Strain identifier

BacDive ID: 13646

Type strain: Yes

Species: Rhizobium vallis

Strain history: <- LMG <- W. X. Chen, State Key Laboratory for Agrobiotechnol., China Agricultural Univ., Beijing, PR China; CCBAU 65647

NCBI tax ID(s): 634290 (species)

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

@ref: 18221

BacDive-ID: 13646

DSM-Number: 26437

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile

description: Rhizobium vallis DSM 26437 is a mesophilic, motile bacterium that was isolated from root nodules of Phaseolus vulgaris.

NCBI tax id

  • NCBI tax id: 634290
  • Matching level: species

strain history

  • @ref: 18221
  • history: <- LMG <- W. X. Chen, State Key Laboratory for Agrobiotechnol., China Agricultural Univ., Beijing, PR China; CCBAU 65647

doi: 10.13145/bacdive13646.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Rhizobiaceae
  • genus: Rhizobium
  • species: Rhizobium vallis
  • full scientific name: Rhizobium vallis Wang et al. 2011

@ref: 18221

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Rhizobiaceae

genus: Rhizobium

species: Rhizobium vallis

full scientific name: Rhizobium vallis Wang et al. 2011

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes91.639
6948099.984negative

colony morphology

  • @ref: 18221
  • incubation period: 2-3 days

Culture and growth conditions

culture medium

  • @ref: 18221
  • name: RHIZOBIUM MEDIUM (DSMZ Medium 98)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/98
  • composition: Name: 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

  • @ref: 18221
  • growth: positive
  • type: growth
  • temperature: 30
  • range: mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.997

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

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

metabolite tests

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

enzymes

@refvalueactivityec
18221cytochrome-c 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_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
18221----++-+-+/---+/-+/-+/------

Isolation, sampling and environmental information

isolation

  • @ref: 18221
  • sample type: root nodules of Phaseolus vulgaris
  • host species: Phaseolus vulgaris
  • geographic location: Yunnan Province, valley of Red River
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

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

Safety information

risk assessment

  • @ref: 18221
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 18221
  • description: Rhizobium vallis strain CCBAU 65647 16S ribosomal RNA gene, partial sequence
  • accession: FJ839677
  • length: 1382
  • database: ena
  • NCBI tax ID: 634290

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhizobium vallis CCBAU 65647GCA_003985155scaffoldncbi634290
66792Rhizobium vallis strain CCBAU 65647634290.7wgspatric634290
66792Rhizobium vallis LMG 252952739367694draftimg634290

GC content

  • @ref: 18221
  • GC-content: 60.9
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes87.827no
flagellatedno82.885no
gram-positiveno97.747no
anaerobicno98.786no
aerobicyes92.981no
halophileno93.861no
spore-formingno92.486no
thermophileno99.127no
glucose-utilyes83.414yes
glucose-fermentno89.559yes

External links

@ref: 18221

culture collection no.: DSM 26437, CCBAU 65647, HAMBI 3073, LMG 25295

straininfo link

  • @ref: 82829
  • straininfo: 378476

literature

  • topic: Phylogeny
  • Pubmed-ID: 21131504
  • title: Rhizobium vallis sp. nov., isolated from nodules of three leguminous species.
  • authors: Wang F, Wang ET, Wu LJ, Sui XH, Li Y, Chen WX
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.026484-0
  • year: 2010
  • mesh: Bacterial Proteins/genetics/metabolism, Base Composition, China, DNA, Bacterial/genetics, Fabaceae/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobium/classification/genetics/*isolation & purification/metabolism, Root Nodules, Plant/*microbiology
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitle
18221Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26437)https://www.dsmz.de/collection/catalogue/details/culture/DSM-26437
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
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
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
82829Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID378476.1StrainInfo: A central database for resolving microbial strain identifiers