Strain identifier
BacDive ID: 13646
Type strain:
Species: Rhizobium vallis
Strain history: <- LMG <- W. X. Chen, State Key Laboratory for Agrobiotechnol., China Agricultural Univ., Beijing, PR China; CCBAU 65647
NCBI tax ID(s): 634290 (species)
General
@ref: 18221
BacDive-ID: 13646
DSM-Number: 26437
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile
description: Rhizobium vallis DSM 26437 is a mesophilic, motile bacterium that was isolated from root nodules of Phaseolus vulgaris.
NCBI tax id
- NCBI tax id: 634290
- Matching level: species
strain history
- @ref: 18221
- history: <- LMG <- W. X. Chen, State Key Laboratory for Agrobiotechnol., China Agricultural Univ., Beijing, PR China; CCBAU 65647
doi: 10.13145/bacdive13646.20230509.8.1
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 vallis
- full scientific name: Rhizobium vallis Wang et al. 2011
@ref: 18221
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Rhizobiaceae
genus: Rhizobium
species: Rhizobium vallis
full scientific name: Rhizobium vallis Wang et al. 2011
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | yes | 91.639 | |
69480 | 99.984 | negative |
colony morphology
- @ref: 18221
- incubation period: 2-3 days
Culture and growth conditions
culture medium
- @ref: 18221
- name: RHIZOBIUM MEDIUM (DSMZ Medium 98)
- growth: yes
- link: https://mediadive.dsmz.de/medium/98
- composition: Name: 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
culture temp
- @ref: 18221
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.997 |
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 | 16899 | D-mannitol | - | assimilation |
68369 | 16024 | D-mannose | - | 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 |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
18221 | cytochrome-c 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 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18221 | - | - | - | - | + | + | - | + | - | +/- | - | - | +/- | +/- | +/- | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
- @ref: 18221
- sample type: root nodules of Phaseolus vulgaris
- host species: Phaseolus vulgaris
- geographic location: Yunnan Province, valley of Red River
- country: China
- origin.country: CHN
- continent: Asia
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Plants | #Herbaceous plants (Grass,Crops) |
#Host Body-Site | #Plant | #Root nodule |
Safety information
risk assessment
- @ref: 18221
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 18221
- description: Rhizobium vallis strain CCBAU 65647 16S ribosomal RNA gene, partial sequence
- accession: FJ839677
- length: 1382
- database: ena
- NCBI tax ID: 634290
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Rhizobium vallis CCBAU 65647 | GCA_003985155 | scaffold | ncbi | 634290 |
66792 | Rhizobium vallis strain CCBAU 65647 | 634290.7 | wgs | patric | 634290 |
66792 | Rhizobium vallis LMG 25295 | 2739367694 | draft | img | 634290 |
GC content
- @ref: 18221
- GC-content: 60.9
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 87.827 | no |
flagellated | no | 82.885 | no |
gram-positive | no | 97.747 | no |
anaerobic | no | 98.786 | no |
aerobic | yes | 92.981 | no |
halophile | no | 93.861 | no |
spore-forming | no | 92.486 | no |
thermophile | no | 99.127 | no |
glucose-util | yes | 83.414 | yes |
glucose-ferment | no | 89.559 | yes |
External links
@ref: 18221
culture collection no.: DSM 26437, CCBAU 65647, HAMBI 3073, LMG 25295
straininfo link
- @ref: 82829
- straininfo: 378476
literature
- topic: Phylogeny
- Pubmed-ID: 21131504
- title: Rhizobium vallis sp. nov., isolated from nodules of three leguminous species.
- authors: Wang F, Wang ET, Wu LJ, Sui XH, Li Y, Chen WX
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.026484-0
- year: 2010
- mesh: Bacterial 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/*microbiology
- topic2: Metabolism
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
18221 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26437) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-26437 | |
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 | |
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) | |
68369 | Automatically annotated from API 20NE | |||
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 | |
82829 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID378476.1 | StrainInfo: A central database for resolving microbial strain identifiers |