Name: Halorubrum californiense SF3-213
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5953

Type strain:

Species: Halorubrum californiense

Strain Designation: SF3-213

Culture col. no.: DSM 19288, CECT 7256, JCM 14715

Strain history: A. Ventosa SF3-213.

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

SI-ID 360272

CECT 7256, DSM 19288, JCM 14715

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Archaea"
	Phylum	*Methanobacteriota*
	Class	*Halobacteria*
	Order	*Haloferacales*
	Family	*Halorubraceae*
	Genus	*Halorubrum*
	Species	**Halorubrum californiense**
	Full Scientific Name (LPSN)	Halorubrum californiense Pesenti et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #31210]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.971

[Ref.: #31210]	Cell length	1-1.5 µm

[Ref.: #31210]	Cell width	0.5 µm

[Ref.: #31210]	Cell shape	rod-shaped

[Ref.: #31210]	Motility	yes

[Ref.: #31210]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7999]

Culture medium

HALORUBRUM CALIFORNIENSE MEDIUM (DSMZ Medium 1194)

[Ref.: #7999]

Culture medium growth

[Ref.: #7999]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7999]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7999]	growth	37 °C
[Ref.: #31210]	growth	25-42 °C
[Ref.: #31210]	optimum	37 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #7999]	Temperature range	mesophilic
[Ref.: #31210]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31210]			optimum	7.3
[Ref.: #31210]			growth	6.8-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31210]

Oxygen tolerance

aerobe

[Ref.: #31210]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %99
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.975

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31210]		NaCl		growth	14.5-29	%
[Ref.: #31210]		NaCl		optimum	20.3-26.1	%

[Ref.: #31210]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31210]	esculin ChEBI	+	hydrolysis
[Ref.: #31210]	galactose ChEBI	+	carbon source
[Ref.: #31210]	glucose ChEBI	+	carbon source
[Ref.: #31210]	lactose ChEBI	+	carbon source
[Ref.: #31210]	nitrate ChEBI	+	reduction

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #31210]		catalase	+	1.11.1.6
[Ref.: #31210]		cytochrome oxidase	+	1.9.3.1

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #7999]	Sample type/isolated from	crystallizer pond at the Cargill Solar Salt Plant
[Ref.: #7999]	Geographic location (country and/or sea, region)	California, Newark (37° 29' N 122° 1' W)
[Ref.: #7999]	Country	USA
[Ref.: #7999]	Country ISO 3 Code	USA
[Ref.: #7999]	Continent	North America
[Ref.: #7999]	Geographic location	37.4833°/-122.0170°

[Ref.: #67770]	Sample type/isolated from	Crystallizer pond at the Cargill Solar Salt Plant
[Ref.: #67770]	Geographic location (country and/or sea, region)	Newark, CA
[Ref.: #67770]	Country	USA
[Ref.: #67770]	Country ISO 3 Code	USA
[Ref.: #67770]	Continent	North America
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #7999]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #7999]	Halorubrum californiense strain SF3-213 16S ribosomal RNA gene, partial sequence	EF139654	1436	ENA	416585 tax ID
[Ref.: #20218]	Halorubrum californiense gene for 16S rRNA, complete sequence, strain: JCM 14715	AB663406	1470	ENA	416585 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Halorubrum californiense DSM 19288	GCA_000336875	contig	GenBank	1227465 tax ID
[Ref.: #66792]	Halorubrum californiense SF3-213	2554235496	draft	JGI IMG/M	1227465 tax ID	*
[Ref.: #66792]	Halorubrum californiensis DSM 19288	1227465.4	wgs	PATRIC	1227465 tax ID	*

[Ref.: #7999]	GC-content	69.4 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #31210]	GC-content	69.4 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Halorubrum californiensis DSM 19288 DSM 19288 NCBI: GCA_000336875.1
[Ref.: #69481]	spore-forming	no	99	no

Availability in culture collections External links

[Ref.: #7999]

Culture collection no.

DSM 19288, CECT 7256, JCM 14715

[Ref.: #75442]

SI-ID 360272

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Halorubrum californiense sp. nov., an extreme archaeal halophile isolated from a crystallizer pond at a solar salt plant in California, USA.	Pesenti PT, Sikaroodi M, Gillevet PM, Sanchez-Porro C, Ventosa A, Litchfield CD	Int J Syst Evol Microbiol	10.1099/ijs.0.2008/002410-0	2008	*

References

#7999

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19288

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#31210

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #27537 (see below)

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#75442

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID360272.1 )

#27537

IJSEM 2710 2008 ( DOI 10.1099/ijs.0.2008/002410-0 , PubMed 19060045 )

* These data were automatically processed and therefore are not curated

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Halorubrum californiensis DSM 19288 DSM 19288

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