Methanogenic Archaea dominate mature heartwood habitats of Eastern Cottonwood (Populus deltoides).
Identifieur interne : 000841 ( Main/Exploration ); précédent : 000840; suivant : 000842Methanogenic Archaea dominate mature heartwood habitats of Eastern Cottonwood (Populus deltoides).
Auteurs : Daniel Z. Yip [États-Unis] ; Allison M. Veach [États-Unis] ; Zamin K. Yang [États-Unis] ; Melissa A. Cregger [États-Unis] ; Christopher W. Schadt [États-Unis]Source :
- The New phytologist [ 1469-8137 ] ; 2019.
Descripteurs français
- KwdFr :
- MESH :
- croissance et développement : Bactéries.
- microbiologie : Bois, Populus.
- métabolisme : Archéobactéries, Méthane.
- Analyse en composantes principales, Biodiversité, Microbiote, Écosystème.
English descriptors
- KwdEn :
- MESH :
- chemical , metabolism : Methane.
- growth & development : Bacteria.
- metabolism : Archaea.
- microbiology : Populus, Wood.
- Biodiversity, Ecosystem, Microbiota, Principal Component Analysis.
Abstract
While recent reports demonstrate that the direct emission of methane from living tree trunks may be a significant terrestrial emission source, there has been debate whether tree emissions are due to transport from soils or produced in the wood environment itself. Reports of methanogens from wood of trees were prominent in the literature 40 years ago but have not been revisited with molecular ecology approaches. We examined communities associated with Populus deltoides using rRNA gene sequence analyses and how these vary with tree and wood properties. Our data indicate that wood environments are dominated by anaerobic microbiomes. Methanogens are prominent in heartwood (mean 34% relative abundance) compared to sapwood environments (13%), and dominant operational taxonomic units (OTUs) were classified as the Methanobacterium sp. Members of the Firmicutes phylum comprised 39% of total sequences and were in 42% greater abundance in sapwood over heartwood niches. Tree diameter was the strongest predictor of methanogen abundance, but wood moisture content and pH were also significant predictors of taxon abundance and overall community composition. Unlike microbiomes of the soil, rhizosphere and phyllosphere, wood associated communities are shaped by unique environmental conditions and may be prominent and overlooked sources of methane emissions in temperate forest systems.
DOI: 10.1111/nph.15346
PubMed: 29978909
Affiliations:
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Yip</name><affiliation wicri:level="1"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831</wicri:regionArea><wicri:noRegion>37831</wicri:noRegion></affiliation></author><author><name sortKey="Veach, Allison M" sort="Veach, Allison M" uniqKey="Veach A" first="Allison M" last="Veach">Allison M. Veach</name><affiliation wicri:level="1"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831</wicri:regionArea><wicri:noRegion>37831</wicri:noRegion></affiliation></author><author><name sortKey="Yang, Zamin K" sort="Yang, Zamin K" uniqKey="Yang Z" first="Zamin K" last="Yang">Zamin K. Yang</name><affiliation wicri:level="1"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831</wicri:regionArea><wicri:noRegion>37831</wicri:noRegion></affiliation></author><author><name sortKey="Cregger, Melissa A" sort="Cregger, Melissa A" uniqKey="Cregger M" first="Melissa A" last="Cregger">Melissa A. Cregger</name><affiliation wicri:level="1"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831</wicri:regionArea><wicri:noRegion>37831</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996</wicri:regionArea><wicri:noRegion>37996</wicri:noRegion></affiliation></author><author><name sortKey="Schadt, Christopher W" sort="Schadt, Christopher W" uniqKey="Schadt C" first="Christopher W" last="Schadt">Christopher W. Schadt</name><affiliation wicri:level="1"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831</wicri:regionArea><wicri:noRegion>37831</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Microbiology, University of Tennessee, Knoxville, TN, 37996</wicri:regionArea><wicri:noRegion>37996</wicri:noRegion></affiliation></author></analytic><series><title level="j">The New phytologist</title><idno type="eISSN">1469-8137</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Archaea (metabolism)</term><term>Bacteria (growth & development)</term><term>Biodiversity (MeSH)</term><term>Ecosystem (MeSH)</term><term>Methane (metabolism)</term><term>Microbiota (MeSH)</term><term>Populus (microbiology)</term><term>Principal Component Analysis (MeSH)</term><term>Wood (microbiology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse en composantes principales (MeSH)</term><term>Archéobactéries (métabolisme)</term><term>Bactéries (croissance et développement)</term><term>Biodiversité (MeSH)</term><term>Bois (microbiologie)</term><term>Microbiote (MeSH)</term><term>Méthane (métabolisme)</term><term>Populus (microbiologie)</term><term>Écosystème (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Methane</term></keywords><keywords scheme="MESH" qualifier="croissance et développement" xml:lang="fr"><term>Bactéries</term></keywords><keywords scheme="MESH" qualifier="growth & development" xml:lang="en"><term>Bacteria</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Archaea</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Bois</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Populus</term><term>Wood</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Archéobactéries</term><term>Méthane</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Biodiversity</term><term>Ecosystem</term><term>Microbiota</term><term>Principal Component Analysis</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse en composantes principales</term><term>Biodiversité</term><term>Microbiote</term><term>Écosystème</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">While recent reports demonstrate that the direct emission of methane from living tree trunks may be a significant terrestrial emission source, there has been debate whether tree emissions are due to transport from soils or produced in the wood environment itself. Reports of methanogens from wood of trees were prominent in the literature 40 years ago but have not been revisited with molecular ecology approaches. We examined communities associated with Populus deltoides using rRNA gene sequence analyses and how these vary with tree and wood properties. Our data indicate that wood environments are dominated by anaerobic microbiomes. Methanogens are prominent in heartwood (mean 34% relative abundance) compared to sapwood environments (13%), and dominant operational taxonomic units (OTUs) were classified as the Methanobacterium sp. Members of the Firmicutes phylum comprised 39% of total sequences and were in 42% greater abundance in sapwood over heartwood niches. Tree diameter was the strongest predictor of methanogen abundance, but wood moisture content and pH were also significant predictors of taxon abundance and overall community composition. Unlike microbiomes of the soil, rhizosphere and phyllosphere, wood associated communities are shaped by unique environmental conditions and may be prominent and overlooked sources of methane emissions in temperate forest systems.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">29978909</PMID><DateCompleted><Year>2020</Year><Month>02</Month><Day>27</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1469-8137</ISSN><JournalIssue CitedMedium="Internet"><Volume>222</Volume><Issue>1</Issue><PubDate><Year>2019</Year><Month>04</Month></PubDate></JournalIssue><Title>The New phytologist</Title><ISOAbbreviation>New Phytol</ISOAbbreviation></Journal><ArticleTitle>Methanogenic Archaea dominate mature heartwood habitats of Eastern Cottonwood (Populus deltoides).</ArticleTitle><Pagination><MedlinePgn>115-121</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/nph.15346</ELocationID><Abstract><AbstractText>While recent reports demonstrate that the direct emission of methane from living tree trunks may be a significant terrestrial emission source, there has been debate whether tree emissions are due to transport from soils or produced in the wood environment itself. Reports of methanogens from wood of trees were prominent in the literature 40 years ago but have not been revisited with molecular ecology approaches. We examined communities associated with Populus deltoides using rRNA gene sequence analyses and how these vary with tree and wood properties. Our data indicate that wood environments are dominated by anaerobic microbiomes. Methanogens are prominent in heartwood (mean 34% relative abundance) compared to sapwood environments (13%), and dominant operational taxonomic units (OTUs) were classified as the Methanobacterium sp. Members of the Firmicutes phylum comprised 39% of total sequences and were in 42% greater abundance in sapwood over heartwood niches. Tree diameter was the strongest predictor of methanogen abundance, but wood moisture content and pH were also significant predictors of taxon abundance and overall community composition. Unlike microbiomes of the soil, rhizosphere and phyllosphere, wood associated communities are shaped by unique environmental conditions and may be prominent and overlooked sources of methane emissions in temperate forest systems.</AbstractText><CopyrightInformation>© 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Yip</LastName><ForeName>Daniel Z</ForeName><Initials>DZ</Initials><AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Veach</LastName><ForeName>Allison M</ForeName><Initials>AM</Initials><AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Zamin K</ForeName><Initials>ZK</Initials><AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cregger</LastName><ForeName>Melissa A</ForeName><Initials>MA</Initials><AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Schadt</LastName><ForeName>Christopher W</ForeName><Initials>CW</Initials><AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>DEAC05-00OR22725</GrantID><Agency>US Department of Energy</Agency><Country>International</Country></Grant><Grant><Agency>Office of Science</Agency><Country>International</Country></Grant><Grant><Agency>Biological and Environmental Research</Agency><Country>International</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2018</Year><Month>07</Month><Day>06</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>New Phytol</MedlineTA><NlmUniqueID>9882884</NlmUniqueID><ISSNLinking>0028-646X</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>OP0UW79H66</RegistryNumber><NameOfSubstance UI="D008697">Methane</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001105" MajorTopicYN="N">Archaea</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D001419" MajorTopicYN="N">Bacteria</DescriptorName><QualifierName UI="Q000254" MajorTopicYN="N">growth & development</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D044822" MajorTopicYN="N">Biodiversity</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017753" MajorTopicYN="Y">Ecosystem</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008697" MajorTopicYN="N">Methane</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D064307" MajorTopicYN="N">Microbiota</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D025341" MajorTopicYN="N">Principal Component Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014934" MajorTopicYN="N">Wood</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Populus deltoides
</Keyword><Keyword MajorTopicYN="Y">Archaea</Keyword><Keyword MajorTopicYN="Y">heartwood</Keyword><Keyword MajorTopicYN="Y">methanogenesis</Keyword><Keyword MajorTopicYN="Y">sapwood</Keyword><Keyword MajorTopicYN="Y">wood microbiome</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>04</Month><Day>18</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2018</Year><Month>06</Month><Day>14</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2018</Year><Month>7</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>2</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2018</Year><Month>7</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">29978909</ArticleId><ArticleId IdType="doi">10.1111/nph.15346</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country></list><tree><country name="États-Unis"><noRegion><name sortKey="Yip, Daniel Z" sort="Yip, Daniel Z" uniqKey="Yip D" first="Daniel Z" last="Yip">Daniel Z. Yip</name></noRegion><name sortKey="Cregger, Melissa A" sort="Cregger, Melissa A" uniqKey="Cregger M" first="Melissa A" last="Cregger">Melissa A. Cregger</name><name sortKey="Cregger, Melissa A" sort="Cregger, Melissa A" uniqKey="Cregger M" first="Melissa A" last="Cregger">Melissa A. Cregger</name><name sortKey="Schadt, Christopher W" sort="Schadt, Christopher W" uniqKey="Schadt C" first="Christopher W" last="Schadt">Christopher W. Schadt</name><name sortKey="Schadt, Christopher W" sort="Schadt, Christopher W" uniqKey="Schadt C" first="Christopher W" last="Schadt">Christopher W. Schadt</name><name sortKey="Veach, Allison M" sort="Veach, Allison M" uniqKey="Veach A" first="Allison M" last="Veach">Allison M. Veach</name><name sortKey="Yang, Zamin K" sort="Yang, Zamin K" uniqKey="Yang Z" first="Zamin K" last="Yang">Zamin K. Yang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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