Strain identifier

BacDive ID: 4167

Type strain: Yes

Species: Desulfovibrio psychrotolerans

Strain Designation: JS, JS1

Strain history: <- Ch Sasikala, India

NCBI tax ID(s): 1121461 (strain), 415242 (species)

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General

@ref: 8011

BacDive-ID: 4167

DSM-Number: 19430

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, chemoorganoheterotroph, Gram-negative, motile, vibrio-shaped

description: Desulfovibrio psychrotolerans JS is an anaerobe, chemoorganoheterotroph, Gram-negative bacterium that was isolated from mud sample.

NCBI tax id

NCBI tax idMatching level
415242species
1121461strain

strain history

@refhistory
8011<- C. Sasikala; JS1
67771<- Ch Sasikala, India

doi: 10.13145/bacdive4167.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Deltaproteobacteria
  • order: Desulfovibrionales
  • family: Desulfovibrionaceae
  • genus: Desulfovibrio
  • species: Desulfovibrio psychrotolerans
  • full scientific name: Desulfovibrio psychrotolerans Sasi Jyothsna et al. 2008

  • synonyms

    • @ref: 20215
    • synonym: Psychrodesulfovibrio psychrotolerans

@ref: 8011

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Desulfovibrionales

family: Desulfovibrionaceae

genus: Desulfovibrio

species: Desulfovibrio psychrotolerans

full scientific name: Desulfovibrio psychrotolerans Sasi Jyothsna et al. 2008

strain designation: JS, JS1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
23215negative0.5-2.0 µm0.3-0.8 µmvibrio-shapedyespolar
67771yesmonotrichous, polar
67771negative
69480yes96.546
69480negative99.977

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
23215positivegrowth10-50
67771positivegrowth25mesophilic

culture pH

  • @ref: 23215
  • ability: positive
  • type: optimum
  • pH: 8.5-9.0
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8011anaerobe
23215anaerobe
23215aerotolerant
67771anaerobe
69480anaerobe99.039

nutrition type

  • @ref: 23215
  • type: chemoorganoheterotroph

spore formation

@refspore formationconfidence
23215no
67771no
69481no100
69480no98.808

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2321527897tryptophan-energy source
2321516189sulfate+electron acceptor
2321528885butanol+growth
2321516236ethanol+growth
2321515740formate+growth
2321524996lactate+growth
2321515361pyruvate+growth
2321530031succinate+growth
2321528017starch+hydrolysis
23215178364-aminobenzoate+required for growth

metabolite production

  • @ref: 23215
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 23215
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
23215acid phosphatase-3.1.3.2
23215carbohydrates-1.14.14.9
23215catalase+1.11.1.6
23215lipase-
23215tryptophan deaminase-4.1.99.1
23215urease-3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8011mud sampleLake Pangong, Leh DistrictIndiaINDAsia
23215salt-water lake Pangong situated in the Himalayas
67771From mud and water of Pangong salt water lakeHimalayas, Leh DistrictIndiaINDAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Lake (large)
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_58002.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15981;96_22690;97_32224;98_41310;99_58002&stattab=map
  • Last taxonomy: Desulfovibrio psychrotolerans subclade
  • 16S sequence: AM418397
  • Sequence Identity:
  • Total samples: 358
  • soil counts: 31
  • aquatic counts: 205
  • animal counts: 115
  • plant counts: 7

Safety information

risk assessment

  • @ref: 8011
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8011
  • description: Desulfovibrio psychrotolerans 16S rRNA gene, type strain PWCT
  • accession: AM418397
  • length: 1488
  • database: ena
  • NCBI tax ID: 1121461

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Desulfovibrio psychrotolerans JS1GCA_013340305scaffoldncbi415242
66792Desulfovibrio psychrotolerans strain JS1415242.3wgspatric415242

GC content

  • @ref: 8011
  • GC-content: 49.3
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes92.646no
flagellatedyes72.49yes
gram-positiveno99.522yes
anaerobicyes99.001no
aerobicno99.105yes
halophileno74.395no
spore-formingno93.993yes
glucose-utilno54.657no
thermophileno97.453no
glucose-fermentno74.39no

External links

@ref: 8011

culture collection no.: DSM 19430, JCM 14597, KCTC 5573

straininfo link

  • @ref: 73669
  • straininfo: 343791

literature

  • topic: Phylogeny
  • Pubmed-ID: 18398176
  • title: Desulfovibrio psychrotolerans sp. nov., a psychrotolerant and moderately alkaliphilic sulfate-reducing deltaproteobacterium from the Himalayas.
  • authors: Sasi Jyothsna TS, Sasikala Ch, Ramana ChV
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65402-0
  • year: 2008
  • mesh: Base Composition, DNA, Bacterial/chemistry/genetics, Desulfovibrio/classification/genetics/*isolation & purification/*metabolism, Fresh Water/microbiology, Genes, Bacterial, India, Molecular Sequence Data, Oxidation-Reduction, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sodium Chloride/metabolism, Species Specificity, Sulfates/metabolism, Terminology as Topic
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8011Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19430)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19430
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
23215T. S. Sasi Jyothsna, Ch. Sasikala, Ch. V. Ramana10.1099/ijs.0.65402-0Desulfovibrio psychrotolerans sp. nov., a psychrotolerant and moderately alkaliphilic sulfate-reducing deltaproteobacterium from the HimalayasIJSEM 58: 821-825 200818398176
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
69479João 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
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
73669Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID343791.1StrainInfo: A central database for resolving microbial strain identifiers