Assessment of functional and structural changes of soil fungal and oomycete communities in holm oak declined dehesas through metabarcoding analysis.
Identifieur interne : 000578 ( Main/Exploration ); précédent : 000577; suivant : 000579Assessment of functional and structural changes of soil fungal and oomycete communities in holm oak declined dehesas through metabarcoding analysis.
Auteurs : Francisco J. Ruiz G Mez [Espagne] ; Rafael M. Navarro-Cerrillo [Espagne] ; Alejandro Pérez-De-Luque [Espagne] ; Wolfgang O Wald [Allemagne] ; Andrea Vannini [Italie] ; Carmen Morales-Rodríguez [Allemagne, Italie]Source :
- Scientific reports [ 2045-2322 ] ; 2019.
Descripteurs français
- KwdFr :
- MESH :
- microbiologie : Maladies des plantes, Quercus.
- métabolisme : Champignons, Oomycetes.
- Analyse de regroupements, Biodiversité, Forêts, Microbiologie du sol, Microbiote, Écosystème.
English descriptors
- KwdEn :
- MESH :
- metabolism : Fungi, Oomycetes.
- microbiology : Plant Diseases, Quercus.
- Biodiversity, Cluster Analysis, Ecosystem, Forests, Microbiota, Soil Microbiology.
Abstract
Forest decline is nowadays a major challenge for ecosystem sustainability. Dehesas, which consists of savannah-like mediterranean ecosystems, are threatened by the holm oak decline in the south-west of Iberian Peninsula. Phytophthora cinnamomi is considered the main agent of holm oak root rot, but little is known about the relationship between diversity of soilborne microbial community and the decline syndrome of holm oak. It would be hypothesized that the changes in the structure and functionality of the soil microbiome might influence tree health status through changes in richness and diversity of beneficial organisms such as mycorrhizal species, or fungal plant pathogens such as Fusarium spp. or Alternaria spp. Total DNA of soil samples from declined oak dehesas was extracted and analyzed through metabarcoding techniques, to evaluate the specific composition and diversity of the fungal and oomycete communities and their relationship with the disease symptoms. The fungal community included a wide range of pathogens and abundance of ectomycorrhizal key taxa related with low defoliation degree. Phytophthora cinnamomi and Pythium spiculum did not appear among the most abundant oomycetes, nor were they related directly to defoliation levels. Moreover, a particular taxon belonging to the genus Trichoderma was strongly correlated with the scarcity of pathogenic Phytophthora spp. The diversity and composition of fungal and oomycete communities were related to the severity of the decline symptoms. The metabarcoding study of microbiome represents a powerful tool to develop biocontrol strategies for the management of the holm oak root rot.
DOI: 10.1038/s41598-019-41804-y
PubMed: 30926869
PubMed Central: PMC6441054
Affiliations:
Links toward previous steps (curation, corpus...)
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Hans-Carl-von-Carlowitz-Platz 2, 85354, Freising, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Fachgebiet Pathologie der Waldbäume, Technische Universität München. Hans-Carl-von-Carlowitz-Platz 2, 85354, Freising</wicri:regionArea><wicri:noRegion>85354, Freising</wicri:noRegion><wicri:noRegion>85354, Freising</wicri:noRegion><wicri:noRegion>Freising</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department for Innovation in Biological, Agro-food and Forest systems (DIBAF) -University of Tuscia, Via San Camillo de Lellis snc, Viterbo, 01100, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Department for Innovation in Biological, Agro-food and Forest systems (DIBAF) -University of Tuscia, Via San Camillo de Lellis snc, Viterbo, 01100</wicri:regionArea><wicri:noRegion>01100</wicri:noRegion></affiliation></author></analytic><series><title level="j">Scientific reports</title><idno type="eISSN">2045-2322</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Biodiversity (MeSH)</term><term>Cluster Analysis (MeSH)</term><term>Ecosystem (MeSH)</term><term>Forests (MeSH)</term><term>Fungi (metabolism)</term><term>Microbiota (MeSH)</term><term>Oomycetes (metabolism)</term><term>Plant Diseases (microbiology)</term><term>Quercus (microbiology)</term><term>Soil Microbiology (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de regroupements (MeSH)</term><term>Biodiversité (MeSH)</term><term>Champignons (métabolisme)</term><term>Forêts (MeSH)</term><term>Maladies des plantes (microbiologie)</term><term>Microbiologie du sol (MeSH)</term><term>Microbiote (MeSH)</term><term>Oomycetes (métabolisme)</term><term>Quercus (microbiologie)</term><term>Écosystème (MeSH)</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Fungi</term><term>Oomycetes</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Maladies des plantes</term><term>Quercus</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Plant Diseases</term><term>Quercus</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Champignons</term><term>Oomycetes</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Biodiversity</term><term>Cluster Analysis</term><term>Ecosystem</term><term>Forests</term><term>Microbiota</term><term>Soil Microbiology</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de regroupements</term><term>Biodiversité</term><term>Forêts</term><term>Microbiologie du sol</term><term>Microbiote</term><term>Écosystème</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Forest decline is nowadays a major challenge for ecosystem sustainability. Dehesas, which consists of savannah-like mediterranean ecosystems, are threatened by the holm oak decline in the south-west of Iberian Peninsula. Phytophthora cinnamomi is considered the main agent of holm oak root rot, but little is known about the relationship between diversity of soilborne microbial community and the decline syndrome of holm oak. It would be hypothesized that the changes in the structure and functionality of the soil microbiome might influence tree health status through changes in richness and diversity of beneficial organisms such as mycorrhizal species, or fungal plant pathogens such as Fusarium spp. or Alternaria spp. Total DNA of soil samples from declined oak dehesas was extracted and analyzed through metabarcoding techniques, to evaluate the specific composition and diversity of the fungal and oomycete communities and their relationship with the disease symptoms. The fungal community included a wide range of pathogens and abundance of ectomycorrhizal key taxa related with low defoliation degree. Phytophthora cinnamomi and Pythium spiculum did not appear among the most abundant oomycetes, nor were they related directly to defoliation levels. Moreover, a particular taxon belonging to the genus Trichoderma was strongly correlated with the scarcity of pathogenic Phytophthora spp. The diversity and composition of fungal and oomycete communities were related to the severity of the decline symptoms. The metabarcoding study of microbiome represents a powerful tool to develop biocontrol strategies for the management of the holm oak root rot.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">30926869</PMID><DateCompleted><Year>2020</Year><Month>10</Month><Day>09</Day></DateCompleted><DateRevised><Year>2020</Year><Month>10</Month><Day>09</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">2045-2322</ISSN><JournalIssue CitedMedium="Internet"><Volume>9</Volume><Issue>1</Issue><PubDate><Year>2019</Year><Month>03</Month><Day>29</Day></PubDate></JournalIssue><Title>Scientific reports</Title><ISOAbbreviation>Sci Rep</ISOAbbreviation></Journal><ArticleTitle>Assessment of functional and structural changes of soil fungal and oomycete communities in holm oak declined dehesas through metabarcoding analysis.</ArticleTitle><Pagination><MedlinePgn>5315</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1038/s41598-019-41804-y</ELocationID><Abstract><AbstractText>Forest decline is nowadays a major challenge for ecosystem sustainability. Dehesas, which consists of savannah-like mediterranean ecosystems, are threatened by the holm oak decline in the south-west of Iberian Peninsula. Phytophthora cinnamomi is considered the main agent of holm oak root rot, but little is known about the relationship between diversity of soilborne microbial community and the decline syndrome of holm oak. It would be hypothesized that the changes in the structure and functionality of the soil microbiome might influence tree health status through changes in richness and diversity of beneficial organisms such as mycorrhizal species, or fungal plant pathogens such as Fusarium spp. or Alternaria spp. Total DNA of soil samples from declined oak dehesas was extracted and analyzed through metabarcoding techniques, to evaluate the specific composition and diversity of the fungal and oomycete communities and their relationship with the disease symptoms. The fungal community included a wide range of pathogens and abundance of ectomycorrhizal key taxa related with low defoliation degree. Phytophthora cinnamomi and Pythium spiculum did not appear among the most abundant oomycetes, nor were they related directly to defoliation levels. Moreover, a particular taxon belonging to the genus Trichoderma was strongly correlated with the scarcity of pathogenic Phytophthora spp. The diversity and composition of fungal and oomycete communities were related to the severity of the decline symptoms. The metabarcoding study of microbiome represents a powerful tool to develop biocontrol strategies for the management of the holm oak root rot.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ruiz Gómez</LastName><ForeName>Francisco J</ForeName><Initials>FJ</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-1999-3415</Identifier><AffiliationInfo><Affiliation>Departamento de Ingeniería Forestal, Laboratorio de Ecofisiología de Sistemas Forestales ECSIFOR- ERSAF. Universidad de Córdoba. Campus de Rabanales, Crta. IV, km. 396, E-14071, Córdoba, Spain. g72rugof@uco.es.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Navarro-Cerrillo</LastName><ForeName>Rafael M</ForeName><Initials>RM</Initials><AffiliationInfo><Affiliation>Departamento de Ingeniería Forestal, Laboratorio de Ecofisiología de Sistemas Forestales ECSIFOR- ERSAF. Universidad de Córdoba. Campus de Rabanales, Crta. IV, km. 396, E-14071, Córdoba, Spain.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pérez-de-Luque</LastName><ForeName>Alejandro</ForeName><Initials>A</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-5609-0354</Identifier><AffiliationInfo><Affiliation>Área de Genómica y Biotecnología, IFAPA, Centro Alameda del Obispo, Avda. Menéndez Pidal s/n, Apdo, 3092, 14080, Córdoba, Spain.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Oβwald</LastName><ForeName>Wolfgang</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Fachgebiet Pathologie der Waldbäume, Technische Universität München. Hans-Carl-von-Carlowitz-Platz 2, 85354, Freising, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vannini</LastName><ForeName>Andrea</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department for Innovation in Biological, Agro-food and Forest systems (DIBAF) -University of Tuscia, Via San Camillo de Lellis snc, Viterbo, 01100, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Morales-Rodríguez</LastName><ForeName>Carmen</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Fachgebiet Pathologie der Waldbäume, Technische Universität München. Hans-Carl-von-Carlowitz-Platz 2, 85354, Freising, Germany.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department for Innovation in Biological, Agro-food and Forest systems (DIBAF) -University of Tuscia, Via San Camillo de Lellis snc, Viterbo, 01100, Italy.</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>2019</Year><Month>03</Month><Day>29</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Sci Rep</MedlineTA><NlmUniqueID>101563288</NlmUniqueID><ISSNLinking>2045-2322</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D044822" MajorTopicYN="Y">Biodiversity</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016000" MajorTopicYN="N">Cluster Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017753" MajorTopicYN="N">Ecosystem</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D065928" MajorTopicYN="N">Forests</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005658" MajorTopicYN="N">Fungi</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D064307" MajorTopicYN="Y">Microbiota</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009868" MajorTopicYN="N">Oomycetes</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010935" MajorTopicYN="N">Plant Diseases</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D029963" MajorTopicYN="N">Quercus</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012988" MajorTopicYN="Y">Soil Microbiology</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>12</Month><Day>21</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>03</Month><Day>15</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>3</Month><Day>31</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>3</Month><Day>31</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>10</Month><Day>10</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">30926869</ArticleId><ArticleId IdType="doi">10.1038/s41598-019-41804-y</ArticleId><ArticleId IdType="pii">10.1038/s41598-019-41804-y</ArticleId><ArticleId IdType="pmc">PMC6441054</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Allemagne</li><li>Espagne</li><li>Italie</li></country></list><tree><country name="Espagne"><noRegion><name sortKey="Ruiz G Mez, Francisco J" sort="Ruiz G Mez, Francisco J" uniqKey="Ruiz G Mez F" first="Francisco J" last="Ruiz G Mez">Francisco J. 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Navarro-Cerrillo</name><name sortKey="Perez De Luque, Alejandro" sort="Perez De Luque, Alejandro" uniqKey="Perez De Luque A" first="Alejandro" last="Pérez-De-Luque">Alejandro Pérez-De-Luque</name></country><country name="Allemagne"><noRegion><name sortKey="O Wald, Wolfgang" sort="O Wald, Wolfgang" uniqKey="O Wald W" first="Wolfgang" last="O Wald">Wolfgang O Wald</name></noRegion><name sortKey="Morales Rodriguez, Carmen" sort="Morales Rodriguez, Carmen" uniqKey="Morales Rodriguez C" first="Carmen" last="Morales-Rodríguez">Carmen Morales-Rodríguez</name></country><country name="Italie"><noRegion><name sortKey="Vannini, Andrea" sort="Vannini, Andrea" uniqKey="Vannini A" first="Andrea" last="Vannini">Andrea Vannini</name></noRegion><name sortKey="Morales Rodriguez, Carmen" sort="Morales Rodriguez, Carmen" uniqKey="Morales Rodriguez C" first="Carmen" last="Morales-Rodríguez">Carmen Morales-Rodríguez</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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