Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment.
Identifieur interne : 001C54 ( Main/Exploration ); précédent : 001C53; suivant : 001C55Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment.
Auteurs : Collin M. Timm [États-Unis] ; Alisha G. Campbell [États-Unis] ; Sagar M. Utturkar [États-Unis] ; Se-Ran Jun [États-Unis] ; Rebecca E. Parales [États-Unis] ; Watumesa A. Tan [États-Unis] ; Michael S. Robeson [États-Unis] ; Tse-Yuan S. Lu [États-Unis] ; Sara Jawdy [États-Unis] ; Steven D. Brown [États-Unis] ; David W. Ussery [États-Unis] ; Christopher W. Schadt [États-Unis] ; Gerald A. Tuskan [États-Unis] ; Mitchel J. Doktycz [États-Unis] ; David J. Weston [États-Unis] ; Dale A. Pelletier [États-Unis]Source :
- Frontiers in microbiology [ 1664-302X ] ; 2015.
Abstract
The bacterial microbiota of plants is diverse, with 1000s of operational taxonomic units (OTUs) associated with any individual plant. In this work, we used phenotypic analysis, comparative genomics, and metabolic models to investigate the differences between 19 sequenced Pseudomonas fluorescens strains. These isolates represent a single OTU and were collected from the rhizosphere and endosphere of Populus deltoides. While no traits were exclusive to either endosphere or rhizosphere P. fluorescens isolates, multiple pathways relevant for plant-bacterial interactions are enriched in endosphere isolate genomes. Further, growth phenotypes such as phosphate solubilization, protease activity, denitrification and root growth promotion are biased toward endosphere isolates. Endosphere isolates have significantly more metabolic pathways for plant signaling compounds and an increased metabolic range that includes utilization of energy rich nucleotides and sugars, consistent with endosphere colonization. Rhizosphere P. fluorescens have fewer pathways representative of plant-bacterial interactions but show metabolic bias toward chemical substrates often found in root exudates. This work reveals the diverse functions that may contribute to colonization of the endosphere by bacteria and are enriched among closely related isolates.
DOI: 10.3389/fmicb.2015.01118
PubMed: 26528266
PubMed Central: PMC4604316
Affiliations:
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Timm</name><affiliation wicri:level="2"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author><author><name sortKey="Campbell, Alisha G" sort="Campbell, Alisha G" uniqKey="Campbell A" first="Alisha G" last="Campbell">Alisha G. Campbell</name><affiliation wicri:level="2"><nlm:affiliation>Department of Natural Sciences, Northwest Missouri State University Maryville, MO, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Natural Sciences, Northwest Missouri State University Maryville, MO</wicri:regionArea><placeName><region type="state">Missouri (État)</region></placeName></affiliation></author><author><name sortKey="Utturkar, Sagar M" sort="Utturkar, Sagar M" uniqKey="Utturkar S" first="Sagar M" last="Utturkar">Sagar M. Utturkar</name><affiliation wicri:level="2"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville Knoxville, TN, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville Knoxville, TN</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author><author><name sortKey="Jun, Se Ran" sort="Jun, Se Ran" uniqKey="Jun S" first="Se-Ran" last="Jun">Se-Ran Jun</name><affiliation wicri:level="2"><nlm:affiliation>Joint Institute for Computational Sciences, University of Tennessee, Knoxville Knoxville, TN, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Joint Institute for Computational Sciences, University of Tennessee, Knoxville Knoxville, TN</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author><author><name sortKey="Parales, Rebecca E" sort="Parales, Rebecca E" uniqKey="Parales R" first="Rebecca E" last="Parales">Rebecca E. Parales</name><affiliation wicri:level="2"><nlm:affiliation>Microbiology and Molecular Genetics, University of California, Davis Davis, CA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Microbiology and Molecular Genetics, University of California, Davis Davis, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Tan, Watumesa A" sort="Tan, Watumesa A" uniqKey="Tan W" first="Watumesa A" last="Tan">Watumesa A. Tan</name><affiliation wicri:level="2"><nlm:affiliation>Microbiology and Molecular Genetics, University of California, Davis Davis, CA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Microbiology and Molecular Genetics, University of California, Davis Davis, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Robeson, Michael S" sort="Robeson, Michael S" uniqKey="Robeson M" first="Michael S" last="Robeson">Michael S. Robeson</name><affiliation wicri:level="2"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Fish, Wildlife and Conservation Biology, Colorado State University Fort Collins, CO, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Fish, Wildlife and Conservation Biology, Colorado State University Fort Collins, CO</wicri:regionArea><placeName><region type="state">Colorado</region></placeName></affiliation></author><author><name sortKey="Lu, Tse Yuan S" sort="Lu, Tse Yuan S" uniqKey="Lu T" first="Tse-Yuan S" last="Lu">Tse-Yuan S. Lu</name><affiliation wicri:level="2"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author><author><name sortKey="Jawdy, Sara" sort="Jawdy, Sara" uniqKey="Jawdy S" first="Sara" last="Jawdy">Sara Jawdy</name><affiliation wicri:level="2"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author><author><name sortKey="Brown, Steven D" sort="Brown, Steven D" uniqKey="Brown S" first="Steven D" last="Brown">Steven D. Brown</name><affiliation wicri:level="2"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville Knoxville, TN, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville Knoxville, TN</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author><author><name sortKey="Ussery, David W" sort="Ussery, David W" uniqKey="Ussery D" first="David W" last="Ussery">David W. Ussery</name><affiliation wicri:level="2"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></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="2"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Department of Microbiology, University of Tennessee, Knoxville Knoxville, TN, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Department of Microbiology, University of Tennessee, Knoxville Knoxville, TN</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author><author><name sortKey="Tuskan, Gerald A" sort="Tuskan, Gerald A" uniqKey="Tuskan G" first="Gerald A" last="Tuskan">Gerald A. Tuskan</name><affiliation wicri:level="2"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author><author><name sortKey="Doktycz, Mitchel J" sort="Doktycz, Mitchel J" uniqKey="Doktycz M" first="Mitchel J" last="Doktycz">Mitchel J. Doktycz</name><affiliation wicri:level="2"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author><author><name sortKey="Weston, David J" sort="Weston, David J" uniqKey="Weston D" first="David J" last="Weston">David J. Weston</name><affiliation wicri:level="2"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author><author><name sortKey="Pelletier, Dale A" sort="Pelletier, Dale A" uniqKey="Pelletier D" first="Dale A" last="Pelletier">Dale A. Pelletier</name><affiliation wicri:level="2"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author></analytic><series><title level="j">Frontiers in microbiology</title><idno type="ISSN">1664-302X</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The bacterial microbiota of plants is diverse, with 1000s of operational taxonomic units (OTUs) associated with any individual plant. In this work, we used phenotypic analysis, comparative genomics, and metabolic models to investigate the differences between 19 sequenced Pseudomonas fluorescens strains. These isolates represent a single OTU and were collected from the rhizosphere and endosphere of Populus deltoides. While no traits were exclusive to either endosphere or rhizosphere P. fluorescens isolates, multiple pathways relevant for plant-bacterial interactions are enriched in endosphere isolate genomes. Further, growth phenotypes such as phosphate solubilization, protease activity, denitrification and root growth promotion are biased toward endosphere isolates. Endosphere isolates have significantly more metabolic pathways for plant signaling compounds and an increased metabolic range that includes utilization of energy rich nucleotides and sugars, consistent with endosphere colonization. Rhizosphere P. fluorescens have fewer pathways representative of plant-bacterial interactions but show metabolic bias toward chemical substrates often found in root exudates. This work reveals the diverse functions that may contribute to colonization of the endosphere by bacteria and are enriched among closely related isolates. </div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">26528266</PMID><DateCompleted><Year>2015</Year><Month>11</Month><Day>03</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-302X</ISSN><JournalIssue CitedMedium="Print"><Volume>6</Volume><PubDate><Year>2015</Year></PubDate></JournalIssue><Title>Frontiers in microbiology</Title><ISOAbbreviation>Front Microbiol</ISOAbbreviation></Journal><ArticleTitle>Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment.</ArticleTitle><Pagination><MedlinePgn>1118</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3389/fmicb.2015.01118</ELocationID><Abstract><AbstractText>The bacterial microbiota of plants is diverse, with 1000s of operational taxonomic units (OTUs) associated with any individual plant. In this work, we used phenotypic analysis, comparative genomics, and metabolic models to investigate the differences between 19 sequenced Pseudomonas fluorescens strains. These isolates represent a single OTU and were collected from the rhizosphere and endosphere of Populus deltoides. While no traits were exclusive to either endosphere or rhizosphere P. fluorescens isolates, multiple pathways relevant for plant-bacterial interactions are enriched in endosphere isolate genomes. Further, growth phenotypes such as phosphate solubilization, protease activity, denitrification and root growth promotion are biased toward endosphere isolates. Endosphere isolates have significantly more metabolic pathways for plant signaling compounds and an increased metabolic range that includes utilization of energy rich nucleotides and sugars, consistent with endosphere colonization. Rhizosphere P. fluorescens have fewer pathways representative of plant-bacterial interactions but show metabolic bias toward chemical substrates often found in root exudates. This work reveals the diverse functions that may contribute to colonization of the endosphere by bacteria and are enriched among closely related isolates. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Timm</LastName><ForeName>Collin M</ForeName><Initials>CM</Initials><AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Campbell</LastName><ForeName>Alisha G</ForeName><Initials>AG</Initials><AffiliationInfo><Affiliation>Department of Natural Sciences, Northwest Missouri State University Maryville, MO, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Utturkar</LastName><ForeName>Sagar M</ForeName><Initials>SM</Initials><AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville Knoxville, TN, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jun</LastName><ForeName>Se-Ran</ForeName><Initials>SR</Initials><AffiliationInfo><Affiliation>Joint Institute for Computational Sciences, University of Tennessee, Knoxville Knoxville, TN, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Parales</LastName><ForeName>Rebecca E</ForeName><Initials>RE</Initials><AffiliationInfo><Affiliation>Microbiology and Molecular Genetics, University of California, Davis Davis, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tan</LastName><ForeName>Watumesa A</ForeName><Initials>WA</Initials><AffiliationInfo><Affiliation>Microbiology and Molecular Genetics, University of California, Davis Davis, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Robeson</LastName><ForeName>Michael S</ForeName><Initials>MS</Initials><AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Fish, Wildlife and Conservation Biology, Colorado State University Fort Collins, CO, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lu</LastName><ForeName>Tse-Yuan S</ForeName><Initials>TY</Initials><AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jawdy</LastName><ForeName>Sara</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Brown</LastName><ForeName>Steven D</ForeName><Initials>SD</Initials><AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville Knoxville, TN, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ussery</LastName><ForeName>David W</ForeName><Initials>DW</Initials><AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, 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, USA ; Department of Microbiology, University of Tennessee, Knoxville Knoxville, TN, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tuskan</LastName><ForeName>Gerald A</ForeName><Initials>GA</Initials><AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Doktycz</LastName><ForeName>Mitchel J</ForeName><Initials>MJ</Initials><AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, 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