Strain identifier

BacDive ID: 133740

Type strain: Yes

Species: Bradyrhizobium daqingense

NCBI tax ID(s): 993502 (species)

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General

@ref: 30354

BacDive-ID: 133740

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped

description: Bradyrhizobium daqingense LMG 26137 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from plant associated.

NCBI tax id

  • NCBI tax id: 993502
  • Matching level: species

doi: 10.13145/bacdive133740.20230509.8.1

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 daqingense
  • full scientific name: Bradyrhizobium daqingense Wang et al. 2013

@ref: 30354

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Bradyrhizobiaceae

genus: Bradyrhizobium

species: Bradyrhizobium daqingense

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
30354negativerod-shaped
69480yes95.619
69480negative99.985

pigmentation

  • @ref: 30354
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
30354positivegrowth28-37mesophilic
30354positiveoptimum28mesophilic

culture pH

@refabilitytypepHPH range
30354positivegrowth06-09alkaliphile
30354positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 30354
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30354no
69481no100
69480no99.964

halophily

  • @ref: 30354
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3035430089acetate+carbon source
3035421217L-alaninamide+carbon source
3035422599arabinose+carbon source
3035418403L-arabitol+carbon source
3035422653asparagine+carbon source
3035435391aspartate+carbon source
3035415740formate+carbon source
3035428757fructose+carbon source
3035433984fucose+carbon source
3035424148galactonate+carbon source
3035428260galactose+carbon source
3035424175galacturonate+carbon source
3035424265gluconate+carbon source
3035417234glucose+carbon source
3035432323glucuronamide+carbon source
3035429987glutamate+carbon source
3035424996lactate+carbon source
3035429864mannitol+carbon source
3035437684mannose+carbon source
3035417272propionate+carbon source
3035451850methyl pyruvate+carbon source
3035426490quinate+carbon source
3035426546rhamnose+carbon source
3035430031succinate+carbon source
3035453426tween 80+carbon source
3035417632nitrate+reduction

Isolation, sampling and environmental information

isolation

  • @ref: 30354
  • sample type: plant associated

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants

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: HQ231274
  • Sequence Identity:
  • Total samples: 12887
  • soil counts: 5001
  • aquatic counts: 2827
  • animal counts: 4320
  • plant counts: 739

Sequence information

16S sequences

  • @ref: 30354
  • description: Bradyrhizobium daqingense strain CCBAU 15774 16S ribosomal RNA gene, partial sequence
  • accession: HQ231274
  • length: 1300
  • database: nuccore
  • NCBI tax ID: 993502

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bradyrhizobium daqingense CGMCC 1.10947GCA_007830205scaffoldncbi993502
66792Bradyrhizobium daqingense strain CGMCC 1.10947993502.3wgspatric993502
66792Bradyrhizobium daqingense CGMCC 1.109472596583556draftimg993502
66792Bradyrhizobium daqingense CCBAU 15774GCA_021044685completencbi993502
66792Bradyrhizobium daqingense strain CCBAU 15774993502.5completepatric993502

GC content

  • @ref: 30354
  • GC-content: 61.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno73.868no
gram-positiveno97.628no
anaerobicno98.033no
aerobicyes93.205yes
halophileno96.219yes
spore-formingno92.14yes
motileyes79.853no
thermophileno98.968yes
glucose-utilyes89.794yes
glucose-fermentno91.37no

External links

@ref: 30354

culture collection no.: LMG 26137, HAMBI 3184, CGMCC 1.10947, CCBAU 15774

straininfo link

  • @ref: 91578
  • straininfo: 389445

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
Phylogeny27394069Bradyrhizobium centrosemae (symbiovar centrosemae) sp. nov., Bradyrhizobium americanum (symbiovar phaseolarum) sp. nov. and a new symbiovar (tropici) of Bradyrhizobium viridifuturi establish symbiosis with Centrosema species native to America.Ramirez-Bahena MH, Flores-Felix JD, Chahboune R, Toro M, Velazquez E, Peix ASyst Appl Microbiol10.1016/j.syapm.2016.06.0012016*Bacterial Typing Techniques, Base Sequence, Bradyrhizobium/*classification/*genetics/isolation & purification, DNA, Bacterial/genetics, Fabaceae/*microbiology, N-Acetylglucosaminyltransferases/genetics, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Rec A Recombinases/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, Symbiosis, VenezuelaTranscriptome
Phylogeny28671523Bradyrhizobium cajani sp. nov. isolated from nodules of Cajanus cajan.Araujo J, Flores-Felix JD, Igual JM, Peix A, Gonzalez-Andres F, Diaz-Alcantara CA, Velazquez EInt J Syst Evol Microbiol10.1099/ijsem.0.0019322017Bacterial Typing Techniques, Base Composition, Bradyrhizobium/*classification/genetics/isolation & purification, Cajanus/*microbiology, DNA, Bacterial/genetics, Dominican Republic, Genes, Bacterial, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, SymbiosisTranscriptome

Reference

@idauthorstitledoi/urlID_cross_referencepubmed
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
30354Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172669428776041
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/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91578Reimer, 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-ID389445.1