Survey of High-Affinity H2-Oxidizing Bacteria in Soil Reveals Their Vast Diversity Yet Underrepresentation in Genomic Databases.
Identifieur interne : 001179 ( Main/Exploration ); précédent : 001178; suivant : 001180Survey of High-Affinity H2-Oxidizing Bacteria in Soil Reveals Their Vast Diversity Yet Underrepresentation in Genomic Databases.
Auteurs : Sarah Piché-Choquette [Canada] ; Mondher Khdhiri [Canada] ; Philippe Constant [Canada]Source :
- Microbial ecology [ 1432-184X ] ; 2017.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Bactéries.
- isolement et purification : Bactéries.
- classification : Bactéries, Bases de données génétiques, Gènes bactériens, Microbiologie du sol, Microbiote, Oxydoréduction, Phylogenèse.
English descriptors
- KwdEn :
- MESH :
- classification : Bacteria.
- genetics : Bacteria.
- isolation & purification : Bacteria.
- Databases, Genetic, Genes, Bacterial, Microbiota, Oxidation-Reduction, Phylogeny, Soil Microbiology.
Abstract
While high-affinity H2-oxidizing bacteria (HA-HOB) serve as the main sink of atmospheric H2, the ecology of this specialist functional group is rather unknown due to its recent discovery. The main purpose of our study is to provide the first extensive survey of HA-HOB in farmland, larch, and poplar soils exposed to 0.5 and 10,000 ppmv H2. Using qPCR and qRT-PCR assays along with PCR amplicon high-throughput sequencing of hhyL gene encoding for the large subunit of high-affinity [NiFe]-hydrogenases (HAH), we found that hhyL gene expression ratio explained better variation in measured H2 oxidation rates than HA-HOB species richness. Carbon, nitrogen, pH, and bacterial species richness appeared as the most important drivers of HA-HOB community structure. Our study also highlights the need to cultivate HA-HOB due to the huge gap in current genomic databases.
DOI: 10.1007/s00248-017-1011-1
PubMed: 28623391
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Philippe.Constant@iaf.inrs.ca.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>INRS-Institut Armand-Frappier, 531 Boulevard des Prairies, Laval, Québec, H7V 1B7</wicri:regionArea><wicri:noRegion>H7V 1B7</wicri:noRegion></affiliation></author></analytic><series><title level="j">Microbial ecology</title><idno type="eISSN">1432-184X</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Bacteria (classification)</term><term>Bacteria (genetics)</term><term>Bacteria (isolation & purification)</term><term>Databases, Genetic (MeSH)</term><term>Genes, Bacterial (MeSH)</term><term>Microbiota (MeSH)</term><term>Oxidation-Reduction (MeSH)</term><term>Phylogeny (MeSH)</term><term>Soil Microbiology (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Bactéries (classification)</term><term>Bactéries (génétique)</term><term>Bactéries (isolement et purification)</term><term>Bases de données génétiques (MeSH)</term><term>Gènes bactériens (MeSH)</term><term>Microbiologie du sol (MeSH)</term><term>Microbiote (MeSH)</term><term>Oxydoréduction (MeSH)</term><term>Phylogenèse (MeSH)</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Bacteria</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Bacteria</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Bactéries</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Bacteria</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Bactéries</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Databases, Genetic</term><term>Genes, Bacterial</term><term>Microbiota</term><term>Oxidation-Reduction</term><term>Phylogeny</term><term>Soil Microbiology</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="fr"><term>Bactéries</term><term>Bases de données génétiques</term><term>Gènes bactériens</term><term>Microbiologie du sol</term><term>Microbiote</term><term>Oxydoréduction</term><term>Phylogenèse</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">While high-affinity H<sub>2</sub>-oxidizing bacteria (HA-HOB) serve as the main sink of atmospheric H<sub>2</sub>, the ecology of this specialist functional group is rather unknown due to its recent discovery. The main purpose of our study is to provide the first extensive survey of HA-HOB in farmland, larch, and poplar soils exposed to 0.5 and 10,000 ppmv H<sub>2</sub>. Using qPCR and qRT-PCR assays along with PCR amplicon high-throughput sequencing of hhyL gene encoding for the large subunit of high-affinity [NiFe]-hydrogenases (HAH), we found that hhyL gene expression ratio explained better variation in measured H<sub>2</sub> oxidation rates than HA-HOB species richness. Carbon, nitrogen, pH, and bacterial species richness appeared as the most important drivers of HA-HOB community structure. Our study also highlights the need to cultivate HA-HOB due to the huge gap in current genomic databases.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">28623391</PMID><DateCompleted><Year>2018</Year><Month>05</Month><Day>14</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1432-184X</ISSN><JournalIssue CitedMedium="Internet"><Volume>74</Volume><Issue>4</Issue><PubDate><Year>2017</Year><Month>11</Month></PubDate></JournalIssue><Title>Microbial ecology</Title><ISOAbbreviation>Microb Ecol</ISOAbbreviation></Journal><ArticleTitle>Survey of High-Affinity H<sub>2</sub>-Oxidizing Bacteria in Soil Reveals Their Vast Diversity Yet Underrepresentation in Genomic Databases.</ArticleTitle><Pagination><MedlinePgn>771-775</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s00248-017-1011-1</ELocationID><Abstract><AbstractText>While high-affinity H<sub>2</sub>-oxidizing bacteria (HA-HOB) serve as the main sink of atmospheric H<sub>2</sub>, the ecology of this specialist functional group is rather unknown due to its recent discovery. The main purpose of our study is to provide the first extensive survey of HA-HOB in farmland, larch, and poplar soils exposed to 0.5 and 10,000 ppmv H<sub>2</sub>. Using qPCR and qRT-PCR assays along with PCR amplicon high-throughput sequencing of hhyL gene encoding for the large subunit of high-affinity [NiFe]-hydrogenases (HAH), we found that hhyL gene expression ratio explained better variation in measured H<sub>2</sub> oxidation rates than HA-HOB species richness. Carbon, nitrogen, pH, and bacterial species richness appeared as the most important drivers of HA-HOB community structure. Our study also highlights the need to cultivate HA-HOB due to the huge gap in current genomic databases.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Piché-Choquette</LastName><ForeName>Sarah</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>INRS-Institut Armand-Frappier, 531 Boulevard des Prairies, Laval, Québec, H7V 1B7, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Khdhiri</LastName><ForeName>Mondher</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>INRS-Institut Armand-Frappier, 531 Boulevard des Prairies, Laval, Québec, H7V 1B7, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Constant</LastName><ForeName>Philippe</ForeName><Initials>P</Initials><Identifier Source="ORCID">0000-0003-2739-2801</Identifier><AffiliationInfo><Affiliation>INRS-Institut Armand-Frappier, 531 Boulevard des Prairies, Laval, Québec, H7V 1B7, Canada. 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17;83(11):</Citation><ArticleIdList><ArticleId IdType="pubmed">28363961</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>Canada</li></country></list><tree><country name="Canada"><noRegion><name sortKey="Piche Choquette, Sarah" sort="Piche Choquette, Sarah" uniqKey="Piche Choquette S" first="Sarah" last="Piché-Choquette">Sarah Piché-Choquette</name></noRegion><name sortKey="Constant, Philippe" sort="Constant, Philippe" uniqKey="Constant P" first="Philippe" last="Constant">Philippe Constant</name><name sortKey="Khdhiri, Mondher" sort="Khdhiri, Mondher" uniqKey="Khdhiri M" first="Mondher" last="Khdhiri">Mondher Khdhiri</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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