Strain identifier

BacDive ID: 5953

Type strain: Yes

Species: Halorubrum californiense

Strain Designation: SF3-213

Strain history: A. Ventosa SF3-213.

NCBI tax ID(s): 1227465 (strain), 416585 (species)

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General

@ref: 7999

BacDive-ID: 5953

DSM-Number: 19288

keywords: genome sequence, 16S sequence, Archaea, aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Halorubrum californiense SF3-213 is an aerobe, mesophilic, Gram-negative archaeon that was isolated from crystallizer pond at the Cargill Solar Salt Plant.

NCBI tax id

NCBI tax idMatching level
416585species
1227465strain

strain history

@refhistory
7999<- A. Ventosa, Univ. Seville, Dept. Microbiol. Parasitol., Spain; SF3-213 <- C. D. Litchfield, Dept. Environmental Sci. and Policy, George Mason Univ., Manassas, USA
67770A. Ventosa SF3-213.

doi: 10.13145/bacdive5953.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/methanobacteriota
  • domain: Archaea
  • phylum: Methanobacteriota
  • class: Halobacteria
  • order: Haloferacales
  • family: Halorubraceae
  • genus: Halorubrum
  • species: Halorubrum californiense
  • full scientific name: Halorubrum californiense Pesenti et al. 2008

@ref: 7999

domain: Archaea

phylum: Euryarchaeota

class: Halobacteria

order: Halobacteriales

family: Halorubraceae

genus: Halorubrum

species: Halorubrum californiense

full scientific name: Halorubrum californiense Pesenti et al. 2008

strain designation: SF3-213

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31210negative1-1.5 µm0.5 µmrod-shapedyes
69480negative99.971

pigmentation

  • @ref: 31210
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 7999
  • name: HALORUBRUM CALIFORNIENSE MEDIUM (DSMZ Medium 1194)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1194
  • composition: Name: HALORUBRUM CALIFORNIENSE MEDIUM (DSMZ Medium 1194) Composition: NaCl 156.0 g/l MgSO4 x 7 H2O 40.6 g/l MgCl2 x 6 H2O 26.0 g/l Agar 20.0 g/l Yeast extract 10.0 g/l KCl 4.0 g/l CaCl2 x 2 H2O 0.66 g/l NaBr 0.46 g/l NaHCO3 0.12 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
7999positivegrowth37mesophilic
31210positivegrowth25-42
31210positiveoptimum37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
31210positivegrowth6.8-8.5alkaliphile
31210positiveoptimum7.3

Physiology and metabolism

oxygen tolerance

  • @ref: 31210
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31210no
69481no99
69480no99.975

halophily

@refsaltgrowthtested relationconcentration
31210NaClpositivegrowth14.5-29 %
31210NaClpositiveoptimum20.3-26.1 %

observation

  • @ref: 31210
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3121028260galactose+carbon source
3121017234glucose+carbon source
3121017716lactose+carbon source
312104853esculin+hydrolysis
3121017632nitrate+reduction

enzymes

@refvalueactivityec
31210catalase+1.11.1.6
31210cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
7999crystallizer pond at the Cargill Solar Salt PlantCalifornia, Newark (37° 29' N 122° 1' W)USAUSANorth America37.4833-122.017
67770Crystallizer pond at the Cargill Solar Salt PlantNewark, CAUSAUSANorth America

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial#Plant (Factory)
#Environmental#Aquatic#Pond (small)
#Condition#Saline

Safety information

risk assessment

  • @ref: 7999
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Halorubrum californiense gene for 16S rRNA, complete sequence, strain: JCM 14715AB6634061470ena416585
7999Halorubrum californiense strain SF3-213 16S ribosomal RNA gene, partial sequenceEF1396541436ena416585

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halorubrum californiense SF3-2132554235496draftimg1227465
67770Halorubrum californiense DSM 19288GCA_000336875contigncbi1227465
66792Halorubrum californiensis DSM 192881227465.4wgspatric1227465

GC content

@refGC-contentmethod
799969.4thermal denaturation, midpoint method (Tm)
3121069.4

Genome-based predictions

predictions

  • trait: spore-forming
  • prediction: no
  • confidence: 99
  • training_data: no

External links

@ref: 7999

culture collection no.: DSM 19288, CECT 7256, JCM 14715

straininfo link

  • @ref: 75442
  • straininfo: 360272

literature

  • topic: Phylogeny
  • Pubmed-ID: 19060045
  • title: Halorubrum californiense sp. nov., an extreme archaeal halophile isolated from a crystallizer pond at a solar salt plant in California, USA.
  • authors: Pesenti PT, Sikaroodi M, Gillevet PM, Sanchez-Porro C, Ventosa A, Litchfield CD
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.2008/002410-0
  • year: 2008
  • mesh: California, Crystallization, Halorubrum/*classification/genetics/*physiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Species Specificity
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
7999Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19288)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19288
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
31210Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127537
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
75442Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID360272.1StrainInfo: A central database for resolving microbial strain identifiers