Pyrosequencing reveals fungal communities in the rhizosphere of Xinjiang Jujube.
Identifieur interne : 001551 ( Main/Corpus ); précédent : 001550; suivant : 001552Pyrosequencing reveals fungal communities in the rhizosphere of Xinjiang Jujube.
Auteurs : Peng Liu ; Xiao-Hui Wang ; Jian-Gui Li ; Wei Qin ; Cheng-Ze Xiao ; Xu Zhao ; Hong-Xia Jiang ; Jun-Kang Sui ; Rong-Bo Sa ; Wei-Yan Wang ; Xun-Li LiuSource :
- BioMed research international [ 2314-6141 ] ; 2015.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : DNA, Fungal, DNA, Ribosomal.
- genetics : Mycorrhizae.
- microbiology : Rhizome, Ziziphus.
- Biodiversity, High-Throughput Nucleotide Sequencing, Soil Microbiology.
Abstract
Fungi are important soil components as both decomposers and plant symbionts and play a major role in ecological and biogeochemical processes. However, little is known about the richness and structure of fungal communities. DNA sequencing technologies allow for the direct estimation of microbial community diversity, avoiding culture-based biases. We therefore used 454 pyrosequencing to investigate the fungal communities in the rhizosphere of Xinjiang jujube. We obtained no less than 40,488 internal transcribed spacer (ITS) rDNA reads, the number of each sample was 6943, 6647, 6584, 6550, 6860, and 6904, and we used bioinformatics and multivariate statistics to analyze the results. The index of diversity showed greater richness in the rhizosphere fungal community of a 3-year-old jujube than in that of an 8-year-old jujube. Most operational taxonomic units belonged to Ascomycota, and taxonomic analyses identified Hypocreales as the dominant fungal order. Our results demonstrated that the fungal orders are present in different proportions in different sampling areas. Redundancy analysis (RDA) revealed a significant correlation between soil properties and the abundance of fungal phyla. Our results indicated lower fungal diversity in the rhizosphere of Xinjiang jujube than that reported in other studies, and we hope our findings provide a reference for future research.
DOI: 10.1155/2015/972481
PubMed: 25685820
PubMed Central: PMC4313056
Links to Exploration step
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China.</nlm:affiliation></affiliation></author><author><name sortKey="Qin, Wei" sort="Qin, Wei" uniqKey="Qin W" first="Wei" last="Qin">Wei Qin</name><affiliation><nlm:affiliation>Research Institute of Forest in Xinjiang Agricultural University, Urumqi, Xinjiang 830052, China.</nlm:affiliation></affiliation></author><author><name sortKey="Xiao, Cheng Ze" sort="Xiao, Cheng Ze" uniqKey="Xiao C" first="Cheng-Ze" last="Xiao">Cheng-Ze Xiao</name><affiliation><nlm:affiliation>College of Forest, Shandong Agricultural University, No. 61, Daizong Street, Taian, Shandong 271018, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhao, Xu" sort="Zhao, Xu" uniqKey="Zhao X" first="Xu" last="Zhao">Xu Zhao</name><affiliation><nlm:affiliation>College of Forest, Shandong Agricultural University, No. 61, Daizong Street, Taian, Shandong 271018, China.</nlm:affiliation></affiliation></author><author><name sortKey="Jiang, Hong Xia" sort="Jiang, Hong Xia" uniqKey="Jiang H" first="Hong-Xia" 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271018, China.</nlm:affiliation></affiliation></author><author><name sortKey="Liu, Xun Li" sort="Liu, Xun Li" uniqKey="Liu X" first="Xun-Li" last="Liu">Xun-Li Liu</name><affiliation><nlm:affiliation>College of Forest, Shandong Agricultural University, No. 61, Daizong Street, Taian, Shandong 271018, China.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:25685820</idno><idno type="pmid">25685820</idno><idno type="doi">10.1155/2015/972481</idno><idno type="pmc">PMC4313056</idno><idno type="wicri:Area/Main/Corpus">001551</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">001551</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Pyrosequencing reveals fungal communities in the rhizosphere of Xinjiang Jujube.</title><author><name sortKey="Liu, Peng" sort="Liu, Peng" uniqKey="Liu P" first="Peng" last="Liu">Peng Liu</name><affiliation><nlm:affiliation>College of Forest, Shandong Agricultural University, No. 61, Daizong Street, Taian, Shandong 271018, China.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Xiao Hui" sort="Wang, Xiao Hui" uniqKey="Wang X" first="Xiao-Hui" last="Wang">Xiao-Hui Wang</name><affiliation><nlm:affiliation>College of Life Science, Shandong Agricultural University, Taian, Shandong 271018, China.</nlm:affiliation></affiliation></author><author><name sortKey="Li, Jian Gui" sort="Li, Jian Gui" uniqKey="Li J" first="Jian-Gui" last="Li">Jian-Gui Li</name><affiliation><nlm:affiliation>Research Institute of Forest in Xinjiang Agricultural University, Urumqi, Xinjiang 830052, China.</nlm:affiliation></affiliation></author><author><name sortKey="Qin, Wei" sort="Qin, Wei" uniqKey="Qin W" first="Wei" last="Qin">Wei Qin</name><affiliation><nlm:affiliation>Research Institute of Forest in Xinjiang Agricultural University, Urumqi, Xinjiang 830052, China.</nlm:affiliation></affiliation></author><author><name sortKey="Xiao, Cheng Ze" sort="Xiao, Cheng Ze" uniqKey="Xiao C" first="Cheng-Ze" last="Xiao">Cheng-Ze Xiao</name><affiliation><nlm:affiliation>College of Forest, Shandong Agricultural University, No. 61, Daizong Street, Taian, Shandong 271018, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhao, Xu" sort="Zhao, Xu" uniqKey="Zhao X" first="Xu" last="Zhao">Xu Zhao</name><affiliation><nlm:affiliation>College of Forest, Shandong Agricultural University, No. 61, Daizong Street, Taian, Shandong 271018, China.</nlm:affiliation></affiliation></author><author><name sortKey="Jiang, Hong Xia" sort="Jiang, Hong Xia" uniqKey="Jiang H" first="Hong-Xia" last="Jiang">Hong-Xia Jiang</name><affiliation><nlm:affiliation>College of Life Science, Shandong Agricultural University, Taian, Shandong 271018, China.</nlm:affiliation></affiliation></author><author><name sortKey="Sui, Jun Kang" sort="Sui, Jun Kang" uniqKey="Sui J" first="Jun-Kang" last="Sui">Jun-Kang Sui</name><affiliation><nlm:affiliation>College of Life Science, Shandong Agricultural University, Taian, Shandong 271018, China.</nlm:affiliation></affiliation></author><author><name sortKey="Sa, Rong Bo" sort="Sa, Rong Bo" uniqKey="Sa R" first="Rong-Bo" last="Sa">Rong-Bo Sa</name><affiliation><nlm:affiliation>College of Life Science, Shandong Agricultural University, Taian, Shandong 271018, China.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Wei Yan" sort="Wang, Wei Yan" uniqKey="Wang W" first="Wei-Yan" last="Wang">Wei-Yan Wang</name><affiliation><nlm:affiliation>College of Forest, Shandong Agricultural University, No. 61, Daizong Street, Taian, Shandong 271018, China.</nlm:affiliation></affiliation></author><author><name sortKey="Liu, Xun Li" sort="Liu, Xun Li" uniqKey="Liu X" first="Xun-Li" last="Liu">Xun-Li Liu</name><affiliation><nlm:affiliation>College of Forest, Shandong Agricultural University, No. 61, Daizong Street, Taian, Shandong 271018, China.</nlm:affiliation></affiliation></author></analytic><series><title level="j">BioMed research international</title><idno type="eISSN">2314-6141</idno><imprint><date when="2015" type="published">2015</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 (genetics)</term><term>High-Throughput Nucleotide Sequencing (MeSH)</term><term>Mycorrhizae (genetics)</term><term>Rhizome (microbiology)</term><term>Soil Microbiology (MeSH)</term><term>Ziziphus (microbiology)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Fungal</term><term>DNA, Ribosomal</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Mycorrhizae</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Rhizome</term><term>Ziziphus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Biodiversity</term><term>High-Throughput Nucleotide Sequencing</term><term>Soil Microbiology</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Fungi are important soil components as both decomposers and plant symbionts and play a major role in ecological and biogeochemical processes. However, little is known about the richness and structure of fungal communities. DNA sequencing technologies allow for the direct estimation of microbial community diversity, avoiding culture-based biases. We therefore used 454 pyrosequencing to investigate the fungal communities in the rhizosphere of Xinjiang jujube. We obtained no less than 40,488 internal transcribed spacer (ITS) rDNA reads, the number of each sample was 6943, 6647, 6584, 6550, 6860, and 6904, and we used bioinformatics and multivariate statistics to analyze the results. The index of diversity showed greater richness in the rhizosphere fungal community of a 3-year-old jujube than in that of an 8-year-old jujube. Most operational taxonomic units belonged to Ascomycota, and taxonomic analyses identified Hypocreales as the dominant fungal order. Our results demonstrated that the fungal orders are present in different proportions in different sampling areas. Redundancy analysis (RDA) revealed a significant correlation between soil properties and the abundance of fungal phyla. Our results indicated lower fungal diversity in the rhizosphere of Xinjiang jujube than that reported in other studies, and we hope our findings provide a reference for future research. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25685820</PMID><DateCompleted><Year>2015</Year><Month>11</Month><Day>06</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">2314-6141</ISSN><JournalIssue CitedMedium="Internet"><Volume>2015</Volume><PubDate><Year>2015</Year></PubDate></JournalIssue><Title>BioMed research international</Title><ISOAbbreviation>Biomed Res Int</ISOAbbreviation></Journal><ArticleTitle>Pyrosequencing reveals fungal communities in the rhizosphere of Xinjiang Jujube.</ArticleTitle><Pagination><MedlinePgn>972481</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1155/2015/972481</ELocationID><Abstract><AbstractText>Fungi are important soil components as both decomposers and plant symbionts and play a major role in ecological and biogeochemical processes. However, little is known about the richness and structure of fungal communities. DNA sequencing technologies allow for the direct estimation of microbial community diversity, avoiding culture-based biases. We therefore used 454 pyrosequencing to investigate the fungal communities in the rhizosphere of Xinjiang jujube. We obtained no less than 40,488 internal transcribed spacer (ITS) rDNA reads, the number of each sample was 6943, 6647, 6584, 6550, 6860, and 6904, and we used bioinformatics and multivariate statistics to analyze the results. The index of diversity showed greater richness in the rhizosphere fungal community of a 3-year-old jujube than in that of an 8-year-old jujube. Most operational taxonomic units belonged to Ascomycota, and taxonomic analyses identified Hypocreales as the dominant fungal order. Our results demonstrated that the fungal orders are present in different proportions in different sampling areas. Redundancy analysis (RDA) revealed a significant correlation between soil properties and the abundance of fungal phyla. Our results indicated lower fungal diversity in the rhizosphere of Xinjiang jujube than that reported in other studies, and we hope our findings provide a reference for future research. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Peng</ForeName><Initials>P</Initials><Identifier Source="ORCID">0000-0003-4997-0713</Identifier><AffiliationInfo><Affiliation>College of Forest, Shandong Agricultural University, No. 61, Daizong Street, Taian, Shandong 271018, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Xiao-Hui</ForeName><Initials>XH</Initials><AffiliationInfo><Affiliation>College of Life Science, Shandong Agricultural University, Taian, Shandong 271018, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Jian-Gui</ForeName><Initials>JG</Initials><AffiliationInfo><Affiliation>Research Institute of Forest in Xinjiang Agricultural University, Urumqi, Xinjiang 830052, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Qin</LastName><ForeName>Wei</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Research Institute of Forest in Xinjiang Agricultural University, Urumqi, Xinjiang 830052, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xiao</LastName><ForeName>Cheng-Ze</ForeName><Initials>CZ</Initials><AffiliationInfo><Affiliation>College of Forest, Shandong Agricultural University, No. 61, Daizong Street, Taian, Shandong 271018, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhao</LastName><ForeName>Xu</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>College of Forest, Shandong Agricultural University, No. 61, Daizong Street, Taian, Shandong 271018, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jiang</LastName><ForeName>Hong-Xia</ForeName><Initials>HX</Initials><AffiliationInfo><Affiliation>College of Life Science, Shandong Agricultural University, Taian, Shandong 271018, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sui</LastName><ForeName>Jun-Kang</ForeName><Initials>JK</Initials><AffiliationInfo><Affiliation>College of Life Science, Shandong Agricultural University, Taian, Shandong 271018, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sa</LastName><ForeName>Rong-Bo</ForeName><Initials>RB</Initials><AffiliationInfo><Affiliation>College of Life Science, Shandong Agricultural University, Taian, Shandong 271018, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Wei-Yan</ForeName><Initials>WY</Initials><AffiliationInfo><Affiliation>College of Forest, Shandong Agricultural University, No. 61, Daizong Street, Taian, Shandong 271018, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Xun-Li</ForeName><Initials>XL</Initials><AffiliationInfo><Affiliation>College of Forest, Shandong Agricultural University, No. 61, Daizong Street, Taian, Shandong 271018, China.</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>2015</Year><Month>01</Month><Day>05</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Biomed Res Int</MedlineTA><NlmUniqueID>101600173</NlmUniqueID></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004271">DNA, Fungal</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004275">DNA, 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="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004275" MajorTopicYN="N">DNA, Ribosomal</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D038821" MajorTopicYN="N">Mycorrhizae</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D027343" MajorTopicYN="N">Rhizome</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012988" MajorTopicYN="Y">Soil Microbiology</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D031957" MajorTopicYN="N">Ziziphus</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2014</Year><Month>09</Month><Day>18</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2014</Year><Month>11</Month><Day>26</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2014</Year><Month>11</Month><Day>29</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2015</Year><Month>2</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2015</Year><Month>2</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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