Strain identifier

BacDive ID: 13571

Type strain: Yes

Species: Rhizobium rhizogenes

Strain history: CIP <- 1995, ATCC <- A.J. Riker

NCBI tax ID(s): 1220581 (strain), 359 (species)

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General

@ref: 9168

BacDive-ID: 13571

DSM-Number: 30148

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

description: Rhizobium rhizogenes DSM 30148 is a mesophilic, Gram-negative, rod-shaped plant pathogen that was isolated from Apple.

NCBI tax id

NCBI tax idMatching level
359species
1220581strain

strain history

@refhistory
9168<- ATCC <- A.J. Riker
67770IAM 13570 <-- ATCC 11325 <-- A. J. Riker.
122199CIP <- 1995, ATCC <- A.J. Riker

doi: 10.13145/bacdive13571.20230509.8.1

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 rhizogenes
  • full scientific name: Rhizobium rhizogenes (Riker et al. 1930) Young et al. 2001

  • synonyms

    @refsynonym
    20215Phytomonas rhizogenes
    20215Agrobacterium rhizogenes

@ref: 9168

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Rhizobiaceae

genus: Rhizobium

species: Rhizobium rhizogenes

full scientific name: Rhizobium rhizogenes (Riker et al. 1930) Young et al. 2001

type strain: yes

Morphology

cell morphology

  • @ref: 122199
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 9168
  • incubation period: 3-7 days

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
41763MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
9168NUTRIENT AGAR (DSMZ Medium 1)yesName: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/1
68368MacConkey mediumno
122199CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
122199CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
41763positivegrowth25mesophilic
9168positivegrowth26mesophilic
67770positivegrowth25mesophilic
122199positivegrowth25-30mesophilic
122199nogrowth5psychrophilic
122199nogrowth10psychrophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836927689decanoate-assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836929016arginine-hydrolysis
6836927897tryptophan-energy source
6836817632nitrate-reduction
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose+fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine+hydrolysis
1221994853esculin+hydrolysis
12219917632nitrate-reduction
12219916301nitrite-reduction
12219917234glucose-degradation

antibiotic resistance

  • @ref: 122199
  • 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
6836816301nitriteno
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12219935581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
6836935581indole-
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
9168catalase+1.11.1.6
9168cytochrome-c oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369arginine dihydrolase-3.5.3.6
68368cytochrome oxidase-1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase-3.2.1.23
122199oxidase-
122199beta-galactosidase+3.2.1.23
122199alcohol dehydrogenase-1.1.1.1
122199gelatinase-
122199amylase-
122199caseinase-3.4.21.50
122199catalase+1.11.1.6
122199tween esterase-
122199lecithinase-
122199lipase-
122199lysine decarboxylase-4.1.1.18
122199ornithine decarboxylase-4.1.1.17
122199urease+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
122199-+++-+----+-++-+++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOXNO2MAC
9168-+-------+-+----+------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
9168----++-+++++-+---+--+
9168+-+--+-++++++-+--++-
9168----++-++++++++--++-+
9168----++-++++++++-++--
9168----+/-+-+--+/---+/----+/---+
9168----++-+-+++-+---+---
45734--++-+-------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122199+++++-+++-+++++++++++++++-++++++++++++-++--+-+--++------------+++--------------++-----+--+++-+----+

Isolation, sampling and environmental information

isolation

@refsample type
67770Apple
122199Food, Apple

taxonmaps

  • @ref: 69479
  • File name: preview.99_1577.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_62;97_65;98_1244;99_1577&stattab=map
  • Last taxonomy: Rhizobiaceae
  • 16S sequence: AB680381
  • Sequence Identity:
  • Total samples: 5839
  • soil counts: 3171
  • aquatic counts: 403
  • animal counts: 1252
  • plant counts: 1013

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
9168yes1Risk group (German classification)
1221991Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Agrobacterium rhizogenes strain ATCC 11325 16S ribosomal RNA gene, partial sequenceAY9459551473ena359
20218Agrobacterium rhizogenes strain CCT 4832T 16S-23S ribosomal DNA intergenic spacer region, 3' endAF091794741ena359
20218Agrobacterium rhizogenes strain CCT 4832T 16S-23S ribosomal DNA intergenic spacer region, 5' endAF091795716ena359
20218Rhizobium rhizogenes strain DSM 30148 16S ribosomal RNA gene, partial sequence; internal transcribed spacer, complete sequence; and 23S ribosomal RNA, partial sequenceAF3452751281ena359
20218Agrobacterium rhizogenes gene for 16S rRNA, strain: IAM 13570D127881434ena359
20218Agrobacterium rhizogenes gene for 16S ribosomal RNA, complete sequenceD145011468ena359
20218Agrobacterium rhizogenes genes for 16S rRNA, tRNA-Ile, tRNA-Ala, 23S rRNA 150-b fragment, IVS, 23S rRNA 1.3-kb fragment A, partial and complete sequence, strain: NBRC 13257AB2476043027ena359
20218Agrobacterium rhizogenes gene for 16S rRNA, partial sequence, strain: NBRC 13257AB6803811406ena359
67770Bifidobacterium longum subsp. infantis strain BIC1401212621a, whole genome shotgun sequenceD01257239227ena1682

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Agrobacterium rhizogenes strain LMG150359.176wgspatric359
66792Rhizobium rhizogenes NBRC 132571220581.4wgspatric1220581
66792Agrobacterium rhizogenes NBRC 132572588253840draftimg1220581
67770Rhizobium rhizogenes NBRC 13257GCA_000696095contigncbi1220581
67770Rhizobium rhizogenes LMG150GCA_007002985contigncbi359

GC content

  • @ref: 67770
  • GC-content: 61.4
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes87.48no
gram-positiveno97.637no
anaerobicno98.095no
aerobicyes90.836no
halophileno94.249no
spore-formingno92.476no
thermophileno99.594no
glucose-utilyes88.125no
flagellatedno77.78no
glucose-fermentno84.21yes

External links

@ref: 9168

culture collection no.: DSM 30148, ATCC 11325, IFO 13257, NBRC 13257, NCPPB 2991, CCUG 12534 C, JCM 20919, CFBP 5520, CIP 104328, HAMBI 1816, IAM 13570, ICMP 5794, IMET 11180, KCTC 12403, LMG 150

straininfo link

  • @ref: 82758
  • straininfo: 443

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16478052The coexistence of symbiosis and pathogenicity-determining genes in Rhizobium rhizogenes strains enables them to induce nodules and tumors or hairy roots in plants.Velazquez E, Peix A, Zurdo-Pineiro JL, Palomo JL, Mateos PF, Rivas R, Munoz-Adelantado E, Toro N, Garcia-Benavides P, Martinez-Molina EMol Plant Microbe Interact10.1094/MPMI-18-13252005Bacterial Proteins/*genetics/*metabolism, Gene Expression Profiling, Molecular Sequence Data, Phaseolus/metabolism/microbiology, Phylogeny, Plant Roots/*microbiology, Plasmids/genetics, RNA, Ribosomal, 16S/genetics, Rhizobium/classification/*genetics/*pathogenicity/physiology, Symbiosis/*genetics, Virulence/geneticsMetabolism
Metabolism16972092Genetic transformation of Gentiana macrophylla with Agrobacterium rhizogenes: growth and production of secoiridoid glucoside gentiopicroside in transformed hairy root cultures.Tiwari RK, Trivedi M, Guang ZC, Guo GQ, Zheng GCPlant Cell Rep10.1007/s00299-006-0236-02006DNA, Bacterial/genetics, Genome, Plant, Gentiana/genetics/*growth & development/*metabolism, Glucosides/*biosynthesis, Iridoid Glucosides, Iridoids, Plant Roots/genetics/growth & development/metabolism, Plants, Genetically Modified/genetics/growth & development/metabolism, Plants, Medicinal/genetics, Pyrans, Rhizobium/*genetics, *Transformation, GeneticGenetics
Phylogeny17082403Rhizobium lusitanum sp. nov. a bacterium that nodulates Phaseolus vulgaris.Valverde A, Igual JM, Peix A, Cervantes E, Velazquez EInt J Syst Evol Microbiol10.1099/ijs.0.64402-02006Anti-Bacterial Agents/pharmacology, Bacterial Proteins/genetics, Bacterial Typing Techniques, Carbohydrate Metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA, Ribosomal Spacer/genetics, Genes, rRNA, Medicago sativa/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidoreductases/genetics, Phaseolus/*microbiology, Phylogeny, Portugal, RNA, Ribosomal, 16S/genetics, Rec A Recombinases/genetics, Rhizobium/*classification/genetics/*isolation & purification/physiology, Sequence Homology, Nucleic Acid, Transcription Factors/genetics, Virulence/geneticsGenetics
Metabolism18050745[Increasing the content of active constituents in Polygonum cuspidatum hairy root by gene transformation technology].Miao XY, Yu SH, Shen YZ, Huang ZJYao Xue Xue Bao2007Acyltransferases/*genetics/metabolism, DNA Primers, DNA, Plant/genetics, Drugs, Chinese Herbal/analysis, Fallopia japonica/*genetics/metabolism, Genetic Vectors, Glucosides/*analysis, Molecular Sequence Data, Plant Roots/genetics/metabolism, *Plants, Genetically Modified, Plants, Medicinal/genetics/metabolism, Resveratrol, Rhizobium/genetics, Stilbenes/*analysis, Transformation, GeneticGenetics
Phylogeny18599718Rhizobium multihospitium sp. nov., isolated from multiple legume species native of Xinjiang, China.Han TX, Wang ET, Wu LJ, Chen WF, Gu JG, Gu CT, Tian CF, Chen WXInt J Syst Evol Microbiol10.1099/ijs.0.65568-02008China, DNA, Ribosomal Spacer/genetics, Fabaceae/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/*isolation & purification, Sequence Homology, Nucleic Acid, Species SpecificityGenetics
Phylogeny21131504Rhizobium vallis sp. nov., isolated from nodules of three leguminous species.Wang F, Wang ET, Wu LJ, Sui XH, Li Y, Chen WXInt J Syst Evol Microbiol10.1099/ijs.0.026484-02010Bacterial Proteins/genetics/metabolism, Base Composition, China, DNA, Bacterial/genetics, Fabaceae/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobium/classification/genetics/*isolation & purification/metabolism, Root Nodules, Plant/*microbiologyMetabolism
24221400Agrobacterium rhizogenes-mediated transformation of Echinacea purpurea.Trypsteen M, Van Lijsebettens M, Van Severen R, Van Montagu MPlant Cell Rep10.1007/BF002364631991
35044833Development of a New Recombineering System for Agrobacterium Species.Bian Z, Li S, Yang R, Yin J, Zhang Y, Tu Q, Fu J, Li RAppl Environ Microbiol10.1128/aem.02499-212022Agrobacterium tumefaciens/genetics, Genetic Engineering, Recombinases, *Rhizobium/genetics, *Rhizobium leguminosarum

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9168Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 30148)https://www.dsmz.de/collection/catalogue/details/culture/DSM-30148
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
41763Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16225
45734Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 12534 C)https://www.ccug.se/strain?id=12534
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/
68368Automatically annotated from API 20E
68369Automatically annotated from API 20NE
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
82758Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID443.1StrainInfo: A central database for resolving microbial strain identifiers
122199Curators of the CIPCollection of Institut Pasteur (CIP 104328)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104328