Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees.
Identifieur interne : 000129 ( Main/Exploration ); précédent : 000128; suivant : 000130Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees.
Auteurs : Bram Beckers [Belgique] ; Michiel Op De Beeck [Belgique, Suède] ; Nele Weyens [Belgique] ; Wout Boerjan [Belgique] ; Jaco Vangronsveld [Belgique]Source :
- Microbiome [ 2049-2618 ] ; 2017.
Descripteurs français
- KwdFr :
- ARN ribosomique 16S (MeSH), Bactéries (classification), Bactéries (isolement et purification), Bactéries (métabolisme), Consortiums microbiens (MeSH), Dépollution biologique de l'environnement (MeSH), Feuilles de plante (microbiologie), Microbiologie du sol (MeSH), Microbiote (génétique), Métabolisme secondaire (MeSH), Populus (microbiologie), Racines de plante (microbiologie), Rhizosphère (MeSH), Séquençage nucléotidique à haut débit (MeSH).
- MESH :
- génétique : Microbiote.
- isolement et purification : Bactéries.
- microbiologie : Feuilles de plante, Populus, Racines de plante.
- métabolisme : Bactéries.
- ARN ribosomique 16S, Bactéries, Consortiums microbiens, Dépollution biologique de l'environnement, Microbiologie du sol, Métabolisme secondaire, Rhizosphère, Séquençage nucléotidique à haut débit.
English descriptors
- KwdEn :
- Bacteria (classification), Bacteria (isolation & purification), Bacteria (metabolism), Biodegradation, Environmental (MeSH), High-Throughput Nucleotide Sequencing (MeSH), Microbial Consortia (MeSH), Microbiota (genetics), Plant Leaves (microbiology), Plant Roots (microbiology), Populus (microbiology), RNA, Ribosomal, 16S (MeSH), Rhizosphere (MeSH), Secondary Metabolism (MeSH), Soil Microbiology (MeSH).
- MESH :
- chemical : RNA, Ribosomal, 16S.
- classification : Bacteria.
- genetics : Microbiota.
- isolation & purification : Bacteria.
- metabolism : Bacteria.
- microbiology : Plant Leaves, Plant Roots, Populus.
- Biodegradation, Environmental, High-Throughput Nucleotide Sequencing, Microbial Consortia, Rhizosphere, Secondary Metabolism, Soil Microbiology.
Abstract
BACKGROUND
The plant microbiome represents one of the key determinants of plant health and productivity by providing a plethora of functional capacities such as access to low-abundance nutrients, suppression of phytopathogens, and resistance to biotic and/or abiotic stressors. However, a robust understanding of the structural composition of the bacterial microbiome present in different plant microenvironments and especially the relationship between below-ground and above-ground communities has remained elusive. In this work, we addressed hypotheses regarding microbiome niche differentiation and structural stability of the bacterial communities within different ecological plant niches.
METHODS
We sampled the rhizosphere soil, root, stem, and leaf endosphere of field-grown poplar trees (Populus tremula × Populus alba) and applied 16S rRNA amplicon pyrosequencing to unravel the bacterial communities associated with the different plant habitats.
RESULTS
We found that the structural variability of rhizosphere microbiomes in field-grown poplar trees (P. tremula × P. alba) is much lower than that of the endosphere microbiomes. Furthermore, our data not only confirm microbiome niche differentiation reports at the rhizosphere soil-root interface but also clearly show additional fine-tuning and adaptation of the endosphere microbiome in the stem and leaf compartment. Each plant compartment represents an unique ecological niche for the bacterial communities. Finally, we identified the core bacterial microbiome associated with the different ecological niches of Populus.
CONCLUSIONS
Understanding the complex host-microbe interactions of Populus could provide the basis for the exploitation of the eukaryote-prokaryote associations in phytoremediation applications, sustainable crop production (bio-energy efficiency), and/or the production of secondary metabolites.
DOI: 10.1186/s40168-017-0241-2
PubMed: 28231859
PubMed Central: PMC5324219
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Diepenbeek</wicri:regionArea><wicri:noRegion>Diepenbeek</wicri:noRegion></affiliation></author></analytic><series><title level="j">Microbiome</title><idno type="eISSN">2049-2618</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 (isolation & purification)</term><term>Bacteria (metabolism)</term><term>Biodegradation, Environmental (MeSH)</term><term>High-Throughput Nucleotide Sequencing (MeSH)</term><term>Microbial Consortia (MeSH)</term><term>Microbiota (genetics)</term><term>Plant Leaves (microbiology)</term><term>Plant Roots (microbiology)</term><term>Populus (microbiology)</term><term>RNA, Ribosomal, 16S (MeSH)</term><term>Rhizosphere (MeSH)</term><term>Secondary Metabolism (MeSH)</term><term>Soil Microbiology (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN ribosomique 16S (MeSH)</term><term>Bactéries (classification)</term><term>Bactéries (isolement et purification)</term><term>Bactéries (métabolisme)</term><term>Consortiums microbiens (MeSH)</term><term>Dépollution biologique de l'environnement (MeSH)</term><term>Feuilles de plante (microbiologie)</term><term>Microbiologie du sol (MeSH)</term><term>Microbiote (génétique)</term><term>Métabolisme secondaire (MeSH)</term><term>Populus (microbiologie)</term><term>Racines de plante (microbiologie)</term><term>Rhizosphère (MeSH)</term><term>Séquençage nucléotidique à haut débit (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>RNA, Ribosomal, 16S</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Bacteria</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Microbiota</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Microbiote</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" qualifier="metabolism" xml:lang="en"><term>Bacteria</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Feuilles de plante</term><term>Populus</term><term>Racines de plante</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Plant Leaves</term><term>Plant Roots</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Bactéries</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Biodegradation, Environmental</term><term>High-Throughput Nucleotide Sequencing</term><term>Microbial Consortia</term><term>Rhizosphere</term><term>Secondary Metabolism</term><term>Soil Microbiology</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ARN ribosomique 16S</term><term>Bactéries</term><term>Consortiums microbiens</term><term>Dépollution biologique de l'environnement</term><term>Microbiologie du sol</term><term>Métabolisme secondaire</term><term>Rhizosphère</term><term>Séquençage nucléotidique à haut débit</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>The plant microbiome represents one of the key determinants of plant health and productivity by providing a plethora of functional capacities such as access to low-abundance nutrients, suppression of phytopathogens, and resistance to biotic and/or abiotic stressors. However, a robust understanding of the structural composition of the bacterial microbiome present in different plant microenvironments and especially the relationship between below-ground and above-ground communities has remained elusive. In this work, we addressed hypotheses regarding microbiome niche differentiation and structural stability of the bacterial communities within different ecological plant niches.</p></div><div type="abstract" xml:lang="en"><p><b>METHODS</b></p><p>We sampled the rhizosphere soil, root, stem, and leaf endosphere of field-grown poplar trees (Populus tremula × Populus alba) and applied 16S rRNA amplicon pyrosequencing to unravel the bacterial communities associated with the different plant habitats.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>We found that the structural variability of rhizosphere microbiomes in field-grown poplar trees (P. tremula × P. alba) is much lower than that of the endosphere microbiomes. Furthermore, our data not only confirm microbiome niche differentiation reports at the rhizosphere soil-root interface but also clearly show additional fine-tuning and adaptation of the endosphere microbiome in the stem and leaf compartment. Each plant compartment represents an unique ecological niche for the bacterial communities. Finally, we identified the core bacterial microbiome associated with the different ecological niches of Populus.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>Understanding the complex host-microbe interactions of Populus could provide the basis for the exploitation of the eukaryote-prokaryote associations in phytoremediation applications, sustainable crop production (bio-energy efficiency), and/or the production of secondary metabolites.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">28231859</PMID><DateCompleted><Year>2017</Year><Month>07</Month><Day>27</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">2049-2618</ISSN><JournalIssue CitedMedium="Internet"><Volume>5</Volume><Issue>1</Issue><PubDate><Year>2017</Year><Month>02</Month><Day>23</Day></PubDate></JournalIssue><Title>Microbiome</Title><ISOAbbreviation>Microbiome</ISOAbbreviation></Journal><ArticleTitle>Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees.</ArticleTitle><Pagination><MedlinePgn>25</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s40168-017-0241-2</ELocationID><Abstract><AbstractText Label="BACKGROUND">The plant microbiome represents one of the key determinants of plant health and productivity by providing a plethora of functional capacities such as access to low-abundance nutrients, suppression of phytopathogens, and resistance to biotic and/or abiotic stressors. However, a robust understanding of the structural composition of the bacterial microbiome present in different plant microenvironments and especially the relationship between below-ground and above-ground communities has remained elusive. In this work, we addressed hypotheses regarding microbiome niche differentiation and structural stability of the bacterial communities within different ecological plant niches.</AbstractText><AbstractText Label="METHODS">We sampled the rhizosphere soil, root, stem, and leaf endosphere of field-grown poplar trees (Populus tremula × Populus alba) and applied 16S rRNA amplicon pyrosequencing to unravel the bacterial communities associated with the different plant habitats.</AbstractText><AbstractText Label="RESULTS">We found that the structural variability of rhizosphere microbiomes in field-grown poplar trees (P. tremula × P. alba) is much lower than that of the endosphere microbiomes. Furthermore, our data not only confirm microbiome niche differentiation reports at the rhizosphere soil-root interface but also clearly show additional fine-tuning and adaptation of the endosphere microbiome in the stem and leaf compartment. Each plant compartment represents an unique ecological niche for the bacterial communities. Finally, we identified the core bacterial microbiome associated with the different ecological niches of Populus.</AbstractText><AbstractText Label="CONCLUSIONS">Understanding the complex host-microbe interactions of Populus could provide the basis for the exploitation of the eukaryote-prokaryote associations in phytoremediation applications, sustainable crop production (bio-energy efficiency), and/or the production of secondary metabolites.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Beckers</LastName><ForeName>Bram</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Centre for Environmental Sciences, Hasselt University, Agoralaan building D, B-3590, Diepenbeek, Belgium. bram.beckers@uhasselt.be.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Op De Beeck</LastName><ForeName>Michiel</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Centre for Environmental Sciences, Hasselt University, Agoralaan building D, B-3590, Diepenbeek, Belgium.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Current address: Department of Biology, Lund University, Ecology Building, SE-22 362, Lund, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Weyens</LastName><ForeName>Nele</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Centre for Environmental Sciences, Hasselt University, Agoralaan building D, B-3590, Diepenbeek, Belgium.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Boerjan</LastName><ForeName>Wout</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Ghent, Belgium.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Plant Biotechnology and Bioinformatics, UGent, Technologiepark 927, B-9052, Ghent, Belgium.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vangronsveld</LastName><ForeName>Jaco</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Centre for Environmental Sciences, Hasselt University, Agoralaan building D, B-3590, Diepenbeek, Belgium.</Affiliation></AffiliationInfo></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>2017</Year><Month>02</Month><Day>23</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Microbiome</MedlineTA><NlmUniqueID>101615147</NlmUniqueID><ISSNLinking>2049-2618</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012336">RNA, Ribosomal, 16S</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001419" MajorTopicYN="N">Bacteria</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000302" MajorTopicYN="Y">isolation & purification</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D001673" MajorTopicYN="N">Biodegradation, Environmental</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059013" MajorTopicYN="N">Microbial Consortia</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D064307" MajorTopicYN="Y">Microbiota</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018515" MajorTopicYN="N">Plant Leaves</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018517" MajorTopicYN="N">Plant Roots</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012336" MajorTopicYN="N">RNA, Ribosomal, 16S</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D058441" MajorTopicYN="Y">Rhizosphere</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D064210" MajorTopicYN="N">Secondary Metabolism</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012988" MajorTopicYN="Y">Soil Microbiology</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">16S rRNA amplicon pyrosequencing</Keyword><Keyword MajorTopicYN="Y">Bacterial microbiome</Keyword><Keyword MajorTopicYN="Y">Endosphere</Keyword><Keyword MajorTopicYN="Y">Microbiome niche differentiation</Keyword><Keyword MajorTopicYN="Y">Populus tremula × Populus alba</Keyword><Keyword MajorTopicYN="Y">Rhizosphere</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2016</Year><Month>10</Month><Day>11</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>02</Month><Day>03</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>2</Month><Day>25</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>2</Month><Day>25</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2017</Year><Month>7</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId 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