Strain identifier

BacDive ID: 141148

Type strain: Yes

Species: Bradyrhizobium namibiense

Strain Designation: 5-10

NCBI tax ID(s): 1549938 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 44069

BacDive-ID: 141148

DSM-Number: 100300

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

description: Bradyrhizobium namibiense 5-10 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from effective nodule of Lablab purpureus.

NCBI tax id

  • NCBI tax id: 1549938
  • Matching level: species

doi: 10.13145/bacdive141148.20230509.8.1

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 namibiense
  • full scientific name: Bradyrhizobium namibiense Grönemeyer et al. 2017

@ref: 44069

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Bradyrhizobiaceae

genus: Bradyrhizobium

species: Bradyrhizobium namibiense

strain designation: 5-10

type strain: yes

Morphology

cell morphology

  • @ref: 44069
  • gram stain: negative
  • cell length: 2-3 µm
  • cell width: 0.7 µm
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 44069
  • colony size: 0.2 mm
  • colony color: beige-whitish
  • colony shape: circular
  • incubation period: 8 days
  • medium used: YMA

Culture and growth conditions

culture medium

@refnamegrowth
44069LB (Luria-Bertani) MEDIUMno
44069MAGyes
44069YMAyes
44069YMByes

culture temp

@refgrowthtypetemperaturerange
44069positivegrowth35mesophilic
44069positiveoptimum28-32mesophilic

culture pH

@refabilitytypepHPH range
44069positivegrowth5.5-9alkaliphile
44069positiveoptimum6.6

Physiology and metabolism

oxygen tolerance

  • @ref: 44069
  • oxygen tolerance: aerobe

spore formation

  • @ref: 44069
  • spore formation: no

halophily

  • @ref: 44069
  • salt: NaCl
  • growth: no
  • tested relation: growth
  • concentration: 1 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
44069620642,3-butanediol-growth
44069182404-hydroxy-L-proline-growth
4406915963ribitol-growth
4406940585alpha-cyclodextrin-growth
4406917057cellobiose-growth
4406916383cis-aconitate-growth
4406916947citrate-growth
4406918333D-arabitol-growth
4406917784D-glucosaminic acid-growth
4406914314D-glucose 6-phosphate-growth
4406915748D-glucuronate-growth
4406916899D-mannitol-growth
4406916024D-mannose-growth
4406927605D-psicose-growth
4406916523D-serine-growth
4406917924D-sorbitol-growth
4406917126DL-carnitine-growth
4406917113erythritol-growth
4406916000ethanolamine-growth
4406916865gamma-aminobutyric acid-growth
4406928066gentiobiose-growth
4406929042glucose 1-phosphate-growth
4406928087glycogen-growth
4406917596inosine-growth
4406917268myo-inositol-growth
4406973786L-alanylglycine-growth
4406917196L-asparagine-growth
4406929991L-aspartate-growth
4406915971L-histidine-growth
4406915729L-ornithine-growth
4406962345L-rhamnose-growth
4406917115L-serine-growth
4406916857L-threonine-growth
4406917716lactose-growth
440696359lactulose-growth
4406915792malonate-growth
4406917306maltose-growth
4406928053melibiose-growth
4406937657methyl D-glucoside-growth
4406928037N-acetylgalactosamine-growth
44069506227N-acetylglucosamine-growth
4406950048phenylethylamine-growth
4406917148putrescine-growth
4406916634raffinose-growth
4406917992sucrose-growth
4406917748thymidine-growth
4406927082trehalose-growth
4406932528turanose-growth
4406916704uridine-growth
4406927248urocanic acid-growth
4406917151xylitol-growth
44069286442-oxopentanoate+assimilation
4406930089acetate+assimilation
44069645522-hydroxybutyrate+assimilation
440698295beta-hydroxybutyrate+assimilation
4406924996lactate+assimilation
4406930849L-arabinose+assimilation
4406951850methyl pyruvate+assimilation
4406975146monomethyl succinate+assimilation
4406917272propionate+assimilation
4406941865sebacic acid+assimilation
4406953423tween 40+assimilation
4406953426tween 80+assimilation
44069167632-oxobutanoate+/-assimilation
44069309162-oxoglutarate+/-assimilation
4406917925alpha-D-glucose+/-assimilation
4406912936D-galactose+/-assimilation
440698391D-gluconate+/-assimilation
4406965327D-xylose+/-assimilation
4406916449dl-alanine+/-assimilation
4406915740formate+/-assimilation
44069167244-hydroxybutyrate+/-assimilation
4406929985L-glutamate+/-assimilation
4406973784glycyl-l-glutamate+/-assimilation
44069143136succinamate+/-assimilation

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
4406927902tetracyclineyesyes15 µg/mL
4406948923erythromycinyesyes50 µg/mL
4406928971ampicillinyesyes50 µg/mL
4406917698chloramphenicolyesyes50 µg/mL
440696104kanamycinyesyes20 µg/mL
4406917076streptomycinyesyes5 µg/mL

enzymes

@refvalueactivityec
44069alkaline phosphatase+3.1.3.1
44069esterase (C 4)+
44069esterase Lipase (C 8)+
44069leucine arylamidase+3.4.11.1
44069trypsin+3.4.21.4
44069acid phosphatase+3.1.3.2
44069naphthol-AS-BI-phosphohydrolase+
44069lipase (C 14)-
44069valine arylamidase-
44069cystine arylamidase-3.4.11.3
44069alpha-chymotrypsin-3.4.21.1
44069alpha-galactosidase-3.2.1.22
44069beta-galactosidase-3.2.1.23
44069beta-glucuronidase-3.2.1.31
44069alpha-glucosidase-3.2.1.20
44069beta-glucosidase-3.2.1.21
44069N-acetyl-beta-glucosaminidase-3.2.1.52
44069alpha-mannosidase-3.2.1.24
44069alpha-fucosidase-3.2.1.51

Isolation, sampling and environmental information

isolation

  • @ref: 44069
  • sample type: effective nodule of Lablab purpureus
  • geographic location: Mashare, Kavango region
  • country: Namibia
  • origin.country: NAM
  • continent: Africa
  • latitude: -17.8958
  • longitude: 20.2124
  • enrichment culture: modified arabinose gluconate (MAG) medium

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_843.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_297;97_582;98_669;99_843&stattab=map
  • Last taxonomy: Bradyrhizobium
  • 16S sequence: KX661401
  • Sequence Identity:
  • Total samples: 29181
  • soil counts: 14338
  • aquatic counts: 4833
  • animal counts: 6732
  • plant counts: 3278

Sequence information

16S sequences

  • @ref: 44069
  • description: 16S rRNA gene sequence
  • accession: KX661401
  • database: nuccore

GC content

  • @ref: 44069
  • GC-content: 63.3
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 44069

culture collection no.: LMG 28789, DSM 100300, NTCCM 0017

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29034855Bradyrhizobium namibiense sp. nov., a symbiotic nitrogen-fixing bacterium from root nodules of Lablab purpureus, hyacinth bean, in Namibia.Gronemeyer JL, Bunger W, Reinhold-Hurek BInt J Syst Evol Microbiol10.1099/ijsem.0.0020392017Bacterial Typing Techniques, Bradyrhizobium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fabaceae/*microbiology, Genes, Bacterial, Namibia, *Nitrogen Fixation, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, SymbiosisTranscriptome
33584615Root Nodule Rhizobia From Undomesticated Shrubs of the Dry Woodlands of Southern Africa Can Nodulate Angolan Teak Pterocarpus angolensis, an Important Source of Timber.Bunger W, Sarkar A, Gronemeyer JL, Zielinski J, Revermann R, Hurek T, Reinhold-Hurek BFront Microbiol10.3389/fmicb.2021.6117042021

Reference

@idauthorstitledoi/urljournalpubmed
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
44069Jann Lasse Grönemeyer, Wiebke Bünger and Barbara Reinhold-HurekBradyrhizobium namibiense sp. nov., a symbiotic nitrogen-fixing bacterium from root nodules of Lablab purpureus, hyacinth bean, in Namibia10.1099/ijsem.0.002039IJSEM 67: 4884-4891 201729034855
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/