Strain identifier
BacDive ID: 13746
Type strain: 
Species: Rhodovulum robiginosum
Strain Designation: N2
Strain history: <- K. L. Straub, Max-Planck-Inst., Bremen; N2
NCBI tax ID(s): 68292 (species)
version 8.1 (current version)
General
@ref: 4695
BacDive-ID: 13746
DSM-Number: 12329
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative
description: Rhodovulum robiginosum N2 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from marine sediment samples.
NCBI tax id
- NCBI tax id: 68292
- Matching level: species
strain history
- @ref: 4695
- history: <- K. L. Straub, Max-Planck-Inst., Bremen; N2
doi: 10.13145/bacdive13746.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Roseobacteraceae
- genus: Rhodovulum
- species: Rhodovulum robiginosum
- full scientific name: Rhodovulum robiginosum Straub et al. 1999
@ref: 4695
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Rhodovulum
species: Rhodovulum robiginosum
full scientific name: Rhodovulum robiginosum Straub et al. 1999
strain designation: N2
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.999
Culture and growth conditions
culture medium
- @ref: 4695
- name: RHODOVULUM IODOSUM AND R. ROBIGINOSUM MEDIUM (DSMZ Medium 929)
- growth: yes
- link: https://mediadive.dsmz.de/medium/929
- composition: Name: RHODOVULUM IODOSUM AND R. ROBIGINOSUM MEDIUM (DSMZ Medium 929) Composition: NaCl 26.4 g/l MgSO4 x 7 H2O 6.8 g/l MgCl2 x 6 H2O 5.7 g/l NaHCO3 2.52 g/l FeSO4 1.5191 g/l CaCl2 x 2 H2O 1.5 g/l KCl 0.66 g/l KH2PO4 0.4 g/l Acetate 0.29522 g/l NH4Cl 0.25 g/l Na2S2O3 0.214257 g/l KBr 0.09 g/l Na2-EDTA 0.0052 g/l FeSO4 x 7 H2O 0.0021 g/l NaOH 0.0002 g/l CoCl2 x 6 H2O 0.00019 g/l Pyridoxin 0.00015 g/l ZnSO4 x 7 H2O 0.000144 g/l Thiamine 0.0001 g/l MnCl2 x 4 H2O 0.0001 g/l Nicotinate 0.0001 g/l Cyanocobalamine 5e-05 g/l Pantothenate 5e-05 g/l Para-aminobenzoic acid 4e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l H3BO3 3e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l Biotin 1e-05 g/l Na2WO4 x 2 H2O 8e-06 g/l Na2SeO3 x 5 H2O 6e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Distilled water
culture temp
- @ref: 4695
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 4695
- oxygen tolerance: anaerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 97 |
| 69480 | no | 99.994 |
Isolation, sampling and environmental information
isolation
- @ref: 4695
- sample type: marine sediment samples
- geographic location: North Sea, Jadebusen
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Aquatic | #Sediment |
Safety information
risk assessment
- @ref: 4695
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20218
- description: Rhodovulum robiginosum 16S rRNA gene
- accession: Y15012
- length: 1414
- database: ena
- NCBI tax ID: 68292
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Rhodovulum robiginosum DSM 12329 | GCA_003944755 | scaffold | ncbi | 68292 |
| 66792 | Rhodovulum robiginosum strain DSM 12329 | 68292.5 | wgs | patric | 68292 |
| 66792 | Rhodovulum robiginosum DSM 12329 | 2894590789 | draft | img | 68292 |
GC content
- @ref: 4695
- GC-content: 69
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 97 | no |
| motile | no | 50.537 | no |
| flagellated | no | 92.614 | no |
| gram-positive | no | 98.808 | no |
| anaerobic | no | 77.005 | yes |
| aerobic | no | 72.608 | yes |
| halophile | yes | 71.626 | no |
| spore-forming | no | 97.519 | no |
| glucose-util | yes | 68.794 | no |
| thermophile | no | 90.513 | yes |
| glucose-ferment | no | 88.282 | no |
External links
@ref: 4695
culture collection no.: DSM 12329
straininfo link
- @ref: 82928
- straininfo: 100912
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 10319496 | Rhodovulum iodosum sp. nov. and Rhodovulum robiginosum sp. nov., two new marine phototrophic ferrous-iron-oxidizing purple bacteria. | Straub KL, Rainey FA, Widdel F | Int J Syst Bacteriol | 10.1099/00207713-49-2-729 | 1999 | Bacteria/*classification/genetics/isolation & purification, Bacterial Physiological Phenomena, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Ferrous Compounds/*metabolism, Genes, rRNA, Geologic Sediments/*microbiology, Light-Harvesting Protein Complexes, Molecular Sequence Data, North Sea, Oxidation-Reduction, Photosynthetic Reaction Center Complex Proteins, Phylogeny, RNA, Ribosomal, 16S/genetics, *Water Microbiology | Genetics |
| Genetics | 30834373 | Draft Genome Sequence of a Marine Photoferrotrophic Bacterium, Rhodovulum robiginosum DSM 12329(T). | Gupta D, Guzman MS, Bose A | Microbiol Resour Announc | 10.1128/MRA.01684-18 | 2019 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 4695 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12329) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-12329 | |||
| 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 | |
| 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 | |||
| 82928 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID100912.1 | StrainInfo: A central database for resolving microbial strain identifiers |