Strain identifier
BacDive ID: 6191
Type strain:
Species: Rhodoplanes serenus
Strain Designation: JA266
Strain history: <- Ch. Sasikala, EMBL, India
NCBI tax ID(s): 444923 (species)
General
@ref: 8403
BacDive-ID: 6191
DSM-Number: 19946
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, motile, rod-shaped
description: Rhodoplanes serenus JA266 is a facultative anaerobe, motile, rod-shaped bacterium that was isolated from water from a freshwater fish pond.
NCBI tax id
- NCBI tax id: 444923
- Matching level: species
strain history
@ref | history |
---|---|
8403 | <- C. Sasikala, Centre Environment, Inst. Sci. and Technol., J. N. T. Univ., Hyderabad, India; JA266 <- S. K. Chakravarthy |
67770 | Ch. Sasikala JA266. |
67771 | <- Ch. Sasikala, EMBL, India |
doi: 10.13145/bacdive6191.20230509.8.1
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 serenus
- full scientific name: Rhodoplanes serenus Okamura et al. 2009
synonyms
- @ref: 20215
- synonym: Rhodoplanes piscinae
@ref: 8403
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Hyphomicrobiaceae
genus: Rhodoplanes
species: Rhodoplanes piscinae
full scientific name: Rhodoplanes piscinae Chakravarthy et al. 2012
strain designation: JA266
type strain: yes
Morphology
cell morphology
@ref | cell length | cell width | cell shape | motility | flagellum arrangement | gram stain |
---|---|---|---|---|---|---|
30507 | 2.5 µm | 0.85 µm | rod-shaped | yes | ||
67771 | rod-shaped | yes | monotrichous, polar | |||
67771 | negative |
pigmentation
- @ref: 30507
- production: yes
Culture and growth conditions
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
30507 | positive | growth | 25-40 | |
30507 | positive | optimum | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
67771 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
30507 | positive | growth | 5.5-9 | alkaliphile |
30507 | positive | optimum | 6.75 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
30507 | facultative anaerobe |
67771 | anaerobe |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
30507 | NaCl | positive | growth | 0-0.5 % |
30507 | NaCl | positive | optimum | 0.25 % |
observation
- @ref: 67771
- observation: quinones: Q10, RQ10
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30507 | 30089 | acetate | + | carbon source |
30507 | 16947 | citrate | + | carbon source |
30507 | 16236 | ethanol | + | carbon source |
30507 | 29987 | glutamate | + | carbon source |
30507 | 24996 | lactate | + | carbon source |
30507 | 25115 | malate | + | carbon source |
30507 | 17272 | propionate | + | carbon source |
30507 | 30031 | succinate | + | carbon source |
30507 | 31011 | valerate | + | carbon source |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
---|---|---|---|---|---|---|---|
8403 | water from a freshwater fish pond | Mangalore (12.5° N 74.5° E) | India | IND | Asia | 12.5 | 74.5 |
67770 | Water sample from a freshwater fish pond at Mangalore | facing the Arabian sea on the west coast of India | India | IND | Asia | ||
67771 | From water from a freshwater fish pond | Mangalore, facing the Arabian sea on the west coast of India(12.5° N 74.5° E) | India | IND | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Freshwater |
#Environmental | #Aquatic | #Pond (small) |
Safety information
risk assessment
- @ref: 8403
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 8403
- description: Rhodoplanes piscinae partial 16S rRNA gene, type strain JA266T
- accession: AM712913
- length: 1398
- database: ena
- NCBI tax ID: 444923
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Rhodoplanes serenus DSM 19946 | GCA_003258855 | scaffold | ncbi | 200615 |
66792 | Rhodoplanes piscinae strain DSM 19946 | 444923.3 | wgs | patric | 444923 |
66792 | Rhodoplanes piscinae DSM 19946 | 2893020018 | draft | img | 444923 |
GC content
@ref | GC-content | method |
---|---|---|
8403 | 71.3 | high performance liquid chromatography (HPLC) |
30507 | 71.3 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
flagellated | yes | 55.485 | yes |
gram-positive | no | 98.642 | yes |
anaerobic | yes | 63.465 | no |
aerobic | no | 59.467 | no |
halophile | no | 93.349 | yes |
spore-forming | no | 94.227 | no |
glucose-util | yes | 85.931 | no |
thermophile | no | 95.353 | no |
motile | yes | 90.086 | yes |
glucose-ferment | no | 91.051 | no |
External links
@ref: 8403
culture collection no.: DSM 19946, JCM 14934, KCTC 5627
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 22228659 | Rhodoplanes piscinae sp. nov. isolated from pond water. | Chakravarthy SK, Ramaprasad EVV, Shobha E, Sasikala C, Ramana CV | Int J Syst Evol Microbiol | 10.1099/ijs.0.037663-0 | 2012 | Bacterial Typing Techniques, Bacteriochlorophyll A/analysis, Base Composition, Carotenoids/analysis, DNA, Bacterial/genetics, Fatty Acids/analysis, Hyphomicrobiaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Ponds/*microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
Phylogeny | 24695055 | Rhodoplanes oryzae sp. nov., a phototrophic alphaproteobacterium isolated from the rhizosphere soil of paddy. | Srinivas A, Sasikala C, Ramana CV | Int J Syst Evol Microbiol | 10.1099/ijs.0.063347-0 | 2014 | 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 | Genetics |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
8403 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19946) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19946 | ||||
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 | ||||
30507 | 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 | 26839 | 28776041 | ||
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 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc |