Name: Halococcus salsus ZJ1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 159820

Type strain:

Species: Halococcus salsus

Strain Designation: ZJ1

Culture col. no.: CGMCC 1.16025, NBRC 112867, JCM 34382

Strain history: CGMCC 1.16025 <-- S. Chen; Anhui Normal Univ., China; ZJ1.

NCBI tax ID(s): 2162894 (species)

Section

Halococcus salsus ZJ1 is a Gram-negative, coccus-shaped archaeon that forms circular colonies and was isolated from rock salt sample.

coccus-shaped
colony-forming
Gram-negative
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	*Halobacteriales*
	Family	*Halococcaceae*
	Genus	*Halococcus*
	Species	**Halococcus salsus**
	Full Scientific Name (LPSN)	Halococcus salsus Chen et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #66759]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.918

[Ref.: #66759]	Cell length	0.8-1.6 µm

[Ref.: #66759]	Cell shape	coccus-shaped

[Ref.: #66759]	Motility	no

[Ref.: #66759]	Colony size	0.3 mm
[Ref.: #66759]	Colony color	pink
[Ref.: #66759]	Colony shape	circular
[Ref.: #66759]	Cultivation medium used	JCM medium No. 168

Information on culture and growth conditions Culture and growth conditions

[Ref.: #66759]

Culture medium

JCM medium No. 168

[Ref.: #66759]

Culture medium growth

		Temperature
[Ref.: #66759]	growth	20-45 °C
[Ref.: #66759]	optimum	38-40 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #67770]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #66759]			optimum	7.5
[Ref.: #66759]			growth	5-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69480]	Ability of spore formation	no Confidence in %99.988
[Ref.: #69481]	Ability of spore formation	no Confidence in %99

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #66759]		NaCl		growth	10-30	%(w/v)
[Ref.: #66759]		NaCl		optimum	20	%(w/v)

[Ref.: #66759]

Observation

The major polar lipids are PG, PGP-Me and SDGD-1.

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #66759]	casein	-	hydrolysis
[Ref.: #66759]	D-fructose ChEBI	-	carbon source
[Ref.: #66759]	D-galactose ChEBI	+	builds acid from
[Ref.: #66759]	D-glucose ChEBI	+	builds acid from
[Ref.: #66759]	D-mannose ChEBI	+	builds acid from
[Ref.: #66759]	D-ribose ChEBI	-	carbon source
[Ref.: #66759]	D-xylose ChEBI	-	carbon source
[Ref.: #66759]	disodium fumarate ChEBI	+	carbon source
[Ref.: #66759]	galactose ChEBI	+	carbon source
[Ref.: #66759]	gelatin ChEBI	-	hydrolysis
[Ref.: #66759]	glucose ChEBI	+	carbon source
[Ref.: #66759]	glycerol ChEBI	+	carbon source
[Ref.: #66759]	glycine ChEBI	-	carbon source
[Ref.: #66759]	L-alanine ChEBI	-	carbon source
[Ref.: #66759]	L-aspartate ChEBI	+	carbon source
[Ref.: #66759]	L-glutamate ChEBI	+	carbon source
[Ref.: #66759]	L-lysine ChEBI	+	carbon source
[Ref.: #66759]	L-malate ChEBI	-	carbon source
[Ref.: #66759]	L-ornithine ChEBI	+	carbon source
[Ref.: #66759]	L-sorbose ChEBI	-	carbon source
[Ref.: #66759]	lactose ChEBI	+	carbon source
[Ref.: #66759]	maltose ChEBI	+	carbon source
[Ref.: #66759]	mannitol ChEBI	+	carbon source
[Ref.: #66759]	mannose ChEBI	+	carbon source
[Ref.: #66759]	sodium citrate ChEBI	+	carbon source
[Ref.: #66759]	sodium succinate ChEBI	-	carbon source
[Ref.: #66759]	sorbitol ChEBI	-	carbon source
[Ref.: #66759]	starch ChEBI	+	carbon source
[Ref.: #66759]	starch ChEBI	+	hydrolysis
[Ref.: #66759]	sucrose ChEBI	+	builds acid from
[Ref.: #66759]	sucrose ChEBI	+	carbon source
[Ref.: #66759]	tween 20 ChEBI	+	hydrolysis
[Ref.: #66759]	tween 40 ChEBI	+	hydrolysis
[Ref.: #66759]	tween 60 ChEBI	+	hydrolysis
[Ref.: #66759]	tween 80 ChEBI	+	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #66759]	ampicillin ChEBI				yes	10	µg (disc)
[Ref.: #66759]	bacitracin ChEBI	yes	0.04	Unit (disc)
[Ref.: #66759]	chloramphenicol ChEBI				yes	30	µg (disc)
[Ref.: #66759]	ciprofloxacin ChEBI				yes	5	µg (disc)
[Ref.: #66759]	erythromycin ChEBI				yes	15	µg (disc)
[Ref.: #66759]	kanamycin ChEBI				yes	10	µg (disc)
[Ref.: #66759]	neomycin ChEBI				yes	30	µg (disc)
[Ref.: #66759]	norfloxacin ChEBI				yes	10	µg (disc)
[Ref.: #66759]	novobiocin ChEBI	yes	30	µg (disc)
[Ref.: #66759]	penicillin ChEBI				yes	10	Unit (disc)
[Ref.: #66759]	rifampicin ChEBI				yes	5	µg (disc)
[Ref.: #66759]	streptomycin ChEBI				yes	10	µg (disc)
[Ref.: #66759]	tetracycline ChEBI				yes	30	µg (disc)
[Ref.: #66759]	vancomycin ChEBI				yes	30	µg (disc)
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #66759]		hydrogen sulfide ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #66759]	catalase	+	1.11.1.6
[Ref.: #66759]	cytochrome oxidase	-	1.9.3.1
[Ref.: #66759]	nitrate reductase	-	1.7.99.4

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

[Ref.: #66759]	Sample type/isolated from	rock salt sample
[Ref.: #66759]	Geographic location (country and/or sea, region)	Yunnan Salt Mine
[Ref.: #66759]	Country	China
[Ref.: #66759]	Country ISO 3 Code	CHN
[Ref.: #66759]	Continent	Asia
[Ref.: #66759]	Geographic location	22.6813°/101.6420°
[Ref.: #66759]	Enrichment culture	JCM medium No. 168
[Ref.: #66759]	Enrichment culture composition	contained (per litre) 200.0 g NaCl, 1 g Casamino acids (Difco), 1.0 g yeast extract (Difco), 3 g trisodium citrate.2H2O, 0.1 g sodium pyruvate, 2.0 g KCl, 20.0 g MgSO4.7H2O, 0.036 g FeSO4.4H2O, 0.00036 g MnSO4.4H2O and 20.0 g Bacto agar (Difco), with pH adjusted to 7.2 with KOH.
[Ref.: #66759]	Enrichment culture duration	2 weeks
[Ref.: #66759]	Enrichment culture temperature	37 ̊C
[Ref.: #66759]	Isolation/enrichment procedure	dissolved in 5% (w/v) sterile NaCl solution. Sediments were removed by using sterile filter paper prior to spreading on agar plates. Approximately 0.2 ml of solution was spread on agar plates,

[Ref.: #67770]	Sample type/isolated from	Rock salt of Yunnan Salt Mine
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Geologic
#Condition	#Saline	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence MG097854 (>99% sequence identity) for Halococcus from Microbeatlas

Aquatic Samples	277
Soil Samples	13
Animal Samples	8
Plant Samples	2
Total Samples	300

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.: #66759]	Halococcus sp. strain ZJ1 16S ribosomal RNA gene, partial sequence	MG097854	1475	ENA	2162894 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Halococcus salsus ZJ1	GCA_009900715	scaffold	GenBank	2162894 tax ID	*

[Ref.: #67770]

GC-content

66.5 mol%

thermal denaturation, midpoint method (Tm)

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: Halococcus salsus ZJ1 NCBI: GCA_009900715.1
[Ref.: #69481]	spore-forming	no	99	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Halococcus salsus ZJ1 NCBI: GCA_009900715.1
[Ref.: #69480]	motile	no	83.145	no
[Ref.: #69480]	flagellated	no	97.422	no
[Ref.: #69480]	gram-positive	no	96.036	yes
[Ref.: #69480]	anaerobic	no	96.959	no
[Ref.: #69480]	aerobic	yes	90.248	no
[Ref.: #69480]	halophile	yes	91.672	yes
[Ref.: #69480]	spore-forming	no	94.933	no
[Ref.: #69480]	glucose-util	yes	89.323	yes
[Ref.: #69480]	thermophile	no	95.44	no
[Ref.: #69480]	glucose-ferment	no	83.94	no

Availability in culture collections External links

[Ref.: #66759]

Culture collection no.

CGMCC 1.16025, NBRC 112867, JCM 34382

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Halococcus salsus sp. nov., a novel halophilic archaeon isolated from rock salt.	Chen S, Sun S, Xu Y, Liu HC	Int J Syst Evol Microbiol	10.1099/ijsem.0.003051	2018	*

References

#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 )

#66759

Shaoxing Chen, Siqi Sun, Yao Xu and Hong-Can Liu: Halococcus salsus sp. nov., a novel halophilic archaeon isolated from rock salt. IJSEM 68: 3754 - 3759 2018 ( DOI 10.1099/ijsem.0.003051 , PubMed 30311879 )

#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;

#69479

João 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.: MicrobeAtlas 1.0 beta .

#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 )

* These data were automatically processed and therefore are not curated

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