Strain identifier

BacDive ID: 6191

Type strain: Yes

Species: Rhodoplanes serenus

Strain Designation: JA266

Strain history: <- Ch. Sasikala, EMBL, India

NCBI tax ID(s): 444923 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refhistory
8403<- C. Sasikala, Centre Environment, Inst. Sci. and Technol., J. N. T. Univ., Hyderabad, India; JA266 <- S. K. Chakravarthy
67770Ch. 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

@refcell lengthcell widthcell shapemotilityflagellum arrangementgram stain
305072.5 µm0.85 µmrod-shapedyes
67771rod-shapedyesmonotrichous, polar
67771negative

pigmentation

  • @ref: 30507
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
30507positivegrowth25-40
30507positiveoptimum30mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
30507positivegrowth5.5-9alkaliphile
30507positiveoptimum6.75

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30507facultative anaerobe
67771anaerobe

halophily

@refsaltgrowthtested relationconcentration
30507NaClpositivegrowth0-0.5 %
30507NaClpositiveoptimum0.25 %

observation

  • @ref: 67771
  • observation: quinones: Q10, RQ10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3050730089acetate+carbon source
3050716947citrate+carbon source
3050716236ethanol+carbon source
3050729987glutamate+carbon source
3050724996lactate+carbon source
3050725115malate+carbon source
3050717272propionate+carbon source
3050730031succinate+carbon source
3050731011valerate+carbon source

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
8403water from a freshwater fish pondMangalore (12.5° N 74.5° E)IndiaINDAsia12.574.5
67770Water sample from a freshwater fish pond at Mangalorefacing the Arabian sea on the west coast of IndiaIndiaINDAsia
67771From water from a freshwater fish pondMangalore, facing the Arabian sea on the west coast of India(12.5° N 74.5° E)IndiaINDAsia

isolation source categories

Cat1Cat2Cat3
#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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodoplanes serenus DSM 19946GCA_003258855scaffoldncbi200615
66792Rhodoplanes piscinae strain DSM 19946444923.3wgspatric444923
66792Rhodoplanes piscinae DSM 199462893020018draftimg444923

GC content

@refGC-contentmethod
840371.3high performance liquid chromatography (HPLC)
3050771.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes55.485yes
gram-positiveno98.642yes
anaerobicyes63.465no
aerobicno59.467no
halophileno93.349yes
spore-formingno94.227no
glucose-utilyes85.931no
thermophileno95.353no
motileyes90.086yes
glucose-fermentno91.051no

External links

@ref: 8403

culture collection no.: DSM 19946, JCM 14934, KCTC 5627

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22228659Rhodoplanes piscinae sp. nov. isolated from pond water.Chakravarthy SK, Ramaprasad EVV, Shobha E, Sasikala C, Ramana CVInt J Syst Evol Microbiol10.1099/ijs.0.037663-02012Bacterial 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, DNAGenetics
Phylogeny24695055Rhodoplanes oryzae sp. nov., a phototrophic alphaproteobacterium isolated from the rhizosphere soil of paddy.Srinivas A, Sasikala C, Ramana CVInt J Syst Evol Microbiol10.1099/ijs.0.063347-02014Bacterial 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/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
8403Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19946)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19946
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
30507Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2683928776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc