Strain identifier

BacDive ID: 1805

Type strain: Yes

Species: Bradyrhizobium japonicum

Strain Designation: 3I1b6

Strain history: CIP <- 1999, ATCC <- L.W. Erdman: strain 3I1b6

NCBI tax ID(s): 375 (species)

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General

@ref: 9152

BacDive-ID: 1805

DSM-Number: 30131

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

description: Bradyrhizobium japonicum 3I1b6 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Soy bean,Glycine hispida,nodule.

NCBI tax id

  • NCBI tax id: 375
  • Matching level: species

strain history

@refhistory
9152<- ATCC <- L.W. Erdman, 3I1b6
67770IAM 12608 <-- ATCC 10324 <-- L. W. Erdman 3I1b6.
120318CIP <- 1999, ATCC <- L.W. Erdman: strain 3I1b6

doi: 10.13145/bacdive1805.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Nitrobacteraceae
  • genus: Bradyrhizobium
  • species: Bradyrhizobium japonicum
  • full scientific name: Bradyrhizobium japonicum (Kirchner 1896) Jordan 1982

  • synonyms

    @refsynonym
    20215Rhizobacterium japonicum
    20215Rhizobium japonicum

@ref: 9152

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: 3I1b6

type strain: yes

Morphology

cell morphology

  • @ref: 120318
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 48990
  • incubation period: 3 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9152RHIZOBIUM 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
32940MEDIUM 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)
120318CIP Medium 296yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=296

culture temp

@refgrowthtypetemperaturerange
9152positivegrowth26mesophilic
32940positivegrowth25mesophilic
48990positivegrowth30mesophilic
67770positivegrowth25mesophilic
120318positivegrowth25-30mesophilic
120318nogrowth10psychrophilic
120318nogrowth37mesophilic
120318nogrowth41thermophilic
120318nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 48990
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
120318NaClpositivegrowth0-2 %
120318NaClnogrowth4 %
120318NaClnogrowth6 %
120318NaClnogrowth8 %
120318NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
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
68371lactose-builds acid from17716
68371maltose+builds acid from17306
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-mannose+builds acid from16024
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
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
120318citrate-carbon source16947
120318esculin-hydrolysis4853
120318hippurate+hydrolysis606565
120318nitrate+reduction17632
120318nitrite-reduction16301

antibiotic resistance

  • @ref: 120318
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 120318
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12031815688acetoin-
12031817234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
120318oxidase+
120318beta-galactosidase-3.2.1.23
120318alcohol dehydrogenase-1.1.1.1
120318gelatinase-
120318catalase+1.11.1.6
120318gamma-glutamyltransferase-2.3.2.2
120318lysine decarboxylase-4.1.1.18
120318ornithine decarboxylase-4.1.1.17
120318phenylalanine ammonia-lyase-4.3.1.24
120318tryptophan deaminase-
120318urease+3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120318--++-+--+-++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120318----+/------+++--------+-++++/-+---+---++------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
48990Soy bean,Glycine hispida,noduleJapanJPNAsia
120318Soybean

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: X66024
  • Sequence Identity:
  • Total samples: 12887
  • soil counts: 5001
  • aquatic counts: 2827
  • animal counts: 4320
  • plant counts: 739

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
91521Risk group (German classification)
1203181Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bradyrhizobium sp. (ATCC 10324) 16S ribosomal RNA (16S rRNA) gene fragmentL41530264ena376
20218Bradyrhizobium japonicum 16S ribosomal RNA gene, partial sequence; tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, complete sequenceU696385146ena1037409
20218Bradyrhizobium japonicum strain DSM 30131 16S-23S intergenic spacer, partial sequenceAF271643815ena375
20218Bradyrhizobium japonicum bv. glycinearum strain DSM 30131 16S-23S ribosomal RNA intergenic spacer, tRNA-Ile and tRNA-Ala genes, complete sequenceAY599102791ena305581
20218B.japonicum 16S rRNA geneX718402882ena375
20218B.japonicum 16S rRNA geneX872721484ena375
20218Bradyrhizobium japonicum gene for 16S rRNA, complete sequenceD113451484ena375
20218Bradyrhizobium japonicum gene for 16S rRNA, strain: IAM 12608D127811441ena375
20218Bradyrhizobium japonicum strain LMG 6138 16S ribosomal RNA gene, partial sequence; internal transcribed spacer, complete sequence; and 23S ribosomal RNA, partial sequenceAF345255839ena375
2021816S rRNA [Bradyrhizobium japonicum, LMG 6138T, rRNA Partial, 1440 nt]S469161440ena375
20218Bradyrhizobium japonicum partial 16S rRNA gene, strain LMG 6138X660241441ena375
20218Bradyrhizobium japonicum gene for 16S ribosomal RNA, partial sequence, strain: NBRC 14783AB5100021414ena375
20218Bradyrhizobium japonicum DNA, 16S-23S rRNA ITS region, tRNA-Ile, tRNA-Ala, strain: NBRC 14783AB573865815ena375
20218Bradyrhizobium japonicum 16S ribosomal RNA gene, partial sequenceAF3629431039ena375
20218Bradyrhizobium japonicum DNA, 16S-23S ITS1 region, tRNA-Ile, tRNA-Ala, strain: USDA 6AB100741791ena1037409
20218Bradyrhizobium japonicum gene for 16S ribosomal RNA, partial sequence, strain: USDA6AB2319271400ena1037409
20218Bradyrhizobium japonicum gene for 16S ribosomal RNA, partial sequence, strain:USDA 6D85412264ena1037409
20218Bradyrhizobium japonicum USDA 6 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceHQ143390913ena1037409

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bradyrhizobium japonicum strain NBRC 14783375.87wgspatric375
67770Bradyrhizobium japonicum NBRC 14783GCA_006539645contigncbi375

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno97.916no
anaerobicno98.272yes
halophileno95.269no
spore-formingno92.206no
glucose-utilyes88.504no
aerobicyes91.888no
motileyes86.815no
flagellatedno70.979no
thermophileno99.671yes
glucose-fermentno89.301no

External links

@ref: 9152

culture collection no.: DSM 30131, ATCC 10324, CCUG 27876, LMG 6138, CECT 530, JCM 20679, BCRC 13518, BCRC 80814, CCTM La 3681, CIP 106093, HAMBI 2314, IAM 12608, ICMP 2864, NBRC 14783, NCIMB 11477, NRRL B-4507, NRRL L-241, NZP 5549, OUT 30002, USDA 505, VKM B-1967

straininfo link

  • @ref: 71452
  • straininfo: 1344

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny570016Bacteriocin-like substances produced by Rhizobium japonicum and other slow-growing rhizobia.Gross DC, Vidaver AKAppl Environ Microbiol10.1128/aem.36.6.936-943.19781978Animals, Antibiosis, Bacteriocins/*biosynthesis/pharmacology, Corynebacterium/drug effects, Dogs, Fabaceae/microbiology, Plants, Medicinal, Rhizobium/growth & development/*metabolism, *Soil Microbiology, Soybeans, Species SpecificityPathogenicity
2294083Cell-associated oligosaccharides of Bradyrhizobium spp.Miller KJ, Gore RS, Johnson R, Benesi AJ, Reinhold VNJ Bacteriol10.1128/jb.172.1.136-142.19901990Glucans/analysis, Magnetic Resonance Spectroscopy, Oligosaccharides/*analysis, Rhizobiaceae/*analysis, Rhizobium/analysis
Metabolism5438044Gluconate catabolism in Rhizobium japonicum.Keele BB Jr, Hamilton PB, Elkan GHJ Bacteriol10.1128/jb.101.3.698-704.19701970Acetates/metabolism, Alcohol Oxidoreductases/metabolism, Aldehyde-Lyases/metabolism, Carbon Dioxide/metabolism, Carbon Isotopes, Citric Acid Cycle, Gluconates/*metabolism, Glutamates/metabolism, Phosphogluconate Dehydrogenase/metabolism, Phosphotransferases/metabolism, Pyruvates/metabolism, Rhizobium/enzymology/*metabolism, Spectrophotometry, Succinates/metabolism, Transferases/metabolismEnzymology
Metabolism5776525Glucose catabolism in Rhizobium japonicum.Keele BB Jr, Hamilton PB, Elkan GHJ Bacteriol10.1128/jb.97.3.1184-1191.19691969Acetates/metabolism, Carbon Dioxide/metabolism, Carbon Isotopes, Citric Acid Cycle, Gluconates/metabolism, Glucose/*metabolism, Glutamates/metabolism, Pyruvates/metabolism, Rhizobium/enzymology/*metabolism, Succinates/metabolismEnzymology
Phylogeny7520737Phenotypic and genotypic characterization of bradyrhizobia nodulating the leguminous tree Acacia albida.Dupuy N, Willems A, Pot B, Dewettinck D, Vandenbruaene I, Maestrojuan G, Dreyfus B, Kersters K, Collins MD, Gillis MInt J Syst Bacteriol10.1099/00207713-44-3-4611994Acacia/*microbiology, Bacterial Proteins/isolation & purification, DNA, Bacterial/genetics, Genotype, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhizobiaceae/*classification/*genetics/isolation & purification, Senegal, Soil Microbiology, Species SpecificityGenetics
Phylogeny10528395Phylogenetic analyses of Bradyrhizobium strains nodulating soybean (Glycine max) in Thailand with reference to the USDA strains of Bradyrhizobium.Ando S, Yokoyama TCan J Microbiol10.1139/w99-0611999Base Sequence, Bradyrhizobium/*classification/*genetics, Genes, Bacterial, Genes, rRNA, Molecular Sequence Data, Nitrogen Fixation/genetics, *Phylogeny, Polymorphism, Restriction Fragment Length, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soybeans/*microbiology, Thailand, United States, United States Department of AgricultureGenetics
Phylogeny13130002Bosea minatitlanensis sp. nov., a strictly aerobic bacterium isolated from an anaerobic digester.Ouattara AS, Assih EA, Thierry S, Cayol JL, Labat M, Monroy O, Macarie HInt J Syst Evol Microbiol10.1099/ijs.0.02540-02003Aerobiosis, Bradyrhizobiaceae/classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Genes, Bacterial, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sewage/microbiology, Species SpecificityGenetics
16347446Conservation of a symbiotic DNA region in soybean root nodule bacteria.Hahn M, Hennecke HAppl Environ Microbiol10.1128/aem.53.9.2253-2255.19871987
Phylogeny29898432Microbial cyclic beta-(1-->3),(1-->6)-glucans as potential drug carriers: Interaction studies between cyclic beta-glucans isolated from Bradyrhizobium japonicum and betulinic acid.Kambhampati NSV, Kar S, Pinnepalli SSK, Chelli J, Doble MSpectrochim Acta A Mol Biomol Spectrosc10.1016/j.saa.2018.05.1062018Bradyrhizobium/*chemistry, Calorimetry, Differential Scanning, Drug Carriers/*chemistry, Glucans/*chemistry/*isolation & purification, Molecular Docking Simulation, Pentacyclic Triterpenes, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Spectrophotometry, Ultraviolet, Thermodynamics, Triterpenes/*chemistry, X-Ray DiffractionPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9152Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 30131)https://www.dsmz.de/collection/catalogue/details/culture/DSM-30131
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
32940Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18184
48990Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 27876)https://www.ccug.se/strain?id=27876
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/
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
71452Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1344.1StrainInfo: A central database for resolving microbial strain identifiers
120318Curators of the CIPCollection of Institut Pasteur (CIP 106093)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106093