Strain identifier

BacDive ID: 13606

Type strain: No

Species: Rhizobium lupini

Strain Designation: 3C231

Strain history: IAM 12610 <-- ATCC 10319 <-- L. W. Erdman 3C231 (Rhizobium lupini).

NCBI tax ID(s): 375 (species)

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General

@ref: 9161

BacDive-ID: 13606

DSM-Number: 30140

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

description: Rhizobium lupini 3C231 is a mesophilic, motile bacterium that was isolated from source of the original strain: lupin root nodules.

NCBI tax id

  • NCBI tax id: 375
  • Matching level: species

strain history

@refhistory
9161<- ATCC <- L.W. Erdman, 3C231
67770IAM 12610 <-- ATCC 10319 <-- L. W. Erdman 3C231 (Rhizobium lupini).

doi: 10.13145/bacdive13606.20230509.8.1

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 lupini
  • full scientific name: Rhizobium lupini (Schroeter 1886) Eckhardt et al. 1931 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Phytomyxa lupini

@ref: 9161

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Nitrobacteraceae

genus: Bradyrhizobium

species: Bradyrhizobium japonicum

full scientific name: Bradyrhizobium japonicum (Kirchner 1896) Jordan 1982

strain designation: 3C231

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes97.023
6948099.989negative

colony morphology

  • @ref: 9161
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9161NUTRIENT 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
9161RHIZOBIUM 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

culture temp

@refgrowthtypetemperaturerange
9161positivegrowth30mesophilic
67770positivegrowth25mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.97

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
683694853esculin-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
9161catalase+1.11.1.6
9161cytochrome-c oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
9161+---+---------------+
9161+-------------------

Isolation, sampling and environmental information

isolation

@refsample typehost species
9161source of the original strain: lupin (Lupinus angustifolius) root nodules
67770Lupine (Lupinus angustifolius)Lupinus angustifolius

isolation source categories

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

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: AB681156
  • Sequence Identity:
  • Total samples: 12887
  • soil counts: 5001
  • aquatic counts: 2827
  • animal counts: 4320
  • plant counts: 739

Safety information

risk assessment

  • @ref: 9161
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bradyrhizobium sp. USDA 3051 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequenceEU8347231220ena546898
20218Rhizobium lupini 16S rRNA gene, type strain DSM 30140TX872731484ena136996
20218Rhizobium lupini gene for 16S rRNA, partial sequence, strain: NBRC 100381AB6811561414ena136996
9161Bradyrhizobium lupini strain DSM 30140 16S ribosomal RNA, partial sequenceNR0448691482ena136996

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bradyrhizobium lupini strain DSM 30140136996.3wgspatric136996
66792Bradyrhizobium lupini DSM 301402861120366draftimg136996

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes86.815no
gram-positiveno97.916no
anaerobicno98.272no
halophileno95.269no
spore-formingno92.206no
thermophileno99.671yes
glucose-utilyes88.504yes
flagellatedno70.83no
aerobicyes91.888no
glucose-fermentno89.301no

External links

@ref: 9161

culture collection no.: DSM 30140, ATCC 10319, JCM 20681, IAM 12610, NBRC 100381, VKM B-1965

straininfo link

  • @ref: 82793
  • straininfo: 35204

literature

Pubmed-IDtitleauthorsjournalDOIyearmeshtopictopic2
2007543Occurrence of lipid A variants with 27-hydroxyoctacosanoic acid in lipopolysaccharides from members of the family Rhizobiaceae.Bhat UR, Mayer H, Yokota A, Hollingsworth RI, Carlson RWJ Bacteriol10.1128/jb.173.7.2155-2159.19911991Fatty Acids/analysis, Hydroxy Acids/*chemistry, Lipid A/*chemistry, Lipopolysaccharides/*chemistry, Rhizobiaceae/*analysis
2228245Cytokine induction by lipopolysaccharide (LPS) corresponds to lethal toxicity and is inhibited by nontoxic Rhodobacter capsulatus LPS.Loppnow H, Libby P, Freudenberg M, Krauss JH, Weckesser J, Mayer HInfect Immun10.1128/iai.58.11.3743-3750.19901990Animals, Cytokines/*biosynthesis, Leukocytes, Mononuclear/drug effects/metabolism, Lipopolysaccharides/chemistry/*toxicity, Mice, Mice, Inbred C57BL, Mortality, *Rhodobacter capsulatus/analysis, Structure-Activity RelationshipPathogenicityMetabolism
25609676Revision of the taxonomic status of the species Rhizobium lupini and reclassification as Bradyrhizobium lupini comb. nov.Peix A, Ramirez-Bahena MH, Flores-Felix JD, Alonso de la Vega P, Rivas R, Mateos PF, Igual JM, Martinez-Molina E, Trujillo ME, Velazquez EInt J Syst Evol Microbiol10.1099/ijs.0.0000822015Bacterial Typing Techniques, Bradyrhizobium/*classification, DNA, Bacterial/genetics, Lupinus/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification, Sequence Analysis, DNA, SymbiosisPhylogenyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9161Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 30140)https://www.dsmz.de/collection/catalogue/details/culture/DSM-30140
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
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
82793Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID35204.1StrainInfo: A central database for resolving microbial strain identifiers