Name: Halococcus dombrowskii H4
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5929

Type strain:

Species: Halococcus dombrowskii

Strain Designation: H4

Culture col. no.: DSM 14522, ATCC BAA-364, NCIMB 13803, JCM 12289, CIP 108355

Strain history: CIP <- 2004, NCIMB <- H. Stan Lotter, Salzburg Univ., Salzburg, Austria: strain H4

NCBI tax ID(s): 179637 (species)

SI-ID 100672

ATCC BAA-364, DSM 14522, NCIMB 13803, JCM 12289, CIP 108355

Section

Halococcus dombrowskii H4 is a mesophilic, Gram-positive, coccus-shaped archaeon that was isolated from dry rock salt from salt mine.

coccus-shaped
Gram-positive
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	*Halobacteriales*
	Family	*Halococcaceae*
	Genus	*Halococcus*
	Species	**Halococcus dombrowskii**
	Full Scientific Name (LPSN)	Halococcus dombrowskii Stan-Lotter et al. 2002

Information on morphological and physiological properties Morphology

[Ref.: #118961]	Gram stain	positive

[Ref.: #118961]	Cell shape	coccus-shaped

[Ref.: #118961]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5282]

Culture medium

MEDIUM FOR H. DOMBROWSKII (DSMZ Medium 954)

[Ref.: #5282]

Culture medium growth

[Ref.: #5282]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5282]

Culture medium composition

expand / minimize

[Ref.: #33060]

Culture medium

MEDIUM 598 - for Halococcus dombrowskii

[Ref.: #33060]

Culture medium growth

[Ref.: #33060]

Culture medium composition

expand / minimize

[Ref.: #118961]

Culture medium

CIP Medium 598

[Ref.: #118961]

Culture medium growth

[Ref.: #118961]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #5282]		growth	37 °C
[Ref.: #33060]		growth	37 °C
[Ref.: #67770]		growth	37 °C
[Ref.: #118961]		growth	25-37 °C
[Ref.: #118961]	no	growth	5 °C
[Ref.: #118961]	no	growth	15 °C
[Ref.: #118961]	no	growth	41 °C
[Ref.: #118961]	no	growth	45 °C

[Ref.: #5282]	Temperature range	mesophilic
[Ref.: #33060]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #118961]	Temperature range	mesophilic
[Ref.: #118961]	Temperature range	psychrophilic
[Ref.: #118961]	Temperature range	thermophilic

Information on physiology and metabolism Physiology and metabolism

	Salt	Tested relation		Salt conc.
[Ref.: #118961]	NaCl	no	growth	0	%
[Ref.: #118961]	NaCl	no	growth	2	%
[Ref.: #118961]	NaCl	no	growth	4	%
[Ref.: #118961]	NaCl	no	growth	6	%
[Ref.: #118961]	NaCl	no	growth	8	%
[Ref.: #118961]	NaCl	no	growth	10	%

[Ref.: #67770]

Observation

quinones: MK-8, MK-8(H₂)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #118961]	citrate ChEBI	-	carbon source
[Ref.: #118961]	esculin ChEBI	-	hydrolysis
[Ref.: #118961]	hippurate ChEBI	+	hydrolysis
[Ref.: #118961]	malonate ChEBI	-	assimilation
[Ref.: #118961]	nitrate ChEBI	-	builds gas from
[Ref.: #118961]	nitrate ChEBI	-	reduction
[Ref.: #118961]	nitrite ChEBI	-	builds gas from
[Ref.: #118961]	nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #118961]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #118961]		acetoin ChEBI	-
[Ref.: #118961]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #118961]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	-	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #118961]	beta-galactosidase	+	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #118961]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #118961]	gelatinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #118961]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #118961]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #118961]	oxidase	+
[Ref.: #118961]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #118961]	tryptophan deaminase	-
[Ref.: #118961]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #118961]	11110	-	-	+	+	-	+	-	-	-	-	-	+	-	-	-	-	-	-	-	-

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

[Ref.: #5282]	Sample type/isolated from	dry rock salt from salt mine
[Ref.: #5282]	Geographic location (country and/or sea, region)	Bad Ischl
[Ref.: #5282]	Country	Austria
[Ref.: #5282]	Country ISO 3 Code	AUT
[Ref.: #5282]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Dry Permina rock salt from the salt mine in Bad Ischl
[Ref.: #67770]	Country	Austria
[Ref.: #67770]	Country ISO 3 Code	AUT
[Ref.: #67770]	Continent	Europe

[Ref.: #118961]	Sample type/isolated from	Dry rock salt
[Ref.: #118961]	Geographic location (country and/or sea, region)	Bad Ischl
[Ref.: #118961]	Country	Austria
[Ref.: #118961]	Country ISO 3 Code	AUT
[Ref.: #118961]	Continent	Europe
[Ref.: #118961]	Isolation date	1997
* marker position based on {}

Isolation sources categories

#Engineered	#Other	#Mine
#Environmental	#Terrestrial	-
#Condition	#Saline	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AJ420376 (>99% sequence identity) for Halococcus from Microbeatlas

Aquatic Samples	97
Soil Samples	14
Animal Samples	164
Plant Samples	1
Total Samples	276

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

[Ref.: #5282]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #118961]	Biosafety level	1	Risk group (French classification)

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.: #5282]	Halococcus dombrowskii partial 16S rRNA gene sequence, strain H4	AJ420376	1472	ENA	179637 tax ID
[Ref.: #20218]	Halococcus dombrowskii strain DSM 14522 16S-23S ribosomal RNA intergenic spacer, partial sequence	EU984226	257	ENA	179637 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Halococcus dombrowskii H4	GCA_022870485	complete	GenBank	179637 tax ID	*

[Ref.: #5282]	GC-content	61.3 mol%
[Ref.: #67770]	GC-content	61.3 mol%	high performance liquid chromatography (HPLC)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Halococcus dombrowskii H4 NCBI: GCA_022870485.1
[Ref.: #69480]	flagellated	no	97.495	no
[Ref.: #69480]	gram-positive	no	95.766	no
[Ref.: #69480]	anaerobic	no	95.249	no
[Ref.: #69480]	aerobic	yes	82.649	no
[Ref.: #69480]	halophile	yes	90.92	no
[Ref.: #69480]	spore-forming	no	93.847	no
[Ref.: #69480]	motile	no	81.642	no
[Ref.: #69480]	glucose-ferment	no	85.16	no
[Ref.: #69480]	thermophile	no	87.469	yes
[Ref.: #69480]	glucose-util	yes	87.104	no

Availability in culture collections External links

[Ref.: #5282]

Culture collection no.

DSM 14522, ATCC BAA-364, NCIMB 13803, JCM 12289, CIP 108355

[Ref.: #75410]

SI-ID 100672

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Halococcus sediminicola sp. nov., an extremely halophilic archaeon isolated from a marine sediment.	Yim KJ, Cha IT, Whon TW, Lee HW, Song HS, Kim KN, Nam YD, Lee SJ, Bae JW, Rhee SK, Choi JS, Seo MJ, Roh SW, Kim D	Antonie Van Leeuwenhoek	10.1007/s10482-013-0054-7	2013	*
Metabolism	Identification of polyhydroxyalkanoates in Halococcus and other haloarchaeal species.	Legat A, Gruber C, Zangger K, Wanner G, Stan-Lotter H	Appl Microbiol Biotechnol	10.1007/s00253-010-2611-6	2010	*
Cultivation	Investigating the effects of simulated martian ultraviolet radiation on Halococcus dombrowskii and other extremely halophilic archaebacteria.	Fendrihan S, Berces A, Lammer H, Musso M, Ronto G, Polacsek TK, Holzinger A, Kolb C, Stan-Lotter H	Astrobiology	10.1089/ast.2007.0234	2009	*
Phylogeny	Halococcus thailandensis sp. nov., from fish sauce in Thailand.	Namwong S, Tanasupawat S, Visessanguan W, Kudo T, Itoh T	Int J Syst Evol Microbiol	10.1099/ijs.0.65218-0	2007	*
Phylogeny	Halococcus qingdaonensis sp. nov., a halophilic archaeon isolated from a crude sea-salt sample.	Wang QF, Li W, Yang H, Liu YL, Cao HH, Dornmayr-Pfaffenhuemer M, Stan-Lotter H, Guo GQ	Int J Syst Evol Microbiol	10.1099/ijs.0.64673-0	2007	*
Phylogeny	Halococcus dombrowskii sp. nov., an archaeal isolate from a Permian alpine salt deposit.	Stan-Lotter H, Pfaffenhuemer M, Legat A, Busse HJ, Radax C, Gruber C	Int J Syst Evol Microbiol	10.1099/00207713-52-5-1807	2002	*

References

#5282

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 14522

#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 )

#33060 ; Curators of the CIP;

#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;

#68382

Automatically annotated from API zym .

#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) .

#75410

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-ID100672.1 )

#118961 Collection of Institut Pasteur ; Curators of the CIP; CIP 108355
* These data were automatically processed and therefore are not curated

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