Strain identifier

BacDive ID: 2468

Type strain: Yes

Species: Thiohalocapsa marina

Strain Designation: JA142

Strain history: Ch. Sasikala JA142.

NCBI tax ID(s): 424902 (species)

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General

@ref: 7870

BacDive-ID: 2468

DSM-Number: 19078

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, coccus-shaped

description: Thiohalocapsa marina JA142 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from marine aquaculture pond.

NCBI tax id

  • NCBI tax id: 424902
  • Matching level: species

strain history

@refhistory
7870<- C. Sasikala, Centre Environment, Inst. Sci. and Technol., J. N. T. Univ., Hyderabad, India; JA142 <- P. A. Kumar
67770Ch. Sasikala JA142.

doi: 10.13145/bacdive2468.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Chromatiales
  • family: Chromatiaceae
  • genus: Thiohalocapsa
  • species: Thiohalocapsa marina
  • full scientific name: Thiohalocapsa marina Anil Kumar et al. 2009

@ref: 7870

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Chromatiales

family: Chromatiaceae

genus: Thiohalocapsa

species: Thiohalocapsa marina

full scientific name: Thiohalocapsa marina Anil Kumar et al. 2009

strain designation: JA142

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
28978negative1.5-2.0 µm1.5-2.0 µmcoccus-shapedno
69480negative99.999

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
28978positivegrowth25-30mesophilic
28978positiveoptimum30mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
28978positivegrowth6.5-8.5alkaliphile
28978positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
7870anaerobe
28978anaerobe
69480anaerobe96.67

spore formation

@refspore formationconfidence
69481no92
69480no99.992

halophily

@refsaltgrowthtested relationconcentration
28978NaClpositivegrowth1.0-6.0 %
28978NaClpositiveoptimum2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2897830089acetate+carbon source
2897817234glucose+carbon source
2897824996lactate+carbon source
2897815361pyruvate+carbon source
2897830031succinate+carbon source

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7870marine aquaculture pondVisakhapatnam, near BheemliIndiaINDAsia
67770Marine aquaculture pond near BheemliVisakhapatnamIndiaINDAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Aquaculture
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Pond (small)

Safety information

risk assessment

  • @ref: 7870
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
28978Thiohalocapsa marina strain JA142 16S ribosomal RNA gene, partial sequenceAM491592.1399nuccore424902
7870Thiohalocapsa marina partial 16S rRNA gene, strain JA142TAM4915921399ena424902

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thiohalocapsa marina strain DSM 19078424902.4wgspatric424902
67770Thiohalocapsa marina DSM 19078GCA_008632335contigncbi424902

GC content

@refGC-contentmethod
787064.8high performance liquid chromatography (HPLC)
2897864.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno92no
gram-positiveno99.133no
anaerobicyes96.15yes
halophileno80.194no
spore-formingno93.181no
glucose-utilyes68.606no
aerobicno95.969yes
flagellatedno91.58no
thermophileno95.58yes
motileno81.392no
glucose-fermentno83.24no

External links

@ref: 7870

culture collection no.: DSM 19078, JCM 14780

literature

  • topic: Phylogeny
  • Pubmed-ID: 19620368
  • title: Thiohalocapsa marina sp. nov., from an Indian marine aquaculture pond.
  • authors: Anil Kumar P, Srinivas TN, Thiel V, Tank M, Sasikala Ch, Ramana ChV, Imhoff JF
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.003053-0
  • year: 2009
  • mesh: Aquaculture, Bacterial Typing Techniques, Bacteriochlorophyll A/analysis, Carotenoids/analysis, Cell Membrane/ultrastructure, Chromatiaceae/*classification/genetics/*isolation & purification/physiology, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, *Geologic Sediments, India, Molecular Sequence Data, Photosynthesis, Phylogeny, Pigments, Biological/biosynthesis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7870Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19078)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19078
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
28978Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2541228776041
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1