Name: Thiohalospira halophila HL 3
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 4300

Type strain:

Species: Thiohalospira halophila

Strain Designation: HL 3

Culture col. no.: DSM 15071, UNIQEM U219

Strain history: <- D.Y. Sorokin; HL 3

NCBI tax ID(s): 1123397 (strain), 381300 (species)

SI-ID 396792

DSM 15071

Special Collections

Other strains from Thiohalospira halophila

Section

Thiohalospira halophila HL 3 is an aerobe, Gram-negative, motile bacterium that was isolated from hypersaline lake.

Gram-negative
motile
rod-shaped
aerobe
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Chromatiales*
	Family	*Ectothiorhodospiraceae*
	Genus	*Thiohalospira*
	Species	**Thiohalospira halophila**
	Full Scientific Name (LPSN)	Thiohalospira halophila Sorokin et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32537]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.5

[Ref.: #32537]	Cell length	02-08 µm

[Ref.: #32537]	Cell width	0.4-0.5 µm

[Ref.: #32537]	Cell shape	rod-shaped

[Ref.: #32537]	Motility	yes

[Ref.: #32537]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5695]

Culture medium

THIOHALOSPIRA HALOPHILA MEDIUM (DSMZ Medium 1058a)

[Ref.: #5695]

Culture medium growth

[Ref.: #5695]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5695]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #5695]	growth	30 °C
[Ref.: #32537]	growth	32-35 °C
[Ref.: #32537]	optimum	32-35 °C

	pH	Kind of pH		pH
[Ref.: #32537]			optimum	7.3-7.8
[Ref.: #32537]			growth	6.5-8.2

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32537]

Oxygen tolerance

aerobe

[Ref.: #32537]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %92.46
[Ref.: #69481]	Ability of spore formation	no Confidence in %99

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32537]		NaCl		growth	14.5-17.4	%
[Ref.: #32537]		NaCl		optimum	11.6-29	%

[Ref.: #32537]

Observation

aggregates in chains

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32537]		glycine ChEBI	+	carbon source

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	phenylmercury acetate degradation	100	2 of 2
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	photosynthesis	100	14 of 14
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	100	8 of 8
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	vitamin B12 metabolism	79.41	27 of 34
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	chorismate metabolism	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	peptidoglycan biosynthesis	66.67	10 of 15
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	UDP-GlcNAc biosynthesis	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	purine metabolism	62.77	59 of 94
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	62.5	5 of 8
[Ref.: #66794]	pyrimidine metabolism	62.22	28 of 45
[Ref.: #66794]	phenylalanine metabolism	61.54	8 of 13
[Ref.: #66794]	glutamate and glutamine metabolism	60.71	17 of 28
[Ref.: #66794]	threonine metabolism	60	6 of 10
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	methionine metabolism	57.69	15 of 26
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	CO2 fixation in Crenarchaeota	55.56	5 of 9
[Ref.: #66794]	NAD metabolism	55.56	10 of 18
[Ref.: #66794]	non-pathway related	55.26	21 of 38
[Ref.: #66794]	flavin biosynthesis	53.33	8 of 15
[Ref.: #66794]	lipid metabolism	51.61	16 of 31
[Ref.: #66794]	isoprenoid biosynthesis	50	13 of 26
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	Entner Doudoroff pathway	50	5 of 10
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	alanine metabolism	48.28	14 of 29
[Ref.: #66794]	histidine metabolism	48.28	14 of 29
[Ref.: #66794]	leucine metabolism	46.15	6 of 13
[Ref.: #66794]	arginine metabolism	45.83	11 of 24
[Ref.: #66794]	cholesterol biosynthesis	45.45	5 of 11
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	oxidative phosphorylation	43.96	40 of 91
[Ref.: #66794]	lysine metabolism	42.86	18 of 42
[Ref.: #66794]	tryptophan metabolism	42.11	16 of 38
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	starch degradation	40	4 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	glycogen metabolism	40	2 of 5
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	L-lactaldehyde degradation	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	urea cycle	30.77	4 of 13
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	propionate fermentation	30	3 of 10
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	proline metabolism	27.27	3 of 11
[Ref.: #66794]	degradation of sugar alcohols	25	4 of 16
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	25	2 of 8
[Ref.: #66794]	carotenoid biosynthesis	22.73	5 of 22
[Ref.: #66794]	arachidonic acid metabolism	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.: #5695]	Sample type/isolated from	hypersaline lake
[Ref.: #5695]	Geographic location (country and/or sea, region)	South West Sibiria
[Ref.: #5695]	Country	Russia
[Ref.: #5695]	Country ISO 3 Code	RUS
[Ref.: #5695]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Lake (large)
#Condition	#Saline	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ469576 (>99% sequence identity) for Thiohalospira halophila subclade from Microbeatlas

Aquatic Samples	51
Soil Samples	7
Animal Samples	8
Plant Samples
Total Samples	66

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

[Ref.: #5695]

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.: #5695]	Thiohalospira halophila strain HL3 16S ribosomal RNA gene, partial sequence	DQ469576	1448	GenBank ENA	1123397 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Thiohalospira halophila DSM 15071 HL 3	GCA_900112605	scaffold	GenBank ENA	1123397 tax ID	*
[Ref.: #66792]	Thiohalospira halophila DSM 15071 strain HL3 strain HL 3	1123397.11	wgs	PATRIC	1123397 tax ID	*

[Ref.: #5695]	GC-content	65.8 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #32537]	GC-content	65.8-67 mol%

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: Thiohalospira halophila DSM 15071 HL 3 NCBI: GCA_900112605.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	99	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Thiohalospira halophila DSM 15071 HL 3 NCBI: GCA_900112605.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	99.5	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	83.287	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	63.389	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	92.46	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	91.625	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	77.601	no

Availability in culture collections External links

[Ref.: #5695]

Culture collection no.

DSM 15071, UNIQEM U219

[Ref.: #73792]

SI-ID 396792

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Thiohalospira halophila gen. nov., sp. nov. and Thiohalospira alkaliphila sp. nov., novel obligately chemolithoautotrophic, halophilic, sulfur-oxidizing gammaproteobacteria from hypersaline habitats.	Sorokin DY, Tourova TP, Muyzer G, Kuenen GJ	Int J Syst Evol Microbiol	10.1099/ijs.0.65654-0	2008	*

References

#5695

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15071

#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 )

#32537

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 #28755 (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) .

#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 )

#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 )

#73792

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-ID396792.1 )

#28755

IJSEM 1685 2008 ( DOI 10.1099/ijs.0.65654-0 , PubMed 18599717 )

* These data were automatically processed and therefore are not curated

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Thiohalospira halophila DSM 15071 HL 3

Thiohalospira halophila DSM 15071 HL 3

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