The Fungal and Bacterial Rhizosphere Microbiome Associated With Grapevine Rootstock Genotypes in Mature and Young Vineyards.
Identifieur interne : 000125 ( Main/Exploration ); précédent : 000124; suivant : 000126The Fungal and Bacterial Rhizosphere Microbiome Associated With Grapevine Rootstock Genotypes in Mature and Young Vineyards.
Auteurs : Carmen Berlanas [Espagne] ; M Nica Berbegal [Espagne] ; Georgina Elena [Espagne] ; Meriem Laidani [Espagne] ; José Félix Cibriain [Espagne] ; Ana Sagües [Espagne] ; David Gramaje [Espagne]Source :
- Frontiers in microbiology [ 1664-302X ] ; 2019.
Abstract
The microbiota colonizing the rhizosphere and the endorhizosphere contribute to plant growth, productivity, carbon sequestration, and phytoremediation. Several studies suggested that different plants types and even genotypes of the same plant species harbor partially different microbiomes. Here, we characterize the rhizosphere bacterial and fungal microbiota across five grapevine rootstock genotypes cultivated in the same soil at two vineyards and sampling dates over 2 years by 16S rRNA gene and ITS high-throughput amplicon sequencing. In addition, we use quantitative PCR (qPCR) approach to measure the relative abundance and dynamic changes of fungal pathogens associated with black-foot disease. The objectives were to (1) unravel the effects of rootstock genotype on microbial communities in the rhizosphere of grapevine and (2) to compare the relative abundances of sequence reads and DNA amount of black-foot disease pathogens. Host genetic control of the microbiome was evident in the rhizosphere of the mature vineyard. Microbiome composition also shifted as year of sampling, and fungal diversity varied with sampling moments. Linear discriminant analysis identified specific bacterial (i.e., Bacillus) and fungal (i.e., Glomus) taxa associated with grapevine rootstocks. Host genotype did not predict any summary metrics of rhizosphere α- and β-diversity in the young vineyard. Regarding black-foot associated pathogens, a significant correlation between sequencing reads and qPCR was observed. In conclusion, grapevine rootstock genotypes in the mature vineyard were associated with different rhizosphere microbiomes. The latter could also have been affected by age of the vineyard, soil properties or field management practices. A more comprehensive study is needed to decipher the cause of the rootstock microbiome selection and the mechanisms by which grapevines are able to shape their associated microbial community. Understanding the vast diversity of bacteria and fungi in the rhizosphere and the interactions between microbiota and grapevine will facilitate the development of future strategies for grapevine protection.
DOI: 10.3389/fmicb.2019.01142
PubMed: 31178845
PubMed Central: PMC6538693
Affiliations:
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Universidad de la Rioja - Gobierno de La Rioja, Logroño, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Instituto de Ciencias de la Vid y del Vino, Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Logroño</wicri:regionArea><wicri:noRegion>Logroño</wicri:noRegion></affiliation></author><author><name sortKey="Berbegal, M Nica" sort="Berbegal, M Nica" uniqKey="Berbegal M" first="M Nica" last="Berbegal">M Nica Berbegal</name><affiliation wicri:level="1"><nlm:affiliation>Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Valencia, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Valencia</wicri:regionArea><wicri:noRegion>Valencia</wicri:noRegion></affiliation></author><author><name sortKey="Elena, Georgina" sort="Elena, Georgina" uniqKey="Elena G" first="Georgina" last="Elena">Georgina Elena</name><affiliation wicri:level="1"><nlm:affiliation>Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Valencia, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Valencia</wicri:regionArea><wicri:noRegion>Valencia</wicri:noRegion></affiliation></author><author><name sortKey="Laidani, Meriem" sort="Laidani, Meriem" uniqKey="Laidani M" first="Meriem" last="Laidani">Meriem Laidani</name><affiliation wicri:level="1"><nlm:affiliation>Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Valencia, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Valencia</wicri:regionArea><wicri:noRegion>Valencia</wicri:noRegion></affiliation></author><author><name sortKey="Cibriain, Jose Felix" sort="Cibriain, Jose Felix" uniqKey="Cibriain J" first="José Félix" last="Cibriain">José Félix Cibriain</name><affiliation wicri:level="1"><nlm:affiliation>EVENA, Sección de Viticultura y Enología del Gobierno de Navarra, Olite, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>EVENA, Sección de Viticultura y Enología del Gobierno de Navarra, Olite</wicri:regionArea><wicri:noRegion>Olite</wicri:noRegion></affiliation></author><author><name sortKey="Sagues, Ana" sort="Sagues, Ana" uniqKey="Sagues A" first="Ana" last="Sagües">Ana Sagües</name><affiliation wicri:level="1"><nlm:affiliation>EVENA, Sección de Viticultura y Enología del Gobierno de Navarra, Olite, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>EVENA, Sección de Viticultura y Enología del Gobierno de Navarra, Olite</wicri:regionArea><wicri:noRegion>Olite</wicri:noRegion></affiliation></author><author><name sortKey="Gramaje, David" sort="Gramaje, David" uniqKey="Gramaje D" first="David" last="Gramaje">David Gramaje</name><affiliation wicri:level="1"><nlm:affiliation>Instituto de Ciencias de la Vid y del Vino, Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Logroño, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Instituto de Ciencias de la Vid y del Vino, Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Logroño</wicri:regionArea><wicri:noRegion>Logroño</wicri:noRegion></affiliation></author></analytic><series><title level="j">Frontiers in microbiology</title><idno type="ISSN">1664-302X</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The microbiota colonizing the rhizosphere and the endorhizosphere contribute to plant growth, productivity, carbon sequestration, and phytoremediation. Several studies suggested that different plants types and even genotypes of the same plant species harbor partially different microbiomes. Here, we characterize the rhizosphere bacterial and fungal microbiota across five grapevine rootstock genotypes cultivated in the same soil at two vineyards and sampling dates over 2 years by 16S rRNA gene and ITS high-throughput amplicon sequencing. In addition, we use quantitative PCR (qPCR) approach to measure the relative abundance and dynamic changes of fungal pathogens associated with black-foot disease. The objectives were to (1) unravel the effects of rootstock genotype on microbial communities in the rhizosphere of grapevine and (2) to compare the relative abundances of sequence reads and DNA amount of black-foot disease pathogens. Host genetic control of the microbiome was evident in the rhizosphere of the mature vineyard. Microbiome composition also shifted as year of sampling, and fungal diversity varied with sampling moments. Linear discriminant analysis identified specific bacterial (i.e., <i>Bacillus</i>) and fungal (i.e., <i>Glomus</i>) taxa associated with grapevine rootstocks. Host genotype did not predict any summary metrics of rhizosphere α- and β-diversity in the young vineyard. Regarding black-foot associated pathogens, a significant correlation between sequencing reads and qPCR was observed. In conclusion, grapevine rootstock genotypes in the mature vineyard were associated with different rhizosphere microbiomes. The latter could also have been affected by age of the vineyard, soil properties or field management practices. A more comprehensive study is needed to decipher the cause of the rootstock microbiome selection and the mechanisms by which grapevines are able to shape their associated microbial community. Understanding the vast diversity of bacteria and fungi in the rhizosphere and the interactions between microbiota and grapevine will facilitate the development of future strategies for grapevine protection.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">31178845</PMID><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>10</Volume><PubDate><Year>2019</Year></PubDate></JournalIssue><Title>Frontiers in microbiology</Title><ISOAbbreviation>Front Microbiol</ISOAbbreviation></Journal><ArticleTitle>The Fungal and Bacterial Rhizosphere Microbiome Associated With Grapevine Rootstock Genotypes in Mature and Young Vineyards.</ArticleTitle><Pagination><MedlinePgn>1142</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3389/fmicb.2019.01142</ELocationID><Abstract><AbstractText>The microbiota colonizing the rhizosphere and the endorhizosphere contribute to plant growth, productivity, carbon sequestration, and phytoremediation. Several studies suggested that different plants types and even genotypes of the same plant species harbor partially different microbiomes. Here, we characterize the rhizosphere bacterial and fungal microbiota across five grapevine rootstock genotypes cultivated in the same soil at two vineyards and sampling dates over 2 years by 16S rRNA gene and ITS high-throughput amplicon sequencing. In addition, we use quantitative PCR (qPCR) approach to measure the relative abundance and dynamic changes of fungal pathogens associated with black-foot disease. The objectives were to (1) unravel the effects of rootstock genotype on microbial communities in the rhizosphere of grapevine and (2) to compare the relative abundances of sequence reads and DNA amount of black-foot disease pathogens. Host genetic control of the microbiome was evident in the rhizosphere of the mature vineyard. Microbiome composition also shifted as year of sampling, and fungal diversity varied with sampling moments. Linear discriminant analysis identified specific bacterial (i.e., <i>Bacillus</i>) and fungal (i.e., <i>Glomus</i>) taxa associated with grapevine rootstocks. Host genotype did not predict any summary metrics of rhizosphere α- and β-diversity in the young vineyard. Regarding black-foot associated pathogens, a significant correlation between sequencing reads and qPCR was observed. In conclusion, grapevine rootstock genotypes in the mature vineyard were associated with different rhizosphere microbiomes. The latter could also have been affected by age of the vineyard, soil properties or field management practices. A more comprehensive study is needed to decipher the cause of the rootstock microbiome selection and the mechanisms by which grapevines are able to shape their associated microbial community. Understanding the vast diversity of bacteria and fungi in the rhizosphere and the interactions between microbiota and grapevine will facilitate the development of future strategies for grapevine protection.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Berlanas</LastName><ForeName>Carmen</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Instituto de Ciencias de la Vid y del Vino, Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Logroño, Spain.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Berbegal</LastName><ForeName>Mónica</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Valencia, Spain.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Elena</LastName><ForeName>Georgina</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Valencia, Spain.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Laidani</LastName><ForeName>Meriem</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Valencia, Spain.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cibriain</LastName><ForeName>José Félix</ForeName><Initials>JF</Initials><AffiliationInfo><Affiliation>EVENA, Sección de Viticultura y Enología del Gobierno de Navarra, Olite, Spain.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sagües</LastName><ForeName>Ana</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>EVENA, Sección de Viticultura y Enología del Gobierno de Navarra, Olite, Spain.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gramaje</LastName><ForeName>David</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Instituto de Ciencias de la Vid y del Vino, Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Logroño, Spain.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>05</Month><Day>22</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Front Microbiol</MedlineTA><NlmUniqueID>101548977</NlmUniqueID><ISSNLinking>1664-302X</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">bacterial and fungal recruitment</Keyword><Keyword MajorTopicYN="N">black-foot disease</Keyword><Keyword MajorTopicYN="N">microbial ecology</Keyword><Keyword MajorTopicYN="N">microbiome</Keyword><Keyword MajorTopicYN="N">rhizosphere</Keyword><Keyword MajorTopicYN="N">rootstock selection</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>09</Month><Day>03</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>05</Month><Day>06</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>6</Month><Day>11</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>6</Month><Day>11</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>6</Month><Day>11</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">31178845</ArticleId><ArticleId IdType="doi">10.3389/fmicb.2019.01142</ArticleId><ArticleId IdType="pmc">PMC6538693</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Microb Ecol. 2001 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