Flavobacterium pokkalii sp. nov., a novel plant growth promoting native rhizobacteria isolated from pokkali rice grown in coastal saline affected agricultural regions of southern India, Kerala.
Identifieur interne : 000034 ( Main/Exploration ); précédent : 000033; suivant : 000035Flavobacterium pokkalii sp. nov., a novel plant growth promoting native rhizobacteria isolated from pokkali rice grown in coastal saline affected agricultural regions of southern India, Kerala.
Auteurs : Rahul R. Menon [Inde] ; Sunitha Kumari [Inde] ; Tomeu Viver [Espagne] ; N. Rameshkumar [Inde]Source :
- Microbiological research [ 1618-0623 ] ; 2020.
Abstract
Nine plant-associated bacterial strains designated as L1I52T, NRK F1, NRK F15, NRK F16, NRK F41, NRK F42, NRK F47, NRK F49, and NRK F50 originating from the roots and rhizosphere region of a coastal saline tolerant pokkali rice were taxonomically characterized in this study. Genomic fingerprinting using Enterobacterial Repetitive Intergenic Consensus (ERIC) primers discriminated the nine strains based on the DNA fingerprint patterns indicating that they were not clonal in origin. Phylogenetic analysis using 16S rRNA and other five housekeeping genes (gyrB, glyA, atpA, dnaK and murG) revealed that the novel strains constituted a single novel species within the genus Flavobacterium. In all tree construction methods, the novel strains formed a distinct phylogenetic branch, with Flavobacterium daejeonense GH1-10T, F. sufflavum BBQ-12T, and F. glycines Gm-149T as their nearest phylogenetic neighbours. However, average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) comparison between the draft genomes of L1I52T (representative isolate) and it's nearest phylogenetic neighbours were well below the proposed threshold values (<95 % and <70 %) used for species discrimination. Thus, based on the phenotypic, genotypic and chemotaxonomic data obtained in this study, we describe a novel Flavobacterium species for which we propose the name Flavobacterium pokkalii sp.nov., with strain L1I52T (=MTCC 12454T=KCTC 42429T) as the type strain. In addition, L1I52T is a potential plant growth promoting rhizobacteria as they can promote pokkali rice growth and we identified several plant associated gene features in the genome of L1I52T that are potentially involved in plant microbe interactions.
DOI: 10.1016/j.micres.2020.126533
PubMed: 32629361
Affiliations:
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Menon</name><affiliation wicri:level="1"><nlm:affiliation>Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695 019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad - 201002, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695 019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad - 201002</wicri:regionArea><wicri:noRegion>Ghaziabad - 201002</wicri:noRegion></affiliation></author><author><name sortKey="Kumari, Sunitha" sort="Kumari, Sunitha" uniqKey="Kumari S" first="Sunitha" last="Kumari">Sunitha Kumari</name><affiliation wicri:level="1"><nlm:affiliation>Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695 019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad - 201002, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695 019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad - 201002</wicri:regionArea><wicri:noRegion>Ghaziabad - 201002</wicri:noRegion></affiliation></author><author><name sortKey="Viver, Tomeu" sort="Viver, Tomeu" uniqKey="Viver T" first="Tomeu" last="Viver">Tomeu Viver</name><affiliation wicri:level="1"><nlm:affiliation>Marine Microbiology Group, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Marine Microbiology Group, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles</wicri:regionArea><wicri:noRegion>Esporles</wicri:noRegion></affiliation></author><author><name sortKey="Rameshkumar, N" sort="Rameshkumar, N" uniqKey="Rameshkumar N" first="N" last="Rameshkumar">N. Rameshkumar</name><affiliation wicri:level="1"><nlm:affiliation>Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695 019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad - 201002, India. Electronic address: rameshkumar@niist.res.in.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695 019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad - 201002</wicri:regionArea><wicri:noRegion>Ghaziabad - 201002</wicri:noRegion></affiliation></author></analytic><series><title level="j">Microbiological research</title><idno type="eISSN">1618-0623</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Nine plant-associated bacterial strains designated as L1I52<sup>T</sup>, NRK F1, NRK F15, NRK F16, NRK F41, NRK F42, NRK F47, NRK F49, and NRK F50 originating from the roots and rhizosphere region of a coastal saline tolerant pokkali rice were taxonomically characterized in this study. Genomic fingerprinting using Enterobacterial Repetitive Intergenic Consensus (ERIC) primers discriminated the nine strains based on the DNA fingerprint patterns indicating that they were not clonal in origin. Phylogenetic analysis using 16S rRNA and other five housekeeping genes (gyrB, glyA, atpA, dnaK and murG) revealed that the novel strains constituted a single novel species within the genus Flavobacterium. In all tree construction methods, the novel strains formed a distinct phylogenetic branch, with Flavobacterium daejeonense GH1-10<sup>T</sup>, F. sufflavum BBQ-12<sup>T</sup>, and F. glycines Gm-149<sup>T</sup> as their nearest phylogenetic neighbours. However, average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) comparison between the draft genomes of L1I52<sup>T</sup> (representative isolate) and it's nearest phylogenetic neighbours were well below the proposed threshold values (<95 % and <70 %) used for species discrimination. Thus, based on the phenotypic, genotypic and chemotaxonomic data obtained in this study, we describe a novel Flavobacterium species for which we propose the name Flavobacterium pokkalii sp.nov., with strain L1I52<sup>T</sup> (=MTCC 12454<sup>T</sup>=KCTC 42429<sup>T</sup>) as the type strain. In addition, L1I52<sup>T</sup> is a potential plant growth promoting rhizobacteria as they can promote pokkali rice growth and we identified several plant associated gene features in the genome of L1I52<sup>T</sup> that are potentially involved in plant microbe interactions.</div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">32629361</PMID><DateRevised><Year>2020</Year><Month>10</Month><Day>16</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1618-0623</ISSN><JournalIssue CitedMedium="Internet"><Volume>240</Volume><PubDate><Year>2020</Year><Month>Nov</Month></PubDate></JournalIssue><Title>Microbiological research</Title><ISOAbbreviation>Microbiol Res</ISOAbbreviation></Journal><ArticleTitle>Flavobacterium pokkalii sp. nov., a novel plant growth promoting native rhizobacteria isolated from pokkali rice grown in coastal saline affected agricultural regions of southern India, Kerala.</ArticleTitle><Pagination><MedlinePgn>126533</MedlinePgn></Pagination><ELocationID EIdType="pii" ValidYN="Y">S0944-5013(20)30401-8</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.micres.2020.126533</ELocationID><Abstract><AbstractText>Nine plant-associated bacterial strains designated as L1I52<sup>T</sup>, NRK F1, NRK F15, NRK F16, NRK F41, NRK F42, NRK F47, NRK F49, and NRK F50 originating from the roots and rhizosphere region of a coastal saline tolerant pokkali rice were taxonomically characterized in this study. Genomic fingerprinting using Enterobacterial Repetitive Intergenic Consensus (ERIC) primers discriminated the nine strains based on the DNA fingerprint patterns indicating that they were not clonal in origin. Phylogenetic analysis using 16S rRNA and other five housekeeping genes (gyrB, glyA, atpA, dnaK and murG) revealed that the novel strains constituted a single novel species within the genus Flavobacterium. In all tree construction methods, the novel strains formed a distinct phylogenetic branch, with Flavobacterium daejeonense GH1-10<sup>T</sup>, F. sufflavum BBQ-12<sup>T</sup>, and F. glycines Gm-149<sup>T</sup> as their nearest phylogenetic neighbours. However, average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) comparison between the draft genomes of L1I52<sup>T</sup> (representative isolate) and it's nearest phylogenetic neighbours were well below the proposed threshold values (<95 % and <70 %) used for species discrimination. Thus, based on the phenotypic, genotypic and chemotaxonomic data obtained in this study, we describe a novel Flavobacterium species for which we propose the name Flavobacterium pokkalii sp.nov., with strain L1I52<sup>T</sup> (=MTCC 12454<sup>T</sup>=KCTC 42429<sup>T</sup>) as the type strain. In addition, L1I52<sup>T</sup> is a potential plant growth promoting rhizobacteria as they can promote pokkali rice growth and we identified several plant associated gene features in the genome of L1I52<sup>T</sup> that are potentially involved in plant microbe interactions.</AbstractText><CopyrightInformation>Copyright © 2020 Elsevier GmbH. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Menon</LastName><ForeName>Rahul R</ForeName><Initials>RR</Initials><AffiliationInfo><Affiliation>Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695 019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad - 201002, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kumari</LastName><ForeName>Sunitha</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695 019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad - 201002, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Viver</LastName><ForeName>Tomeu</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Marine Microbiology Group, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rameshkumar</LastName><ForeName>N</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695 019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad - 201002, India. Electronic address: rameshkumar@niist.res.in.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>06</Month><Day>23</Day></ArticleDate></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>Microbiol Res</MedlineTA><NlmUniqueID>9437794</NlmUniqueID><ISSNLinking>0944-5013</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Brackish rice</Keyword><Keyword MajorTopicYN="N">Flavobacterium</Keyword><Keyword MajorTopicYN="N">PGPR</Keyword><Keyword MajorTopicYN="N">Pokkali</Keyword><Keyword MajorTopicYN="N">Rhizobacteria</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>03</Month><Day>27</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>06</Month><Day>06</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>7</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>7</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>7</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32629361</ArticleId><ArticleId IdType="pii">S0944-5013(20)30401-8</ArticleId><ArticleId IdType="doi">10.1016/j.micres.2020.126533</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Espagne</li><li>Inde</li></country></list><tree><country name="Inde"><noRegion><name sortKey="Menon, Rahul R" sort="Menon, Rahul R" uniqKey="Menon R" first="Rahul R" last="Menon">Rahul R. Menon</name></noRegion><name sortKey="Kumari, Sunitha" sort="Kumari, Sunitha" uniqKey="Kumari S" first="Sunitha" last="Kumari">Sunitha Kumari</name><name sortKey="Rameshkumar, N" sort="Rameshkumar, N" uniqKey="Rameshkumar N" first="N" last="Rameshkumar">N. Rameshkumar</name></country><country name="Espagne"><noRegion><name sortKey="Viver, Tomeu" sort="Viver, Tomeu" uniqKey="Viver T" first="Tomeu" last="Viver">Tomeu Viver</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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