Strain identifier

BacDive ID: 132365

Type strain: Yes

Species: Bradyrhizobium vignae

Strain Designation: 7-2

Strain history: <- B. Reinhold-Hurek, Univ. Bremen, Germany; 7-2 <- J. L. Grönemeyer

NCBI tax ID(s): 1549949 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 24154

BacDive-ID: 132365

DSM-Number: 100297

keywords: genome sequence, 16S sequence, Bacteria, aerobe, thermophilic, Gram-negative, motile, rod-shaped, colony-forming

description: Bradyrhizobium vignae 7-2 is an aerobe, thermophilic, Gram-negative bacterium that forms circular colonies and was isolated from effective nodule of Vigna unguiculata .

NCBI tax id

  • NCBI tax id: 1549949
  • Matching level: species

strain history

  • @ref: 24154
  • history: <- B. Reinhold-Hurek, Univ. Bremen, Germany; 7-2 <- J. L. Grönemeyer

doi: 10.13145/bacdive132365.20230509.8.1

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 vignae
  • full scientific name: Bradyrhizobium vignae Grönemeyer et al. 2016

@ref: 24154

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Nitrobacteraceae

genus: Bradyrhizobium

species: Bradyrhizobium vignae

full scientific name: Bradyrhizobium vignae Grönemeyer et al. 2016

strain designation: 7-2

type strain: yes

Morphology

cell morphology

  • @ref: 44038
  • gram stain: negative
  • cell length: 2-3 µm
  • cell width: 0.7 µm
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 44038
  • colony size: 0.2-1 mm
  • colony color: beige-whitish
  • colony shape: circular
  • incubation period: 8 days
  • medium used: YMA

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
44038YMAyes
24154RHIZOBIUM MEDIUM (DSMZ Medium 98)yeshttps://mediadive.dsmz.de/medium/98Name: RHIZOBIUM MEDIUM (DSMZ Medium 98) Composition: air-dried garden soil 80.0 g/l Agar 15.0 g/l Mannitol 10.0 g/l Yeast extract 1.0 g/l Na2CO3 0.2 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
44038positivegrowth40thermophilic
44038positivegrowth38mesophilic
44038positivegrowth37mesophilic
44038positivegrowth28mesophilic
24154positivegrowth28mesophilic

culture pH

  • @ref: 44038
  • ability: positive
  • type: growth
  • pH: 5-9
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 44038
  • oxygen tolerance: aerobe

spore formation

  • @ref: 44038
  • type of spore: spore
  • spore formation: no

halophily

  • @ref: 44038
  • salt: NaCl
  • growth: no
  • tested relation: growth
  • concentration: 1 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
44038620642,3-butanediol-oxidation
44038182404-hydroxy-L-proline-oxidation
4403815963ribitol-oxidation
4403840585alpha-cyclodextrin-oxidation
4403836219alpha-lactose-oxidation
4403817057cellobiose-oxidation
4403814314D-glucose 6-phosphate-oxidation
4403828053melibiose-oxidation
4403827605D-psicose-oxidation
4403816523D-serine-oxidation
4403817924D-sorbitol-oxidation
4403817126DL-carnitine-oxidation
4403817113erythritol-oxidation
4403816000ethanolamine-oxidation
4403816865gamma-aminobutyric acid-oxidation
4403828066gentiobiose-oxidation
4403829042glucose 1-phosphate-oxidation
4403814336glycerol 1-phosphate-oxidation
4403828087glycogen-oxidation
4403817596inosine-oxidation
4403817268myo-inositol-oxidation
4403821217L-alaninamide-oxidation
4403873786L-alanylglycine-oxidation
4403817196L-asparagine-oxidation
4403815971L-histidine-oxidation
4403815729L-ornithine-oxidation
4403817203L-proline-oxidation
4403817115L-serine-oxidation
4403816857L-threonine-oxidation
440386359lactulose-oxidation
4403817306maltose-oxidation
44038320055methyl beta-D-glucopyranoside-oxidation
4403828037N-acetylgalactosamine-oxidation
44038506227N-acetylglucosamine-oxidation
4403850048phenylethylamine-oxidation
4403817148putrescine-oxidation
4403816634raffinose-oxidation
4403817992sucrose-oxidation
4403817748thymidine-oxidation
4403827082trehalose-oxidation
4403832528turanose-oxidation
4403816704uridine-oxidation
4403817151xylitol-oxidation
44038309162-oxoglutarate+oxidation
44038286442-oxopentanoate+oxidation
4403817925alpha-D-glucose+oxidation
440388295beta-hydroxybutyrate+oxidation
4403873706bromosuccinate+oxidation
4403816383cis-aconitate+oxidation
4403816947citrate+oxidation
4403818333D-arabitol+oxidation
4403815895D-galactonic acid lactone+oxidation
4403812936D-galactose+oxidation
4403818024D-galacturonic acid+oxidation
440388391D-gluconate+oxidation
4403817784D-glucosaminic acid+oxidation
4403816899D-mannitol+oxidation
4403816024D-mannose+oxidation
4403833801D-saccharate+oxidation
4403824996lactate+oxidation
4403815740formate+oxidation
44038167244-hydroxybutyrate+oxidation
4403832323glucuronamide+oxidation
4403817754glycerol+oxidation
4403830849L-arabinose+oxidation
4403829991L-aspartate+oxidation
4403828120L-fructose+oxidation
4403829985L-glutamate+oxidation
4403815603L-leucine+oxidation
4403818183L-pyroglutamic acid+oxidation
4403815792malonate+oxidation
4403851850methyl pyruvate+oxidation
4403875146monomethyl succinate+oxidation
4403817272propionate+oxidation
4403826490quinate+oxidation
4403841865sebacic acid+oxidation
44038143136succinamate+oxidation
4403830031succinate+oxidation
4403853423tween 40+oxidation
4403853426tween 80+oxidation
4403827248urocanic acid+oxidation

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantresistance conc.
4403817698chloramphenicolyesyes50 µg/mL
4403817076streptomycinyesyes5 µg/mL
4403827902tetracyclineyesyes15 µg/mL

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment culture
24154effective nodule of Vigna unguiculata (cowpea)Vigna unguiculataKavango region, near MashareNamibiaNAMAfrica-17.892820.2105
44038effective nodule of Vigna unguiculata (cowpea)Kavango RegionNamibiaNAMAfricaMAG medium (van Berkum, 1990)

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root nodule

taxonmaps

  • @ref: 69479
  • File name: preview.99_445.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_297;97_329;98_370;99_445&stattab=map
  • Last taxonomy: Bradyrhizobium
  • 16S sequence: KP899563
  • Sequence Identity:
  • Total samples: 12887
  • soil counts: 5001
  • aquatic counts: 2827
  • animal counts: 4320
  • plant counts: 739

Safety information

risk assessment

  • @ref: 24154
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24154
  • description: Bradyrhizobium vignae strain 7-2 16S ribosomal RNA gene, partial sequence
  • accession: KP899563
  • length: 1298
  • database: ena
  • NCBI tax ID: 1549949

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bradyrhizobium vignae LMG 28791GCA_004114425scaffoldncbi1549949
66792Bradyrhizobium vignae strain LMG 287911549949.9wgspatric1549949
66792Bradyrhizobium vignae LMG 287912881665667draftimg1549949

GC content

@refGC-contentmethod
4403865.4high performance liquid chromatography (HPLC)
2415465.4thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes81.391no
flagellatedno78.163no
gram-positiveno97.943no
anaerobicno96.902yes
aerobicyes91.839yes
halophileno94.775no
spore-formingno93.157no
thermophileno99.327no
glucose-utilyes90.103no
glucose-fermentno89.729no

External links

@ref: 24154

culture collection no.: DSM 100297, LMG 28791, NTCCM 0018, DSMZ 100297

straininfo link

  • @ref: 90711
  • straininfo: 396451

literature

  • topic: Phylogeny
  • Pubmed-ID: 26463703
  • title: Bradyrhizobium vignae sp. nov., a nitrogen-fixing symbiont isolated from effective nodules of Vigna and Arachis.
  • authors: Gronemeyer JL, Hurek T, Bunger W, Reinhold-Hurek B
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000674
  • year: 2015
  • mesh: Arachis/*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, *Symbiosis
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24154Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100297Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100297)
44038Jann Lasse Grönemeyer, Thomas Hurek, Wiebke Bünger and Barbara Reinhold-HurekBradyrhizobium vignae sp. nov., a nitrogen-fixing symbiont isolated from effective nodules of Vigna and Arachis10.1099/ijsem.0.000674IJSEM 66: 62-69 201626463703
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
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
90711Reimer, 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-ID396451.1