Strain identifier

BacDive ID: 134681

Type strain: Yes

Species: Bradyrhizobium yuanmingense

Strain history: CIP <- 2003, W.X. Chen, China Agric. Univ., Beijing, China: strain CCBAU 10071

NCBI tax ID(s): 108015 (species)

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General

@ref: 33193

BacDive-ID: 134681

keywords: genome sequence, Bacteria, mesophilic, Gram-negative, rod-shaped

description: Bradyrhizobium yuanmingense CIP 108027 is a mesophilic, Gram-negative, rod-shaped bacterium of the family Nitrobacteraceae.

NCBI tax id

  • NCBI tax id: 108015
  • Matching level: species

strain history

@refhistory
331932003, W. X. Chen, China Agric. Univ., Beijing, China: strain CCBAU 10071
33193CIP <- 2003, W.X. Chen, China Agric. Univ., Beijing, China: strain CCBAU 10071

doi: 10.13145/bacdive134681.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Nitrobacteraceae
  • genus: Bradyrhizobium
  • species: Bradyrhizobium yuanmingense
  • full scientific name: Bradyrhizobium yuanmingense Yao et al. 2002

@ref: 33193

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Bradyrhizobiaceae

genus: Bradyrhizobium

species: Bradyrhizobium yuanmingense

type strain: yes

Morphology

cell morphology

  • @ref: 33193
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 33193

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
33193MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
33193CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
33193positivegrowth30mesophilic
33193positivegrowth25-41
33193nogrowth10psychrophilic
33193nogrowth45thermophilic

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
33193NaClnogrowth0 %
33193NaClnogrowth2 %
33193NaClnogrowth4 %
33193NaClnogrowth6 %
33193NaClnogrowth8 %
33193NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3319316947citrate-carbon source
331934853esculin+hydrolysis
33193606565hippurate+hydrolysis
3319317632nitrate+reduction
3319316301nitrite-reduction
3319317632nitrate-respiration

antibiotic resistance

  • @ref: 33193
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 33193
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
3319315688acetoin-
3319317234glucose+

enzymes

@refvalueactivityec
33193oxidase-
33193beta-galactosidase+3.2.1.23
33193alcohol dehydrogenase-1.1.1.1
33193gelatinase+/-
33193amylase-
33193DNase-
33193caseinase+3.4.21.50
33193catalase+1.11.1.6
33193tween esterase-
33193gamma-glutamyltransferase+2.3.2.2
33193lecithinase-
33193lipase-
33193lysine decarboxylase-4.1.1.18
33193ornithine decarboxylase-4.1.1.17
33193phenylalanine ammonia-lyase-4.3.1.24
33193protease+
33193tryptophan deaminase-
33193urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
33193-+-+-+--+--+--------

Isolation, sampling and environmental information

isolation

@refgeographic locationcountryorigin.countrycontinentsample typeisolation date
33193BeijingChinaCHNAsia
33193BeijingChinaCHNAsiaLespedera cuneata1995

Safety information

risk assessment

  • @ref: 33193
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bradyrhizobium yuanmingense CCBAU 10071GCA_900094575scaffoldncbi108015
66792Bradyrhizobium yuanmingense strain CCBAU 10071108015.31wgspatric108015
66792Bradyrhizobium yuanmingense CCBAU 100712617270741draftimg108015

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes80.137no
flagellatedno77.18no
gram-positiveno98.235no
anaerobicno98.264no
aerobicyes92.822no
halophileno96.139no
spore-formingno93.013no
glucose-fermentno90.438no
thermophileno99.258yes
glucose-utilyes90.492no

External links

@ref: 33193

culture collection no.: CIP 108027, CFNEB 101, CCBAU 10071

straininfo link

  • @ref: 92160
  • straininfo: 100569

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12508891Characterization of rhizobia that nodulate legume species of the genus Lespedeza and description of Bradyrhizobium yuanmingense sp. nov.Yao ZY, Kan FL, Wang ET, Wei GH, Chen WXInt J Syst Evol Microbiol10.1099/00207713-52-6-22192002Bacterial Proteins/isolation & purification, Base Composition, Base Sequence, Bradyrhizobium/*classification/genetics/isolation & purification/metabolism, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Genes, Bacterial, Lespedeza/*microbiology, Molecular Sequence Data, Phenotype, Phylogeny, Plasmids/genetics, Polymorphism, Restriction Fragment Length, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity, United StatesEnzymology
Phylogeny22544787Bradyrhizobium daqingense sp. nov., isolated from soybean nodules.Wang JY, Wang R, Zhang YM, Liu HC, Chen WF, Wang ET, Sui XH, Chen WXInt J Syst Evol Microbiol10.1099/ijs.0.034280-02012Bacterial Typing Techniques, Base Composition, Bradyrhizobium/*classification/genetics/isolation & purification, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, Soybeans/*microbiology, Ubiquinone/analysisGenetics
Phylogeny26198108Bradyrhizobium subterraneum sp. nov., a symbiotic nitrogen-fixing bacterium from root nodules of groundnuts.Gronemeyer JL, Chimwamurombe P, Reinhold-Hurek BInt J Syst Evol Microbiol10.1099/ijsem.0.0004032015Arachis/*microbiology, Bacterial Typing Techniques, Base Composition, Bradyrhizobium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Molecular Sequence Data, Namibia, Nitrogen, *Nitrogen Fixation, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, SymbiosisGenetics
Phylogeny26409482Bradyrhizobium guangdongense sp. nov. and Bradyrhizobium guangxiense sp. nov., isolated from effective nodules of peanut.Li YH, Wang R, Zhang XX, Young JPW, Wang ET, Sui XH, Chen WXInt J Syst Evol Microbiol10.1099/ijsem.0.0006292015Arachis/*microbiology, Bacterial Typing Techniques, Base Composition, Bradyrhizobium/*classification/genetics/isolation & purification, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Molecular Sequence Data, Multilocus Sequence Typing, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNAGenetics
Phylogeny26463703Bradyrhizobium vignae sp. nov., a nitrogen-fixing symbiont isolated from effective nodules of Vigna and Arachis.Gronemeyer JL, Hurek T, Bunger W, Reinhold-Hurek BInt J Syst Evol Microbiol10.1099/ijsem.0.0006742015Arachis/*microbiology, Bacterial Typing Techniques, Base Composition, Bradyrhizobium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fabaceae/*microbiology, Fatty Acids/chemistry, Genes, Bacterial, Molecular Sequence Data, Namibia, *Nitrogen Fixation, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/microbiology, Sequence Analysis, DNA, *SymbiosisGenetics
Genetics29225730Draft genome sequences of Bradyrhizobium shewense sp. nov. ERR11(T) and Bradyrhizobium yuanmingense CCBAU 10071(T).Aserse AA, Woyke T, Kyrpides NC, Whitman WB, Lindstrom KStand Genomic Sci10.1186/s40793-017-0283-x2017Phylogeny
Genetics33122079Genome sequence of Bradyrhizobium yuanmingense strain P10 130, a highly efficient nitrogen-fixing bacterium that could be used for Desmodium incanum inoculation.Toniutti MA, Albicoro FJ, Castellani LG, Lopez Garcia SL, Fornasero LV, Zuber NE, Vera LM, Vacca C, Cafiero JH, Winkler A, Kalinowski J, Lagares A, Torres Tejerizo GA, Del Papa MFGene10.1016/j.gene.2020.1452672020Base Composition/genetics, Bradyrhizobium/*genetics, DNA, Bacterial/genetics, Fabaceae/*growth & development/microbiology, Genome, Bacterial/*genetics, Nitrogen Fixation/*genetics, Phylogeny, Plant Growth Regulators/pharmacologyPhylogeny
Phylogeny33709900Bradyrhizobium agreste sp. nov., Bradyrhizobium glycinis sp. nov. and Bradyrhizobium diversitatis sp. nov., isolated from a biodiversity hotspot of the genus Glycine in Western Australia.Klepa MS, Ferraz Helene LC, O'Hara G, Hungria MInt J Syst Evol Microbiol10.1099/ijsem.0.0047422021

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
33193Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108027Collection of Institut Pasteur (CIP 108027)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68382Automatically annotated from API zym
92160Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID100569.1