Strain identifier
BacDive ID: 6187
Type strain: 
Species: Rhodoplanes roseus
Strain Designation: 941
Strain history: <- DSM <- PH Janssen, 941
NCBI tax ID(s): 29409 (species)
version 8.1 (current version)
General
@ref: 2357
BacDive-ID: 6187
DSM-Number: 5909
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile, rod-shaped
description: Rhodoplanes roseus 941 is an anaerobe, mesophilic, motile bacterium of the family Nitrobacteraceae.
NCBI tax id
- NCBI tax id: 29409
- Matching level: species
strain history
| @ref | history |
|---|---|
| 2357 | <- P.H. Janssen, 941 |
| 67771 | <- DSM <- PH Janssen, 941 |
doi: 10.13145/bacdive6187.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Nitrobacteraceae
- genus: Rhodoplanes
- species: Rhodoplanes roseus
- full scientific name: Rhodoplanes roseus (Janssen and Harfoot 1991) Hiraishi and Ueda 1994
synonyms
- @ref: 20215
- synonym: Rhodopseudomonas rosea
@ref: 2357
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Nitrobacteraceae
genus: Rhodoplanes
species: Rhodoplanes roseus
full scientific name: Rhodoplanes roseus (Janssen and Harfoot 1991) Hiraishi and Ueda 1994
strain designation: 941
type strain: yes
Morphology
cell morphology
| @ref | cell shape | motility | gram stain | confidence |
|---|---|---|---|---|
| 67771 | rod-shaped | yes | ||
| 67771 | negative | |||
| 69480 | yes | 92.915 | ||
| 69480 | negative | 99.999 |
Culture and growth conditions
culture medium
- @ref: 2357
- name: RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27)
- growth: yes
- link: https://mediadive.dsmz.de/medium/27
- composition: Name: RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27; with strain-specific modifications) Composition: Disodium succinate 1.0 g/l KH2PO4 0.5 g/l Ammonium acetate 0.5 g/l MgSO4 x 7 H2O 0.4 g/l NH4Cl 0.4 g/l NaCl 0.4 g/l L-Cysteine HCl 0.3 g/l Yeast extract 0.1 g/l CaCl2 x 2 H2O 0.05 g/l Resazurin 0.005 g/l Fe(III) citrate 0.005 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Vitamin B12 Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 2357 | positive | growth | 35 | mesophilic |
| 67771 | positive | growth | 35 | mesophilic |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 2357 | anaerobe |
| 67771 | anaerobe |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.986 |
Isolation, sampling and environmental information
isolation
| @ref | geographic location | country | origin.country | continent | sample type |
|---|---|---|---|---|---|
| 2357 | Cambridbe, Te Kontu park | New Zealand | NZL | Australia and Oceania | |
| 67771 | Te Kontu park, Cambridbe | New Zealand | NZL | Australia and Oceania | From duck pond |
taxonmaps
- @ref: 69479
- File name: preview.99_74447.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_2492;97_3043;98_16748;99_74447&stattab=map
- Last taxonomy: Rhodoplanes roseus
- 16S sequence: D25313
- Sequence Identity:
- Total samples: 498
- soil counts: 150
- aquatic counts: 271
- animal counts: 57
- plant counts: 20
Safety information
risk assessment
- @ref: 2357
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Rhodoplanes roseus gene for 16S rRNA | D25313 | 1413 | ena | 29409 |
| 20218 | Rhodoplanes roseus 16S rRNA | D14429 | 1379 | ena | 29409 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Rhodoplanes roseus DSM 5909 | GCA_003258865 | scaffold | ncbi | 29409 |
| 66792 | Rhodoplanes roseus strain DSM 5909 | 29409.3 | wgs | patric | 29409 |
| 66792 | Rhodoplanes roseus DSM 5909 | 2891101655 | draft | img | 29409 |
GC content
- @ref: 67771
- GC-content: 66.0
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | no | 58.038 | no |
| gram-positive | no | 98.785 | yes |
| anaerobic | no | 56.148 | no |
| aerobic | no | 57.448 | yes |
| halophile | no | 94.005 | no |
| spore-forming | no | 93.65 | no |
| glucose-util | yes | 82.594 | no |
| thermophile | no | 98.646 | yes |
| motile | yes | 86.11 | no |
| glucose-ferment | no | 89.2 | no |
External links
@ref: 2357
culture collection no.: DSM 5909, KCTC 15222, NCIMB 13363, ATCC 49724
straininfo link
- @ref: 75668
- straininfo: 92732
literature
- topic: Phylogeny
- Pubmed-ID: 24695055
- title: Rhodoplanes oryzae sp. nov., a phototrophic alphaproteobacterium isolated from the rhizosphere soil of paddy.
- authors: Srinivas A, Sasikala C, Ramana CV
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.063347-0
- year: 2014
- mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hyphomicrobiaceae/*classification/genetics/isolation & purification, India, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analogs & derivatives/chemistry
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 2357 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5909) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-5909 | |||
| 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) | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
| 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 | |||
| 75668 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID92732.1 | StrainInfo: A central database for resolving microbial strain identifiers |