Strain identifier
BacDive ID: 13747
Type strain: 
Species: Rhodovulum marinum
Strain Designation: 3Vi, JA 128
Strain history: Ch. Sasikala and Ch. V. Romana JA128.
NCBI tax ID(s): 320662 (species)
version 9.1 (current version)
General
@ref: 7356
BacDive-ID: 13747
DSM-Number: 18063
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, Gram-negative, ovoid-shaped
description: Rhodovulum marinum 3Vi is an anaerobe, Gram-negative, ovoid-shaped bacterium that was isolated from Sea shore water.
NCBI tax id
- NCBI tax id: 320662
- Matching level: species
strain history
| @ref | history |
|---|---|
| 7356 | <- C. Sasikala, Centre Environment, Inst. Sci. and Technol., J. N. T. Univ., Hyderabad, India; JA 128 <- P. Anil Kumar |
| 67770 | Ch. Sasikala and Ch. V. Romana JA128. |
doi: 10.13145/bacdive13747.20240916.9.1
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 marinum
- full scientific name: Rhodovulum marinum Srinivas et al. 2006
@ref: 7356
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Rhodovulum
species: Rhodovulum marinum
full scientific name: Rhodovulum marinum Srinivas et al. 2006
strain designation: 3Vi, JA 128
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 31665 | negative | 01-02 µm | 0.6-0.8 µm | ovoid-shaped | no | |
| 69480 | negative | 99 |
colony morphology
- @ref: 59456
- incubation period: 2 days
pigmentation
- @ref: 31665
- production: yes
Culture and growth conditions
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 31665 | positive | growth | 25-35 |
| 31665 | positive | optimum | 30 |
| 59456 | positive | growth | 30 |
| 67770 | positive | growth | 30 |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 31665 | positive | growth | 5.5-7.5 |
| 31665 | positive | optimum | 6-6.8 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 7356 | anaerobe |
| 31665 | anaerobe |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 31665 | no | |
| 69480 | no | 93.484 |
| 69481 | no | 90 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 31665 | NaCl | positive | growth | 0.5-3 % |
| 31665 | NaCl | positive | optimum | 0.5-3 % |
observation
- @ref: 31665
- observation: aggregates in chains
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 31665 | 30089 | acetate | + | carbon source |
| 31665 | 16236 | ethanol | + | carbon source |
| 31665 | 17754 | glycerol | + | carbon source |
| 31665 | 24996 | lactate | + | carbon source |
| 31665 | 29864 | mannitol | + | carbon source |
| 31665 | 15361 | pyruvate | + | carbon source |
| 31665 | 30911 | sorbitol | + | carbon source |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 7356 | Sea shore water | Visakhapatnam | India | IND | Asia |
| 59456 | Water,tidal | Visakhapatnam,R.K.beach | India | IND | Asia |
| 67770 | Marine tides | Visakhapatnam | India | IND | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Terrestrial | #Coast |
taxonmaps
- @ref: 69479
- File name: preview.99_25026.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_12514;97_15191;98_18814;99_25026&stattab=map
- Last taxonomy: Rhodovulum marinum subclade
- 16S sequence: AJ891122
- Sequence Identity:
- Total samples: 28
- soil counts: 3
- aquatic counts: 20
- animal counts: 5
Safety information
risk assessment
- @ref: 7356
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7356
- description: Rhodovulum marinum partial 16S rRNA gene, type strain JA128
- accession: AJ891122
- length: 1376
- database: nuccore
- NCBI tax ID: 320662
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Rhodovulum marinum strain DSM 18063 | 320662.3 | wgs | patric | 320662 |
| 66792 | Rhodovulum marinum DSM 18063 | 2795385476 | draft | img | 320662 |
| 67770 | Rhodovulum marinum DSM 18063 | GCA_004343075 | scaffold | ncbi | 320662 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 31665 | 62 | |
| 67770 | 62 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 90 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 99 | yes |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 64.126 | yes |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 93.484 | yes |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 56.767 | yes |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 93.569 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 68.841 | no |
External links
@ref: 7356
culture collection no.: DSM 18063, CCUG 52183, JCM 13300, ATCC BAA-1215, BCRC 80541
straininfo link
- @ref: 82929
- straininfo: 297331
literature
- topic: Phylogeny
- Pubmed-ID: 16825644
- title: Rhodovulum marinum sp. nov., a novel phototrophic purple non-sulfur alphaproteobacterium from marine tides of Visakhapatnam, India.
- authors: Srinivas TNR, Kumar PA, Sasikala C, Ramana CV, Suling J, Imhoff JF
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.64005-0
- year: 2006
- mesh: Carotenoids/analysis, Cell Membrane/ultrastructure, Chlorophyll/analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Hydrogen-Ion Concentration, India, Microscopy, Electron, Transmission, Microscopy, Phase-Contrast, Molecular Sequence Data, Organic Chemicals/metabolism, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhodovulum/*classification/cytology/*isolation & purification/physiology, Saline Solution, Hypertonic, Seawater/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Temperature, Thiamine/pharmacology, Vitamin B Complex/pharmacology, Water Microbiology
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 7356 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18063) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18063 | |||
| 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 | |||
| 31665 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 27945 | 28776041 | |
| 59456 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 52183) | https://www.ccug.se/strain?id=52183 | |||
| 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) | |||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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 | |||
| 82929 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297331.1 | StrainInfo: A central database for resolving microbial strain identifiers |