Microbial community assembly differs across minerals in a rhizosphere microcosm.
Identifieur interne : 000792 ( Main/Corpus ); précédent : 000791; suivant : 000793Microbial community assembly differs across minerals in a rhizosphere microcosm.
Auteurs : Thea Whitman ; Rachel Neurath ; Adele Perera ; Ilexis Chu-Jacoby ; Daliang Ning ; Jizhong Zhou ; Peter Nico ; Jennifer Pett-Ridge ; Mary FirestoneSource :
- Environmental microbiology [ 1462-2920 ] ; 2018.
English descriptors
- KwdEn :
- MESH :
- chemical , metabolism : Minerals.
- growth & development : Bacteria.
- metabolism : Bacteria, Mycorrhizae.
- microbiology : Avena, Plant Roots.
- Microbiota, Rhizosphere, Soil Microbiology.
Abstract
Mineral-associated microbes drive many critical soil processes, including mineral weathering, soil aggregation and cycling of mineral-sorbed organic matter. To investigate the interactions between soil minerals and microbes in the rhizosphere, we incubated three types of minerals (ferrihydrite, kaolinite and quartz) and a native soil mineral fraction near roots of a common Californian annual grass, Avena barbata, growing in its resident soil. We followed microbial colonization of these minerals for up to 2.5 months - the plant's lifespan. Bacteria and fungi that colonized mineral surfaces during this experiment differed across mineral types and differed from those in the background soil, implying that microbial colonization was the result of processes in addition to passive movement with water to mineral surfaces. Null model analysis revealed that dispersal limitation was a dominant factor structuring mineral-associated microbial communities for all mineral types. Once bacteria arrived at a mineral surface, capacity for rapid growth appeared important, as ribosomal copy number was significantly correlated with relative enrichment on minerals. Glomeromycota (a phylum associated with arbuscular mycorrhizal fungi) appeared to preferentially associate with ferrihydrite surfaces. The mechanisms enabling the colonization of soil minerals may be foundational in shaping the overall soil microbiome composition and development of persistent organic matter in soils.
DOI: 10.1111/1462-2920.14366
PubMed: 30047192
Links to Exploration step
pubmed:30047192Le document en format XML
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Life Science Directorate, Livermore, CA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Perera, Adele" sort="Perera, Adele" uniqKey="Perera A" first="Adele" last="Perera">Adele Perera</name><affiliation><nlm:affiliation>Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Chu Jacoby, Ilexis" sort="Chu Jacoby, Ilexis" uniqKey="Chu Jacoby I" first="Ilexis" last="Chu-Jacoby">Ilexis Chu-Jacoby</name><affiliation><nlm:affiliation>Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Ning, Daliang" sort="Ning, Daliang" uniqKey="Ning D" first="Daliang" last="Ning">Daliang Ning</name><affiliation><nlm:affiliation>Consolidated Core Laboratory, University of Oklahoma, Norman, OK, USA.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Zhou, Jizhong" sort="Zhou, Jizhong" uniqKey="Zhou J" first="Jizhong" last="Zhou">Jizhong Zhou</name><affiliation><nlm:affiliation>Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Lawrence Berkeley National Laboratory, Earth and Environmental 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Firestone</name><affiliation><nlm:affiliation>Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Lawrence Berkeley National Laboratory, Earth and Environmental Sciences, Berkeley, CA, USA.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2018">2018</date><idno type="RBID">pubmed:30047192</idno><idno type="pmid">30047192</idno><idno type="doi">10.1111/1462-2920.14366</idno><idno type="wicri:Area/Main/Corpus">000792</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000792</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Microbial community assembly differs across minerals in a rhizosphere microcosm.</title><author><name sortKey="Whitman, Thea" sort="Whitman, Thea" uniqKey="Whitman T" first="Thea" last="Whitman">Thea Whitman</name><affiliation><nlm:affiliation>Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Soil Science, University of Wisconsin-Madison, Madison, WI, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Neurath, Rachel" sort="Neurath, Rachel" uniqKey="Neurath R" first="Rachel" last="Neurath">Rachel Neurath</name><affiliation><nlm:affiliation>Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Lawrence Livermore National Laboratory, Physical and Life Science Directorate, Livermore, CA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Perera, Adele" sort="Perera, Adele" uniqKey="Perera A" first="Adele" last="Perera">Adele Perera</name><affiliation><nlm:affiliation>Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Chu Jacoby, Ilexis" sort="Chu Jacoby, Ilexis" uniqKey="Chu Jacoby I" first="Ilexis" last="Chu-Jacoby">Ilexis Chu-Jacoby</name><affiliation><nlm:affiliation>Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Ning, Daliang" sort="Ning, Daliang" uniqKey="Ning D" first="Daliang" last="Ning">Daliang Ning</name><affiliation><nlm:affiliation>Consolidated Core Laboratory, University of Oklahoma, Norman, OK, USA.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Zhou, Jizhong" sort="Zhou, Jizhong" uniqKey="Zhou J" first="Jizhong" last="Zhou">Jizhong Zhou</name><affiliation><nlm:affiliation>Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Lawrence Berkeley National Laboratory, Earth and Environmental Sciences, Berkeley, CA, USA.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.</nlm:affiliation></affiliation></author><author><name sortKey="Nico, Peter" sort="Nico, Peter" uniqKey="Nico P" first="Peter" last="Nico">Peter Nico</name><affiliation><nlm:affiliation>Lawrence Berkeley National Laboratory, Earth and Environmental Sciences, Berkeley, CA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Pett Ridge, Jennifer" sort="Pett Ridge, Jennifer" uniqKey="Pett Ridge J" first="Jennifer" last="Pett-Ridge">Jennifer Pett-Ridge</name><affiliation><nlm:affiliation>Lawrence Livermore National Laboratory, Physical and Life Science Directorate, Livermore, CA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Firestone, Mary" sort="Firestone, Mary" uniqKey="Firestone M" first="Mary" last="Firestone">Mary Firestone</name><affiliation><nlm:affiliation>Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Lawrence Berkeley National Laboratory, Earth and Environmental Sciences, Berkeley, CA, USA.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Environmental microbiology</title><idno type="eISSN">1462-2920</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Avena (microbiology)</term><term>Bacteria (growth & development)</term><term>Bacteria (metabolism)</term><term>Microbiota (MeSH)</term><term>Minerals (metabolism)</term><term>Mycorrhizae (metabolism)</term><term>Plant Roots (microbiology)</term><term>Rhizosphere (MeSH)</term><term>Soil Microbiology (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Minerals</term></keywords><keywords scheme="MESH" qualifier="growth & development" xml:lang="en"><term>Bacteria</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Bacteria</term><term>Mycorrhizae</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Avena</term><term>Plant Roots</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Microbiota</term><term>Rhizosphere</term><term>Soil Microbiology</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Mineral-associated microbes drive many critical soil processes, including mineral weathering, soil aggregation and cycling of mineral-sorbed organic matter. To investigate the interactions between soil minerals and microbes in the rhizosphere, we incubated three types of minerals (ferrihydrite, kaolinite and quartz) and a native soil mineral fraction near roots of a common Californian annual grass, Avena barbata, growing in its resident soil. We followed microbial colonization of these minerals for up to 2.5 months - the plant's lifespan. Bacteria and fungi that colonized mineral surfaces during this experiment differed across mineral types and differed from those in the background soil, implying that microbial colonization was the result of processes in addition to passive movement with water to mineral surfaces. Null model analysis revealed that dispersal limitation was a dominant factor structuring mineral-associated microbial communities for all mineral types. Once bacteria arrived at a mineral surface, capacity for rapid growth appeared important, as ribosomal copy number was significantly correlated with relative enrichment on minerals. Glomeromycota (a phylum associated with arbuscular mycorrhizal fungi) appeared to preferentially associate with ferrihydrite surfaces. The mechanisms enabling the colonization of soil minerals may be foundational in shaping the overall soil microbiome composition and development of persistent organic matter in soils.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">30047192</PMID><DateCompleted><Year>2019</Year><Month>09</Month><Day>25</Day></DateCompleted><DateRevised><Year>2019</Year><Month>09</Month><Day>25</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1462-2920</ISSN><JournalIssue CitedMedium="Internet"><Volume>20</Volume><Issue>12</Issue><PubDate><Year>2018</Year><Month>12</Month></PubDate></JournalIssue><Title>Environmental microbiology</Title><ISOAbbreviation>Environ Microbiol</ISOAbbreviation></Journal><ArticleTitle>Microbial community assembly differs across minerals in a rhizosphere microcosm.</ArticleTitle><Pagination><MedlinePgn>4444-4460</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/1462-2920.14366</ELocationID><Abstract><AbstractText>Mineral-associated microbes drive many critical soil processes, including mineral weathering, soil aggregation and cycling of mineral-sorbed organic matter. To investigate the interactions between soil minerals and microbes in the rhizosphere, we incubated three types of minerals (ferrihydrite, kaolinite and quartz) and a native soil mineral fraction near roots of a common Californian annual grass, Avena barbata, growing in its resident soil. We followed microbial colonization of these minerals for up to 2.5 months - the plant's lifespan. Bacteria and fungi that colonized mineral surfaces during this experiment differed across mineral types and differed from those in the background soil, implying that microbial colonization was the result of processes in addition to passive movement with water to mineral surfaces. Null model analysis revealed that dispersal limitation was a dominant factor structuring mineral-associated microbial communities for all mineral types. Once bacteria arrived at a mineral surface, capacity for rapid growth appeared important, as ribosomal copy number was significantly correlated with relative enrichment on minerals. Glomeromycota (a phylum associated with arbuscular mycorrhizal fungi) appeared to preferentially associate with ferrihydrite surfaces. The mechanisms enabling the colonization of soil minerals may be foundational in shaping the overall soil microbiome composition and development of persistent organic matter in soils.</AbstractText><CopyrightInformation>© 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Whitman</LastName><ForeName>Thea</ForeName><Initials>T</Initials><Identifier Source="ORCID">0000-0003-2269-5598</Identifier><AffiliationInfo><Affiliation>Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Soil Science, University of Wisconsin-Madison, Madison, WI, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Neurath</LastName><ForeName>Rachel</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Lawrence Livermore National Laboratory, Physical and Life Science Directorate, Livermore, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Perera</LastName><ForeName>Adele</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chu-Jacoby</LastName><ForeName>Ilexis</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ning</LastName><ForeName>Daliang</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Consolidated Core Laboratory, University of Oklahoma, Norman, OK, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhou</LastName><ForeName>Jizhong</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Lawrence Berkeley National Laboratory, Earth and Environmental Sciences, Berkeley, CA, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nico</LastName><ForeName>Peter</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Lawrence Berkeley National Laboratory, Earth and Environmental Sciences, Berkeley, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pett-Ridge</LastName><ForeName>Jennifer</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Lawrence Livermore National Laboratory, Physical and Life Science Directorate, Livermore, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Firestone</LastName><ForeName>Mary</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Lawrence Berkeley National Laboratory, Earth and Environmental Sciences, Berkeley, CA, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>DE-SC0010570</GrantID><Agency>Biological and Environmental Research</Agency><Country>International</Country></Grant><Grant><Agency>University of California Hopland Research and Extension Center</Agency><Country>International</Country></Grant><Grant><GrantID>DE-AC52-07NA27344</GrantID><Agency>Lawrence Livermore National Laboratory</Agency><Country>International</Country></Grant><Grant><Agency>U.S. Department of Energy</Agency><Country>International</Country></Grant><Grant><Agency>University of Oklahoma</Agency><Country>International</Country></Grant><Grant><Agency>UC Berkeley</Agency><Country>International</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2018</Year><Month>09</Month><Day>10</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Environ Microbiol</MedlineTA><NlmUniqueID>100883692</NlmUniqueID><ISSNLinking>1462-2912</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D008903">Minerals</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D018554" MajorTopicYN="N">Avena</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D001419" MajorTopicYN="N">Bacteria</DescriptorName><QualifierName UI="Q000254" MajorTopicYN="N">growth & development</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D064307" MajorTopicYN="Y">Microbiota</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008903" MajorTopicYN="N">Minerals</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D038821" MajorTopicYN="N">Mycorrhizae</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018517" MajorTopicYN="N">Plant Roots</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D058441" MajorTopicYN="Y">Rhizosphere</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012988" MajorTopicYN="Y">Soil Microbiology</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>01</Month><Day>22</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2018</Year><Month>07</Month><Day>20</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2018</Year><Month>07</Month><Day>20</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2018</Year><Month>7</Month><Day>27</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>9</Month><Day>26</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2018</Year><Month>7</Month><Day>27</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId 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