Strain identifier

BacDive ID: 13593

Type strain: No

Species: Rhizobium leguminosarum

Strain Designation: 3D1K2

Strain history: <- ATCC <- U.M. Means, 3D1K2

NCBI tax ID(s): 384 (species)

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General

@ref: 2212

BacDive-ID: 13593

DSM-Number: 6040

keywords: genome sequence, Bacteria, psychrophilic, motile

description: Rhizobium leguminosarum 3D1K2 is a psychrophilic, motile bacterium of the family Rhizobiaceae.

NCBI tax id

  • NCBI tax id: 384
  • Matching level: species

strain history

  • @ref: 2212
  • history: <- ATCC <- U.M. Means, 3D1K2

doi: 10.13145/bacdive13593.20230509.8.1

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 leguminosarum
  • full scientific name: Rhizobium leguminosarum (Frank 1879) Frank 1889 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Schinzia leguminosarum
    20215Rhizobium trifolii

@ref: 2212

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Rhizobiaceae

genus: Rhizobium

species: Rhizobium leguminosarum

full scientific name: Rhizobium leguminosarum (Frank 1879) Frank 1889 emend. Ramírez-Bahena et al. 2008

strain designation: 3D1K2

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes93.891
6948099.975negative

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2212RHIZOBIUM 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
2212NUTRIENT 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

culture temp

@refgrowthtypetemperaturerange
2212positivegrowth22psychrophilic
2212positivegrowth26mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.995

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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
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
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
2212-----+/--+------------+

Safety information

risk assessment

  • @ref: 2212
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhizobium leguminosarum ATCC 14479GCA_003290405completencbi384
66792Rhizobium leguminosarum strain ATCC 14479384.95completepatric384
66792Rhizobium leguminosarum ATCC 144792859840839completeimg384

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes86.338no
flagellatedno79.024no
gram-positiveno98.149no
anaerobicno98.079no
aerobicyes91.338no
halophileno94.774no
spore-formingno93.575no
glucose-utilyes85.422yes
thermophileno99.611no
glucose-fermentno89.665yes

External links

@ref: 2212

culture collection no.: DSM 6040, ATCC 14479

straininfo link

  • @ref: 82780
  • straininfo: 36091

literature

  • topic: Metabolism
  • Pubmed-ID: 23361163
  • title: Isolation and structural identification of the trihydroxamate siderophore vicibactin and its degradative products from Rhizobium leguminosarum ATCC 14479 bv. trifolii.
  • authors: Wright W, Little J, Liu F, Chakraborty R
  • journal: Biometals
  • DOI: 10.1007/s10534-013-9609-3
  • year: 2013
  • mesh: Iron/metabolism, Peptides, Cyclic/*biosynthesis, Plant Roots/metabolism/microbiology, Rhizobium leguminosarum/*metabolism, Siderophores/biosynthesis, Soil Microbiology, *Symbiosis, Trifolium/*metabolism
  • topic2: Phylogeny

Reference

@idauthorscataloguedoi/urltitle
2212Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6040)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6040
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
82780Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID36091.1StrainInfo: A central database for resolving microbial strain identifiers