Strain identifier
BacDive ID: 132365
Type strain:
Species: Bradyrhizobium vignae
Strain Designation: 7-2
Strain history: <- B. Reinhold-Hurek, Univ. Bremen, Germany; 7-2 <- J. L. Grönemeyer
NCBI tax ID(s): 1549949 (species)
General
@ref: 24154
BacDive-ID: 132365
DSM-Number: 100297
keywords: genome sequence, 16S sequence, Bacteria, aerobe, thermophilic, Gram-negative, motile, rod-shaped, colony-forming
description: Bradyrhizobium vignae 7-2 is an aerobe, thermophilic, Gram-negative bacterium that forms circular colonies and was isolated from effective nodule of Vigna unguiculata .
NCBI tax id
- NCBI tax id: 1549949
- Matching level: species
strain history
- @ref: 24154
- history: <- B. Reinhold-Hurek, Univ. Bremen, Germany; 7-2 <- J. L. Grönemeyer
doi: 10.13145/bacdive132365.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Nitrobacteraceae
- genus: Bradyrhizobium
- species: Bradyrhizobium vignae
- full scientific name: Bradyrhizobium vignae Grönemeyer et al. 2016
@ref: 24154
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Nitrobacteraceae
genus: Bradyrhizobium
species: Bradyrhizobium vignae
full scientific name: Bradyrhizobium vignae Grönemeyer et al. 2016
strain designation: 7-2
type strain: yes
Morphology
cell morphology
- @ref: 44038
- gram stain: negative
- cell length: 2-3 µm
- cell width: 0.7 µm
- cell shape: rod-shaped
- motility: yes
colony morphology
- @ref: 44038
- colony size: 0.2-1 mm
- colony color: beige-whitish
- colony shape: circular
- incubation period: 8 days
- medium used: YMA
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
44038 | YMA | yes | ||
24154 | RHIZOBIUM MEDIUM (DSMZ Medium 98) | yes | https://mediadive.dsmz.de/medium/98 | 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 | growth | type | temperature | range |
---|---|---|---|---|
44038 | positive | growth | 40 | thermophilic |
44038 | positive | growth | 38 | mesophilic |
44038 | positive | growth | 37 | mesophilic |
44038 | positive | growth | 28 | mesophilic |
24154 | positive | growth | 28 | mesophilic |
culture pH
- @ref: 44038
- ability: positive
- type: growth
- pH: 5-9
- PH range: alkaliphile
Physiology and metabolism
oxygen tolerance
- @ref: 44038
- oxygen tolerance: aerobe
spore formation
- @ref: 44038
- type of spore: spore
- spore formation: no
halophily
- @ref: 44038
- salt: NaCl
- growth: no
- tested relation: growth
- concentration: 1 %(w/v)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
44038 | 62064 | 2,3-butanediol | - | oxidation |
44038 | 18240 | 4-hydroxy-L-proline | - | oxidation |
44038 | 15963 | ribitol | - | oxidation |
44038 | 40585 | alpha-cyclodextrin | - | oxidation |
44038 | 36219 | alpha-lactose | - | oxidation |
44038 | 17057 | cellobiose | - | oxidation |
44038 | 14314 | D-glucose 6-phosphate | - | oxidation |
44038 | 28053 | melibiose | - | oxidation |
44038 | 27605 | D-psicose | - | oxidation |
44038 | 16523 | D-serine | - | oxidation |
44038 | 17924 | D-sorbitol | - | oxidation |
44038 | 17126 | DL-carnitine | - | oxidation |
44038 | 17113 | erythritol | - | oxidation |
44038 | 16000 | ethanolamine | - | oxidation |
44038 | 16865 | gamma-aminobutyric acid | - | oxidation |
44038 | 28066 | gentiobiose | - | oxidation |
44038 | 29042 | glucose 1-phosphate | - | oxidation |
44038 | 14336 | glycerol 1-phosphate | - | oxidation |
44038 | 28087 | glycogen | - | oxidation |
44038 | 17596 | inosine | - | oxidation |
44038 | 17268 | myo-inositol | - | oxidation |
44038 | 21217 | L-alaninamide | - | oxidation |
44038 | 73786 | L-alanylglycine | - | oxidation |
44038 | 17196 | L-asparagine | - | oxidation |
44038 | 15971 | L-histidine | - | oxidation |
44038 | 15729 | L-ornithine | - | oxidation |
44038 | 17203 | L-proline | - | oxidation |
44038 | 17115 | L-serine | - | oxidation |
44038 | 16857 | L-threonine | - | oxidation |
44038 | 6359 | lactulose | - | oxidation |
44038 | 17306 | maltose | - | oxidation |
44038 | 320055 | methyl beta-D-glucopyranoside | - | oxidation |
44038 | 28037 | N-acetylgalactosamine | - | oxidation |
44038 | 506227 | N-acetylglucosamine | - | oxidation |
44038 | 50048 | phenylethylamine | - | oxidation |
44038 | 17148 | putrescine | - | oxidation |
44038 | 16634 | raffinose | - | oxidation |
44038 | 17992 | sucrose | - | oxidation |
44038 | 17748 | thymidine | - | oxidation |
44038 | 27082 | trehalose | - | oxidation |
44038 | 32528 | turanose | - | oxidation |
44038 | 16704 | uridine | - | oxidation |
44038 | 17151 | xylitol | - | oxidation |
44038 | 30916 | 2-oxoglutarate | + | oxidation |
44038 | 28644 | 2-oxopentanoate | + | oxidation |
44038 | 17925 | alpha-D-glucose | + | oxidation |
44038 | 8295 | beta-hydroxybutyrate | + | oxidation |
44038 | 73706 | bromosuccinate | + | oxidation |
44038 | 16383 | cis-aconitate | + | oxidation |
44038 | 16947 | citrate | + | oxidation |
44038 | 18333 | D-arabitol | + | oxidation |
44038 | 15895 | D-galactonic acid lactone | + | oxidation |
44038 | 12936 | D-galactose | + | oxidation |
44038 | 18024 | D-galacturonic acid | + | oxidation |
44038 | 8391 | D-gluconate | + | oxidation |
44038 | 17784 | D-glucosaminic acid | + | oxidation |
44038 | 16899 | D-mannitol | + | oxidation |
44038 | 16024 | D-mannose | + | oxidation |
44038 | 33801 | D-saccharate | + | oxidation |
44038 | 24996 | lactate | + | oxidation |
44038 | 15740 | formate | + | oxidation |
44038 | 16724 | 4-hydroxybutyrate | + | oxidation |
44038 | 32323 | glucuronamide | + | oxidation |
44038 | 17754 | glycerol | + | oxidation |
44038 | 30849 | L-arabinose | + | oxidation |
44038 | 29991 | L-aspartate | + | oxidation |
44038 | 28120 | L-fructose | + | oxidation |
44038 | 29985 | L-glutamate | + | oxidation |
44038 | 15603 | L-leucine | + | oxidation |
44038 | 18183 | L-pyroglutamic acid | + | oxidation |
44038 | 15792 | malonate | + | oxidation |
44038 | 51850 | methyl pyruvate | + | oxidation |
44038 | 75146 | monomethyl succinate | + | oxidation |
44038 | 17272 | propionate | + | oxidation |
44038 | 26490 | quinate | + | oxidation |
44038 | 41865 | sebacic acid | + | oxidation |
44038 | 143136 | succinamate | + | oxidation |
44038 | 30031 | succinate | + | oxidation |
44038 | 53423 | tween 40 | + | oxidation |
44038 | 53426 | tween 80 | + | oxidation |
44038 | 27248 | urocanic acid | + | oxidation |
antibiotic resistance
@ref | ChEBI | metabolite | is antibiotic | is resistant | resistance conc. |
---|---|---|---|---|---|
44038 | 17698 | chloramphenicol | yes | yes | 50 µg/mL |
44038 | 17076 | streptomycin | yes | yes | 5 µg/mL |
44038 | 27902 | tetracycline | yes | yes | 15 µg/mL |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | geographic location | country | origin.country | continent | latitude | longitude | enrichment culture |
---|---|---|---|---|---|---|---|---|---|
24154 | effective nodule of Vigna unguiculata (cowpea) | Vigna unguiculata | Kavango region, near Mashare | Namibia | NAM | Africa | -17.8928 | 20.2105 | |
44038 | effective nodule of Vigna unguiculata (cowpea) | Kavango Region | Namibia | NAM | Africa | MAG medium (van Berkum, 1990) |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Plants | #Herbaceous plants (Grass,Crops) |
#Host Body-Site | #Plant | #Root nodule |
taxonmaps
- @ref: 69479
- File name: preview.99_445.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_297;97_329;98_370;99_445&stattab=map
- Last taxonomy: Bradyrhizobium
- 16S sequence: KP899563
- Sequence Identity:
- Total samples: 12887
- soil counts: 5001
- aquatic counts: 2827
- animal counts: 4320
- plant counts: 739
Safety information
risk assessment
- @ref: 24154
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24154
- description: Bradyrhizobium vignae strain 7-2 16S ribosomal RNA gene, partial sequence
- accession: KP899563
- length: 1298
- database: ena
- NCBI tax ID: 1549949
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Bradyrhizobium vignae LMG 28791 | GCA_004114425 | scaffold | ncbi | 1549949 |
66792 | Bradyrhizobium vignae strain LMG 28791 | 1549949.9 | wgs | patric | 1549949 |
66792 | Bradyrhizobium vignae LMG 28791 | 2881665667 | draft | img | 1549949 |
GC content
@ref | GC-content | method |
---|---|---|
44038 | 65.4 | high performance liquid chromatography (HPLC) |
24154 | 65.4 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 81.391 | no |
flagellated | no | 78.163 | no |
gram-positive | no | 97.943 | no |
anaerobic | no | 96.902 | yes |
aerobic | yes | 91.839 | yes |
halophile | no | 94.775 | no |
spore-forming | no | 93.157 | no |
thermophile | no | 99.327 | no |
glucose-util | yes | 90.103 | no |
glucose-ferment | no | 89.729 | no |
External links
@ref: 24154
culture collection no.: DSM 100297, LMG 28791, NTCCM 0018, DSMZ 100297
straininfo link
- @ref: 90711
- straininfo: 396451
literature
- topic: Phylogeny
- Pubmed-ID: 26463703
- title: Bradyrhizobium vignae sp. nov., a nitrogen-fixing symbiont isolated from effective nodules of Vigna and Arachis.
- authors: Gronemeyer JL, Hurek T, Bunger W, Reinhold-Hurek B
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.000674
- year: 2015
- mesh: Arachis/*microbiology, Bacterial Typing Techniques, Base Composition, Bradyrhizobium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fabaceae/*microbiology, Fatty Acids/chemistry, Genes, Bacterial, Molecular Sequence Data, Namibia, *Nitrogen Fixation, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/microbiology, Sequence Analysis, DNA, *Symbiosis
- topic2: Genetics
Reference
@id | authors | title | doi/url | catalogue | journal | pubmed |
---|---|---|---|---|---|---|
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |||
24154 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-100297 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100297) | |||
44038 | Jann Lasse Grönemeyer, Thomas Hurek, Wiebke Bünger and Barbara Reinhold-Hurek | Bradyrhizobium vignae sp. nov., a nitrogen-fixing symbiont isolated from effective nodules of Vigna and Arachis | 10.1099/ijsem.0.000674 | IJSEM 66: 62-69 2016 | 26463703 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
90711 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID396451.1 |