Strain identifier

BacDive ID: 13537

Type strain: No

Species: Agrobacterium rosae

Strain Designation: B 2326, KGR

Strain history: IAM 13558 <-- NCPPB 1650 (Agrobacterium tumefaciens) <-- A. C. Hayward B2326 <-- B. H. Boelema strain KGR.

NCBI tax ID(s): 361 (species)

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General

@ref: 9200

BacDive-ID: 13537

DSM-Number: 30203

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

description: Agrobacterium rosae B 2326 is a mesophilic, Gram-negative bacterium that was isolated from Rosa sp..

NCBI tax id

  • NCBI tax id: 361
  • Matching level: species

strain history

@refhistory
9200<- DSM 60566 <- J. De Ley <- NCPPB (Agrobacterium tumefaciens) <- A.C. Hayward, B 2326 <- B.H. Boelema, KGR
67770IAM 13558 <-- NCPPB 1650 (Agrobacterium tumefaciens) <-- A. C. Hayward B2326 <-- B. H. Boelema strain KGR.

doi: 10.13145/bacdive13537.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Rhizobiaceae
  • genus: Agrobacterium
  • species: Agrobacterium rosae
  • full scientific name: Agrobacterium rosae Kuzmanovi? et al. 2019

@ref: 9200

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Rhizobiaceae

genus: Agrobacterium

species: Agrobacterium sp.

full scientific name: Agrobacterium sp.

strain designation: B 2326, KGR

type strain: no

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.985

Culture and growth conditions

culture medium

  • @ref: 9200
  • name: NUTRIENT AGAR (DSMZ Medium 1)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1
  • composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
9200positivegrowth26mesophilic
67770positivegrowth25mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.986

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
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
6836827613amygdalin-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

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
6836817997dinitrogenyes
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

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

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
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

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOXN2
9200+--------+-+-----+/--+/--+

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
9200-----+-+-----++--+--+

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
9200Rosa sp.RosaSouth AfricaZAFAfrica
67770Crown gall of Rosa sp.Rosa sp.South AfricaZAFAfrica

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Shrub (Scrub)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3457.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_6;97_6;98_6;99_3457&stattab=map
  • Last taxonomy: Agrobacterium
  • 16S sequence: MF443188
  • Sequence Identity:
  • Total samples: 1548
  • soil counts: 173
  • aquatic counts: 101
  • animal counts: 477
  • plant counts: 797

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Agrobacterium sp. NCPPB 1650 gene for 16S ribosomal RNA, complete sequenceD145061472ena759702
67770Agrobacterium tumefaciens 16S rRNA geneD139431402ena358
67770Agrobacterium sp. strain NCPPB 1650 16S ribosomal RNA gene, partial sequenceMF4431881489ena361

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Agrobacterium rosae strain NCPPB 16501972867.3wgspatric1972867
66792Agrobacterium rosae NCPPB 16502858625304draftimg1972867
67770Agrobacterium rosae NCPPB 1650GCA_002915175scaffoldncbi1972867

GC content

@refGC-contentmethod
920057.8
6777056.5genome sequence analysis
6777057.8thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes84.483no
gram-positiveno98.117no
anaerobicno97.251no
aerobicyes85.77no
halophileno90.206no
spore-formingno95.148no
glucose-utilyes86.281yes
flagellatedno82.209no
thermophileno99.605yes
glucose-fermentno86.858no

External links

@ref: 9200

culture collection no.: DSM 30203, DSM 60566, NCPPB 1650, JCM 20915, CFBP 4470, IAM 13558, LMG 230

straininfo link

  • @ref: 82728
  • straininfo: 589

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20521039Rapid and efficient identification of Agrobacterium species by recA allele analysis: Agrobacterium recA diversity.Costechareyre D, Rhouma A, Lavire C, Portier P, Chapulliot D, Bertolla F, Boubaker A, Dessaux Y, Nesme XMicrob Ecol10.1007/s00248-010-9685-72010Alleles, Amplified Fragment Length Polymorphism Analysis, Bacterial Proteins/*genetics, Bacterial Typing Techniques/*methods, *Genetic Variation, Molecular Sequence Data, Phylogeny, Rec A Recombinases/*genetics, Rhizobium/classification/*enzymology/genetics/*isolation & purification, Sequence Analysis, DNAGenetics
Phylogeny24440816Single acquisition of protelomerase gave rise to speciation of a large and diverse clade within the Agrobacterium/Rhizobium supercluster characterized by the presence of a linear chromid.Ramirez-Bahena MH, Vial L, Lassalle F, Diel B, Chapulliot D, Daubin V, Nesme X, Muller DMol Phylogenet Evol10.1016/j.ympev.2014.01.0052014Agrobacterium/classification/*enzymology/*genetics, Base Sequence, Chromosomes, Bacterial/*genetics, *Evolution, Molecular, *Genetic Speciation, Genome, Bacterial/genetics, *Phylogeny, Rhizobium/classification/*enzymology/*genetics, Telomerase/*geneticsEnzymology
Phylogeny29426637Agrobacterium rosae sp. nov., isolated from galls on different agricultural crops.Kuzmanovic N, Pulawska J, Smalla K, Nesme XSyst Appl Microbiol10.1016/j.syapm.2018.01.0042018Agrobacterium/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Crops, Agricultural/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry, Genes, Bacterial, Genes, Essential, Multilocus Sequence Typing, Nucleic Acid Hybridization, *Phylogeny, Plant Tumors/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome
34328363Occurrence of Crown Gall Disease on Japanese Spindle (Euonymus japonicas var. Green Rocket) Caused by Agrobacterium rosae in Iran.Mafakheri H, Taghavi SM, Zarei S, Kuzmanovic N, Osdaghi EPlant Dis10.1094/PDIS-03-21-0580-PDN2021

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9200Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 30203)https://www.dsmz.de/collection/catalogue/details/culture/DSM-30203
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/
68368Automatically annotated from API 20E
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
82728Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID589.1StrainInfo: A central database for resolving microbial strain identifiers