Description of Deinococcus populi sp. nov. from the trunk surface of a Japanese aspen tree.
Identifieur interne : 000F65 ( Main/Exploration ); précédent : 000F64; suivant : 000F66Description of Deinococcus populi sp. nov. from the trunk surface of a Japanese aspen tree.
Auteurs : Juan Li [Japon] ; Chisaki Kudo [Japon] ; Akio Tonouchi [Japon]Source :
- Archives of microbiology [ 1432-072X ] ; 2018.
Descripteurs français
- KwdFr :
- ADN bactérien (génétique), ARN ribosomique 16S (génétique), Acides gras (analyse), Analyse de séquence d'ADN (MeSH), Composition en bases nucléiques (génétique), Deinococcus (classification), Deinococcus (génétique), Deinococcus (isolement et purification), Glycolipides (analyse), Hybridation d'acides nucléiques (MeSH), Peptidoglycane (composition chimique), Phospholipides (analyse), Phylogenèse (MeSH), Populus (microbiologie), Techniques de typage bactérien (MeSH), Vitamine K2 (analogues et dérivés), Vitamine K2 (analyse), Écorce (microbiologie).
- MESH :
- analogues et dérivés : Vitamine K2.
- analyse : Acides gras, Glycolipides, Phospholipides, Vitamine K2.
- composition chimique : Deinococcus, Peptidoglycane.
- génétique : ADN bactérien, ARN ribosomique 16S, Composition en bases nucléiques, Deinococcus.
- isolement et purification : Deinococcus.
- microbiologie : Populus, Écorce.
- Analyse de séquence d'ADN, Hybridation d'acides nucléiques, Phylogenèse, Techniques de typage bactérien.
English descriptors
- KwdEn :
- Bacterial Typing Techniques (MeSH), Base Composition (genetics), DNA, Bacterial (genetics), Deinococcus (classification), Deinococcus (genetics), Deinococcus (isolation & purification), Fatty Acids (analysis), Glycolipids (analysis), Nucleic Acid Hybridization (MeSH), Peptidoglycan (chemistry), Phospholipids (analysis), Phylogeny (MeSH), Plant Bark (microbiology), Populus (microbiology), RNA, Ribosomal, 16S (genetics), Sequence Analysis, DNA (MeSH), Vitamin K 2 (analogs & derivatives), Vitamin K 2 (analysis).
- MESH :
- chemical , analogs & derivatives : Vitamin K 2.
- chemical , analysis : Fatty Acids, Glycolipids, Phospholipids, Vitamin K 2.
- chemical , chemistry : Peptidoglycan.
- chemical , genetics : DNA, Bacterial, RNA, Ribosomal, 16S.
- classification : Deinococcus.
- genetics : Base Composition, Deinococcus.
- isolation & purification : Deinococcus.
- microbiology : Plant Bark, Populus.
- Bacterial Typing Techniques, Nucleic Acid Hybridization, Phylogeny, Sequence Analysis, DNA.
Abstract
A bacterial strain designated PtRA-8T was isolated from the trunk surface of a Japanese aspen tree (Populus tremula var. sieboldii). Cells of strain PtRA-8T were aerobic, non-motile, non-spore forming, Gram-stain-negative rods, 1.0‒2.0 µm in width and 3.0‒10.0 µm in length. The pH range for growth was between 5.5 and 7.5, with an optimum at 6.5. The temperature range for growth was between 10 and 37 °C, with an optimum at around 25‒30 °C. Strain PtRA-8T was highly resistant to UV irradiation, similar to its Deinococcus relatives. The respiratory quinone was menaquinone MK-8. The major cellular fatty acids (> 10% of the total fatty acid content) were iso-C15:0 (17.8%), C16:0 (15.0%), iso-C17:0 (10.4%), and iso-C17:1 ω9c/C16:010-methyl (22.2%). The polar lipids consisted of four unidentified glycolipids, two unidentified aminolipids, two unidentified phospholipids, and three unidentified polar lipids. The peptidoglycan was A3β-type containing glutamic acid, glycine, alanine, and ornithine. The DNA G + C content of strain PtRA-8T was 68.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PtRA-8T was closely related to "Deinococcus radioresistens" 8AT (97.4%), Deinococcus metalli DSM 27521T (95.7%), and Deinococcus yunweiensis YIM 007T (94.5%). The DNA-DNA hybridization experiments between strain PtRA-8T and its relatives yielded relatedness values below 70%. Based on the polyphasic evidence, we concluded that strain PtRA-8T represents a novel species within the genus Deinococcus, for which the name Deinococcus populi is proposed. The type strain of D. populi is PtRA-8T (= DSM 29820T= NBRC 110763T; DPD TaxonNumber TA00271).
DOI: 10.1007/s00203-017-1443-5
PubMed: 29080938
Affiliations:
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Ueda 3-chome, Morioka, Iwate, 020-8550</wicri:regionArea><wicri:noRegion>020-8550</wicri:noRegion></affiliation></author><author><name sortKey="Kudo, Chisaki" sort="Kudo, Chisaki" uniqKey="Kudo C" first="Chisaki" last="Kudo">Chisaki Kudo</name><affiliation wicri:level="1"><nlm:affiliation>Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561</wicri:regionArea><wicri:noRegion>036-8561</wicri:noRegion></affiliation></author><author><name sortKey="Tonouchi, Akio" sort="Tonouchi, Akio" uniqKey="Tonouchi A" first="Akio" last="Tonouchi">Akio Tonouchi</name><affiliation wicri:level="1"><nlm:affiliation>Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan. symbio@hirosaki-u.ac.jp.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561</wicri:regionArea><wicri:noRegion>036-8561</wicri:noRegion></affiliation></author></analytic><series><title level="j">Archives of microbiology</title><idno type="eISSN">1432-072X</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Bacterial Typing Techniques (MeSH)</term><term>Base Composition (genetics)</term><term>DNA, Bacterial (genetics)</term><term>Deinococcus (classification)</term><term>Deinococcus (genetics)</term><term>Deinococcus (isolation & purification)</term><term>Fatty Acids (analysis)</term><term>Glycolipids (analysis)</term><term>Nucleic Acid Hybridization (MeSH)</term><term>Peptidoglycan (chemistry)</term><term>Phospholipids (analysis)</term><term>Phylogeny (MeSH)</term><term>Plant Bark (microbiology)</term><term>Populus (microbiology)</term><term>RNA, Ribosomal, 16S (genetics)</term><term>Sequence Analysis, DNA (MeSH)</term><term>Vitamin K 2 (analogs & derivatives)</term><term>Vitamin K 2 (analysis)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN bactérien (génétique)</term><term>ARN ribosomique 16S (génétique)</term><term>Acides gras (analyse)</term><term>Analyse de séquence d'ADN (MeSH)</term><term>Composition en bases nucléiques (génétique)</term><term>Deinococcus (classification)</term><term>Deinococcus (génétique)</term><term>Deinococcus (isolement et purification)</term><term>Glycolipides (analyse)</term><term>Hybridation d'acides nucléiques (MeSH)</term><term>Peptidoglycane (composition chimique)</term><term>Phospholipides (analyse)</term><term>Phylogenèse (MeSH)</term><term>Populus (microbiologie)</term><term>Techniques de typage bactérien (MeSH)</term><term>Vitamine K2 (analogues et dérivés)</term><term>Vitamine K2 (analyse)</term><term>Écorce (microbiologie)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analogs & derivatives" xml:lang="en"><term>Vitamin K 2</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>Fatty Acids</term><term>Glycolipids</term><term>Phospholipids</term><term>Vitamin K 2</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Peptidoglycan</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Bacterial</term><term>RNA, Ribosomal, 16S</term></keywords><keywords scheme="MESH" qualifier="analogues et dérivés" xml:lang="fr"><term>Vitamine K2</term></keywords><keywords scheme="MESH" qualifier="analyse" xml:lang="fr"><term>Acides gras</term><term>Glycolipides</term><term>Phospholipides</term><term>Vitamine K2</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Deinococcus</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Deinococcus</term><term>Peptidoglycane</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Base Composition</term><term>Deinococcus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN bactérien</term><term>ARN ribosomique 16S</term><term>Composition en bases nucléiques</term><term>Deinococcus</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Deinococcus</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Deinococcus</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Populus</term><term>Écorce</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Plant Bark</term><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Bacterial Typing Techniques</term><term>Nucleic Acid Hybridization</term><term>Phylogeny</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Hybridation d'acides nucléiques</term><term>Phylogenèse</term><term>Techniques de typage bactérien</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">A bacterial strain designated PtRA-8<sup>T</sup> was isolated from the trunk surface of a Japanese aspen tree (Populus tremula var. sieboldii). Cells of strain PtRA-8<sup>T</sup> were aerobic, non-motile, non-spore forming, Gram-stain-negative rods, 1.0‒2.0 µm in width and 3.0‒10.0 µm in length. The pH range for growth was between 5.5 and 7.5, with an optimum at 6.5. The temperature range for growth was between 10 and 37 °C, with an optimum at around 25‒30 °C. Strain PtRA-8<sup>T</sup> was highly resistant to UV irradiation, similar to its Deinococcus relatives. The respiratory quinone was menaquinone MK-8. The major cellular fatty acids (> 10% of the total fatty acid content) were iso-C<sub>15:0</sub> (17.8%), C<sub>16:0</sub> (15.0%), iso-C<sub>17:0</sub> (10.4%), and iso-C<sub>17:1</sub> ω9c/C<sub>16:0</sub>10-methyl (22.2%). The polar lipids consisted of four unidentified glycolipids, two unidentified aminolipids, two unidentified phospholipids, and three unidentified polar lipids. The peptidoglycan was A3β-type containing glutamic acid, glycine, alanine, and ornithine. The DNA G + C content of strain PtRA-8<sup>T</sup> was 68.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PtRA-8<sup>T</sup> was closely related to "Deinococcus radioresistens" 8A<sup>T</sup> (97.4%), Deinococcus metalli DSM 27521<sup>T</sup> (95.7%), and Deinococcus yunweiensis YIM 007<sup>T</sup> (94.5%). The DNA-DNA hybridization experiments between strain PtRA-8<sup>T</sup> and its relatives yielded relatedness values below 70%. Based on the polyphasic evidence, we concluded that strain PtRA-8<sup>T</sup> represents a novel species within the genus Deinococcus, for which the name Deinococcus populi is proposed. The type strain of D. populi is PtRA-8<sup>T</sup> (= DSM 29820<sup>T</sup>= NBRC 110763<sup>T</sup>; DPD TaxonNumber TA00271).</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">29080938</PMID><DateCompleted><Year>2018</Year><Month>05</Month><Day>10</Day></DateCompleted><DateRevised><Year>2018</Year><Month>12</Month><Day>02</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1432-072X</ISSN><JournalIssue CitedMedium="Internet"><Volume>200</Volume><Issue>2</Issue><PubDate><Year>2018</Year><Month>Mar</Month></PubDate></JournalIssue><Title>Archives of microbiology</Title><ISOAbbreviation>Arch Microbiol</ISOAbbreviation></Journal><ArticleTitle>Description of Deinococcus populi sp. nov. from the trunk surface of a Japanese aspen tree.</ArticleTitle><Pagination><MedlinePgn>291-297</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s00203-017-1443-5</ELocationID><Abstract><AbstractText>A bacterial strain designated PtRA-8<sup>T</sup> was isolated from the trunk surface of a Japanese aspen tree (Populus tremula var. sieboldii). Cells of strain PtRA-8<sup>T</sup> were aerobic, non-motile, non-spore forming, Gram-stain-negative rods, 1.0‒2.0 µm in width and 3.0‒10.0 µm in length. The pH range for growth was between 5.5 and 7.5, with an optimum at 6.5. The temperature range for growth was between 10 and 37 °C, with an optimum at around 25‒30 °C. Strain PtRA-8<sup>T</sup> was highly resistant to UV irradiation, similar to its Deinococcus relatives. The respiratory quinone was menaquinone MK-8. The major cellular fatty acids (> 10% of the total fatty acid content) were iso-C<sub>15:0</sub> (17.8%), C<sub>16:0</sub> (15.0%), iso-C<sub>17:0</sub> (10.4%), and iso-C<sub>17:1</sub> ω9c/C<sub>16:0</sub>10-methyl (22.2%). The polar lipids consisted of four unidentified glycolipids, two unidentified aminolipids, two unidentified phospholipids, and three unidentified polar lipids. The peptidoglycan was A3β-type containing glutamic acid, glycine, alanine, and ornithine. The DNA G + C content of strain PtRA-8<sup>T</sup> was 68.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PtRA-8<sup>T</sup> was closely related to "Deinococcus radioresistens" 8A<sup>T</sup> (97.4%), Deinococcus metalli DSM 27521<sup>T</sup> (95.7%), and Deinococcus yunweiensis YIM 007<sup>T</sup> (94.5%). The DNA-DNA hybridization experiments between strain PtRA-8<sup>T</sup> and its relatives yielded relatedness values below 70%. Based on the polyphasic evidence, we concluded that strain PtRA-8<sup>T</sup> represents a novel species within the genus Deinococcus, for which the name Deinococcus populi is proposed. The type strain of D. populi is PtRA-8<sup>T</sup> (= DSM 29820<sup>T</sup>= NBRC 110763<sup>T</sup>; DPD TaxonNumber TA00271).</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Juan</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>United Graduate School of Agricultural Sciences, Iwate University, 18-8 Ueda 3-chome, Morioka, Iwate, 020-8550, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kudo</LastName><ForeName>Chisaki</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tonouchi</LastName><ForeName>Akio</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan. symbio@hirosaki-u.ac.jp.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>10</Month><Day>28</Day></ArticleDate></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>Arch Microbiol</MedlineTA><NlmUniqueID>0410427</NlmUniqueID><ISSNLinking>0302-8933</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004269">DNA, Bacterial</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005227">Fatty Acids</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D006017">Glycolipids</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010457">Peptidoglycan</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010743">Phospholipids</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012336">RNA, Ribosomal, 16S</NameOfSubstance></Chemical><Chemical><RegistryNumber>11032-49-8</RegistryNumber><NameOfSubstance UI="D024482">Vitamin K 2</NameOfSubstance></Chemical><Chemical><RegistryNumber>523-38-6</RegistryNumber><NameOfSubstance UI="C024223">vitamin MK 8</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D015373" MajorTopicYN="N">Bacterial Typing Techniques</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001482" MajorTopicYN="N">Base Composition</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004269" MajorTopicYN="N">DNA, Bacterial</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D034301" MajorTopicYN="N">Deinococcus</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="Y">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000302" MajorTopicYN="Y">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005227" MajorTopicYN="N">Fatty Acids</DescriptorName><QualifierName UI="Q000032" MajorTopicYN="N">analysis</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006017" MajorTopicYN="N">Glycolipids</DescriptorName><QualifierName UI="Q000032" MajorTopicYN="N">analysis</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D009693" MajorTopicYN="N">Nucleic Acid Hybridization</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010457" MajorTopicYN="N">Peptidoglycan</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010743" MajorTopicYN="N">Phospholipids</DescriptorName><QualifierName UI="Q000032" MajorTopicYN="N">analysis</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D024301" MajorTopicYN="N">Plant Bark</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012336" MajorTopicYN="N">RNA, Ribosomal, 16S</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D024482" MajorTopicYN="N">Vitamin K 2</DescriptorName><QualifierName UI="Q000031" MajorTopicYN="N">analogs & derivatives</QualifierName><QualifierName UI="Q000032" MajorTopicYN="N">analysis</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Deinococcus</Keyword><Keyword MajorTopicYN="N">Japanese aspen tree</Keyword><Keyword MajorTopicYN="N">Phyllosphere</Keyword><Keyword MajorTopicYN="N">Populus tremula var. sieboldii</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>06</Month><Day>28</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>10</Month><Day>19</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2017</Year><Month>09</Month><Day>29</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>10</Month><Day>31</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2018</Year><Month>5</Month><Day>11</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>10</Month><Day>30</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">29080938</ArticleId><ArticleId IdType="doi">10.1007/s00203-017-1443-5</ArticleId><ArticleId IdType="pii">10.1007/s00203-017-1443-5</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Japon</li></country></list><tree><country name="Japon"><noRegion><name sortKey="Li, Juan" sort="Li, Juan" uniqKey="Li J" first="Juan" last="Li">Juan Li</name></noRegion><name sortKey="Kudo, Chisaki" sort="Kudo, Chisaki" uniqKey="Kudo C" first="Chisaki" last="Kudo">Chisaki Kudo</name><name sortKey="Tonouchi, Akio" 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