Network hubs in root-associated fungal metacommunities.
Identifieur interne : 000835 ( Main/Corpus ); précédent : 000834; suivant : 000836Network hubs in root-associated fungal metacommunities.
Auteurs : Hirokazu Toju ; Akifumi S. Tanabe ; Hirotoshi SatoSource :
- Microbiome [ 2049-2618 ] ; 2018.
English descriptors
- KwdEn :
- Base Sequence (MeSH), Biodiversity (MeSH), DNA, Fungal (genetics), Endophytes (classification), Endophytes (genetics), Endophytes (isolation & purification), Forests (MeSH), Fungi (classification), Fungi (genetics), Fungi (isolation & purification), Host Specificity (MeSH), Japan (MeSH), Microbiota (genetics), Mycorrhizae (physiology), Plant Roots (microbiology), Plants (microbiology), Sequence Analysis, DNA (MeSH), Soil Microbiology (MeSH).
- MESH :
- chemical , genetics : DNA, Fungal.
- geographic : Japan.
- classification : Endophytes, Fungi.
- genetics : Endophytes, Fungi, Microbiota.
- isolation & purification : Endophytes, Fungi.
- microbiology : Plant Roots, Plants.
- physiology : Mycorrhizae.
- Base Sequence, Biodiversity, Forests, Host Specificity, Sequence Analysis, DNA, Soil Microbiology.
Abstract
BACKGROUND
Although a number of recent studies have uncovered remarkable diversity of microbes associated with plants, understanding and managing dynamics of plant microbiomes remain major scientific challenges. In this respect, network analytical methods have provided a basis for exploring "hub" microbial species, which potentially organize community-scale processes of plant-microbe interactions.
METHODS
By compiling Illumina sequencing data of root-associated fungi in eight forest ecosystems across the Japanese Archipelago, we explored hubs within "metacommunity-scale" networks of plant-fungus associations. In total, the metadata included 8080 fungal operational taxonomic units (OTUs) detected from 227 local populations of 150 plant species/taxa.
RESULTS
Few fungal OTUs were common across all the eight forests. However, in each of the metacommunity-scale networks representing northern four localities or southern four localities, diverse mycorrhizal, endophytic, and pathogenic fungi were classified as "metacommunity hubs," which were detected from diverse host plant taxa throughout a climatic region. Specifically, Mortierella (Mortierellales), Cladophialophora (Chaetothyriales), Ilyonectria (Hypocreales), Pezicula (Helotiales), and Cadophora (incertae sedis) had broad geographic and host ranges across the northern (cool-temperate) region, while Saitozyma/Cryptococcus (Tremellales/Trichosporonales) and Mortierella as well as some arbuscular mycorrhizal fungi were placed at the central positions of the metacommunity-scale network representing warm-temperate and subtropical forests in southern Japan.
CONCLUSIONS
The network theoretical framework presented in this study will help us explore prospective fungi and bacteria, which have high potentials for agricultural application to diverse plant species within each climatic region. As some of those fungal taxa with broad geographic and host ranges have been known to promote the survival and growth of host plants, further studies elucidating their functional roles are awaited.
DOI: 10.1186/s40168-018-0497-1
PubMed: 29935536
PubMed Central: PMC6015470
Links to Exploration step
pubmed:29935536Le document en format XML
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Tanabe</name><affiliation><nlm:affiliation>Faculty of Science and Technology, Ryukoku University, Seta Oe, Otsu, Shiga, 520-2194, Japan.</nlm:affiliation></affiliation></author><author><name sortKey="Sato, Hirotoshi" sort="Sato, Hirotoshi" uniqKey="Sato H" first="Hirotoshi" last="Sato">Hirotoshi Sato</name><affiliation><nlm:affiliation>Graduate School of Human and Environmental Studies, Kyoto University, Sakyo, Kyoto, 606-8501, Japan.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2018">2018</date><idno type="RBID">pubmed:29935536</idno><idno type="pmid">29935536</idno><idno type="doi">10.1186/s40168-018-0497-1</idno><idno type="pmc">PMC6015470</idno><idno type="wicri:Area/Main/Corpus">000835</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000835</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Network hubs in root-associated fungal metacommunities.</title><author><name sortKey="Toju, Hirokazu" sort="Toju, Hirokazu" uniqKey="Toju H" first="Hirokazu" last="Toju">Hirokazu Toju</name><affiliation><nlm:affiliation>Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2113, Japan. toju.hirokazu.4c@kyoto-u.ac.jp.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Kawaguchi, Saitama, 332-0012, Japan. toju.hirokazu.4c@kyoto-u.ac.jp.</nlm:affiliation></affiliation></author><author><name sortKey="Tanabe, Akifumi S" sort="Tanabe, Akifumi S" uniqKey="Tanabe A" first="Akifumi S" last="Tanabe">Akifumi S. Tanabe</name><affiliation><nlm:affiliation>Faculty of Science and Technology, Ryukoku University, Seta Oe, Otsu, Shiga, 520-2194, Japan.</nlm:affiliation></affiliation></author><author><name sortKey="Sato, Hirotoshi" sort="Sato, Hirotoshi" uniqKey="Sato H" first="Hirotoshi" last="Sato">Hirotoshi Sato</name><affiliation><nlm:affiliation>Graduate School of Human and Environmental Studies, Kyoto University, Sakyo, Kyoto, 606-8501, Japan.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Microbiome</title><idno type="eISSN">2049-2618</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence (MeSH)</term><term>Biodiversity (MeSH)</term><term>DNA, Fungal (genetics)</term><term>Endophytes (classification)</term><term>Endophytes (genetics)</term><term>Endophytes (isolation & purification)</term><term>Forests (MeSH)</term><term>Fungi (classification)</term><term>Fungi (genetics)</term><term>Fungi (isolation & purification)</term><term>Host Specificity (MeSH)</term><term>Japan (MeSH)</term><term>Microbiota (genetics)</term><term>Mycorrhizae (physiology)</term><term>Plant Roots (microbiology)</term><term>Plants (microbiology)</term><term>Sequence Analysis, DNA (MeSH)</term><term>Soil Microbiology (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Fungal</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>Japan</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Endophytes</term><term>Fungi</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Endophytes</term><term>Fungi</term><term>Microbiota</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Endophytes</term><term>Fungi</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Plant Roots</term><term>Plants</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Mycorrhizae</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Biodiversity</term><term>Forests</term><term>Host Specificity</term><term>Sequence Analysis, DNA</term><term>Soil Microbiology</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Although a number of recent studies have uncovered remarkable diversity of microbes associated with plants, understanding and managing dynamics of plant microbiomes remain major scientific challenges. In this respect, network analytical methods have provided a basis for exploring "hub" microbial species, which potentially organize community-scale processes of plant-microbe interactions.</p></div><div type="abstract" xml:lang="en"><p><b>METHODS</b></p><p>By compiling Illumina sequencing data of root-associated fungi in eight forest ecosystems across the Japanese Archipelago, we explored hubs within "metacommunity-scale" networks of plant-fungus associations. In total, the metadata included 8080 fungal operational taxonomic units (OTUs) detected from 227 local populations of 150 plant species/taxa.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>Few fungal OTUs were common across all the eight forests. However, in each of the metacommunity-scale networks representing northern four localities or southern four localities, diverse mycorrhizal, endophytic, and pathogenic fungi were classified as "metacommunity hubs," which were detected from diverse host plant taxa throughout a climatic region. Specifically, Mortierella (Mortierellales), Cladophialophora (Chaetothyriales), Ilyonectria (Hypocreales), Pezicula (Helotiales), and Cadophora (incertae sedis) had broad geographic and host ranges across the northern (cool-temperate) region, while Saitozyma/Cryptococcus (Tremellales/Trichosporonales) and Mortierella as well as some arbuscular mycorrhizal fungi were placed at the central positions of the metacommunity-scale network representing warm-temperate and subtropical forests in southern Japan.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>The network theoretical framework presented in this study will help us explore prospective fungi and bacteria, which have high potentials for agricultural application to diverse plant species within each climatic region. As some of those fungal taxa with broad geographic and host ranges have been known to promote the survival and growth of host plants, further studies elucidating their functional roles are awaited.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">29935536</PMID><DateCompleted><Year>2019</Year><Month>01</Month><Day>28</Day></DateCompleted><DateRevised><Year>2019</Year><Month>01</Month><Day>28</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">2049-2618</ISSN><JournalIssue CitedMedium="Internet"><Volume>6</Volume><Issue>1</Issue><PubDate><Year>2018</Year><Month>06</Month><Day>23</Day></PubDate></JournalIssue><Title>Microbiome</Title><ISOAbbreviation>Microbiome</ISOAbbreviation></Journal><ArticleTitle>Network hubs in root-associated fungal metacommunities.</ArticleTitle><Pagination><MedlinePgn>116</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s40168-018-0497-1</ELocationID><Abstract><AbstractText Label="BACKGROUND">Although a number of recent studies have uncovered remarkable diversity of microbes associated with plants, understanding and managing dynamics of plant microbiomes remain major scientific challenges. In this respect, network analytical methods have provided a basis for exploring "hub" microbial species, which potentially organize community-scale processes of plant-microbe interactions.</AbstractText><AbstractText Label="METHODS">By compiling Illumina sequencing data of root-associated fungi in eight forest ecosystems across the Japanese Archipelago, we explored hubs within "metacommunity-scale" networks of plant-fungus associations. In total, the metadata included 8080 fungal operational taxonomic units (OTUs) detected from 227 local populations of 150 plant species/taxa.</AbstractText><AbstractText Label="RESULTS">Few fungal OTUs were common across all the eight forests. However, in each of the metacommunity-scale networks representing northern four localities or southern four localities, diverse mycorrhizal, endophytic, and pathogenic fungi were classified as "metacommunity hubs," which were detected from diverse host plant taxa throughout a climatic region. Specifically, Mortierella (Mortierellales), Cladophialophora (Chaetothyriales), Ilyonectria (Hypocreales), Pezicula (Helotiales), and Cadophora (incertae sedis) had broad geographic and host ranges across the northern (cool-temperate) region, while Saitozyma/Cryptococcus (Tremellales/Trichosporonales) and Mortierella as well as some arbuscular mycorrhizal fungi were placed at the central positions of the metacommunity-scale network representing warm-temperate and subtropical forests in southern Japan.</AbstractText><AbstractText Label="CONCLUSIONS">The network theoretical framework presented in this study will help us explore prospective fungi and bacteria, which have high potentials for agricultural application to diverse plant species within each climatic region. As some of those fungal taxa with broad geographic and host ranges have been known to promote the survival and growth of host plants, further studies elucidating their functional roles are awaited.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Toju</LastName><ForeName>Hirokazu</ForeName><Initials>H</Initials><Identifier Source="ORCID">0000-0002-3362-3285</Identifier><AffiliationInfo><Affiliation>Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2113, Japan. toju.hirokazu.4c@kyoto-u.ac.jp.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Kawaguchi, Saitama, 332-0012, Japan. toju.hirokazu.4c@kyoto-u.ac.jp.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tanabe</LastName><ForeName>Akifumi S</ForeName><Initials>AS</Initials><AffiliationInfo><Affiliation>Faculty of Science and Technology, Ryukoku University, Seta Oe, Otsu, Shiga, 520-2194, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sato</LastName><ForeName>Hirotoshi</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Graduate School of Human and Environmental Studies, Kyoto University, Sakyo, Kyoto, 606-8501, Japan.</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>2018</Year><Month>06</Month><Day>23</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Microbiome</MedlineTA><NlmUniqueID>101615147</NlmUniqueID><ISSNLinking>2049-2618</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004271">DNA, 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