Metagenome data of bacterial diversity in pear (Pyrus communis L.) rhizospheres associated with Phytophthora infection and amino acid treatment.
Identifieur interne : 000455 ( Main/Exploration ); précédent : 000454; suivant : 000456Metagenome data of bacterial diversity in pear (Pyrus communis L.) rhizospheres associated with Phytophthora infection and amino acid treatment.
Auteurs : Antonios Zambounis [Grèce] ; Maslin Osathanunkul [Thaïlande] ; Panagiotis Madesis [Grèce]Source :
- Data in brief [ 2352-3409 ] ; 2019.
Abstract
The bacterial diversity in rhizosphere soil of pear trees (Pyrus communis L. cv. Krystalli) from an orchard at Thessaly region of Greece was characterized employing amplicon-based metagenomics analysis. Pathogenic filamentous oomycetes of the genus Phytophthora comprises more than 150 recognized species and cause highly destructive soil-borne diseases in deciduous trees crops worldwide. Moreover, the treatment of soil microbiota with amino acids is an alternative strategy to achieve desirable effects even against phytopathogenic oomycetes. In our study, samples from rhizosphere soil were collected either from naturally Phytophthora-infected trees, from completely asymptomatic ones, or from trees as above subjected also to treatments with amino acids (Amino16®) under different fertilization regimes. The interactions of bacterial communities with plant pathogenic oomycetes are crucial to determine the course of infection and the pathogenicity encompassing various functional contexts like biofilm formation. Thus, for deciphering the structure and diversity of these soil bacterial communities, we applied a 16S rRNA Illumina sequencing approach targeting the V3-V4 gene region. After quality check 478,479 sequences were obtained in the dataset comprising a total read length of 192,291,625 base pairs. Proteobacteria were the dominant phylum (46.1%) followed by Acidobacteria (13.2%) and Actinobacteria (12.4%). Different distributions of phyla were observed among our samples which is indicative of various alterations of soil bacterial communities in rhizosphere. The metagenome data from this survey are available at NCBI Sequence Read Archive (SRA) database and Biosample under accession number PRJNA542725.
DOI: 10.1016/j.dib.2019.104396
PubMed: 31667217
PubMed Central: PMC6811883
Affiliations:
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Madesis</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Applied Biosciences (INAB), CERTH, 6th Km Charilaou-Thermi Road, 57001, Thessaloniki, Greece.</nlm:affiliation><country xml:lang="fr">Grèce</country><wicri:regionArea>Institute of Applied Biosciences (INAB), CERTH, 6th Km Charilaou-Thermi Road, 57001, Thessaloniki</wicri:regionArea><wicri:noRegion>Thessaloniki</wicri:noRegion></affiliation></author></analytic><series><title level="j">Data in brief</title><idno type="eISSN">2352-3409</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The bacterial diversity in rhizosphere soil of pear trees (<i>Pyrus communis</i> L. cv. <i>Krystalli</i>) from an orchard at Thessaly region of Greece was characterized employing amplicon-based metagenomics analysis. Pathogenic filamentous oomycetes of the genus <i>Phytophthora</i> comprises more than 150 recognized species and cause highly destructive soil-borne diseases in deciduous trees crops worldwide. Moreover, the treatment of soil microbiota with amino acids is an alternative strategy to achieve desirable effects even against phytopathogenic oomycetes. In our study, samples from rhizosphere soil were collected either from naturally <i>Phytophthora</i>-infected trees, from completely asymptomatic ones, or from trees as above subjected also to treatments with amino acids (Amino16®) under different fertilization regimes. The interactions of bacterial communities with plant pathogenic oomycetes are crucial to determine the course of infection and the pathogenicity encompassing various functional contexts like biofilm formation. Thus, for deciphering the structure and diversity of these soil bacterial communities, we applied a 16S rRNA Illumina sequencing approach targeting the V3-V4 gene region. After quality check 478,479 sequences were obtained in the dataset comprising a total read length of 192,291,625 base pairs. <i>Proteobacteria</i> were the dominant phylum (46.1%) followed by <i>Acidobacteria</i> (13.2%) and <i>Actinobacteria</i> (12.4%). Different distributions of phyla were observed among our samples which is indicative of various alterations of soil bacterial communities in rhizosphere. The metagenome data from this survey are available at NCBI Sequence Read Archive (SRA) database and Biosample under accession number PRJNA542725.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">31667217</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">2352-3409</ISSN><JournalIssue CitedMedium="Internet"><Volume>26</Volume><PubDate><Year>2019</Year><Month>Oct</Month></PubDate></JournalIssue><Title>Data in brief</Title><ISOAbbreviation>Data Brief</ISOAbbreviation></Journal><ArticleTitle>Metagenome data of bacterial diversity in pear (<i>Pyrus communis</i> L.) rhizospheres associated with <i>Phytophthora</i> infection and amino acid treatment.</ArticleTitle><Pagination><MedlinePgn>104396</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.dib.2019.104396</ELocationID><Abstract><AbstractText>The bacterial diversity in rhizosphere soil of pear trees (<i>Pyrus communis</i> L. cv. <i>Krystalli</i>) from an orchard at Thessaly region of Greece was characterized employing amplicon-based metagenomics analysis. Pathogenic filamentous oomycetes of the genus <i>Phytophthora</i> comprises more than 150 recognized species and cause highly destructive soil-borne diseases in deciduous trees crops worldwide. Moreover, the treatment of soil microbiota with amino acids is an alternative strategy to achieve desirable effects even against phytopathogenic oomycetes. In our study, samples from rhizosphere soil were collected either from naturally <i>Phytophthora</i>-infected trees, from completely asymptomatic ones, or from trees as above subjected also to treatments with amino acids (Amino16®) under different fertilization regimes. The interactions of bacterial communities with plant pathogenic oomycetes are crucial to determine the course of infection and the pathogenicity encompassing various functional contexts like biofilm formation. Thus, for deciphering the structure and diversity of these soil bacterial communities, we applied a 16S rRNA Illumina sequencing approach targeting the V3-V4 gene region. After quality check 478,479 sequences were obtained in the dataset comprising a total read length of 192,291,625 base pairs. <i>Proteobacteria</i> were the dominant phylum (46.1%) followed by <i>Acidobacteria</i> (13.2%) and <i>Actinobacteria</i> (12.4%). Different distributions of phyla were observed among our samples which is indicative of various alterations of soil bacterial communities in rhizosphere. The metagenome data from this survey are available at NCBI Sequence Read Archive (SRA) database and Biosample under accession number PRJNA542725.</AbstractText><CopyrightInformation>© 2019 The Authors.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zambounis</LastName><ForeName>Antonios</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Institute of Plant Breeding and Genetic Resources, Department of Deciduous Fruit Trees, HAO, 'Demeter', Naoussa, Greece.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Osathanunkul</LastName><ForeName>Maslin</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Center of Excellence in Bioresources for Agriculture, Industry and Medicine Chiang Mai University, Chiang Mai, 50200, Thailand.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Madesis</LastName><ForeName>Panagiotis</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Institute of Applied Biosciences (INAB), CERTH, 6th Km Charilaou-Thermi Road, 57001, Thessaloniki, Greece.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>08</Month><Day>24</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>Data Brief</MedlineTA><NlmUniqueID>101654995</NlmUniqueID><ISSNLinking>2352-3409</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">16S bacteriome communities</Keyword><Keyword MajorTopicYN="N">Deep amplicon sequencing</Keyword><Keyword MajorTopicYN="N">Metagenomics</Keyword><Keyword MajorTopicYN="N">Oomycetes</Keyword><Keyword MajorTopicYN="N">Phytophthora</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>06</Month><Day>10</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2019</Year><Month>08</Month><Day>01</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>08</Month><Day>06</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>11</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>11</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>11</Month><Day>2</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">31667217</ArticleId><ArticleId 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IdType="pubmed">21700674</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>Grèce</li><li>Thaïlande</li></country></list><tree><country name="Grèce"><noRegion><name sortKey="Zambounis, Antonios" sort="Zambounis, Antonios" uniqKey="Zambounis A" first="Antonios" last="Zambounis">Antonios Zambounis</name></noRegion><name sortKey="Madesis, Panagiotis" sort="Madesis, Panagiotis" uniqKey="Madesis P" first="Panagiotis" last="Madesis">Panagiotis Madesis</name></country><country name="Thaïlande"><noRegion><name sortKey="Osathanunkul, Maslin" sort="Osathanunkul, Maslin" uniqKey="Osathanunkul M" first="Maslin" last="Osathanunkul">Maslin Osathanunkul</name></noRegion><name sortKey="Osathanunkul, Maslin" sort="Osathanunkul, Maslin" uniqKey="Osathanunkul M" first="Maslin" last="Osathanunkul">Maslin Osathanunkul</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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