Strain identifier
BacDive ID: 1827
Type strain: 
Species: Rhodopseudomonas rhenobacensis
Strain Designation: R1
Strain history: 2000, J.H. Klemme, IFMB, Univ. Bonn, Germany: strain Rb
NCBI tax ID(s): 87461 (species)
version 7.1 (current version)
General
@ref: 4793
BacDive-ID: 1827
DSM-Number: 12706
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Rhodopseudomonas rhenobacensis R1 is an anaerobe, mesophilic bacterium that was isolated from sediment of eutrophic pond.
NCBI tax id
- NCBI tax id: 87461
- Matching level: species
strain history
doi: 10.13145/bacdive1827.20221219.7.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Nitrobacteraceae
- genus: Rhodopseudomonas
- species: Rhodopseudomonas rhenobacensis
- full scientific name: Rhodopseudomonas rhenobacensis Hougardy et al. 2000
@ref: 4793
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Nitrobacteraceae
genus: Rhodopseudomonas
species: Rhodopseudomonas rhenobacensis
full scientific name: Rhodopseudomonas rhenobacensis Hougardy et al. 2000
strain designation: R1
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 53.297 | |
| 69480 | 99.37 | negative |
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 4793 | ACID RHODOSPIRILLACEAE MEDIUM (DSMZ Medium 26) | yes | https://mediadive.dsmz.de/medium/26 | Name: ACID RHODOSPIRILLACEAE MEDIUM (DSMZ Medium 26) Composition: Disodium succinate 1.0 g/l Ammonium acetate 0.5 g/l KH2PO4 0.5 g/l MgSO4 x 7 H2O 0.4 g/l NaCl 0.4 g/l NH4Cl 0.4 g/l L-Cysteine HCl 0.3 g/l Yeast extract 0.2 g/l CaCl2 x 2 H2O 0.05 g/l Fe(III) citrate 0.005 g/l Resazurin 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 |
| 39553 | MEDIUM 374 - for Rhodopseudomonas rhenobacensis | yes | Distilled water make up to (944.500 ml);Agar (20.000 g);Yeast extract (1.000 ml);Solution A - M00720 (40.000 ml);Solution B - M00721 (10.000 ml);Solution C - M00722 (2.000 ml);Solution D - M00723 (1.000 ml);Solution E - M00724 (1.500 ml);Solution trace el |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 4793 | positive | growth | 28 | mesophilic |
| 39553 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 4793
- oxygen tolerance: anaerobe
spore formation
- @ref: 69480
- spore formation: no
- confidence: 96.923
halophily
- @ref: 69480
- halophily level: non-halophilic
- confidence: 98.819
Isolation, sampling and environmental information
isolation
- @ref: 4793
- sample type: sediment of eutrophic pond
- geographic location: Rheinbach
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Pond (small) |
| #Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_2375.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_297;97_329;98_1850;99_2375&stattab=map
- Last taxonomy: Rhodopseudomonas
- 16S sequence: AB087719
- Sequence Identity:
- Total samples: 555
- soil counts: 280
- aquatic counts: 158
- animal counts: 55
- plant counts: 62
Safety information
risk assessment
- @ref: 4793
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Rhodopseudomonas rhenobacensis genes for 16S rRNA, 16S-23S ribosomal RNA intergeic spacer, tRNA-Ile, tRNA-Ala, 23S rRNA, partial and complete sequence, strain: Rb, clone: a | AB498835 | 1115 | ena | 87461 |
| 20218 | Rhodopseudomonas rhenobacensis genes for 16S rRNA, 16S-23S ribosomal RNA intergeic spacer, tRNA-Ile, tRNA-Ala, 23S rRNA, partial and complete sequence, strain: Rb, clone: d | AB498836 | 1082 | ena | 87461 |
| 20218 | Rhodopseudomonas rhenobacensis genes for 16S rRNA, 16S-23S ribosomal RNA intergeic spacer, tRNA-Ile, tRNA-Ala, 23S rRNA, partial and complete sequence, strain: Rb, clone: e | AB498837 | 1107 | ena | 87461 |
| 20218 | Rhodopseudomonas rhenobacensis 16S rRNA gene, partial, clone 1 | AJ132401 | 405 | ena | 87461 |
| 20218 | Rhodopseudomonas rhenobacensis 16S rRNA gene, partial, clone 2 | AJ132402 | 665 | ena | 87461 |
| 4793 | Rhodopseudomonas rhenobacensis gene for 16S rRNA, complete sequence | AB087719 | 1485 | ena | 87461 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Rhodopseudomonas rhenobacensis DSM 12706 | GCA_014203125 | scaffold | ncbi | 87461 |
| 66792 | Rhodopseudomonas rhenobacensis strain DSM 12706 | 87461.3 | wgs | patric | 87461 |
| 66792 | Rhodopseudomonas rhenobacensis DSM 12706 | 2861707373 | draft | img | 87461 |
| 66792 | Escherichia coli S455 | GCA_019879485 | scaffold | patric | 562 |
External links
@ref: 4793
culture collection no.: DSM 12706
straininfo link
- @ref: 20218
- passport: http://www.straininfo.net/strains/163318
literature
- topic: Phylogeny
- Pubmed-ID: 21986724
- title: Descriptions of Rhodopseudomonas parapalustris sp. nov., Rhodopseudomonas harwoodiae sp. nov. and Rhodopseudomonas pseudopalustris sp. nov., and emended description of Rhodopseudomonas palustris.
- authors: Ramana VV, Chakravarthy SK, Raj PS, Kumar BV, Shobha E, Ramaprasad EVV, Sasikala C, Ramana CV
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.026815-0
- year: 2011
- mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fresh Water/microbiology, Geologic Sediments/microbiology, India, Lipids/analysis, Molecular Sequence Data, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodopseudomonas/*classification/genetics/isolation & purification, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 4793 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12706) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-12706 | |||
| 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 | |
| 39553 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/18839 | ||||
| 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 | |||
| 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) |