Strain identifier
BacDive ID: 13537
Type strain:
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)
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
@ref | history |
---|---|
9200 | <- DSM 60566 <- J. De Ley <- NCPPB (Agrobacterium tumefaciens) <- A.C. Hayward, B 2326 <- B.H. Boelema, KGR |
67770 | IAM 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
@ref | growth | type | temperature | range |
---|---|---|---|---|
9200 | positive | growth | 26 | mesophilic |
67770 | positive | growth | 25 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.986 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68369 | 25115 | malate | + | assimilation |
68369 | 17128 | adipate | - | assimilation |
68369 | 27689 | decanoate | - | assimilation |
68369 | 24265 | gluconate | + | assimilation |
68369 | 17306 | maltose | + | assimilation |
68369 | 59640 | N-acetylglucosamine | - | assimilation |
68369 | 16899 | D-mannitol | - | assimilation |
68369 | 16024 | D-mannose | - | assimilation |
68369 | 30849 | L-arabinose | - | assimilation |
68369 | 17634 | D-glucose | - | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 4853 | esculin | + | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | - | reduction |
68368 | 27613 | amygdalin | - | fermentation |
68368 | 17992 | sucrose | - | fermentation |
68368 | 62345 | L-rhamnose | - | fermentation |
68368 | 30911 | sorbitol | - | fermentation |
68368 | 17268 | myo-inositol | - | fermentation |
68368 | 16899 | D-mannitol | - | fermentation |
68368 | 17634 | D-glucose | + | fermentation |
68368 | 5291 | gelatin | - | hydrolysis |
68368 | 27897 | tryptophan | - | energy source |
68368 | 16199 | urea | - | hydrolysis |
68368 | 16947 | citrate | - | assimilation |
68368 | 18257 | ornithine | - | degradation |
68368 | 25094 | lysine | - | degradation |
68368 | 29016 | arginine | - | hydrolysis |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | no |
68368 | 17997 | dinitrogen | yes |
68368 | 15688 | acetoin | yes |
68368 | 35581 | indole | no |
68368 | 16136 | hydrogen sulfide | no |
metabolite tests
@ref | Chebi-ID | metabolite | indole test | voges-proskauer-test |
---|---|---|---|---|
68369 | 35581 | indole | - | |
68368 | 15688 | acetoin | + | |
68368 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68369 | cytochrome oxidase | + | 1.9.3.1 |
68369 | gelatinase | - | |
68369 | beta-glucosidase | + | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
68368 | cytochrome oxidase | - | 1.9.3.1 |
68368 | gelatinase | - | |
68368 | tryptophan deaminase | - | 4.1.99.1 |
68368 | urease | - | 3.5.1.5 |
68368 | ornithine decarboxylase | - | 4.1.1.17 |
68368 | lysine decarboxylase | - | 4.1.1.18 |
68368 | arginine dihydrolase | - | 3.5.3.6 |
68368 | beta-galactosidase | + | 3.2.1.23 |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL | GLU | MAN | INO | Sor | RHA | SAC | MEL | AMY | ARA | OX | N2 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
9200 | + | - | - | - | - | - | - | - | - | + | - | + | - | - | - | - | - | +/- | - | +/- | - | + |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
9200 | - | - | - | - | - | + | - | + | - | - | - | - | - | + | + | - | - | + | - | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | country | origin.country | continent |
---|---|---|---|---|---|
9200 | Rosa sp. | Rosa | South Africa | ZAF | Africa |
67770 | Crown gall of Rosa sp. | Rosa sp. | South Africa | ZAF | Africa |
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
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Agrobacterium sp. NCPPB 1650 gene for 16S ribosomal RNA, complete sequence | D14506 | 1472 | ena | 759702 |
67770 | Agrobacterium tumefaciens 16S rRNA gene | D13943 | 1402 | ena | 358 |
67770 | Agrobacterium sp. strain NCPPB 1650 16S ribosomal RNA gene, partial sequence | MF443188 | 1489 | ena | 361 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Agrobacterium rosae strain NCPPB 1650 | 1972867.3 | wgs | patric | 1972867 |
66792 | Agrobacterium rosae NCPPB 1650 | 2858625304 | draft | img | 1972867 |
67770 | Agrobacterium rosae NCPPB 1650 | GCA_002915175 | scaffold | ncbi | 1972867 |
GC content
@ref | GC-content | method |
---|---|---|
9200 | 57.8 | |
67770 | 56.5 | genome sequence analysis |
67770 | 57.8 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 84.483 | no |
gram-positive | no | 98.117 | no |
anaerobic | no | 97.251 | no |
aerobic | yes | 85.77 | no |
halophile | no | 90.206 | no |
spore-forming | no | 95.148 | no |
glucose-util | yes | 86.281 | yes |
flagellated | no | 82.209 | no |
thermophile | no | 99.605 | yes |
glucose-ferment | no | 86.858 | no |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 20521039 | Rapid 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 X | Microb Ecol | 10.1007/s00248-010-9685-7 | 2010 | Alleles, 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, DNA | Genetics |
Phylogeny | 24440816 | Single 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 D | Mol Phylogenet Evol | 10.1016/j.ympev.2014.01.005 | 2014 | Agrobacterium/classification/*enzymology/*genetics, Base Sequence, Chromosomes, Bacterial/*genetics, *Evolution, Molecular, *Genetic Speciation, Genome, Bacterial/genetics, *Phylogeny, Rhizobium/classification/*enzymology/*genetics, Telomerase/*genetics | Enzymology |
Phylogeny | 29426637 | Agrobacterium rosae sp. nov., isolated from galls on different agricultural crops. | Kuzmanovic N, Pulawska J, Smalla K, Nesme X | Syst Appl Microbiol | 10.1016/j.syapm.2018.01.004 | 2018 | Agrobacterium/*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, DNA | Transcriptome |
34328363 | Occurrence 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 E | Plant Dis | 10.1094/PDIS-03-21-0580-PDN | 2021 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
9200 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 30203) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-30203 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68368 | Automatically annotated from API 20E | |||||
68369 | Automatically annotated from API 20NE | |||||
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
82728 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID589.1 | StrainInfo: A central database for resolving microbial strain identifiers |