hits that met the cut‐off criteria for spuC but had a higher bit score against argD were removed from the final list of spuC homologues. Fig. S1. Non‐metric multidimensional scaling analysis (MDS) of the composition of PUT, SPD and CTRL libraries based on transcript sequence assignments to COG categories with normalization for size differences between metatranscriptomes. Fig. S2. Phylogenetic placement of spuC (A) and kauB (B) transcript sequences into reference gene trees built from the Moore Foundation Microbial Genome Sequencing Project (MMGSP) database using the pplacer program (Matsen et al., 2010). The output of gene alignments for reference sequences from pplacer were imported into MEGA 4 (Tamura et al., 2011), where bootstrapped maximum likelihood trees were built. Bootstrap values higher than 50% are indicated at the pplacer branch nodes. The scale bar indicates the amount of genetic change in terms of number of amino acid residue substitutions per site. The sequence IDs of putative genes in the experimental metatranscriptomes are in blue font. NCBI or CAMERA accession numbers of the references sequences are included in brackets following the taxonomic IDs. Out‐groups are shown in gray boxes. Table S1. Initial environmental and biological conditions in the microcosms. Table S2. Significantly depleted COG groups (marked with a negative sign) in the PUT and SPD metatranscriptomic libraries relative to CTRL. Table S3. Twenty‐two diagnostic polyamine genes used in tBLASTn searches of bacterioplankton metatranscriptomic libraries with a bit score cut‐off of > 40. The acetylornithine aminotransferase gene (argD) has a sequence similar to spuC but a different function unrelated to polyamine degradation. To distinguish between these two genes, the blast hits that met the cut‐off criteria for spuC but had a higher bit score against argD were removed from the final list of spuC homologues. Fig. S1. Non‐metric multidimensional scaling analysis (MDS) of the composition of PUT, SPD and CTRL libraries based on transcript sequence assignments to COG categories with normalization for size differences between metatranscriptomes. Fig. S2. Phylogenetic placement of spuC (A) and kauB (B) transcript sequences into reference gene trees built from the Moore Foundation Microbial Genome Sequencing Project (MMGSP) database using the pplacer program (Matsen et al., 2010). The output of gene alignments for reference sequences from pplacer were imported into MEGA 4 (Tamura et al., 2011), where bootstrapped maximum likelihood trees were built. Bootstrap values higher than 50% are indicated at the pplacer branch nodes. The scale bar indicates the amount of genetic change in terms of number of amino acid residue substitutions per site. The sequence IDs of putative genes in the experimental metatranscriptomes are in blue font. NCBI or CAMERA accession numbers of the references sequences are included in brackets following the taxonomic IDs. Out‐groups are shown in gray boxes. Table S1. Initial environmental and biological conditions in the microcosms. Table S2. Significantly depleted COG groups (marked with a negative sign) in the PUT and SPD metatranscriptomic libraries relative to CTRL. Table S3. Twenty‐two diagnostic polyamine genes used in tBLASTn searches of bacterioplankton metatranscriptomic libraries with a bit score cut‐off of > 40. The acetylornithine aminotransferase gene (argD) has a sequence similar to spuC but a different function unrelated to polyamine degradation. To distinguish between these two genes, the blast hits that met the cut‐off criteria for spuC but had a higher bit score against argD were removed from the final list of spuC homologues.Supporting Info Item: Supporting info item - </note><identifier type="ISSN">1758-2229</identifier><identifier type="eISSN">1758-2229</identifier><identifier type="DOI">10.1111/(ISSN)1758-2229</identifier><identifier type="PublisherID">EMI4</identifier><part><date>2011</date><detail type="volume"><caption>vol.</caption><number>3</number></detail><detail type="issue"><caption>no.</caption><number>6</number></detail><extent unit="pages"><start>798</start><end>806</end><total>9</total></extent></part></relatedItem><identifier type="istex">B317ED09EF7C55D5683C5D3E9FD719D54EFCA893</identifier><identifier type="DOI">10.1111/j.1758-2229.2011.00289.x</identifier><identifier type="ArticleID">EMI4289</identifier><accessCondition type="use and reproduction" contentType="copyright">© 2011 Society for Applied Microbiology and 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/B317ED09EF7C55D5683C5D3E9FD719D54EFCA893/enrichments/multicat</uri></json:item></enrichments><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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