TreeMicInterV1, Main, Exploration, bibRecord, 000100

Poplar phyllosphere harbors disparate isoprene-degrading bacteria.

Identifieur interne : 000100 ( Main/Exploration ); précédent : 000099; suivant : 000101

Poplar phyllosphere harbors disparate isoprene-degrading bacteria.

Auteurs : Andrew T. Crombie [Royaume-Uni] ; Nasmille L. Larke-Mejia [Royaume-Uni] ; Helen Emery [Royaume-Uni] ; Robin Dawson [Royaume-Uni] ; Jennifer Pratscher [Royaume-Uni] ; Gordon P. Murphy [Royaume-Uni] ; Terry J. Mcgenity [Royaume-Uni] ; J Colin Murrell [Royaume-Uni]

Source :

Proceedings of the National Academy of Sciences of the United States of America [ 1091-6490 ] ; 2018.

RBID : pubmed:30498029

Descripteurs français

KwdFr :
- ADN bactérien (génétique), Butadiènes (métabolisme), Comamonadaceae (classification), Comamonadaceae (génétique), Comamonadaceae (métabolisme), Dépollution biologique de l'environnement (MeSH), Génome bactérien (MeSH), Hémiterpènes (métabolisme), Microbiologie du sol (MeSH), Mixed function oxygenases (génétique), Mixed function oxygenases (métabolisme), Métagénomique (MeSH), Phylogenèse (MeSH), Populus (microbiologie), Populus (métabolisme), Rhodococcus (classification), Rhodococcus (génétique), Rhodococcus (métabolisme).
MESH :
- génétique : ADN bactérien, Comamonadaceae, Mixed function oxygenases, Rhodococcus.
- microbiologie : Populus.
- métabolisme : Butadiènes, Comamonadaceae, Hémiterpènes, Mixed function oxygenases, Populus, Rhodococcus.
- Dépollution biologique de l'environnement, Génome bactérien, Microbiologie du sol, Métagénomique, Phylogenèse.

English descriptors

KwdEn :
- Biodegradation, Environmental (MeSH), Butadienes (metabolism), Comamonadaceae (classification), Comamonadaceae (genetics), Comamonadaceae (metabolism), DNA, Bacterial (genetics), Genome, Bacterial (MeSH), Hemiterpenes (metabolism), Metagenomics (MeSH), Mixed Function Oxygenases (genetics), Mixed Function Oxygenases (metabolism), Phylogeny (MeSH), Populus (metabolism), Populus (microbiology), Rhodococcus (classification), Rhodococcus (genetics), Rhodococcus (metabolism), Soil Microbiology (MeSH).
MESH :
- chemical , genetics : DNA, Bacterial, Mixed Function Oxygenases.
- chemical , metabolism : Butadienes, Hemiterpenes, Mixed Function Oxygenases.
- classification : Comamonadaceae, Rhodococcus.
- genetics : Comamonadaceae, Rhodococcus.
- metabolism : Comamonadaceae, Populus, Rhodococcus.
- microbiology : Populus.
- Biodegradation, Environmental, Genome, Bacterial, Metagenomics, Phylogeny, Soil Microbiology.

Abstract

The climate-active gas isoprene (2-methyl-1,3-butadiene) is released to the atmosphere in huge quantities, almost equaling that of methane, yet we know little about the biological cycling of isoprene in the environment. Although bacteria capable of growth on isoprene as the sole source of carbon and energy have previously been isolated from soils and sediments, no microbiological studies have targeted the major source of isoprene and examined the phyllosphere of isoprene-emitting trees for the presence of degraders of this abundant carbon source. Here, we identified isoprene-degrading bacteria in poplar tree-derived microcosms by DNA stable isotope probing. The genomes of isoprene-degrading taxa were reconstructed, putative isoprene metabolic genes were identified, and isoprene-related gene transcription was analyzed by shotgun metagenomics and metatranscriptomics. Gram-positive bacteria of the genus Rhodococcus proved to be the dominant isoprene degraders, as previously found in soil. However, a wider diversity of isoprene utilizers was also revealed, notably Variovorax, a genus not previously associated with this trait. This finding was confirmed by expression of the isoprene monooxygenase from Variovorax in a heterologous host. A Variovorax strain that could grow on isoprene as the sole carbon and energy source was isolated. Analysis of its genome confirmed that it contained isoprene metabolic genes with an identical layout and high similarity to those identified by DNA-stable isotope probing and metagenomics. This study provides evidence of a wide diversity of isoprene-degrading bacteria in the isoprene-emitting tree phyllosphere and greatly enhances our understanding of the biodegradation of this important metabolite and climate-active gas.

DOI: 10.1073/pnas.1812668115
PubMed: 30498029
PubMed Central: PMC6304962

Affiliations:

Royaume-Uni

Links toward previous steps (curation, corpus...)

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Le document en format XML

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<series><title level="j">Proceedings of the National Academy of Sciences of the United States of America</title>
<idno type="eISSN">1091-6490</idno>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Biodegradation, Environmental (MeSH)</term>
<term>Butadienes (metabolism)</term>
<term>Comamonadaceae (classification)</term>
<term>Comamonadaceae (genetics)</term>
<term>Comamonadaceae (metabolism)</term>
<term>DNA, Bacterial (genetics)</term>
<term>Genome, Bacterial (MeSH)</term>
<term>Hemiterpenes (metabolism)</term>
<term>Metagenomics (MeSH)</term>
<term>Mixed Function Oxygenases (genetics)</term>
<term>Mixed Function Oxygenases (metabolism)</term>
<term>Phylogeny (MeSH)</term>
<term>Populus (metabolism)</term>
<term>Populus (microbiology)</term>
<term>Rhodococcus (classification)</term>
<term>Rhodococcus (genetics)</term>
<term>Rhodococcus (metabolism)</term>
<term>Soil Microbiology (MeSH)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>ADN bactérien (génétique)</term>
<term>Butadiènes (métabolisme)</term>
<term>Comamonadaceae (classification)</term>
<term>Comamonadaceae (génétique)</term>
<term>Comamonadaceae (métabolisme)</term>
<term>Dépollution biologique de l'environnement (MeSH)</term>
<term>Génome bactérien (MeSH)</term>
<term>Hémiterpènes (métabolisme)</term>
<term>Microbiologie du sol (MeSH)</term>
<term>Mixed function oxygenases (génétique)</term>
<term>Mixed function oxygenases (métabolisme)</term>
<term>Métagénomique (MeSH)</term>
<term>Phylogenèse (MeSH)</term>
<term>Populus (microbiologie)</term>
<term>Populus (métabolisme)</term>
<term>Rhodococcus (classification)</term>
<term>Rhodococcus (génétique)</term>
<term>Rhodococcus (métabolisme)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Bacterial</term>
<term>Mixed Function Oxygenases</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Butadienes</term>
<term>Hemiterpenes</term>
<term>Mixed Function Oxygenases</term>
</keywords>
<keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Comamonadaceae</term>
<term>Rhodococcus</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Comamonadaceae</term>
<term>Rhodococcus</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN bactérien</term>
<term>Comamonadaceae</term>
<term>Mixed function oxygenases</term>
<term>Rhodococcus</term>
</keywords>
<keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Comamonadaceae</term>
<term>Populus</term>
<term>Rhodococcus</term>
</keywords>
<keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Populus</term>
</keywords>
<keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Populus</term>
</keywords>
<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Butadiènes</term>
<term>Comamonadaceae</term>
<term>Hémiterpènes</term>
<term>Mixed function oxygenases</term>
<term>Populus</term>
<term>Rhodococcus</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Biodegradation, Environmental</term>
<term>Genome, Bacterial</term>
<term>Metagenomics</term>
<term>Phylogeny</term>
<term>Soil Microbiology</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Dépollution biologique de l'environnement</term>
<term>Génome bactérien</term>
<term>Microbiologie du sol</term>
<term>Métagénomique</term>
<term>Phylogenèse</term>
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<front><div type="abstract" xml:lang="en">The climate-active gas isoprene (2-methyl-1,3-butadiene) is released to the atmosphere in huge quantities, almost equaling that of methane, yet we know little about the biological cycling of isoprene in the environment. Although bacteria capable of growth on isoprene as the sole source of carbon and energy have previously been isolated from soils and sediments, no microbiological studies have targeted the major source of isoprene and examined the phyllosphere of isoprene-emitting trees for the presence of degraders of this abundant carbon source. Here, we identified isoprene-degrading bacteria in poplar tree-derived microcosms by DNA stable isotope probing. The genomes of isoprene-degrading taxa were reconstructed, putative isoprene metabolic genes were identified, and isoprene-related gene transcription was analyzed by shotgun metagenomics and metatranscriptomics. Gram-positive bacteria of the genus <i>Rhodococcus</i>
 proved to be the dominant isoprene degraders, as previously found in soil. However, a wider diversity of isoprene utilizers was also revealed, notably <i>Variovorax</i>
, a genus not previously associated with this trait. This finding was confirmed by expression of the isoprene monooxygenase from <i>Variovorax</i>
 in a heterologous host. A <i>Variovorax</i>
 strain that could grow on isoprene as the sole carbon and energy source was isolated. Analysis of its genome confirmed that it contained isoprene metabolic genes with an identical layout and high similarity to those identified by DNA-stable isotope probing and metagenomics. This study provides evidence of a wide diversity of isoprene-degrading bacteria in the isoprene-emitting tree phyllosphere and greatly enhances our understanding of the biodegradation of this important metabolite and climate-active gas.</div>
</front>
</TEI>
<pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">30498029</PMID>
<DateCompleted><Year>2019</Year>
<Month>02</Month>
<Day>19</Day>
</DateCompleted>
<DateRevised><Year>2020</Year>
<Month>02</Month>
<Day>25</Day>
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<Issue>51</Issue>
<PubDate><Year>2018</Year>
<Month>12</Month>
<Day>18</Day>
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<Title>Proceedings of the National Academy of Sciences of the United States of America</Title>
<ISOAbbreviation>Proc Natl Acad Sci U S A</ISOAbbreviation>
</Journal>
<ArticleTitle>Poplar phyllosphere harbors disparate isoprene-degrading bacteria.</ArticleTitle>
<Pagination><MedlinePgn>13081-13086</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1073/pnas.1812668115</ELocationID>
<Abstract><AbstractText>The climate-active gas isoprene (2-methyl-1,3-butadiene) is released to the atmosphere in huge quantities, almost equaling that of methane, yet we know little about the biological cycling of isoprene in the environment. Although bacteria capable of growth on isoprene as the sole source of carbon and energy have previously been isolated from soils and sediments, no microbiological studies have targeted the major source of isoprene and examined the phyllosphere of isoprene-emitting trees for the presence of degraders of this abundant carbon source. Here, we identified isoprene-degrading bacteria in poplar tree-derived microcosms by DNA stable isotope probing. The genomes of isoprene-degrading taxa were reconstructed, putative isoprene metabolic genes were identified, and isoprene-related gene transcription was analyzed by shotgun metagenomics and metatranscriptomics. Gram-positive bacteria of the genus <i>Rhodococcus</i>
 proved to be the dominant isoprene degraders, as previously found in soil. However, a wider diversity of isoprene utilizers was also revealed, notably <i>Variovorax</i>
, a genus not previously associated with this trait. This finding was confirmed by expression of the isoprene monooxygenase from <i>Variovorax</i>
 in a heterologous host. A <i>Variovorax</i>
 strain that could grow on isoprene as the sole carbon and energy source was isolated. Analysis of its genome confirmed that it contained isoprene metabolic genes with an identical layout and high similarity to those identified by DNA-stable isotope probing and metagenomics. This study provides evidence of a wide diversity of isoprene-degrading bacteria in the isoprene-emitting tree phyllosphere and greatly enhances our understanding of the biodegradation of this important metabolite and climate-active gas.</AbstractText>
<CopyrightInformation>Copyright © 2018 the Author(s). Published by PNAS.</CopyrightInformation>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Crombie</LastName>
<ForeName>Andrew T</ForeName>
<Initials>AT</Initials>
<Identifier Source="ORCID">0000-0002-8577-2602</Identifier>
<AffiliationInfo><Affiliation>School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom; a.crombie@uea.ac.uk.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Larke-Mejia</LastName>
<ForeName>Nasmille L</ForeName>
<Initials>NL</Initials>
<AffiliationInfo><Affiliation>School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Emery</LastName>
<ForeName>Helen</ForeName>
<Initials>H</Initials>
<AffiliationInfo><Affiliation>School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Dawson</LastName>
<ForeName>Robin</ForeName>
<Initials>R</Initials>
<AffiliationInfo><Affiliation>School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Pratscher</LastName>
<ForeName>Jennifer</ForeName>
<Initials>J</Initials>
<AffiliationInfo><Affiliation>Lyell Centre, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Murphy</LastName>
<ForeName>Gordon P</ForeName>
<Initials>GP</Initials>
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</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>McGenity</LastName>
<ForeName>Terry J</ForeName>
<Initials>TJ</Initials>
<AffiliationInfo><Affiliation>School of Biological Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Murrell</LastName>
<ForeName>J Colin</ForeName>
<Initials>JC</Initials>
<AffiliationInfo><Affiliation>School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom.</Affiliation>
</AffiliationInfo>
</Author>
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	Serveur d'exploration sur les interactions arbre microorganisme
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Poplar phyllosphere harbors disparate isoprene-degrading bacteria.

Poplar phyllosphere harbors disparate isoprene-degrading bacteria.

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