191 lines
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191 lines
14 KiB
XML
<document ID-DOI="http://doi.org/10.5281/zenodo.5728362" ID-GBIF-Dataset="a4edc281-0cb2-4c24-b652-aa6157ac84af" ID-GBIF-Taxon="190793284" ID-ISSN="1055-7903" ID-Zenodo-Dep="5728362" approvalRequired="5" approvalRequired_for_bibRefs="1" approvalRequired_for_document="1" approvalRequired_for_treatments="3" checkinTime="1637882316881" checkinUser="felipe" docAuthor="Avontuur, Juanita R., Palmer, Marike, Beukes, Chrizelle W., Chan, Wai Y., Tasiya, Taponeswa, Zyl, Elritha van, Coetzee, Martin P. A., Stepkowski, Tomasz, Venter, Stephanus N. & Steenkamp, Emma T." docDate="2022" docId="C069AB7BFF98FF88FFDFE9F52EDF8161" docLanguage="en" docName="MolecularPhylogeneticsEvolution.166.107338.pdf" docOrigin="Molecular Phylogenetics and Evolution (107338) 167" docTitle="Bradyrhizobium oropedii Avontuur & Palmer & Beukes & Chan & Tasiya & Zyl & Coetzee & Stepkowski & Venter & Steenkamp 2022, sp. nov." docType="treatment" docVersion="5" lastPageNumber="10" masterDocId="3C50D303FF91FF81FFBBED6B2D748077" masterDocTitle="Bradyrhizobium altum sp. nov., Bradyrhizobium oropedii sp. nov. and Bradyrhizobium acaciae sp. nov. from South Africa show locally restricted and pantropical nodA phylogeographic patterns" masterLastPageNumber="13" masterPageNumber="1" pageId="9" pageNumber="10" updateTime="1637888292042" updateUser="ExternalLinkService">
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<mods:mods xmlns:mods="http://www.loc.gov/mods/v3">
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<mods:titleInfo>
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<mods:title>Bradyrhizobium altum sp. nov., Bradyrhizobium oropedii sp. nov. and Bradyrhizobium acaciae sp. nov. from South Africa show locally restricted and pantropical nodA phylogeographic patterns</mods:title>
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</mods:titleInfo>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Avontuur, Juanita R.</mods:namePart>
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<mods:affiliation>Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa</mods:affiliation>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Palmer, Marike</mods:namePart>
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<mods:affiliation>School of Life Sciences, University of Nevada, Las Vegas, Nevada, United States</mods:affiliation>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Beukes, Chrizelle W.</mods:namePart>
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<mods:affiliation>Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa</mods:affiliation>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Chan, Wai Y.</mods:namePart>
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<mods:affiliation>Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa & National Institute for Communicable Disease, National Health Laboratory Service, Johannesburg, South Africa</mods:affiliation>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Tasiya, Taponeswa</mods:namePart>
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<mods:affiliation>Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa</mods:affiliation>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Zyl, Elritha van</mods:namePart>
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<mods:affiliation>Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa</mods:affiliation>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Coetzee, Martin P. A.</mods:namePart>
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<mods:affiliation>Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa</mods:affiliation>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Stepkowski, Tomasz</mods:namePart>
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<mods:affiliation>Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Poland</mods:affiliation>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Venter, Stephanus N.</mods:namePart>
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<mods:affiliation>Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa</mods:affiliation>
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<mods:nameIdentifier type="email">fanus.venter@up.ac.za</mods:nameIdentifier>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Steenkamp, Emma T.</mods:namePart>
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<mods:affiliation>Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa</mods:affiliation>
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</mods:name>
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<mods:typeOfResource>text</mods:typeOfResource>
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<mods:relatedItem type="host">
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<mods:titleInfo>
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<mods:title>Molecular Phylogenetics and Evolution</mods:title>
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</mods:titleInfo>
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<mods:part>
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<mods:date>2022</mods:date>
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<mods:detail type="series">
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<mods:title>107338</mods:title>
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</mods:detail>
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<mods:detail type="pubDate">
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<mods:number>2021-10-29</mods:number>
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</mods:detail>
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<mods:detail type="volume">
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<mods:number>167</mods:number>
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</mods:detail>
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<mods:extent unit="page">
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<mods:start>1</mods:start>
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<mods:end>13</mods:end>
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</mods:extent>
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</mods:part>
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</mods:relatedItem>
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<mods:classification>journal article</mods:classification>
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<mods:identifier type="DOI">10.1016/j.ympev.2021.107338</mods:identifier>
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<mods:identifier type="GBIF-Dataset">a4edc281-0cb2-4c24-b652-aa6157ac84af</mods:identifier>
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<mods:identifier type="ISSN">1055-7903</mods:identifier>
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<mods:identifier type="Zenodo-Dep">5728354</mods:identifier>
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</mods:mods>
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<treatment ID-DOI="http://doi.org/10.5281/zenodo.5728362" ID-GBIF-Taxon="190793284" ID-Zenodo-Dep="5728362" LSID="urn:lsid:plazi:treatment:C069AB7BFF98FF88FFDFE9F52EDF8161" httpUri="http://treatment.plazi.org/id/C069AB7BFF98FF88FFDFE9F52EDF8161" lastPageNumber="10" pageId="9" pageNumber="10">
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<subSubSection box="[100,577,1181,1201]" pageId="9" pageNumber="10" type="nomenclature">
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<paragraph blockId="9.[100,577,1181,1201]" box="[100,577,1181,1201]" pageId="9" pageNumber="10">
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<heading box="[100,577,1181,1201]" level="2" pageId="9" pageNumber="10">
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<emphasis bold="true" box="[100,577,1181,1201]" italics="true" pageId="9" pageNumber="10">
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4.2. Description of
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<taxonomicName authority="Avontuur & Palmer & Beukes & Chan & Tasiya & Zyl & Coetzee & Stepkowski & Venter & Steenkamp, 2022" authorityName="Avontuur & Palmer & Beukes & Chan & Tasiya & Zyl & Coetzee & Stepkowski & Venter & Steenkamp" authorityYear="2022" box="[280,501,1181,1200]" class="Alphaproteobacteria" family="Bradyrhizobiaceae" genus="Bradyrhizobium" kingdom="Bacteria" order="Rhizobiales" pageId="9" pageNumber="10" phylum="Proteobacteria" rank="species" species="oropedii" status="sp. nov.">Bradyrhizobium oropedii</taxonomicName>
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<taxonomicNameLabel box="[508,577,1182,1201]" pageId="9" pageNumber="10" rank="species">sp. nov.</taxonomicNameLabel>
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</emphasis>
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</heading>
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</paragraph>
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</subSubSection>
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<subSubSection pageId="9" pageNumber="10" type="etymology">
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<paragraph blockId="9.[100,771,1237,1982]" pageId="9" pageNumber="10">
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<taxonomicName authorityName="Avontuur & Palmer & Beukes & Chan & Tasiya & Zyl & Coetzee & Stepkowski & Venter & Steenkamp" authorityYear="2022" box="[132,351,1237,1256]" class="Alphaproteobacteria" family="Bradyrhizobiaceae" genus="Bradyrhizobium" kingdom="Bacteria" order="Rhizobiales" pageId="9" pageNumber="10" phylum="Proteobacteria" rank="species" species="oropedii">
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<emphasis bold="true" box="[132,351,1237,1256]" italics="true" pageId="9" pageNumber="10">Bradyrhizobium oropedii</emphasis>
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</taxonomicName>
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(o.ro.pe’ di.i. Gr. neut. n.
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<emphasis bold="true" box="[587,675,1237,1256]" italics="true" pageId="9" pageNumber="10">oropedion</emphasis>
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mountain plain; N.L. gen. n.
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<taxonomicName authorityName="Avontuur & Palmer & Beukes & Chan & Tasiya & Zyl & Coetzee & Stepkowski & Venter & Steenkamp" authorityYear="2022" box="[270,342,1265,1284]" class="Alphaproteobacteria" family="Bradyrhizobiaceae" genus="Bradyrhizobium" kingdom="Bacteria" order="Rhizobiales" pageId="9" pageNumber="10" phylum="Proteobacteria" rank="species" species="oropedii">
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<emphasis bold="true" box="[270,342,1265,1284]" italics="true" pageId="9" pageNumber="10">oropedii</emphasis>
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</taxonomicName>
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, of the central Southern African plateau, from where the species was isolated).
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</paragraph>
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</subSubSection>
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<subSubSection pageId="9" pageNumber="10" type="description">
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<paragraph blockId="9.[100,771,1237,1982]" pageId="9" pageNumber="10">
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Cells are motile, Gram-negative, rod shaped and approximately 1.87 × 0.48 μm in size. Growth occurs on YMA at 28
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<superScript attach="right" box="[581,588,1346,1359]" fontSize="6" pageId="9" pageNumber="10">◦</superScript>
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C after 7 days and colonies are translucent to opaque, circular, convex and cream in colour. Grows at pH values ranging from 5 to 10 and at temperatures ranging from 15 to 35
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<superScript attach="right" box="[241,248,1429,1442]" fontSize="6" pageId="9" pageNumber="10">◦</superScript>
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C. Isolates are unable to grow in the presence of more than 0.5% NaCl (w/v). Strains tested positive for oxidase, catalase, urease and β- glucosidase activity as well as the production of Tween 40 and Tween 80. Tested positive for the following carbon sources: Dfructose, L-fructose, D-gluconic acid, D-mannitol, α and β- hydroxy butyric acid, p-hydroxy phenylacetic acid, L-alaninamide, L-lactic acid, L-leucine, D-saccharic acid, and urocanic acid. Negative reactions were recorded for indole production and the assimilation of capric acid, adipic acid, malic acid, glycogen, α- D-lactose, N-acetyl-D-galactosamine, α- cyclodextrin, Adonitol, D-cellobiose, D-raffinose, i-erythritol, maltose, lactulose, D-melibiose, sucrose, D-trehalose, turanose, xylitol, L-threonine, uridine, inosine, thymine, glucose-1-phosphate and glucose-6-phosphate, and m-inositol. Resistant to ampicillin (10 μg/ml), chloramphenicol (30 μg/ml), tetracycline (30 μg/ml), penicillin (10 μg/ ml), and susceptible to streptomycin (25 μg/ml).
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</paragraph>
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</subSubSection>
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<subSubSection pageId="9" pageNumber="10" type="materials_examined">
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<paragraph blockId="9.[100,771,1237,1982]" lastBlockId="9.[818,1488,148,278]" pageId="9" pageNumber="10">
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The type strain, Pear76
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<superScript attach="left" box="[352,362,1845,1859]" fontSize="6" pageId="9" pageNumber="10">T</superScript>
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(=SARCC 731 = LMG 31408) was isolated from root nodules of
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<taxonomicName box="[310,476,1878,1898]" class="Magnoliopsida" family="Fabaceae" genus="Pearsonia" kingdom="Plantae" order="Fabales" pageId="9" pageNumber="10" phylum="Tracheophyta" rank="species" species="obovata">
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<emphasis bold="true" box="[310,476,1878,1898]" italics="true" pageId="9" pageNumber="10">Pearsonia obovata</emphasis>
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</taxonomicName>
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in the Dullstroom area of the Mpumalanga Province, South Africa and forms effective nodules on cowpea (
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<taxonomicName box="[189,353,1934,1954]" class="Magnoliopsida" family="Fabaceae" genus="Vigna" kingdom="Plantae" order="Fabales" pageId="9" pageNumber="10" phylum="Tracheophyta" rank="species" species="unguiculata">
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<emphasis bold="true" box="[189,353,1934,1954]" italics="true" pageId="9" pageNumber="10">Vigna unguiculata</emphasis>
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</taxonomicName>
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) and siratro (
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<taxonomicName box="[495,755,1934,1954]" class="Magnoliopsida" family="Fabaceae" genus="Macroptilium" kingdom="Plantae" order="Fabales" pageId="9" pageNumber="10" phylum="Tracheophyta" rank="species" species="atropurpureum">
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<emphasis bold="true" box="[495,755,1934,1954]" italics="true" pageId="9" pageNumber="10">Macroptilium atropurpureum</emphasis>
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</taxonomicName>
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). The DNA G + Ccontent of the type strain is 63.5 mol%. GenBank/ EMBL/DDBJ accession numbers for the genome sequence and the gene sequences of this type strain are:
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<materialsCitation ID-GBIF-Occurrence="3411891302" pageId="9" pageNumber="10" specimenCount="1">
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whole genome (
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<accessionNumber box="[1284,1481,176,195]" pageId="9" pageNumber="10">JACMYO000000000</accessionNumber>
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) and 16S rRNA (
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<accessionNumber box="[968,1071,204,223]" pageId="9" pageNumber="10">LR877297</accessionNumber>
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),
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<emphasis bold="true" box="[1088,1130,204,223]" italics="true" pageId="9" pageNumber="10">atpD</emphasis>
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(
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<accessionNumber box="[1144,1248,203,222]" pageId="9" pageNumber="10">LN650103</accessionNumber>
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),
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<emphasis bold="true" box="[1265,1305,203,222]" italics="true" pageId="9" pageNumber="10">glnII</emphasis>
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(
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<accessionNumber box="[1318,1423,203,222]" pageId="9" pageNumber="10">LN650145</accessionNumber>
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),
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<emphasis bold="true" box="[1440,1487,203,222]" italics="true" pageId="9" pageNumber="10">dnaK</emphasis>
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(
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<accessionNumber box="[824,926,231,250]" pageId="9" pageNumber="10">LN650124</accessionNumber>
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),
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<emphasis bold="true" box="[963,1004,232,251]" italics="true" pageId="9" pageNumber="10">gyrB</emphasis>
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(
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<accessionNumber box="[1035,1139,231,250]" pageId="9" pageNumber="10">LN650208</accessionNumber>
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),
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<emphasis bold="true" box="[1174,1216,232,251]" italics="true" pageId="9" pageNumber="10">rpoB</emphasis>
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(
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<accessionNumber box="[1247,1348,231,250]" pageId="9" pageNumber="10">LN650187</accessionNumber>
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) and
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<emphasis bold="true" box="[1440,1488,231,250]" italics="true" pageId="9" pageNumber="10">nodA</emphasis>
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(
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<accessionNumber box="[824,929,259,278]" pageId="9" pageNumber="10">LN650250</accessionNumber>
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).
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</materialsCitation>
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</paragraph>
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</subSubSection>
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</treatment>
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</document> |