Name: Haloquadratum walsbyi HBSQ001
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 5879

Type strain:

Species: Haloquadratum walsbyi

Strain Designation: HBSQ001

Culture col. no.: DSM 16790, JCM 12895

Strain history: H. Bolhuis HBSQ001.

NCBI tax ID(s): 362976 (strain), 293091 (species)

SI-ID 294527

DSM 16790, JCM 12895

Special Collections

DSMZ
JCM

Other strains from Haloquadratum walsbyi

Section

Haloquadratum walsbyi HBSQ001 is a Gram-negative archaeon that was isolated from 39% total salinity crystallizer pond.

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	*Haloferacales*
	Family	*Haloferacaceae*
	Genus	*Haloquadratum*
	Species	**Haloquadratum walsbyi**
	Full Scientific Name (LPSN)	Haloquadratum walsbyi Burns et al. 2007

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6603]

Culture medium

HALOQUADRATUM WALSBYI MEDIUM (DSMZ Medium 1091)

[Ref.: #6603]

Culture medium growth

[Ref.: #6603]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6603]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #6603]			growth	37 °C
[Ref.: #67770]			growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]

Ability of spore formation

no Confidence in %100

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	pyrimidine metabolism	77.78	35 of 45
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	palmitate biosynthesis	77.27	17 of 22
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	purine metabolism	76.6	72 of 94
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	vitamin B12 metabolism	70.59	24 of 34
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	nitrate assimilation	66.67	6 of 9
[Ref.: #66794]	arginine metabolism	66.67	16 of 24
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	alanine metabolism	65.52	19 of 29
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	oxidative phosphorylation	60.44	55 of 91
[Ref.: #66794]	3-chlorocatechol degradation	60	3 of 5
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	carotenoid biosynthesis	59.09	13 of 22
[Ref.: #66794]	histidine metabolism	58.62	17 of 29
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	57.14	8 of 14
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	tryptophan metabolism	52.63	20 of 38
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	degradation of sugar alcohols	50	8 of 16
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	degradation of sugar acids	48	12 of 25
[Ref.: #66794]	lysine metabolism	47.62	20 of 42
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	methionine metabolism	46.15	12 of 26
[Ref.: #66794]	cysteine metabolism	44.44	8 of 18
[Ref.: #66794]	arachidonic acid metabolism	44.44	8 of 18
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	degradation of pentoses	35.71	10 of 28
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	isoprenoid biosynthesis	34.62	9 of 26
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	methanogenesis from CO2	33.33	4 of 12
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	ppGpp biosynthesis	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	phenol degradation	25	5 of 20
[Ref.: #66794]	dTDPLrhamnose biosynthesis	25	2 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	sulfopterin metabolism	25	1 of 4
[Ref.: #66794]	butanoate fermentation	25	1 of 4
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	degradation of hexoses	22.22	4 of 18
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #6603]	Sample type/isolated from	39% total salinity crystallizer pond
[Ref.: #6603]	Geographic location (country and/or sea, region)	Brac del Port, Alicante
[Ref.: #6603]	Country	Spain
[Ref.: #6603]	Country ISO 3 Code	ESP
[Ref.: #6603]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Salt-saturated crystallizer ponds of a solar saltern in Brac del Port
[Ref.: #67770]	Geographic location (country and/or sea, region)	Alicante
[Ref.: #67770]	Country	Spain
[Ref.: #67770]	Country ISO 3 Code	ESP
[Ref.: #67770]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Pond (small)
#Condition	#Saline	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AM180088 (>99% sequence identity) for Haloquadratum walsbyi subclade from Microbeatlas

Aquatic Samples	167
Soil Samples	16
Animal Samples	12
Plant Samples	4
Total Samples	199

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

[Ref.: #6603]

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.: #67770]	Haloquadratum walsbyi DSM 16790 complete genome	AM180088	3132494	GenBank ENA	362976 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Haloquadratum walsbyi DSM 16790 DSM 16790 = HBSQ001	GCA_000009185	complete	GenBank ENA	362976 tax ID	*
[Ref.: #66792]	Haloquadratum walsbyi HBSQ001, DSM 16790	637000129	complete	JGI IMG/M	362976 tax ID	*
[Ref.: #66792]	Haloquadratum walsbyi DSM 16790 strain DSM 16790 = HBSQ001	362976.27	plasmid	PATRIC	362976 tax ID	*
[Ref.: #66792]	Haloquadratum walsbyi DSM 16790	362976.22	complete	PATRIC	362976 tax ID	*

[Ref.: #67770]

GC-content

46.9 mol%

high performance liquid chromatography (HPLC)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Haloquadratum walsbyi DSM 16790 DSM 16790 = HBSQ001 NCBI: GCA_000009185.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Haloquadratum walsbyi DSM 16790 DSM 16790 = HBSQ001 NCBI: GCA_000009185.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	75.198	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	72.035	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	71.965	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	87.387	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	81.312	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	85	no

Availability in culture collections External links

[Ref.: #6603]

Culture collection no.

DSM 16790, JCM 12895

[Ref.: #75358]

SI-ID 294527

Literature:

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

Topic	Title	Authors	Journal	DOI	Year
Transcriptome	Transcriptome analysis of Haloquadratum walsbyi: vanity is but the surface.	Bolhuis H, Martin-Cuadrado AB, Rosselli R, Pasic L, Rodriguez-Valera F	BMC Genomics	10.1186/s12864-017-3892-2	2017	*
Genetics	Haloquadratum walsbyi: limited diversity in a global pond.	Dyall-Smith ML, Pfeiffer F, Klee K, Palm P, Gross K, Schuster SC, Rampp M, Oesterhelt D	PLoS One	10.1371/journal.pone.0020968	2011	*
Genetics	MUST: a system for identification of miniature inverted-repeat transposable elements and applications to Anabaena variabilis and Haloquadratum walsbyi.	Chen Y, Zhou F, Li G, Xu Y	Gene	10.1016/j.gene.2009.01.019	2009	*
Genetics	Genomic plasticity in prokaryotes: the case of the square haloarchaeon.	Cuadros-Orellana S, Martin-Cuadrado AB, Legault B, D'Auria G, Zhaxybayeva O, Papke RT, Rodriguez-Valera F	ISME J	10.1038/ismej.2007.35	2007	*
Phylogeny	Haloquadratum walsbyi gen. nov., sp. nov., the square haloarchaeon of Walsby, isolated from saltern crystallizers in Australia and Spain.	Burns DG, Janssen PH, Itoh T, Kamekura M, Li Z, Jensen G, Rodriguez-Valera F, Bolhuis H, Dyall-Smith ML	Int J Syst Evol Microbiol	10.1099/ijs.0.64690-0	2007	*
Genetics	Environmental genomics of "Haloquadratum walsbyi" in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species.	Legault BA, Lopez-Lopez A, Alba-Casado JC, Doolittle WF, Bolhuis H, Rodriguez-Valera F, Papke RT	BMC Genomics	10.1186/1471-2164-7-171	2006	*
	A manual curation strategy to improve genome annotation: application to a set of haloarchael genomes.	Pfeiffer F, Oesterhelt D	Life (Basel)	10.3390/life5021427	2015	*
	Fluorescence microscopy visualization of halomucin, a secreted 927 kDa protein surrounding Haloquadratum walsbyi cells.	Zenke R, von Gronau S, Bolhuis H, Gruska M, Pfeiffer F, Oesterhelt D	Front Microbiol	10.3389/fmicb.2015.00249	2015	*
	Differences in gene expression patterns between cultured and natural Haloquadratum walsbyi ecotypes.	Rosselli R, Lopez-Perez M, Martin-Cuadrado AB, Rodriguez-Valera F, Bolhuis H	Front Microbiol	10.3389/fmicb.2022.1044446	2022	*

References

#6603

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16790

#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 )

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#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 )

#75358

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-ID294527.1 )

* These data were automatically processed and therefore are not curated

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Haloquadratum walsbyi DSM 16790 DSM 16790 = HBSQ001

Haloquadratum walsbyi DSM 16790 DSM 16790 = HBSQ001

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