Strain identifier

BacDive ID: 138443

Type strain: Yes

Species: Rhizobium leguminosarum

Strain Designation: 3Hoq18

Strain history: CIP <- 2001, IFO <- Toyama Dept Biol. <- H. Oyaizu <- IAM <- ATCC <- L.W. Erdman

NCBI tax ID(s): 384 (species)

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

@ref: 64388

BacDive-ID: 138443

DSM-Number: 106839

keywords: genome sequence, Bacteria, mesophilic, Gram-negative

description: Rhizobium leguminosarum 3Hoq18 is a mesophilic, Gram-negative bacterium of the family Rhizobiaceae.

NCBI tax id

  • NCBI tax id: 384
  • Matching level: species

strain history

@refhistory
64388<- C. Vereecke, LMG; LMG 14904 <- 1994, American Type Culture Collection (ATCC), Bacteriology Program (Rhizobium leguminosarum biovar. viceae) <- L.Erdman (Rhizobium leguminosarum)
39741CIP <- 2001, IFO <- Toyama Dept Biol. <- H. Oyaizu <- IAM <- ATCC <- L.W. Erdman

doi: 10.13145/bacdive138443.20230509.8.1

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: 64388

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: 3Hoq18

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.945
39741negativerod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
64388R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
39741MEDIUM 296 - for RhizobiumyesDistilled water make up to (800.000 ml);Agar (15.000 g);Yeast extract (1.000 g);Mannitol (10.000 g);Earth extract - M0541 (200.000 ml)
39741CIP Medium 296yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=296

culture temp

@refgrowthtypetemperaturerange
64388positivegrowth28mesophilic
39741positivegrowth30mesophilic
39741positivegrowth25-37mesophilic
39741nogrowth10psychrophilic
39741nogrowth41thermophilic
39741nogrowth45thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.995

halophily

  • @ref: 39741
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371melibiose-builds acid from28053
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371galactitol-builds acid from16813
68371L-sorbose-builds acid from17266
68371erythritol-builds acid from17113
68369malate-assimilation25115
68369adipate-assimilation17128
68369decanoate-assimilation27689
68369gluconate-assimilation24265
68369maltose-assimilation17306
68369N-acetylglucosamine-assimilation59640
68369D-mannitol-assimilation16899
68369D-mannose-assimilation16024
68369L-arabinose-assimilation30849
68369D-glucose-assimilation17634
68369gelatin-hydrolysis5291
68369esculin+hydrolysis4853
68369urea+hydrolysis16199
68369arginine-hydrolysis29016
68369D-glucose-fermentation17634
68369tryptophan-energy source27897
68369nitrate-reduction17632
39741citrate-carbon source16947
39741esculin-hydrolysis4853
39741hippurate-hydrolysis606565
39741nitrate-reduction17632
39741nitrite-reduction16301

antibiotic resistance

  • @ref: 39741
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
3974135581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
3974115688acetoin-
3974117234glucose-

enzymes

@refvalueactivityec
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6
39741oxidase+
39741beta-galactosidase+3.2.1.23
39741alcohol dehydrogenase-1.1.1.1
39741gelatinase-
39741catalase-1.11.1.6
39741gamma-glutamyltransferase+2.3.2.2
39741lysine decarboxylase-4.1.1.18
39741ornithine decarboxylase-4.1.1.17
39741phenylalanine ammonia-lyase-4.3.1.24
39741tryptophan deaminase-
39741urease+3.5.1.5
68382esterase (C 4)-
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382cystine arylamidase-3.4.11.3
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382alpha-galactosidase-3.2.1.22
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
64388-----+--+/--+----+++/---
39741-+---++-+-++-+-+++++

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
64388----++-+------------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
39741+/--+/-+/-+/-+/-+/-+/-+/-+/-+/-+/-+/--+/--+/---+/-+/-+/-+/-+/-+/-+/-+/-+/-+/--+/-+/---+/---+/-+/-+/-+/-+/-+/-+/-+/-+/----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
39741+++-+-++--++---++-++-+-++------++--+++-+--------+----------+-----------+---------------------------

Isolation, sampling and environmental information

isolation

@refgeographic locationsample type
64388country of origin unknown
39741Effective nodules of Pisum sativum

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
643881Risk group (German classification)
397411Risk group (French classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhizobium leguminosarum DSM 106839GCA_014202125scaffoldncbi384
66792Rhizobium leguminosarum strain DSM 106839384.421wgspatric384
66792Rhizobium leguminosarum DSM 1068392861339494draftimg384

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno76.966no
gram-positiveno97.671no
anaerobicno98.773no
aerobicyes93.604no
halophileno93.679no
spore-formingno92.577no
glucose-utilyes83.293yes
thermophileno99.344yes
motileyes86.031no
glucose-fermentno89.086yes

External links

@ref: 64388

culture collection no.: CIP 106959, ATCC 10004, IAM 12609, OUT 30008, IFO 14778, DSM 106839, LMG 14904

straininfo link

  • @ref: 95170
  • straininfo: 4782

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny1377901Phylogenetic position of Rhizobium sp. strain Or 191, a symbiont of both Medicago sativa and Phaseolus vulgaris, based on partial sequences of the 16S rRNA and nifH genes.Eardly BD, Young JP, Selander RKAppl Environ Microbiol10.1128/aem.58.6.1809-1815.19921992Base Sequence, DNA, Bacterial/genetics, Fabaceae/microbiology, Genes, Bacterial, Hydrogen-Ion Concentration, Medicago sativa/microbiology, Microscopy, Electron, Molecular Sequence Data, Nitrogen Fixation/*genetics, Phylogeny, Plants, Medicinal, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/*genetics, Rhizobium/classification/*genetics/ultrastructure, Sequence Homology, Nucleic Acid, Symbiosis, TemperatureGenetics
Phylogeny9336913Classification of Austrian rhizobia and the Mexican isolate FL27 obtained from Phaseolus vulgaris L. as Rhizobium gallicum.Sessitsch A, Ramirez-Saad H, Hardarson G, Akkermans AD, de Vos WMInt J Syst Bacteriol10.1099/00207713-47-4-10971997Austria, DNA, Bacterial/*analysis, Fabaceae/microbiology/physiology, Mexico, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plants, Medicinal, Plasmids/genetics, RNA, Ribosomal, 16S/*analysis, Rhizobium/*classification/*genetics, Rickettsiaceae/physiologyGenetics
Metabolism12029033Atypical processing in domain III of 23S rRNA of Rhizobium leguminosarum ATCC 10004(T) at a position homologous to an rRNA fragmentation site in protozoa.Klein F, Samorski R, Klug G, Evguenieva-Hackenberg EJ Bacteriol10.1128/JB.184.12.3176-3185.20022002Animals, Base Sequence, Crithidia, Endoribonucleases/metabolism, Introns, Molecular Sequence Data, Nucleic Acid Conformation, *RNA Processing, Post-Transcriptional, RNA, Bacterial/metabolism, RNA, Protozoan/*chemistry/metabolism, RNA, Ribosomal, 23S/*chemistry/genetics/*metabolism, Rhizobium leguminosarum/genetics/growth & development/*metabolism, Ribonuclease III, Trypanosomatina/*genetics/metabolismGenetics
Phylogeny18984681Revision of the taxonomic status of the species Rhizobium leguminosarum (Frank 1879) Frank 1889AL, Rhizobium phaseoli Dangeard 1926AL and Rhizobium trifolii Dangeard 1926AL. R. trifolii is a later synonym of R. leguminosarum. Reclassification of the strain R. leguminosarum DSM 30132 (=NCIMB 11478) as Rhizobium pisi sp. nov.Ramirez-Bahena MH, Garcia-Fraile P, Peix A, Valverde A, Rivas R, Igual JM, Mateos PF, Martinez-Molina E, Velazquez EInt J Syst Evol Microbiol10.1099/ijs.0.65621-02008Bacterial Proteins/genetics, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal Spacer/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, Rhizobium/*classification/genetics/physiology, Rhizobium leguminosarum/*classification/genetics/physiology, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny19567587Rhizobium mesosinicum sp. nov., isolated from root nodules of three different legumes.Lin DX, Chen WF, Wang FQ, Hu D, Wang ET, Sui XH, Chen WXInt J Syst Evol Microbiol10.1099/ijs.0.006387-02009Aerobiosis, Bacterial Proteins/genetics, Bacterial Typing Techniques, China, Cluster Analysis, DNA Fingerprinting/methods, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA, Ribosomal Spacer/chemistry/genetics, Fabaceae/*microbiology, Locomotion, Molecular Sequence Data, N-Acetylglucosaminyltransferases/genetics, Nucleic Acid Hybridization, Phylogeny, Plant Roots/*microbiology, Proteome/analysis, RNA, Ribosomal, 16S/genetics, Rec A Recombinases/genetics, Rhizobium/*classification/genetics/*isolation & purification/physiology, Sequence Analysis, DNA, Transcription Factors/geneticsGenetics
Phylogeny29881978A new Rhizobium species isolated from the water of a crater lake, description of Rhizobium aquaticum sp. nov.Mathe I, Toth E, Mentes A, Szabo A, Marialigeti K, Schumann P, Felfoldi TAntonie Van Leeuwenhoek10.1007/s10482-018-1110-02018Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Lakes/*microbiology, Phylogeny, Rhizobium/classification/genetics/*isolation & purification/metabolismMetabolism

Reference

@idauthorstitledoi/urlcatalogue
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
39741Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106959Collection of Institut Pasteur (CIP 106959)
64388Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-106839Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 106839)
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
68369Automatically annotated from API 20NE
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
95170Reimer, 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-ID4782.1