Strain identifier

BacDive ID: 13609

Type strain: Yes

Species: Rhizobium phaseoli

Strain Designation: 3I6c15, 316c15

Strain history: CIP <- 2002, P. De Lajudie, Montpellier, France: strain ORS 662 <- LMG <- 1989, ATCC, Rhizobium leguminosarum biovar phaseoli <- U. Means, Rhizobium phaseoli, USDA: strain 316c15

NCBI tax ID(s): 396 (species)

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

@ref: 9158

BacDive-ID: 13609

DSM-Number: 30137

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, motile, rod-shaped

description: Rhizobium phaseoli 3I6c15 is a mesophilic, Gram-negative, motile bacterium of the family Rhizobiaceae.

NCBI tax id

  • NCBI tax id: 396
  • Matching level: species

strain history

@refhistory
9158<- ATCC <- U. M. Means, USDA, 3I6c15
67770IAM 12612 <-- ATCC 14482 <-- U. M. Means 3I6c15.
121793CIP <- 2002, P. De Lajudie, Montpellier, France: strain ORS 662 <- LMG <- 1989, ATCC, Rhizobium leguminosarum biovar phaseoli <- U. Means, Rhizobium phaseoli, USDA: strain 316c15

doi: 10.13145/bacdive13609.20230509.8.1

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 phaseoli
  • full scientific name: Rhizobium phaseoli Dangeard 1926 (Approved Lists 1980)

@ref: 9158

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Rhizobiaceae

genus: Rhizobium

species: Rhizobium phaseoli

full scientific name: Rhizobium phaseoli Dangeard 1926 emend. Ramírez-Bahena et al. 2008

strain designation: 3I6c15, 316c15

type strain: yes

Morphology

cell morphology

  • @ref: 121793
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 9158
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9158RHIZOBIUM 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
38201MEDIUM 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)
121793CIP Medium 296yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=296

culture temp

@refgrowthtypetemperaturerange
9158positivegrowth26mesophilic
38201positivegrowth30mesophilic
67770positivegrowth25mesophilic
121793positivegrowth25-37mesophilic
121793nogrowth10psychrophilic
121793nogrowth41thermophilic
121793nogrowth45thermophilic

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
121793NaClpositivegrowth0 %
121793NaClnogrowth2 %
121793NaClnogrowth4 %
121793NaClnogrowth6 %
121793NaClnogrowth8 %
121793NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
68369adipate-assimilation17128
68369decanoate-assimilation27689
68369gelatin-hydrolysis5291
68369urea+hydrolysis16199
68369arginine-hydrolysis29016
68369D-glucose-fermentation17634
68369tryptophan-energy source27897
68369nitrate-reduction17632
121793citrate-carbon source16947
121793esculin+hydrolysis4853
121793hippurate-hydrolysis606565
121793nitrate-reduction17632
121793nitrite-reduction16301

antibiotic resistance

  • @ref: 121793
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12179335581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
12179315688acetoin-
12179317234glucose-

enzymes

@refvalueactivityec
9158catalase+1.11.1.6
9158cytochrome-c oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6
121793oxidase-
121793beta-galactosidase+3.2.1.23
121793alcohol dehydrogenase-1.1.1.1
121793gelatinase-
121793catalase+1.11.1.6
121793gamma-glutamyltransferase-2.3.2.2
121793lysine decarboxylase-4.1.1.18
121793ornithine decarboxylase-4.1.1.17
121793phenylalanine ammonia-lyase-4.3.1.24
121793tryptophan deaminase-
121793urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121793-++--+----++-+-+++--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
9158----+--++/-+/-+/-+/-+/-+/-+/---+/---+
9158----++-+------------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121793------------+/----------------+/--------------------+/-

Isolation, sampling and environmental information

isolation

@refgeographic locationcountryorigin.countrycontinentsample type
38201Beltsville, MDUSAUSANorth America
67770Beltsville, MDUSAUSANorth AmericaPlant-derived foodstuff (garden beans)
121793Beltsville, MarylandUnited States of AmericaUSANorth AmericaGarden beans

taxonmaps

  • @ref: 69479
  • File name: preview.99_77.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_62;97_65;98_70;99_77&stattab=map
  • Last taxonomy: Rhizobium
  • 16S sequence: EF141340
  • Sequence Identity:
  • Total samples: 333
  • soil counts: 50
  • aquatic counts: 32
  • animal counts: 28
  • plant counts: 223

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
91581Risk group (German classification)
1217931Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Rhizobium phaseoli strain ATCC 14482 16S ribosomal RNA gene, partial sequenceEF1413401477ena396
20218Rhizobium phaseoli strain ATCC 14482 16S-23S ribosomal RNA intergenic spacer, partial sequenceEF1413411091ena396
20218Rhizobium leguminosarum strain CCT 4168T 16S-23S ribosomal DNA intergenic spacer region, 3' endAF091788784ena384
20218Rhizobium leguminosarum strain CCT 4168T 16S-23S ribosomal DNA intergenic spacer region, 5' endAF091789743ena384
20218R.leguminosarum (LMG 8819) 16S rRNA geneX771221099ena384
20218Rhizobium phaseoli gene for 16S rRNA, partial sequence, strain: NBRC 14785AB6806641406ena396

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhizobium phaseoli strain ATCC 14482396.115wgspatric396
66792Rhizobium phaseoli DSM 301372738541346draftimg396
67770Rhizobium phaseoli ATCC 14482GCA_003985125scaffoldncbi396

GC content

  • @ref: 9158
  • GC-content: 59.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno97.581no
anaerobicno98.745no
halophileno94.003no
spore-formingno94.069no
glucose-utilyes83.603no
aerobicyes93.007no
motileyes83.885no
thermophileno99.251yes
flagellatedno84.117no
glucose-fermentno88.904no

External links

@ref: 9158

culture collection no.: DSM 30137, ATCC 14482, JCM 20683, NBRC 14785, NRRL L-321, VKM B-1966, IAM 12612, CIP 107329, LMG 8819, ORS 662

straininfo link

  • @ref: 82796
  • straininfo: 265209

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
Phylogeny22858268Rhizobium etli taxonomy revised with novel genomic data and analyses.Lopez-Guerrero MG, Ormeno-Orrillo E, Velazquez E, Rogel MA, Acosta JL, Gonzalez V, Martinez J, Martinez-Romero ESyst Appl Microbiol10.1016/j.syapm.2012.06.0092012DNA, Bacterial/genetics, Databases, Genetic, *Genome, Bacterial, Genomics/methods, Nucleic Acid Hybridization, Phaseolus/microbiology, Phylogeny, Rhizobium etli/*classification/*geneticsGenetics
Phylogeny25385989Rhizobium sophorae sp. nov. and Rhizobium sophoriradicis sp. nov., nitrogen-fixing rhizobial symbionts of the medicinal legume Sophora flavescens.Jiao YS, Yan H, Ji ZJ, Liu YH, Sui XH, Wang ET, Guo BL, Chen WX, Chen WFInt J Syst Evol Microbiol10.1099/ijs.0.068916-02014China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Molecular Sequence Data, *Nitrogen Fixation, Nucleic Acid Hybridization, Phaseolus, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/isolation & purification, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, Sophora/*microbiology, *Symbiosis, Ubiquinone/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9158Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 30137)https://www.dsmz.de/collection/catalogue/details/culture/DSM-30137
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
38201Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4753
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
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
82796Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265209.1StrainInfo: A central database for resolving microbial strain identifiers
121793Curators of the CIPCollection of Institut Pasteur (CIP 107329)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107329