Species abundance distributions and richness estimations in fungal metagenomics--lessons learned from community ecology.
Identifieur interne : 002476 ( Main/Curation ); précédent : 002475; suivant : 002477Species abundance distributions and richness estimations in fungal metagenomics--lessons learned from community ecology.
Auteurs : Martin Unterseher [Allemagne] ; Ari Jumpponen ; Maarja Opik ; Leho Tedersoo ; Mari Moora ; Carsten F. Dormann ; Martin SchnittlerSource :
- Molecular ecology [ 1365-294X ] ; 2011.
Descripteurs français
- KwdFr :
- ADN fongique (génétique), ARN ribosomique (MeSH), Analyse de séquence d'ADN (MeSH), Biodiversité (MeSH), Champignons (génétique), Espaceur de l'ADN ribosomique (MeSH), Glomeromycota (génétique), Mycorhizes (génétique), Métagénomique (MeSH), Petite sous-unité du ribosome (MeSH), Phylogenèse (MeSH), Réaction de polymérisation en chaîne (MeSH), Spécificité d'espèce (MeSH), Séquençage nucléotidique à haut débit (MeSH), Écosystème (MeSH), Études par échantillonnage (MeSH).
- MESH :
- génétique : ADN fongique, Champignons, Glomeromycota, Mycorhizes.
- ARN ribosomique, Analyse de séquence d'ADN, Biodiversité, Espaceur de l'ADN ribosomique, Métagénomique, Petite sous-unité du ribosome, Phylogenèse, Réaction de polymérisation en chaîne, Spécificité d'espèce, Séquençage nucléotidique à haut débit, Écosystème, Études par échantillonnage.
English descriptors
- KwdEn :
- Biodiversity (MeSH), DNA, Fungal (genetics), DNA, Ribosomal Spacer (MeSH), Ecosystem (MeSH), Fungi (genetics), Glomeromycota (genetics), High-Throughput Nucleotide Sequencing (MeSH), Metagenomics (MeSH), Mycorrhizae (genetics), Phylogeny (MeSH), Polymerase Chain Reaction (MeSH), RNA, Ribosomal (MeSH), Ribosome Subunits, Small (MeSH), Sampling Studies (MeSH), Sequence Analysis, DNA (MeSH), Species Specificity (MeSH).
- MESH :
- chemical , genetics : DNA, Fungal.
- genetics : Fungi, Glomeromycota, Mycorrhizae.
- Biodiversity, DNA, Ribosomal Spacer, Ecosystem, High-Throughput Nucleotide Sequencing, Metagenomics, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, Ribosome Subunits, Small, Sampling Studies, Sequence Analysis, DNA, Species Specificity.
Abstract
Results of diversity and community ecology studies strongly depend on sampling depth. Completely surveyed communities follow log-normal distribution, whereas power law functions best describe incompletely censused communities. It is arguable whether the statistics behind those theories can be applied to voluminous next generation sequencing data in microbiology by treating individual DNA sequences as counts of molecular taxonomic units (MOTUs). This study addresses the suitability of species abundance models in three groups of plant-associated fungal communities - phyllosphere, ectomycorrhizal and arbuscular mycorrhizal fungi. We tested the impact of differential treatment of molecular singletons on observed and estimated species richness and species abundance distribution models. The arbuscular mycorrhizal community of 48 MOTUs was exhaustively sampled and followed log-normal distribution. The ectomycorrhizal (153 MOTUs) and phyllosphere (327 MOTUs) communities significantly differed from log-normal distribution. The fungal phyllosphere community in particular was clearly undersampled. This undersampling bias resulted in strong sensitivity to the exclusion of molecular singletons and other rare MOTUs that may represent technical artefacts. The analysis of abundant (core) and rare (satellite) MOTUs clearly identified two species abundance distributions in the phyllosphere data - a log-normal model for the core group and a log-series model for the satellite group. The prominent log-series distribution of satellite phyllosphere fungi highlighted the ecological significance of an infrequent fungal component in the phyllosphere community.
DOI: 10.1111/j.1365-294X.2010.04948.x
PubMed: 21155911
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Dormann</name></author><author><name sortKey="Schnittler, Martin" sort="Schnittler, Martin" uniqKey="Schnittler M" first="Martin" last="Schnittler">Martin Schnittler</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2011">2011</date><idno type="RBID">pubmed:21155911</idno><idno type="pmid">21155911</idno><idno type="doi">10.1111/j.1365-294X.2010.04948.x</idno><idno type="wicri:Area/Main/Corpus">002476</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">002476</idno><idno type="wicri:Area/Main/Curation">002476</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">002476</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Species abundance distributions and richness estimations in fungal metagenomics--lessons learned from community ecology.</title><author><name sortKey="Unterseher, Martin" sort="Unterseher, Martin" uniqKey="Unterseher M" first="Martin" last="Unterseher">Martin Unterseher</name><affiliation wicri:level="1"><nlm:affiliation>University Greifswald, Institute of Botany and Landscape Ecology, Greifswald, Germany. martin.unterseher@uni-greifswald.de</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>University Greifswald, Institute of Botany and Landscape Ecology, Greifswald</wicri:regionArea></affiliation></author><author><name sortKey="Jumpponen, Ari" sort="Jumpponen, Ari" uniqKey="Jumpponen A" first="Ari" last="Jumpponen">Ari Jumpponen</name></author><author><name sortKey="Opik, Maarja" sort="Opik, Maarja" uniqKey="Opik M" first="Maarja" last="Opik">Maarja Opik</name></author><author><name sortKey="Tedersoo, Leho" sort="Tedersoo, Leho" uniqKey="Tedersoo L" first="Leho" last="Tedersoo">Leho Tedersoo</name></author><author><name sortKey="Moora, Mari" sort="Moora, Mari" uniqKey="Moora M" first="Mari" last="Moora">Mari Moora</name></author><author><name sortKey="Dormann, Carsten F" sort="Dormann, Carsten F" uniqKey="Dormann C" first="Carsten F" last="Dormann">Carsten F. Dormann</name></author><author><name sortKey="Schnittler, Martin" sort="Schnittler, Martin" uniqKey="Schnittler M" first="Martin" last="Schnittler">Martin Schnittler</name></author></analytic><series><title level="j">Molecular ecology</title><idno type="eISSN">1365-294X</idno><imprint><date when="2011" type="published">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Biodiversity (MeSH)</term><term>DNA, Fungal (genetics)</term><term>DNA, Ribosomal Spacer (MeSH)</term><term>Ecosystem (MeSH)</term><term>Fungi (genetics)</term><term>Glomeromycota (genetics)</term><term>High-Throughput Nucleotide Sequencing (MeSH)</term><term>Metagenomics (MeSH)</term><term>Mycorrhizae (genetics)</term><term>Phylogeny (MeSH)</term><term>Polymerase Chain Reaction (MeSH)</term><term>RNA, Ribosomal (MeSH)</term><term>Ribosome Subunits, Small (MeSH)</term><term>Sampling Studies (MeSH)</term><term>Sequence Analysis, DNA (MeSH)</term><term>Species Specificity (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN fongique (génétique)</term><term>ARN ribosomique (MeSH)</term><term>Analyse de séquence d'ADN (MeSH)</term><term>Biodiversité (MeSH)</term><term>Champignons (génétique)</term><term>Espaceur de l'ADN ribosomique (MeSH)</term><term>Glomeromycota (génétique)</term><term>Mycorhizes (génétique)</term><term>Métagénomique (MeSH)</term><term>Petite sous-unité du ribosome (MeSH)</term><term>Phylogenèse (MeSH)</term><term>Réaction de polymérisation en chaîne (MeSH)</term><term>Spécificité d'espèce (MeSH)</term><term>Séquençage nucléotidique à haut débit (MeSH)</term><term>Écosystème (MeSH)</term><term>Études par échantillonnage (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Fungal</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Fungi</term><term>Glomeromycota</term><term>Mycorrhizae</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN fongique</term><term>Champignons</term><term>Glomeromycota</term><term>Mycorhizes</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Biodiversity</term><term>DNA, Ribosomal Spacer</term><term>Ecosystem</term><term>High-Throughput Nucleotide Sequencing</term><term>Metagenomics</term><term>Phylogeny</term><term>Polymerase Chain Reaction</term><term>RNA, Ribosomal</term><term>Ribosome Subunits, Small</term><term>Sampling Studies</term><term>Sequence Analysis, DNA</term><term>Species Specificity</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ARN ribosomique</term><term>Analyse de séquence d'ADN</term><term>Biodiversité</term><term>Espaceur de l'ADN ribosomique</term><term>Métagénomique</term><term>Petite sous-unité du ribosome</term><term>Phylogenèse</term><term>Réaction de polymérisation en chaîne</term><term>Spécificité d'espèce</term><term>Séquençage nucléotidique à haut débit</term><term>Écosystème</term><term>Études par échantillonnage</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Results of diversity and community ecology studies strongly depend on sampling depth. Completely surveyed communities follow log-normal distribution, whereas power law functions best describe incompletely censused communities. It is arguable whether the statistics behind those theories can be applied to voluminous next generation sequencing data in microbiology by treating individual DNA sequences as counts of molecular taxonomic units (MOTUs). This study addresses the suitability of species abundance models in three groups of plant-associated fungal communities - phyllosphere, ectomycorrhizal and arbuscular mycorrhizal fungi. We tested the impact of differential treatment of molecular singletons on observed and estimated species richness and species abundance distribution models. The arbuscular mycorrhizal community of 48 MOTUs was exhaustively sampled and followed log-normal distribution. The ectomycorrhizal (153 MOTUs) and phyllosphere (327 MOTUs) communities significantly differed from log-normal distribution. The fungal phyllosphere community in particular was clearly undersampled. This undersampling bias resulted in strong sensitivity to the exclusion of molecular singletons and other rare MOTUs that may represent technical artefacts. The analysis of abundant (core) and rare (satellite) MOTUs clearly identified two species abundance distributions in the phyllosphere data - a log-normal model for the core group and a log-series model for the satellite group. The prominent log-series distribution of satellite phyllosphere fungi highlighted the ecological significance of an infrequent fungal component in the phyllosphere community.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">21155911</PMID><DateCompleted><Year>2011</Year><Month>07</Month><Day>19</Day></DateCompleted><DateRevised><Year>2011</Year><Month>01</Month><Day>07</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1365-294X</ISSN><JournalIssue CitedMedium="Internet"><Volume>20</Volume><Issue>2</Issue><PubDate><Year>2011</Year><Month>Jan</Month></PubDate></JournalIssue><Title>Molecular ecology</Title><ISOAbbreviation>Mol Ecol</ISOAbbreviation></Journal><ArticleTitle>Species abundance distributions and richness estimations in fungal metagenomics--lessons learned from community ecology.</ArticleTitle><Pagination><MedlinePgn>275-85</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/j.1365-294X.2010.04948.x</ELocationID><Abstract><AbstractText>Results of diversity and community ecology studies strongly depend on sampling depth. Completely surveyed communities follow log-normal distribution, whereas power law functions best describe incompletely censused communities. It is arguable whether the statistics behind those theories can be applied to voluminous next generation sequencing data in microbiology by treating individual DNA sequences as counts of molecular taxonomic units (MOTUs). This study addresses the suitability of species abundance models in three groups of plant-associated fungal communities - phyllosphere, ectomycorrhizal and arbuscular mycorrhizal fungi. We tested the impact of differential treatment of molecular singletons on observed and estimated species richness and species abundance distribution models. The arbuscular mycorrhizal community of 48 MOTUs was exhaustively sampled and followed log-normal distribution. The ectomycorrhizal (153 MOTUs) and phyllosphere (327 MOTUs) communities significantly differed from log-normal distribution. The fungal phyllosphere community in particular was clearly undersampled. This undersampling bias resulted in strong sensitivity to the exclusion of molecular singletons and other rare MOTUs that may represent technical artefacts. The analysis of abundant (core) and rare (satellite) MOTUs clearly identified two species abundance distributions in the phyllosphere data - a log-normal model for the core group and a log-series model for the satellite group. The prominent log-series distribution of satellite phyllosphere fungi highlighted the ecological significance of an infrequent fungal component in the phyllosphere community.</AbstractText><CopyrightInformation>© 2010 Blackwell Publishing Ltd.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Unterseher</LastName><ForeName>Martin</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>University Greifswald, Institute of Botany and Landscape Ecology, Greifswald, Germany. martin.unterseher@uni-greifswald.de</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jumpponen</LastName><ForeName>Ari</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Opik</LastName><ForeName>Maarja</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Tedersoo</LastName><ForeName>Leho</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Moora</LastName><ForeName>Mari</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Dormann</LastName><ForeName>Carsten F</ForeName><Initials>CF</Initials></Author><Author ValidYN="Y"><LastName>Schnittler</LastName><ForeName>Martin</ForeName><Initials>M</Initials></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>2010</Year><Month>12</Month><Day>13</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Mol Ecol</MedlineTA><NlmUniqueID>9214478</NlmUniqueID><ISSNLinking>0962-1083</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><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012335">RNA, Ribosomal</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D044822" MajorTopicYN="Y">Biodiversity</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></MeshHeading><MeshHeading><DescriptorName UI="D017753" MajorTopicYN="N">Ecosystem</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005658" MajorTopicYN="N">Fungi</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D055137" MajorTopicYN="N">Glomeromycota</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D056186" MajorTopicYN="Y">Metagenomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D038821" MajorTopicYN="N">Mycorrhizae</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016133" MajorTopicYN="N">Polymerase Chain Reaction</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012335" MajorTopicYN="N">RNA, Ribosomal</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D054679" MajorTopicYN="N">Ribosome Subunits, Small</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012494" MajorTopicYN="N">Sampling Studies</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013045" MajorTopicYN="N">Species Specificity</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2010</Year><Month>12</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2010</Year><Month>12</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2011</Year><Month>7</Month><Day>20</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">21155911</ArticleId><ArticleId IdType="doi">10.1111/j.1365-294X.2010.04948.x</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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