Environmental metabarcoding reveals contrasting microbial communities at two poplar phytomanagement sites.
Identifieur interne : 001892 ( Main/Exploration ); précédent : 001891; suivant : 001893Environmental metabarcoding reveals contrasting microbial communities at two poplar phytomanagement sites.
Auteurs : Julie Foulon [France] ; Cyril Zappelini [France] ; Alexis Durand [France] ; Benoit Valot [France] ; Olivier Girardclos [France] ; Damien Blaudez [France] ; Michel Chalot [France]Source :
- The Science of the total environment [ 1879-1026 ] ; 2016.
Descripteurs français
- KwdFr :
- Bactéries (classification), Champignons (classification), Codage à barres de l'ADN pour la taxonomie (MeSH), Dépollution biologique de l'environnement (MeSH), France (MeSH), Installations d'élimination des déchets (MeSH), Microbiologie du sol (MeSH), Microbiote (MeSH), Mycorhizes (MeSH), Populus (croissance et développement).
- MESH :
- croissance et développement : Populus.
- classification : Bactéries, Champignons, Codage à barres de l'ADN pour la taxonomie, Dépollution biologique de l'environnement, France, Installations d'élimination des déchets, Microbiologie du sol, Microbiote, Mycorhizes.
English descriptors
- KwdEn :
- MESH :
- classification : Bacteria, Fungi.
- growth & development : Populus.
- Biodegradation, Environmental, DNA Barcoding, Taxonomic, France, Microbiota, Mycorrhizae, Soil Microbiology, Waste Disposal Facilities.
Abstract
The aim of the present study is to deepen the current understanding of the microbial communities at two poplar phytomanagement sites to reveal the environmental factors that drive the abundance, diversity and composition of microbial communities. A soil analysis revealed that the two soils displayed contrasting physico-chemical characteristics, with significant lower pH and higher Cd, Zn and Mn CaCl2-extractable fractions at Leforest site, compared with Pierrelaye site. The fungal and bacterial community profiles in the poplar roots and soils were assessed through Illumina MiSeq sequencing. Diversity indices and β-diversity measures illustrated that the root microbial communities were well separated from the soil microbial communities at both sites. A detailed study of the fungal composition showed that Ascomycota dominated the overall fungal communities on poplar soil, the root samples at Pierrelaye, and the unplanted soil at the experimental sites. Conversely, Basidiomycota accounted for a much higher percentage of the fungal community in poplar root samples from the Leforest site. The root bacterial communities were dominated by Alphaproteobacteria and Actinobacteria, and the soil samples were dominated by Alphaproteobacteria and Acidobacteria. The occurrence and dominance of the ectomycorrhizal community at Leforest but not at Pierrelaye is the major feature of our data set. Overall, ectomycorrhizal root symbionts appeared to be highly constrained by soil characteristics at the phytomanagement sites. Our data support the view that mycorrhizal inoculation is needed in highly stressed and nutrient-poor environments.
DOI: 10.1016/j.scitotenv.2016.07.151
PubMed: 27474992
Affiliations:
- France
- Bourgogne-Franche-Comté, Franche-Comté, Grand Est, Lorraine (région)
- Montbéliard, Vandœuvre-lès-Nancy
- Université de Lorraine
Links toward previous steps (curation, corpus...)
Le document en format XML
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Université de Lorraine, Faculté des Sciences et Technologies, BP 70239, 54506 Vandoeuvre-les-Nancy, France. 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Montbéliard</wicri:regionArea><placeName><region type="region" nuts="2">Bourgogne-Franche-Comté</region><region type="old region" nuts="2">Franche-Comté</region><settlement type="city">Montbéliard</settlement></placeName></affiliation></author><author><name sortKey="Zappelini, Cyril" sort="Zappelini, Cyril" uniqKey="Zappelini C" first="Cyril" last="Zappelini">Cyril Zappelini</name><affiliation wicri:level="3"><nlm:affiliation>Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard</wicri:regionArea><placeName><region type="region" nuts="2">Bourgogne-Franche-Comté</region><region type="old region" nuts="2">Franche-Comté</region><settlement type="city">Montbéliard</settlement></placeName></affiliation></author><author><name sortKey="Durand, Alexis" sort="Durand, Alexis" uniqKey="Durand A" first="Alexis" last="Durand">Alexis Durand</name><affiliation wicri:level="3"><nlm:affiliation>Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard</wicri:regionArea><placeName><region type="region" nuts="2">Bourgogne-Franche-Comté</region><region type="old region" nuts="2">Franche-Comté</region><settlement type="city">Montbéliard</settlement></placeName></affiliation></author><author><name sortKey="Valot, Benoit" sort="Valot, Benoit" uniqKey="Valot B" first="Benoit" last="Valot">Benoit Valot</name><affiliation wicri:level="3"><nlm:affiliation>Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard</wicri:regionArea><placeName><region type="region" nuts="2">Bourgogne-Franche-Comté</region><region type="old region" nuts="2">Franche-Comté</region><settlement type="city">Montbéliard</settlement></placeName></affiliation></author><author><name sortKey="Girardclos, Olivier" sort="Girardclos, Olivier" uniqKey="Girardclos O" first="Olivier" last="Girardclos">Olivier Girardclos</name><affiliation wicri:level="3"><nlm:affiliation>Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard</wicri:regionArea><placeName><region type="region" nuts="2">Bourgogne-Franche-Comté</region><region type="old region" nuts="2">Franche-Comté</region><settlement type="city">Montbéliard</settlement></placeName></affiliation></author><author><name sortKey="Blaudez, Damien" sort="Blaudez, Damien" uniqKey="Blaudez D" first="Damien" last="Blaudez">Damien Blaudez</name><affiliation wicri:level="4"><nlm:affiliation>CNRS, LIEC UMR7360, Faculté des Sciences et Technologies, BP70239, 54506 Vandoeuvre-lès-Nancy, France; Université de Lorraine, LIEC UMR7360, Faculté des Sciences et Technologies, BP 70239, 54506 Vandoeuvre-lès-Nancy, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>CNRS, LIEC UMR7360, Faculté des Sciences et Technologies, BP70239, 54506 Vandoeuvre-lès-Nancy, France; Université de Lorraine, LIEC UMR7360, Faculté des Sciences et Technologies, BP 70239, 54506 Vandoeuvre-lès-Nancy</wicri:regionArea><placeName><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region><settlement type="city">Vandœuvre-lès-Nancy</settlement></placeName><orgName type="university">Université de Lorraine</orgName></affiliation></author><author><name sortKey="Chalot, Michel" sort="Chalot, Michel" uniqKey="Chalot M" first="Michel" last="Chalot">Michel Chalot</name><affiliation wicri:level="3"><nlm:affiliation>Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France; Université de Lorraine, Faculté des Sciences et Technologies, BP 70239, 54506 Vandoeuvre-les-Nancy, France. Electronic address: michel.chalot@univ-fcomte.fr.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France; Université de Lorraine, Faculté des Sciences et Technologies, BP 70239, 54506 Vandoeuvre-les-Nancy</wicri:regionArea><placeName><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region><settlement type="city">Vandœuvre-lès-Nancy</settlement></placeName></affiliation></author></analytic><series><title level="j">The Science of the total environment</title><idno type="eISSN">1879-1026</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Bacteria (classification)</term><term>Biodegradation, Environmental (MeSH)</term><term>DNA Barcoding, Taxonomic (MeSH)</term><term>France (MeSH)</term><term>Fungi (classification)</term><term>Microbiota (MeSH)</term><term>Mycorrhizae (MeSH)</term><term>Populus (growth & development)</term><term>Soil Microbiology (MeSH)</term><term>Waste Disposal Facilities (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Bactéries (classification)</term><term>Champignons (classification)</term><term>Codage à barres de l'ADN pour la taxonomie (MeSH)</term><term>Dépollution biologique de l'environnement (MeSH)</term><term>France (MeSH)</term><term>Installations d'élimination des déchets (MeSH)</term><term>Microbiologie du sol (MeSH)</term><term>Microbiote (MeSH)</term><term>Mycorhizes (MeSH)</term><term>Populus (croissance et développement)</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Bacteria</term><term>Fungi</term></keywords><keywords scheme="MESH" qualifier="croissance et développement" xml:lang="fr"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="growth & development" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Biodegradation, Environmental</term><term>DNA Barcoding, Taxonomic</term><term>France</term><term>Microbiota</term><term>Mycorrhizae</term><term>Soil Microbiology</term><term>Waste Disposal Facilities</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="fr"><term>Bactéries</term><term>Champignons</term><term>Codage à barres de l'ADN pour la taxonomie</term><term>Dépollution biologique de l'environnement</term><term>France</term><term>Installations d'élimination des déchets</term><term>Microbiologie du sol</term><term>Microbiote</term><term>Mycorhizes</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The aim of the present study is to deepen the current understanding of the microbial communities at two poplar phytomanagement sites to reveal the environmental factors that drive the abundance, diversity and composition of microbial communities. A soil analysis revealed that the two soils displayed contrasting physico-chemical characteristics, with significant lower pH and higher Cd, Zn and Mn CaCl2-extractable fractions at Leforest site, compared with Pierrelaye site. The fungal and bacterial community profiles in the poplar roots and soils were assessed through Illumina MiSeq sequencing. Diversity indices and β-diversity measures illustrated that the root microbial communities were well separated from the soil microbial communities at both sites. A detailed study of the fungal composition showed that Ascomycota dominated the overall fungal communities on poplar soil, the root samples at Pierrelaye, and the unplanted soil at the experimental sites. Conversely, Basidiomycota accounted for a much higher percentage of the fungal community in poplar root samples from the Leforest site. The root bacterial communities were dominated by Alphaproteobacteria and Actinobacteria, and the soil samples were dominated by Alphaproteobacteria and Acidobacteria. The occurrence and dominance of the ectomycorrhizal community at Leforest but not at Pierrelaye is the major feature of our data set. Overall, ectomycorrhizal root symbionts appeared to be highly constrained by soil characteristics at the phytomanagement sites. Our data support the view that mycorrhizal inoculation is needed in highly stressed and nutrient-poor environments. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">27474992</PMID><DateCompleted><Year>2018</Year><Month>03</Month><Day>21</Day></DateCompleted><DateRevised><Year>2018</Year><Month>03</Month><Day>21</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1879-1026</ISSN><JournalIssue CitedMedium="Internet"><Volume>571</Volume><PubDate><Year>2016</Year><Month>Nov</Month><Day>15</Day></PubDate></JournalIssue><Title>The Science of the total environment</Title><ISOAbbreviation>Sci Total Environ</ISOAbbreviation></Journal><ArticleTitle>Environmental metabarcoding reveals contrasting microbial communities at two poplar phytomanagement sites.</ArticleTitle><Pagination><MedlinePgn>1230-40</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.scitotenv.2016.07.151</ELocationID><ELocationID EIdType="pii" ValidYN="Y">S0048-9697(16)31603-5</ELocationID><Abstract><AbstractText>The aim of the present study is to deepen the current understanding of the microbial communities at two poplar phytomanagement sites to reveal the environmental factors that drive the abundance, diversity and composition of microbial communities. A soil analysis revealed that the two soils displayed contrasting physico-chemical characteristics, with significant lower pH and higher Cd, Zn and Mn CaCl2-extractable fractions at Leforest site, compared with Pierrelaye site. The fungal and bacterial community profiles in the poplar roots and soils were assessed through Illumina MiSeq sequencing. Diversity indices and β-diversity measures illustrated that the root microbial communities were well separated from the soil microbial communities at both sites. A detailed study of the fungal composition showed that Ascomycota dominated the overall fungal communities on poplar soil, the root samples at Pierrelaye, and the unplanted soil at the experimental sites. Conversely, Basidiomycota accounted for a much higher percentage of the fungal community in poplar root samples from the Leforest site. The root bacterial communities were dominated by Alphaproteobacteria and Actinobacteria, and the soil samples were dominated by Alphaproteobacteria and Acidobacteria. The occurrence and dominance of the ectomycorrhizal community at Leforest but not at Pierrelaye is the major feature of our data set. Overall, ectomycorrhizal root symbionts appeared to be highly constrained by soil characteristics at the phytomanagement sites. Our data support the view that mycorrhizal inoculation is needed in highly stressed and nutrient-poor environments. </AbstractText><CopyrightInformation>Copyright © 2016 Elsevier B.V. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Foulon</LastName><ForeName>Julie</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zappelini</LastName><ForeName>Cyril</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Durand</LastName><ForeName>Alexis</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Valot</LastName><ForeName>Benoit</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Girardclos</LastName><ForeName>Olivier</ForeName><Initials>O</Initials><AffiliationInfo><Affiliation>Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Blaudez</LastName><ForeName>Damien</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>CNRS, LIEC UMR7360, Faculté des Sciences et Technologies, BP70239, 54506 Vandoeuvre-lès-Nancy, France; Université de Lorraine, LIEC UMR7360, Faculté des Sciences et Technologies, BP 70239, 54506 Vandoeuvre-lès-Nancy, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chalot</LastName><ForeName>Michel</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France; Université de Lorraine, Faculté des Sciences et Technologies, BP 70239, 54506 Vandoeuvre-les-Nancy, France. Electronic address: michel.chalot@univ-fcomte.fr.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>07</Month><Day>28</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>Sci Total Environ</MedlineTA><NlmUniqueID>0330500</NlmUniqueID><ISSNLinking>0048-9697</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001419" MajorTopicYN="N">Bacteria</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="Y">classification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D001673" MajorTopicYN="N">Biodegradation, Environmental</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D058893" MajorTopicYN="N">DNA Barcoding, Taxonomic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005602" MajorTopicYN="N">France</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005658" MajorTopicYN="N">Fungi</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="Y">classification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D064307" MajorTopicYN="Y">Microbiota</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D038821" MajorTopicYN="N">Mycorrhizae</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000254" MajorTopicYN="N">growth & development</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012988" MajorTopicYN="Y">Soil Microbiology</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D064091" MajorTopicYN="Y">Waste Disposal Facilities</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Bacterial 16S</Keyword><Keyword MajorTopicYN="N">Fungal ITS</Keyword><Keyword MajorTopicYN="N">Illumina MiSeq sequencing</Keyword><Keyword MajorTopicYN="N">Phytomanagement</Keyword><Keyword MajorTopicYN="N">Poplar plantation</Keyword><Keyword MajorTopicYN="N">Trace element</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2016</Year><Month>05</Month><Day>23</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2016</Year><Month>07</Month><Day>20</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2016</Year><Month>07</Month><Day>21</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>8</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>8</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2018</Year><Month>3</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">27474992</ArticleId><ArticleId IdType="pii">S0048-9697(16)31603-5</ArticleId><ArticleId IdType="doi">10.1016/j.scitotenv.2016.07.151</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>France</li></country><region><li>Bourgogne-Franche-Comté</li><li>Franche-Comté</li><li>Grand Est</li><li>Lorraine (région)</li></region><settlement><li>Montbéliard</li><li>Vandœuvre-lès-Nancy</li></settlement><orgName><li>Université de Lorraine</li></orgName></list><tree><country name="France"><region name="Bourgogne-Franche-Comté"><name sortKey="Foulon, Julie" sort="Foulon, Julie" uniqKey="Foulon J" first="Julie" last="Foulon">Julie Foulon</name></region><name sortKey="Blaudez, Damien" sort="Blaudez, Damien" uniqKey="Blaudez D" first="Damien" last="Blaudez">Damien Blaudez</name><name sortKey="Chalot, Michel" sort="Chalot, Michel" uniqKey="Chalot M" first="Michel" last="Chalot">Michel Chalot</name><name sortKey="Durand, Alexis" sort="Durand, Alexis" uniqKey="Durand A" first="Alexis" last="Durand">Alexis Durand</name><name sortKey="Girardclos, Olivier" sort="Girardclos, Olivier" uniqKey="Girardclos O" first="Olivier" last="Girardclos">Olivier Girardclos</name><name sortKey="Valot, Benoit" sort="Valot, Benoit" uniqKey="Valot B" first="Benoit" last="Valot">Benoit Valot</name><name sortKey="Zappelini, Cyril" sort="Zappelini, Cyril" uniqKey="Zappelini C" first="Cyril" last="Zappelini">Cyril Zappelini</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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