The contribution of DNA metabarcoding to fungal conservation: diversity assessment, habitat partitioning and mapping red-listed fungi in protected coastal Salix repens communities in the Netherlands.
Identifieur interne : 001091 ( Main/Curation ); précédent : 001090; suivant : 001092The contribution of DNA metabarcoding to fungal conservation: diversity assessment, habitat partitioning and mapping red-listed fungi in protected coastal Salix repens communities in the Netherlands.
Auteurs : J Zsef Geml [Pays-Bas] ; Barbara Gravendeel [Pays-Bas] ; Kristiaan J. Van Der Gaag [Pays-Bas] ; Manon Neilen [Pays-Bas] ; Youri Lammers [Pays-Bas] ; Niels Raes [Pays-Bas] ; Tatiana A. Semenova [Pays-Bas] ; Peter De Knijff [Pays-Bas] ; Machiel E. Noordeloos [Pays-Bas]Source :
- PloS one [ 1932-6203 ] ; 2014.
Descripteurs français
- KwdFr :
- ADN fongique (génétique), Ascomycota (classification), Ascomycota (génétique), Biodiversité (MeSH), Codage à barres de l'ADN pour la taxonomie (MeSH), Conservation des ressources naturelles (MeSH), Espaceur de l'ADN ribosomique (génétique), Microbiologie du sol (MeSH), Pays-Bas (MeSH), Salix (microbiologie), Séquence nucléotidique (MeSH), Écosystème (MeSH).
- MESH :
- Wicri :
- geographic : Pays-Bas.
English descriptors
- KwdEn :
- Ascomycota (classification), Ascomycota (genetics), Base Sequence (MeSH), Biodiversity (MeSH), Conservation of Natural Resources (MeSH), DNA Barcoding, Taxonomic (MeSH), DNA, Fungal (genetics), DNA, Ribosomal Spacer (genetics), Ecosystem (MeSH), Netherlands (MeSH), Salix (microbiology), Soil Microbiology (MeSH).
- MESH :
- chemical , genetics : DNA, Fungal, DNA, Ribosomal Spacer.
- geographic : Netherlands.
- classification : Ascomycota.
- genetics : Ascomycota.
- microbiology : Salix.
- Base Sequence, Biodiversity, Conservation of Natural Resources, DNA Barcoding, Taxonomic, Ecosystem, Soil Microbiology.
Abstract
Western European coastal sand dunes are highly important for nature conservation. Communities of the creeping willow (Salix repens) represent one of the most characteristic and diverse vegetation types in the dunes. We report here the results of the first kingdom-wide fungal diversity assessment in S. repens coastal dune vegetation. We carried out massively parallel pyrosequencing of ITS rDNA from soil samples taken at ten sites in an extended area of joined nature reserves located along the North Sea coast of the Netherlands, representing habitats with varying soil pH and moisture levels. Fungal communities in Salix repens beds are highly diverse and we detected 1211 non-singleton fungal 97% sequence similarity OTUs after analyzing 688,434 ITS2 rDNA sequences. Our comparison along a north-south transect indicated strong correlation between soil pH and fungal community composition. The total fungal richness and the number OTUs of most fungal taxonomic groups negatively correlated with higher soil pH, with some exceptions. With regard to ecological groups, dark-septate endophytic fungi were more diverse in acidic soils, ectomycorrhizal fungi were represented by more OTUs in calcareous sites, while detected arbuscular mycorrhizal genera fungi showed opposing trends regarding pH. Furthermore, we detected numerous red listed species in our samples often from previously unknown locations, indicating that some of the fungal species currently considered rare may be more abundant in Dutch S. repens communities than previously thought.
DOI: 10.1371/journal.pone.0099852
PubMed: 24937200
PubMed Central: PMC4061046
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Communities of the creeping willow (Salix repens) represent one of the most characteristic and diverse vegetation types in the dunes. We report here the results of the first kingdom-wide fungal diversity assessment in S. repens coastal dune vegetation. We carried out massively parallel pyrosequencing of ITS rDNA from soil samples taken at ten sites in an extended area of joined nature reserves located along the North Sea coast of the Netherlands, representing habitats with varying soil pH and moisture levels. Fungal communities in Salix repens beds are highly diverse and we detected 1211 non-singleton fungal 97% sequence similarity OTUs after analyzing 688,434 ITS2 rDNA sequences. Our comparison along a north-south transect indicated strong correlation between soil pH and fungal community composition. The total fungal richness and the number OTUs of most fungal taxonomic groups negatively correlated with higher soil pH, with some exceptions. With regard to ecological groups, dark-septate endophytic fungi were more diverse in acidic soils, ectomycorrhizal fungi were represented by more OTUs in calcareous sites, while detected arbuscular mycorrhizal genera fungi showed opposing trends regarding pH. Furthermore, we detected numerous red listed species in our samples often from previously unknown locations, indicating that some of the fungal species currently considered rare may be more abundant in Dutch S. repens communities than previously thought. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24937200</PMID><DateCompleted><Year>2015</Year><Month>02</Month><Day>12</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>9</Volume><Issue>6</Issue><PubDate><Year>2014</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS One</ISOAbbreviation></Journal><ArticleTitle>The contribution of DNA metabarcoding to fungal conservation: diversity assessment, habitat partitioning and mapping red-listed fungi in protected coastal Salix repens communities in the Netherlands.</ArticleTitle><Pagination><MedlinePgn>e99852</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0099852</ELocationID><Abstract><AbstractText>Western European coastal sand dunes are highly important for nature conservation. Communities of the creeping willow (Salix repens) represent one of the most characteristic and diverse vegetation types in the dunes. We report here the results of the first kingdom-wide fungal diversity assessment in S. repens coastal dune vegetation. We carried out massively parallel pyrosequencing of ITS rDNA from soil samples taken at ten sites in an extended area of joined nature reserves located along the North Sea coast of the Netherlands, representing habitats with varying soil pH and moisture levels. Fungal communities in Salix repens beds are highly diverse and we detected 1211 non-singleton fungal 97% sequence similarity OTUs after analyzing 688,434 ITS2 rDNA sequences. Our comparison along a north-south transect indicated strong correlation between soil pH and fungal community composition. The total fungal richness and the number OTUs of most fungal taxonomic groups negatively correlated with higher soil pH, with some exceptions. With regard to ecological groups, dark-septate endophytic fungi were more diverse in acidic soils, ectomycorrhizal fungi were represented by more OTUs in calcareous sites, while detected arbuscular mycorrhizal genera fungi showed opposing trends regarding pH. Furthermore, we detected numerous red listed species in our samples often from previously unknown locations, indicating that some of the fungal species currently considered rare may be more abundant in Dutch S. repens communities than previously thought. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Geml</LastName><ForeName>József</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Naturalis Biodiversity Center, Leiden, The Netherlands; Faculty of Science, Leiden University, Leiden, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gravendeel</LastName><ForeName>Barbara</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Naturalis Biodiversity Center, Leiden, The Netherlands; Faculty of Science, Leiden University, Leiden, The Netherlands; University of Applied Sciences Leiden, Leiden, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>van der Gaag</LastName><ForeName>Kristiaan J</ForeName><Initials>KJ</Initials><AffiliationInfo><Affiliation>Forensic Laboratory for DNA Research, Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Neilen</LastName><ForeName>Manon</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Naturalis Biodiversity Center, Leiden, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lammers</LastName><ForeName>Youri</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Naturalis Biodiversity Center, Leiden, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Raes</LastName><ForeName>Niels</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Naturalis Biodiversity Center, Leiden, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Semenova</LastName><ForeName>Tatiana A</ForeName><Initials>TA</Initials><AffiliationInfo><Affiliation>Naturalis Biodiversity Center, Leiden, The Netherlands; Faculty of Science, Leiden University, Leiden, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>de Knijff</LastName><ForeName>Peter</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Forensic Laboratory for DNA Research, Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Noordeloos</LastName><ForeName>Machiel E</ForeName><Initials>ME</Initials><AffiliationInfo><Affiliation>Naturalis Biodiversity Center, Leiden, The Netherlands.</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>2014</Year><Month>06</Month><Day>17</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PLoS One</MedlineTA><NlmUniqueID>101285081</NlmUniqueID><ISSNLinking>1932-6203</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004271">DNA, Fungal</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D021903">DNA, Ribosomal Spacer</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001203" MajorTopicYN="N">Ascomycota</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D044822" MajorTopicYN="N">Biodiversity</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003247" MajorTopicYN="N">Conservation of Natural Resources</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D058893" MajorTopicYN="N">DNA Barcoding, Taxonomic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004271" MajorTopicYN="N">DNA, Fungal</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D021903" MajorTopicYN="N">DNA, Ribosomal Spacer</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017753" MajorTopicYN="N">Ecosystem</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009426" MajorTopicYN="N" Type="Geographic">Netherlands</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032108" MajorTopicYN="N">Salix</DescriptorName><QualifierName UI="Q000382" 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