Strain identifier
BacDive ID: 133800
Type strain: 
Species: Rhodobacter viridis
Strain Designation: JA737
Strain history: <- Ch Sasikala, EMBL, India
NCBI tax ID(s): 1054202 (species)
version 8.1 (current version)
General
@ref: 30550
BacDive-ID: 133800
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Rhodobacter viridis JA737 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from freshwater sediment .
NCBI tax id
- NCBI tax id: 1054202
- Matching level: species
strain history
- @ref: 67771
- history: <- Ch Sasikala, EMBL, India
doi: 10.13145/bacdive133800.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Paracoccaceae
- genus: Rhodobacter
- species: Rhodobacter viridis
- full scientific name: Rhodobacter viridis Shalem Raj et al. 2013
@ref: 30550
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Rhodobacter
species: Rhodobacter viridis
strain designation: JA737
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 30550 | negative | 2.25 µm | 0.85 µm | rod-shaped | yes | |
| 67771 | rod-shaped | yes | ||||
| 67771 | negative | |||||
| 69480 | negative | 99.993 |
pigmentation
- @ref: 30550
- production: yes
Culture and growth conditions
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 30550 | positive | optimum | 30 | mesophilic |
| 67771 | positive | growth | 30 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 30550 | positive | growth | 06-09 | alkaliphile |
| 30550 | positive | optimum | 7.25 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 30550 | anaerobe |
| 67771 | anaerobe |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.986
observation
- @ref: 67771
- observation: quinones: Q-10
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30550 | 28757 | fructose | + | carbon source |
| 30550 | 17234 | glucose | + | carbon source |
| 30550 | 24996 | lactate | + | carbon source |
| 30550 | 29864 | mannitol | + | carbon source |
| 30550 | 17272 | propionate | + | carbon source |
| 30550 | 15361 | pyruvate | + | carbon source |
| 30550 | 30911 | sorbitol | + | carbon source |
| 30550 | 17992 | sucrose | + | carbon source |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 30550 | freshwater sediment (river, lake, pond) | ||||
| 67771 | From mud of a stream | Rottikadai Town near Anaimalai Hills, Western Ghats, Tamil Nadu | India | IND | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Freshwater |
| #Environmental | #Aquatic | #Lake (large) |
| #Environmental | #Aquatic | #Pond (small) |
| #Environmental | #Aquatic | #River (Creek) |
taxonmaps
- @ref: 69479
- File name: preview.99_2602.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_1054;97_1659;98_2016;99_2602&stattab=map
- Last taxonomy: Rhodobacter
- 16S sequence: HE572577
- Sequence Identity:
- Total samples: 18101
- soil counts: 1824
- aquatic counts: 12158
- animal counts: 3470
- plant counts: 649
Sequence information
16S sequences
- @ref: 30550
- description: Rhodobacter viridis partial 16S rRNA gene, type strain JA737T
- accession: HE572577
- length: 1391
- database: nuccore
- NCBI tax ID: 1054202
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Rhodobacter viridis JA737 | GCA_003217355 | scaffold | ncbi | 1054202 |
| 66792 | Rhodobacter viridis JA737 | 2740891858 | draft | img | 1054202 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 30550 | 66.4 | |
| 67771 | 66.4 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 75 | no |
| flagellated | no | 79.915 | no |
| gram-positive | no | 98.516 | no |
| anaerobic | no | 77.043 | no |
| halophile | no | 94.221 | no |
| spore-forming | no | 95.717 | no |
| aerobic | no | 92.966 | yes |
| glucose-util | yes | 82.137 | no |
| thermophile | no | 95.147 | yes |
| motile | yes | 61.222 | no |
| glucose-ferment | no | 86.562 | no |
External links
@ref: 30550
culture collection no.: KCTC 15167, MTCC 11105, NBRC 108864
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 22389279 | Rhodobacter viridis sp. nov., a phototrophic bacterium isolated from mud of a stream. | Raj PS, Ramaprasad EVV, Vaseef S, Sasikala C, Ramana CV | Int J Syst Evol Microbiol | 10.1099/ijs.0.038471-0 | 2012 | Bacterial Typing Techniques, Bacteriochlorophyll A/analysis, Carotenoids/analysis, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/microbiology, India, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacter/*classification/genetics/isolation & purification, Rivers/*microbiology, Sequence Analysis, DNA, *Water Microbiology | Genetics |
| Enzymology | 23563697 | Neurosporene is the major carotenoid accumulated by Rhodobacter viridis JA737. | Ramaprasad EV, Sasikala Ch, Ramana ChV | Biotechnol Lett | 10.1007/s10529-013-1181-y | 2013 | Antioxidants/chemistry/isolation & purification, Carotenoids/chemistry/*isolation & purification, Magnetic Resonance Spectroscopy, Radiation-Protective Agents/chemistry/isolation & purification, Rhodobacter/*metabolism | Phylogeny |
| Phylogeny | 24135316 | Paenirhodobacter enshiensis gen. nov., sp. nov., a non-photosynthetic bacterium isolated from soil, and emended descriptions of the genera Rhodobacter and Haematobacter. | Wang D, Liu H, Zheng S, Wang G | Int J Syst Evol Microbiol | 10.1099/ijs.0.050351-0 | 2013 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacter/classification, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry | Genetics |
| Phylogeny | 27150292 | Rhodobacter sediminis sp. nov., isolated from lagoon sediments. | Subhash Y, Lee SS | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001130 | 2016 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/microbiology, North Carolina, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacter/*classification/genetics/isolation & purification, Sequence Analysis, DNA, *Water Microbiology | Transcriptome |
| Phylogeny | 27695993 | Sinorhodobacter hungdaonensis sp. nov. isolated from activated sludge collected from a municipal wastewater treatment plant. | Xi L, Qiao N, Zhang Z, Yan L, Li F, Hu J, Li J | Antonie Van Leeuwenhoek | 10.1007/s10482-016-0770-x | 2016 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/classification/genetics/*isolation & purification/metabolism, Sewage/*microbiology, Waste Water/chemistry/*microbiology | Metabolism |
| Phylogeny | 28829020 | Description of Rhodobacter azollae sp. nov. and Rhodobacter lacus sp. nov. | Suresh G, Sailaja B, Ashif A, Dave BP, Sasikala C, Ramana CV | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002107 | 2017 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, India, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, Ponds/*microbiology, RNA, Ribosomal, 16S/genetics, Rhodobacter/*classification/genetics/isolation & purification, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA | Enzymology |
Reference
| @id | authors | title | doi/url | ID_cross_reference | pubmed |
|---|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | ||
| 30550 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 26881 | 28776041 |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | ||
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | ||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes |