191 lines
14 KiB
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191 lines
14 KiB
XML
<document ID-DOI="http://doi.org/10.5281/zenodo.5728366" ID-GBIF-Dataset="a4edc281-0cb2-4c24-b652-aa6157ac84af" ID-GBIF-Taxon="190793285" ID-ISSN="1055-7903" ID-Zenodo-Dep="5728366" 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="C069AB7BFF98FF88FC89EC24297E851D" docLanguage="en" docName="MolecularPhylogeneticsEvolution.166.107338.pdf" docOrigin="Molecular Phylogenetics and Evolution (107338) 167" docTitle="Bradyrhizobium altum Avontuur & Palmer & Beukes & Chan & Tasiya & Zyl & Coetzee & Stepkowski & Venter & Steenkamp 2022, sp. nov." docType="treatment" docVersion="4" 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.5728366" ID-GBIF-Taxon="190793285" ID-Zenodo-Dep="5728366" LSID="urn:lsid:plazi:treatment:C069AB7BFF98FF88FC89EC24297E851D" httpUri="http://treatment.plazi.org/id/C069AB7BFF98FF88FC89EC24297E851D" lastPageNumber="10" pageId="9" pageNumber="10">
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<subSubSection box="[818,1274,335,354]" pageId="9" pageNumber="10" type="nomenclature">
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<paragraph blockId="9.[818,1274,335,354]" box="[818,1274,335,354]" pageId="9" pageNumber="10">
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<heading box="[818,1274,335,354]" level="2" pageId="9" pageNumber="10">
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<emphasis bold="true" box="[818,1274,335,354]" italics="true" pageId="9" pageNumber="10">
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4.3. 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="[997,1197,335,354]" class="Alphaproteobacteria" family="Bradyrhizobiaceae" genus="Bradyrhizobium" kingdom="Bacteria" order="Rhizobiales" pageId="9" pageNumber="10" phylum="Proteobacteria" rank="species" species="altum" status="sp. nov.">Bradyrhizobium altum</taxonomicName>
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<taxonomicNameLabel box="[1204,1274,335,354]" 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.[818,1488,391,1386]" pageId="9" pageNumber="10">
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<taxonomicName authorityName="Avontuur & Palmer & Beukes & Chan & Tasiya & Zyl & Coetzee & Stepkowski & Venter & Steenkamp" authorityYear="2022" box="[849,1050,391,410]" class="Alphaproteobacteria" family="Bradyrhizobiaceae" genus="Bradyrhizobium" kingdom="Bacteria" order="Rhizobiales" pageId="9" pageNumber="10" phylum="Proteobacteria" rank="species" species="altum">
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<emphasis bold="true" box="[849,1050,391,410]" italics="true" pageId="9" pageNumber="10">Bradyrhizobium altum</emphasis>
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</taxonomicName>
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(al’ tum. L. neut. adj.
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<taxonomicName authorityName="Avontuur & Palmer & Beukes & Chan & Tasiya & Zyl & Coetzee & Stepkowski & Venter & Steenkamp" authorityYear="2022" box="[1260,1311,391,410]" class="Alphaproteobacteria" family="Bradyrhizobiaceae" genus="Bradyrhizobium" kingdom="Bacteria" order="Rhizobiales" pageId="9" pageNumber="10" phylum="Proteobacteria" rank="species" species="altum">
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<emphasis bold="true" box="[1260,1311,391,410]" italics="true" pageId="9" pageNumber="10">altum</emphasis>
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</taxonomicName>
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, high, referring to the high-altitude region where this species was isolated from).
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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.[818,1488,391,1386]" pageId="9" pageNumber="10">
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Cells are motile, Gram-negative rods and is approximately 1.29 × 0.45 μm in size. Colonies are circular, convex, opaque, cream in colour and
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<emphasis box="[852,868,503,522]" italics="true" pageId="9" pageNumber="10"><</emphasis>
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1 mm in diameteron YMA after 7 daysincubation at 28
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<superScript attach="right" box="[1386,1393,499,512]" fontSize="6" pageId="9" pageNumber="10">◦</superScript>
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C. The pH range for growth on YMA is 5 to 10 and growth can occur between 15 and 37
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<superScript attach="right" box="[885,892,555,568]" fontSize="6" pageId="9" pageNumber="10">◦</superScript>
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Cand thesestrainscangrowinthe presenceof upto 2.0 % (w/v) NaCl. Reduction of nitrates, β- glucosidase urease, tested positive. It is also positive for the production of L-arabinose, Tween 40, Tween 80, adonitol, N-acetyl-D-glucosamine, D-cellobiose, D-arabitol, D-galactose, D- and L-fructose, m-inositol, D-mannitol, maltose, D-mannose, Draffinose, D-melibiose, L-rhamnose, D-sorbitol, sucrose, xylitol, Dtrehalose, turanose, methyl pyruvate, D-galacturonic acid, acetic acid, malonic acid, propionic acid, D-saccharic acid, quinic acid, sebacic acid, L-asparagine, D- and L-alanine, L-leucine, L-proline, L-ornithine and glycerol. Negative reactions were recorded for glucose fermentation, indole production, β- galactosidase activity and L-arginine dihydrolase. It is also negative for the assimilation of N-acetyl-glucosamine, potassium gluconate, D-maltose, adipic acid, capric acid, malic acid, phenylacetic acid, glycogen, α- cyclodextrin, L-arabinose, i-erythritol, Lthreonine, D- and L-serine, glucose-1-phosphate and glucose-6- phosphate. Strain is resistant to penicillin (10 μg/ml), ampicillin (10 μg/ml), gentamycin (10 μg/ml), chloramphenicol (30 μg/ml) and neomycin (10 μg/ml) and is susceptible to kanamycin (30 μg/ml), erythromycin (30 μg/ml), streptomycin (10 and 25 μg/ml) and tetracycline (30 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.[818,1488,391,1386]" pageId="9" pageNumber="10">
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The type strain Pear77
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<superScript attach="left" box="[1064,1074,1111,1125]" fontSize="6" pageId="9" pageNumber="10">T</superScript>
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(=SARCC 754 = LMG 31407), was isolated from root nodules of
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<taxonomicName box="[1017,1179,1144,1163]" 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="[1017,1179,1144,1163]" italics="true" pageId="9" pageNumber="10">Pearsonia obovata</emphasis>
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</taxonomicName>
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collected in the Dullstroom area of the Mpumalanga Province, South Africa. This species forms effective nodules on cowpea (
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<taxonomicName box="[1018,1180,1200,1219]" 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="[1018,1180,1200,1219]" 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 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" 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 63.3 mol%. The GenBank/EMBL/DDBJ accession numbers for the genome sequence and gene sequences for this type strain are:
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<materialsCitation ID-GBIF-Occurrence="3411891303" pageId="9" pageNumber="10" specimenCount="1">
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whole genome (
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<accessionNumber pageId="9" pageNumber="10">JACMYP000000000</accessionNumber>
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) and 16S rRNA (
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<accessionNumber box="[1144,1247,1312,1331]" pageId="9" pageNumber="10">LR877298</accessionNumber>
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),
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<emphasis bold="true" box="[1266,1308,1312,1331]" italics="true" pageId="9" pageNumber="10">atpD</emphasis>
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(
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<accessionNumber box="[1324,1428,1311,1330]" pageId="9" pageNumber="10">LN650104</accessionNumber>
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),
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<emphasis bold="true" box="[1448,1488,1311,1330]" italics="true" pageId="9" pageNumber="10">glnII</emphasis>
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(
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<accessionNumber box="[824,928,1339,1358]" pageId="9" pageNumber="10">LN650146</accessionNumber>
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),
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<emphasis bold="true" box="[949,996,1339,1358]" italics="true" pageId="9" pageNumber="10">dnaK</emphasis>
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(
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<accessionNumber box="[1013,1117,1339,1358]" pageId="9" pageNumber="10">LN650125</accessionNumber>
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),
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<emphasis bold="true" box="[1138,1179,1340,1359]" italics="true" pageId="9" pageNumber="10">gyrB</emphasis>
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(
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<accessionNumber box="[1195,1300,1339,1358]" pageId="9" pageNumber="10">LN650209</accessionNumber>
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),
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<emphasis bold="true" box="[1320,1362,1340,1359]" italics="true" pageId="9" pageNumber="10">rpoB</emphasis>
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(
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<accessionNumber box="[1379,1481,1339,1358]" pageId="9" pageNumber="10">LN650188</accessionNumber>
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) and
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<emphasis bold="true" box="[859,907,1367,1386]" italics="true" pageId="9" pageNumber="10">nodA</emphasis>
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(
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<accessionNumber box="[919,1024,1367,1386]" pageId="9" pageNumber="10">LN650251</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> |