Strain identifier
BacDive ID: 1810
Type strain: 
Species: Bradyrhizobium denitrificans
Strain Designation: 222
Strain history: <- P. Hirsch (IFAM) <- M. Müller, 222
NCBI tax ID(s): 328552 (species)
version 8.1 (current version)
General
@ref: 562
BacDive-ID: 1810
DSM-Number: 1113
keywords: genome sequence, 16S sequence, Bacteria, thermophilic
description: Bradyrhizobium denitrificans 222 is a thermophilic bacterium that was isolated from surface lake water.
NCBI tax id
- NCBI tax id: 328552
- Matching level: species
strain history
- @ref: 562
- history: <- P. Hirsch (IFAM) <- M. Müller, 222
doi: 10.13145/bacdive1810.20230509.8.1
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 denitrificans
- full scientific name: Bradyrhizobium denitrificans (Hirsch and Müller 1986) van Berkum et al. 2011
synonyms
- @ref: 20215
- synonym: Blastobacter denitrificans
@ref: 562
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Nitrobacteraceae
genus: Bradyrhizobium
species: Bradyrhizobium denitrificans
full scientific name: Bradyrhizobium denitrificans (Hirsch and Müller 1986) van Berkum et al. 2011
strain designation: 222
type strain: yes
Culture and growth conditions
culture medium
- @ref: 562
- name: PYGV AGAR (DSMZ Medium 621)
- growth: yes
- link: https://mediadive.dsmz.de/medium/621
- composition: Name: PYGV AGAR (DSMZ Medium 621) Composition: Agar 15.0 g/l MgSO4 x 7 H2O 0.625264 g/l Glucose 0.25 g/l Peptone 0.25 g/l Yeast extract 0.25 g/l Nitrilotriacetic acid 0.210526 g/l CaCl2 x 2 H2O 0.0703158 g/l FeSO4 x 7 H2O 0.00208422 g/l Na2MoO4 x 2 H2O 0.000266736 g/l Pyridoxine hydrochloride 0.0001 g/l p-Aminobenzoic acid 5e-05 g/l D-Calcium pantothenate 5e-05 g/l Nicotinamide 5e-05 g/l Thiamine-HCl x 2 H2O 5e-05 g/l Riboflavine 5e-05 g/l Folic acid 2e-05 g/l Biotin 2e-05 g/l Vitamin B12 1e-06 g/l Metall salt sol. 44 Distilled water
culture temp
- @ref: 562
- growth: positive
- type: growth
- temperature: 40
- range: thermophilic
Isolation, sampling and environmental information
isolation
- @ref: 562
- sample type: surface lake water
- geographic location: Schleswig-Holstein, Plubsea
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Lake (large) |
| #Environmental | #Aquatic | #Surface water |
taxonmaps
- @ref: 69479
- File name: preview.99_466.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_297;97_329;98_370;99_466&stattab=map
- Last taxonomy: Bradyrhizobium
- 16S sequence: X66025
- Sequence Identity:
- Total samples: 526
- soil counts: 181
- aquatic counts: 150
- animal counts: 111
- plant counts: 84
Safety information
risk assessment
- @ref: 562
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | 16S rRNA [Blastobacter denitrificans, LMG 8443, rRNA partial, 1443 nt] | S46917 | 1443 | ena | 328552 |
| 562 | Blastobacter denitrificans 16S ribosomal RNA gene, partial sequence; tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequence | AF338176 | 3000 | ena | 328552 |
| 562 | Blastobacter denitrificans partial 16S rRNA gene, strain LMG 8443 | X66025 | 1443 | ena | 328552 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Bradyrhizobium sp. LMG 8443 | GCA_013179005 | scaffold | ncbi | 2734912 |
| 66792 | Bradyrhizobium sp. LMG 8443 | 2734912.3 | wgs | patric | 2734912 |
GC content
- @ref: 562
- GC-content: 64.5±0.8
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | yes | 84.664 | no |
| flagellated | no | 63.459 | no |
| gram-positive | no | 97.909 | no |
| anaerobic | no | 97.299 | no |
| aerobic | yes | 91.796 | no |
| halophile | no | 95.508 | no |
| spore-forming | no | 92.601 | no |
| glucose-util | yes | 90.48 | no |
| thermophile | no | 98.259 | yes |
| glucose-ferment | no | 92.547 | no |
External links
@ref: 562
culture collection no.: DSM 1113, ATCC 43295, HAMBI 2266, IFAM 1005, LMG 8443, VKM B-2062
straininfo link
- @ref: 71456
- straininfo: 92173
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 11872460 | The aquatic budding bacterium Blastobacter denitrificans is a nitrogen-fixing symbiont of Aeschynomene indica. | van Berkum P, Eardly BD | Appl Environ Microbiol | 10.1128/AEM.68.3.1132-1136.2002 | 2002 | DNA, Ribosomal Spacer/genetics, Evolution, Molecular, Fabaceae/*microbiology, Fresh Water/*microbiology, Molecular Sequence Data, *Nitrogen Fixation, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobiaceae/*classification/genetics/growth & development, Sequence Analysis, DNA, Soybeans/microbiology, *Symbiosis | Genetics |
| Phylogeny | 13130002 | Bosea minatitlanensis sp. nov., a strictly aerobic bacterium isolated from an anaerobic digester. | Ouattara AS, Assih EA, Thierry S, Cayol JL, Labat M, Monroy O, Macarie H | Int J Syst Evol Microbiol | 10.1099/ijs.0.02540-0 | 2003 | Aerobiosis, Bradyrhizobiaceae/classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Genes, Bacterial, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sewage/microbiology, Species Specificity | Genetics |
| Phylogeny | 16564957 | Proposal for combining Bradyrhizobium spp. (Aeschynomene indica) with Blastobacter denitrificans and to transfer Blastobacter denitrificans (Hirsch and Muller, 1985) to the genus Bradyrhizobium as Bradyrhizobium denitrificans (comb. nov.). | van Berkum P, Leibold JM, Eardly BD | Syst Appl Microbiol | 10.1016/j.syapm.2005.07.014 | 2005 | Bradyrhizobiaceae/*classification/genetics, Bradyrhizobium/*classification/genetics/ultrastructure, Fabaceae/microbiology, Microscopy, Electron, Molecular Sequence Data, Nitrogen Fixation, RNA, Ribosomal, 23S/chemistry, Symbiosis | Genetics |
| Phylogeny | 22685107 | Reclassification of Agromonas oligotrophica into the genus Bradyrhizobium as Bradyrhizobium oligotrophicum comb. nov. | Ramirez-Bahena MH, Chahboune R, Peix A, Velazquez E | Int J Syst Evol Microbiol | 10.1099/ijs.0.041897-0 | 2012 | Bacterial Typing Techniques, Base Composition, Bradyrhizobium/*classification/genetics, DNA, Bacterial/genetics, Genes, Bacterial, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
| Phylogeny | 35689949 | Bradyrhizobium aeschynomenes sp. nov., a root and stem nodule microsymbiont of Aeschynomene indica. | Sun L, Zhang Z, Dong X, Tang Z, Ju B, Du Z, Wang E, Xie Z | Syst Appl Microbiol | 10.1016/j.syapm.2022.126337 | 2022 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 562 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1113) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-1113 | |||
| 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) | |||
| 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 | |||
| 71456 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID92173.1 | StrainInfo: A central database for resolving microbial strain identifiers |