Strain identifier

BacDive ID: 1813

Type strain: Yes

Species: Bradyrhizobium betae

Strain Designation: P17Hg1, PL7HG1

Strain history: <- E. Velázquez, Univ. Salamanca, Spain; P17Hg1

NCBI tax ID(s): 244734 (species)

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General

@ref: 6873

BacDive-ID: 1813

DSM-Number: 17288

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

description: Bradyrhizobium betae P17Hg1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from roots of sugar beet Beta vulgaris affected by tumour-like deformations.

NCBI tax id

  • NCBI tax id: 244734
  • Matching level: species

strain history

  • @ref: 6873
  • history: <- E. Velázquez, Univ. Salamanca, Spain; P17Hg1

doi: 10.13145/bacdive1813.20230509.8.1

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 betae
  • full scientific name: Bradyrhizobium betae Rivas et al. 2004

@ref: 6873

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Nitrobacteraceae

genus: Bradyrhizobium

species: Bradyrhizobium betae

full scientific name: Bradyrhizobium betae Rivas et al. 2004

strain designation: P17Hg1, PL7HG1

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
23328negative
69480yes98.136
69480negative99.989

colony morphology

  • @ref: 23328
  • colony color: pearl white
  • medium used: YMA

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6873NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
23328YMAyes

culture temp

@refgrowthtypetemperaturerange
6873positivegrowth28mesophilic
23328positiveoptimum28mesophilic
60755positivegrowth30mesophilic

culture pH

  • @ref: 23328
  • ability: positive
  • type: optimum
  • pH: 7.0-7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 60755
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.984

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2332815963ribitol-growth
2332862345L-rhamnose-growth
2332817716lactose-growth
2332816634raffinose-growth
2332817992sucrose-growth
2332827082trehalose-growth
2332817632nitrate-reduction
2332828260galactose+carbon source
2332817234glucose+carbon source
2332830849L-arabinose+carbon source
2332817266L-sorbose+carbon source
2332817306maltose+carbon source
2332829864mannitol+carbon source
2332837684mannose+carbon source
23328506227N-acetylglucosamine+carbon source
233284853esculin+hydrolysis
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantresistance conc.is intermediateintermediate conc.is sensitivesensitivity conc.
2332817334penicillinyesyes10 Unit
233288309polymyxin byesyes300 Unit
2332849566cloxacillinyesyes1 µg
2332817833gentamicinyesyes10 µg
2332827701oxytetracyclineyesyes30 µg
233282676amoxicillinyesyes
2332848923erythromycinyesyes2 µg
233283515cefuroximeyesyes30 µg
23328100241ciprofloxacinyesyes5 µg
233287507neomycinyesyes5 µg

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
233286-phospho-beta-galactosidase+3.2.1.85
23328urease+3.5.1.5
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
60755--------------------+

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentsampling date
6873roots of sugar beet Beta vulgaris affected by tumour-like deformationsBeta vulgarisnorthern SpainSpainESPEurope
60755Beta vulgaris tumor-like deformationsSalamancaSpainESPEurope2002

isolation source categories

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

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: AY372184
  • Sequence Identity:
  • Total samples: 12887
  • soil counts: 5001
  • aquatic counts: 2827
  • animal counts: 4320
  • plant counts: 739

Safety information

risk assessment

  • @ref: 6873
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bradyrhizobium betae gene for 16S rRNA, partial sequence, strain: NBRC 103048AB6819281414ena244734
20218Bradyrhizobium betae internal transcribed spacer between 16S and 23S rRNA genesAJ631967789ena244734
6873Bradyrhizobium betae 16S ribosomal RNA gene, partial sequenceAY3721841483ena244734

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bradyrhizobium betae PL7HG1GCA_008932115completencbi244734
66792Bradyrhizobium betae strain PL7HG1244734.9completepatric244734
66792Bradyrhizobium betae CECT 58292824350403draftimg244734
66792Bradyrhizobium betae CECT 5829GCA_024806875contigncbi244734

GC content

@refGC-contentmethod
687363.7
2332863.7high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes85.669no
flagellatedno64.151no
gram-positiveno98.307yes
anaerobicno97.487yes
aerobicyes91.513yes
halophileno96.172no
spore-formingno93.342no
thermophileno98.92yes
glucose-utilyes86.457no
glucose-fermentno92.377yes

External links

@ref: 6873

culture collection no.: DSM 17288, CECT 5829, LMG 21987, NBRC 103048, CCUG 55850

straininfo link

  • @ref: 71459
  • straininfo: 128240

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15280302Bradyrhizobium betae sp. nov., isolated from roots of Beta vulgaris affected by tumour-like deformations.Rivas R, Willems A, Palomo JL, Garcia-Benavides P, Mateos PF, Martinez-Molina E, Gillis M, Velazquez EInt J Syst Evol Microbiol10.1099/ijs.0.02971-02004Bacterial Typing Techniques, Beta vulgaris/*microbiology, Bradyrhizobium/*classification/genetics/*isolation & purification, DNA Fingerprinting, DNA, Bacterial/chemistry, DNA, Ribosomal/chemistry, DNA, Ribosomal Spacer/chemistry, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Plant Roots/*microbiology, Plant Tumors/*microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Random Amplified Polymorphic DNA Technique, Sequence Analysis, DNA, Sequence Homology, Soil Microbiology, SpainGenetics
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
Genetics31727720Analysis of the Complete Genome Sequence of the Widely Studied Strain Bradyrhizobium betae PL7HG1(T) Reveals the Presence of Photosynthesis Genes and a Putative Plasmid.Cloutier S, Bromfield ESPMicrobiol Resour Announc10.1128/MRA.01282-192019

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6873Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17288)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17288
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
23328Raúl Rivas, Anne Willems, José Luis Palomo, Pablo García-Benavides, Pedro F. Mateos, Eustoquio Martínez-Molina, Monique Gillis, Encarna Velázquez10.1099/ijs.0.02971-0Bradyrhizobium betae sp. nov., isolated from roots of Beta vulgaris affected by tumour-like deformationsIJSEM 54: 1271-1275 200415280302
60755Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55850)https://www.ccug.se/strain?id=55850
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68369Automatically annotated from API 20NE
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
71459Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID128240.1StrainInfo: A central database for resolving microbial strain identifiers