Weak phylogenetic signal in physiological traits of methane-oxidizing bacteria.
Identifieur interne : 000191 ( Main/Exploration ); précédent : 000190; suivant : 000192Weak phylogenetic signal in physiological traits of methane-oxidizing bacteria.
Auteurs : S. Krause [États-Unis] ; P M Van Bodegom ; W K Cornwell ; P L E. BodelierSource :
- Journal of evolutionary biology [ 1420-9101 ] ; 2014.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Methylococcaceae.
- physiologie : Methylococcaceae.
- Marqueurs génétiques, Phylogenèse, Température.
English descriptors
- KwdEn :
- MESH :
- chemical : Genetic Markers.
- genetics : Methylococcaceae.
- physiology : Methylococcaceae.
- Phylogeny, Temperature.
Abstract
The presence of phylogenetic signal is assumed to be ubiquitous. However, for microorganisms, this may not be true given that they display high physiological flexibility and have fast regeneration. This may result in fundamentally different patterns of resemblance, that is, in variable strength of phylogenetic signal. However, in microbiological inferences, trait similarities and therewith microbial interactions with its environment are mostly assumed to follow evolutionary relatedness. Here, we tested whether indeed a straightforward relationship between relatedness and physiological traits exists for aerobic methane-oxidizing bacteria (MOB). We generated a comprehensive data set that included 30 MOB strains with quantitative physiological trait information. Phylogenetic trees were built from the 16S rRNA gene, a common phylogenetic marker, and the pmoA gene which encodes a subunit of the key enzyme involved in the first step of methane oxidation. We used a Blomberg's K from comparative biology to quantify the strength of phylogenetic signal of physiological traits. Phylogenetic signal was strongest for physiological traits associated with optimal growth pH and temperature indicating that adaptations to habitat are very strongly conserved in MOB. However, those physiological traits that are associated with kinetics of methane oxidation had only weak phylogenetic signals and were more pronounced with the pmoA than with the 16S rRNA gene phylogeny. In conclusion, our results give evidence that approaches based solely on taxonomical information will not yield further advancement on microbial eco-evolutionary interactions with its environment. This is a novel insight on the connection between function and phylogeny within microbes and adds new understanding on the evolution of physiological traits across microbes, plants and animals.
DOI: 10.1111/jeb.12401
PubMed: 24797710
Affiliations:
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Krause</name><affiliation wicri:level="4"><nlm:affiliation>Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands; Department of Chemical Engineering, University of Washington, Seattle, WA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands; Department of Chemical Engineering, University of Washington, Seattle, WA</wicri:regionArea><placeName><region type="state">Washington (État)</region><settlement type="city">Seattle</settlement></placeName><orgName type="university">Université de Washington</orgName></affiliation></author><author><name sortKey="Van Bodegom, P M" sort="Van Bodegom, P M" uniqKey="Van Bodegom P" first="P M" last="Van Bodegom">P M Van Bodegom</name></author><author><name sortKey="Cornwell, W K" sort="Cornwell, W K" uniqKey="Cornwell W" first="W K" last="Cornwell">W K Cornwell</name></author><author><name sortKey="Bodelier, P L E" sort="Bodelier, P L E" uniqKey="Bodelier P" first="P L E" last="Bodelier">P L E. 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Krause</name><affiliation wicri:level="4"><nlm:affiliation>Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands; Department of Chemical Engineering, University of Washington, Seattle, WA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands; Department of Chemical Engineering, University of Washington, Seattle, WA</wicri:regionArea><placeName><region type="state">Washington (État)</region><settlement type="city">Seattle</settlement></placeName><orgName type="university">Université de Washington</orgName></affiliation></author><author><name sortKey="Van Bodegom, P M" sort="Van Bodegom, P M" uniqKey="Van Bodegom P" first="P M" last="Van Bodegom">P M Van Bodegom</name></author><author><name sortKey="Cornwell, W K" sort="Cornwell, W K" uniqKey="Cornwell W" first="W K" last="Cornwell">W K Cornwell</name></author><author><name sortKey="Bodelier, P L E" sort="Bodelier, P L E" uniqKey="Bodelier P" first="P L E" last="Bodelier">P L E. Bodelier</name></author></analytic><series><title level="j">Journal of evolutionary biology</title><idno type="eISSN">1420-9101</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Genetic Markers (MeSH)</term><term>Methylococcaceae (genetics)</term><term>Methylococcaceae (physiology)</term><term>Phylogeny (MeSH)</term><term>Temperature (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Marqueurs génétiques (MeSH)</term><term>Methylococcaceae (génétique)</term><term>Methylococcaceae (physiologie)</term><term>Phylogenèse (MeSH)</term><term>Température (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Genetic Markers</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Methylococcaceae</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Methylococcaceae</term></keywords><keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Methylococcaceae</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Methylococcaceae</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Phylogeny</term><term>Temperature</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Marqueurs génétiques</term><term>Phylogenèse</term><term>Température</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The presence of phylogenetic signal is assumed to be ubiquitous. However, for microorganisms, this may not be true given that they display high physiological flexibility and have fast regeneration. This may result in fundamentally different patterns of resemblance, that is, in variable strength of phylogenetic signal. However, in microbiological inferences, trait similarities and therewith microbial interactions with its environment are mostly assumed to follow evolutionary relatedness. Here, we tested whether indeed a straightforward relationship between relatedness and physiological traits exists for aerobic methane-oxidizing bacteria (MOB). We generated a comprehensive data set that included 30 MOB strains with quantitative physiological trait information. Phylogenetic trees were built from the 16S rRNA gene, a common phylogenetic marker, and the pmoA gene which encodes a subunit of the key enzyme involved in the first step of methane oxidation. We used a Blomberg's K from comparative biology to quantify the strength of phylogenetic signal of physiological traits. Phylogenetic signal was strongest for physiological traits associated with optimal growth pH and temperature indicating that adaptations to habitat are very strongly conserved in MOB. However, those physiological traits that are associated with kinetics of methane oxidation had only weak phylogenetic signals and were more pronounced with the pmoA than with the 16S rRNA gene phylogeny. In conclusion, our results give evidence that approaches based solely on taxonomical information will not yield further advancement on microbial eco-evolutionary interactions with its environment. This is a novel insight on the connection between function and phylogeny within microbes and adds new understanding on the evolution of physiological traits across microbes, plants and animals. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24797710</PMID><DateCompleted><Year>2015</Year><Month>01</Month><Day>14</Day></DateCompleted><DateRevised><Year>2014</Year><Month>06</Month><Day>03</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1420-9101</ISSN><JournalIssue CitedMedium="Internet"><Volume>27</Volume><Issue>6</Issue><PubDate><Year>2014</Year><Month>Jun</Month></PubDate></JournalIssue><Title>Journal of evolutionary biology</Title><ISOAbbreviation>J Evol Biol</ISOAbbreviation></Journal><ArticleTitle>Weak phylogenetic signal in physiological traits of methane-oxidizing bacteria.</ArticleTitle><Pagination><MedlinePgn>1240-7</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/jeb.12401</ELocationID><Abstract><AbstractText>The presence of phylogenetic signal is assumed to be ubiquitous. However, for microorganisms, this may not be true given that they display high physiological flexibility and have fast regeneration. This may result in fundamentally different patterns of resemblance, that is, in variable strength of phylogenetic signal. However, in microbiological inferences, trait similarities and therewith microbial interactions with its environment are mostly assumed to follow evolutionary relatedness. Here, we tested whether indeed a straightforward relationship between relatedness and physiological traits exists for aerobic methane-oxidizing bacteria (MOB). We generated a comprehensive data set that included 30 MOB strains with quantitative physiological trait information. Phylogenetic trees were built from the 16S rRNA gene, a common phylogenetic marker, and the pmoA gene which encodes a subunit of the key enzyme involved in the first step of methane oxidation. We used a Blomberg's K from comparative biology to quantify the strength of phylogenetic signal of physiological traits. Phylogenetic signal was strongest for physiological traits associated with optimal growth pH and temperature indicating that adaptations to habitat are very strongly conserved in MOB. However, those physiological traits that are associated with kinetics of methane oxidation had only weak phylogenetic signals and were more pronounced with the pmoA than with the 16S rRNA gene phylogeny. In conclusion, our results give evidence that approaches based solely on taxonomical information will not yield further advancement on microbial eco-evolutionary interactions with its environment. This is a novel insight on the connection between function and phylogeny within microbes and adds new understanding on the evolution of physiological traits across microbes, plants and animals. </AbstractText><CopyrightInformation>© 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Krause</LastName><ForeName>S</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands; Department of Chemical Engineering, University of Washington, Seattle, WA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>van Bodegom</LastName><ForeName>P M</ForeName><Initials>PM</Initials></Author><Author ValidYN="Y"><LastName>Cornwell</LastName><ForeName>W K</ForeName><Initials>WK</Initials></Author><Author ValidYN="Y"><LastName>Bodelier</LastName><ForeName>P L E</ForeName><Initials>PL</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>05</Month><Day>03</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>J Evol Biol</MedlineTA><NlmUniqueID>8809954</NlmUniqueID><ISSNLinking>1010-061X</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005819">Genetic Markers</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D005819" MajorTopicYN="N">Genetic Markers</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008772" MajorTopicYN="N">Methylococcaceae</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000502" MajorTopicYN="N">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="Y">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013696" MajorTopicYN="N">Temperature</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">horizontal gene transfer</Keyword><Keyword MajorTopicYN="N">methane oxidation</Keyword><Keyword MajorTopicYN="N">microorganisms</Keyword><Keyword MajorTopicYN="N">modelling</Keyword><Keyword MajorTopicYN="N">phylogenomics</Keyword><Keyword MajorTopicYN="N">traits</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2013</Year><Month>10</Month><Day>29</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2014</Year><Month>04</Month><Day>01</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2014</Year><Month>04</Month><Day>04</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>5</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2014</Year><Month>5</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2015</Year><Month>1</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">24797710</ArticleId><ArticleId IdType="doi">10.1111/jeb.12401</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Washington (État)</li></region><settlement><li>Seattle</li></settlement><orgName><li>Université de Washington</li></orgName></list><tree><noCountry><name sortKey="Bodelier, P L E" sort="Bodelier, P L E" uniqKey="Bodelier P" first="P L E" last="Bodelier">P L E. Bodelier</name><name sortKey="Cornwell, W K" sort="Cornwell, W K" uniqKey="Cornwell W" first="W K" last="Cornwell">W K Cornwell</name><name sortKey="Van Bodegom, P M" sort="Van Bodegom, P M" uniqKey="Van Bodegom P" first="P M" last="Van Bodegom">P M Van Bodegom</name></noCountry><country name="États-Unis"><region name="Washington (État)"><name sortKey="Krause, S" sort="Krause, S" uniqKey="Krause S" first="S" last="Krause">S. Krause</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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