Strain identifier

BacDive ID: 13573

Type strain: Yes

Species: Agrobacterium rubi

Strain Designation: TR3, TR 3

Strain history: CIP <- 1995, ATCC <- M.P. Starr: strain TR 3 <- E.M. Hildebrand

NCBI tax ID(s): 1368415 (strain), 28099 (species)

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General

@ref: 2810

BacDive-ID: 13573

DSM-Number: 6772

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

description: Agrobacterium rubi TR3 is a mesophilic, Gram-negative plant pathogen that was isolated from probably boysenberry .

NCBI tax id

NCBI tax idMatching level
28099species
1368415strain

strain history

@refhistory
2810<- NCPPB <-ICPB, TR3
67770IAM 13569 <-- ATCC 13335 <-- M. P. Starr TR3 <-- E. M. Hilderbrand.
122281CIP <- 1995, ATCC <- M.P. Starr: strain TR 3 <- E.M. Hildebrand

doi: 10.13145/bacdive13573.20230509.8.1

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 rubi
  • full scientific name: Agrobacterium rubi (Hildebrand 1940) Starr and Weiss 1943 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Phytomonas rubi
    20215Rhizobium rubi

@ref: 2810

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Rhizobiaceae

genus: Agrobacterium

species: Agrobacterium rubi

full scientific name: Agrobacterium rubi (Hildebrand 1940) Starr and Weiss 1943

strain designation: TR3, TR 3

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.975
122281negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
34681MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
2810NUTRIENT 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
122281CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
34681positivegrowth30mesophilic
2810positivegrowth26mesophilic
67770positivegrowth25mesophilic
122281positivegrowth30mesophilic
122281nogrowth5psychrophilic
122281nogrowth10psychrophilic
122281nogrowth41thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.995

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
1222814853esculin-hydrolysis
12228117632nitrate-reduction
12228116301nitrite-reduction
122281132112sodium thiosulfate-builds gas from
12228117234glucose+degradation

antibiotic resistance

  • @ref: 122281
  • 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
12228135581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

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
122281oxidase-
122281beta-galactosidase+3.2.1.23
122281alcohol dehydrogenase-1.1.1.1
122281gelatinase-
122281amylase-
122281caseinase-3.4.21.50
122281catalase-1.11.1.6
122281tween esterase-
122281lecithinase-
122281lysine decarboxylase-4.1.1.18
122281ornithine decarboxylase-4.1.1.17
122281urease+3.5.1.5

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
2810----++-++++++++--+--+

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
2810probably boysenberry (Rubus ursinus var. loganobaccus)Rubus ursinus var. Loganobaccus
67770Cane gall of Rubus ursinusRubus ursinusUSAUSANorth America
122281Black raspberry

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Fruit (Seed)

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
2810yes1Risk group (German classification)
1222811Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Rhizobium rubi strain DSM 6772 clone 1 16S ribosomal RNA gene, partial sequence; internal transcribed spacer, complete sequence; and 23S ribosomal RNA, partial sequenceAF3452761259ena28099
20218Rhizobium rubi strain DSM 6772 clone 2 16S ribosomal RNA gene, partial sequence; internal transcribed spacer, complete sequence; and 23S ribosomal RNA, partial sequenceAF3452771248ena28099
20218Agrobacterium rubi gene for 16S rRNA, strain: IAM 13569D127871438ena28099
20218Agrobacterium rubi strain ICMP 11833 16S ribosomal RNA gene, partial sequenceAY6263951336ena28099
20218Agrobacterium rubi gene for 16S ribosomal RNA, complete sequenceD145031472ena28099
20218Agrobacterium rubi partial 16S rRNA gene, strain LMG 156X672281436ena28099
20218Agrobacterium rubi partial 16S rRNA gene, strain LMG 17935AM1817591426ena28099
20218Agrobacterium rubi gene for 16S rRNA, partial sequence, strain: NBRC 13261AB6803851410ena28099

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Agrobacterium rubi DSM 6772GCA_017873055contigncbi28099
66792Agrobacterium rubi strain DSM 677228099.16wgspatric28099
66792Rhizobium rubi NBRC 132611220582.3wgspatric1368415
66792Agrobacterium rubi NBRC 132612600255076draftimg1368415
66792Rhizobium rubi DSM 67722913290767draftimg28099
67770Agrobacterium rubi TR3 = NBRC 13261GCA_000739935contigncbi1368415

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes81.456no
gram-positiveno98.293no
anaerobicno97.863no
aerobicyes89.437no
halophileno89.656no
spore-formingno96.151no
thermophileno99.666yes
glucose-utilyes90.674yes
flagellatedno81.778no
glucose-fermentno89.695yes

External links

@ref: 2810

culture collection no.: DSM 6772, ATCC 13335, NCPPB 1854, JCM 20918, CFBP 1317, CIP 104332, HAMBI 1812, IAM 13569, ICMP 6428, ICPB TR3, IFO 13261, LMG 13935, LMG 156, NBRC 13261

straininfo link

  • @ref: 82760
  • straininfo: 447

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics17284069Agrobacterium rubi(T) DSM 6772 produces a lipophilic polysaccharide capsule whose degree of acetylation is growth modulated.De Castro C, Gargiulo V, Lanzetta R, Parrilli MBiomacromolecules10.1021/bm061081f2007Acetylation, Antigens, Bacterial, Biochemistry/methods, Capsules/*chemistry, Carbohydrate Conformation, Carbohydrate Sequence, Gas Chromatography-Mass Spectrometry, Macromolecular Substances, Magnetic Resonance Spectroscopy, Models, Molecular, Molecular Sequence Data, Monosaccharides/chemistry, Polysaccharides/*chemistry, Protons, Rhizobium/*metabolism, TemperatureMetabolism
Phylogeny21148676Rhizobium pusense sp. nov., isolated from the rhizosphere of chickpea (Cicer arietinum L.).Panday D, Schumann P, Das SKInt J Syst Evol Microbiol10.1099/ijs.0.028407-02010Base Composition, Cicer/*microbiology, DNA, Bacterial/genetics, Fatty Acids/metabolism, India, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/*isolation & purification/metabolism, *Rhizosphere, *Soil MicrobiologyMetabolism
Phylogeny21642489Rhizobium skierniewicense sp. nov., isolated from tumours on chrysanthemum and cherry plum.Pulawska J, Willems A, Sobiczewski PInt J Syst Evol Microbiol10.1099/ijs.0.032532-02011Chrysanthemum/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Plant Tumors/*microbiology, Prunus/*microbiology, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/isolation & purificationGenetics
Phylogeny29402492Agrobacterium bohemicum sp. nov. isolated from poppy seed wastes in central Bohemia.Zahradnik J, Nunvar J, Parizkova H, Kolarova L, Palyzova A, Maresova H, Grulich M, Kyslikova E, Kyslik PSyst Appl Microbiol10.1016/j.syapm.2018.01.0032018Agrobacterium/*classification/genetics/isolation & purification, Base Composition, Biotransformation, Czech Republic, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Multilocus Sequence Typing, Nucleic Acid Hybridization, Papaver/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seeds/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2810Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6772)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6772
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
34681Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16229
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
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
82760Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID447.1StrainInfo: A central database for resolving microbial strain identifiers
122281Curators of the CIPCollection of Institut Pasteur (CIP 104332)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104332