Name: Sulfodiicoccus acidiphilus HS-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140590

Type strain:

Species: Sulfodiicoccus acidiphilus

Strain Designation: HS-1

Culture col. no.: InaCC Ar79, JCM 31740

Strain history: N. Kurosawa; Fac. of Sci. & Eng., Soka Univ., Japan; HS-1.

NCBI tax ID(s): 1670455 (species)

Section

Sulfodiicoccus acidiphilus HS-1 is an aerobe, heterotroph, spore-forming archaeon that forms circular colonies and was isolated from a terrestrial acidic hot spring.

coccus-shaped
colony-forming
spore-forming
aerobe
heterotroph
thermophilic
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	*Thermoproteota*
	Class	*Thermoprotei*
	Order	*Sulfolobales*
	Family	*Sulfolobaceae*
	Genus	*Sulfodiicoccus*
	Species	**Sulfodiicoccus acidiphilus**
	Full Scientific Name (LPSN)	Sulfodiicoccus acidiphilus Sakai and Kurosawa 2017

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.926

[Ref.: #43238]	Cell width	0.8-1.5 µm

[Ref.: #43238]	Cell shape	coccus-shaped

[Ref.: #43238]	Motility	no

[Ref.: #43238]	Colony size	0.5-1.5 mm
[Ref.: #43238]	Colony color	pale yellow
[Ref.: #43238]	Colony shape	circular
[Ref.: #43238]	Cultivation medium used	MBSY

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43238]

Culture medium

MBSY

[Ref.: #43238]

Culture medium growth

[Ref.: #43238]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #43238]	optimum	65-70 °C
[Ref.: #43238]	growth	50-70 °C
[Ref.: #67770]	growth	68 °C

[Ref.: #43238]	Temperature range	thermophilic
[Ref.: #67770]	Temperature range	thermophilic
[Ref.: #69480]	Temperature range	thermophilic Confidence in %99.999

	pH	Kind of pH		pH
[Ref.: #43238]			optimum	3.0-3.5
[Ref.: #43238]			growth	1.4-5.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43238]

Oxygen tolerance

aerobe

[Ref.: #43238]

Nutrition type

heterotroph

[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.947

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43238]		NaCl		growth	0-2.5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43238]	alanine ChEBI	-	growth
[Ref.: #43238]	arabinose ChEBI	+/-	growth
[Ref.: #43238]	aspartate ChEBI	+	growth
[Ref.: #43238]	beef extract	+	growth
[Ref.: #43238]	casamino acids	+	growth
[Ref.: #43238]	cysteine ChEBI	-	growth
[Ref.: #43238]	dihydrogen ChEBI	+/-	oxidation
[Ref.: #43238]	galactose ChEBI	+	growth
[Ref.: #43238]	glucose ChEBI	+	growth
[Ref.: #43238]	glutamate ChEBI	+	growth
[Ref.: #43238]	lactose ChEBI	+	growth
[Ref.: #43238]	maltose ChEBI	+	growth
[Ref.: #43238]	peptone	+	growth
[Ref.: #43238]	raffinose ChEBI	+	growth
[Ref.: #43238]	sorbose ChEBI	-	growth
[Ref.: #43238]	sucrose ChEBI	+	growth
[Ref.: #43238]	tryptone	+	growth
[Ref.: #43238]	tryptophan ChEBI	-	growth
[Ref.: #43238]	tyrosine ChEBI	-	growth
[Ref.: #43238]	xylose ChEBI	+	growth
[Ref.: #43238]	yeast extract	+	growth
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Antibiotic resistance	Concentration
[Ref.: #43238]	ampicillin ChEBI		yes	100	µg/mL
[Ref.: #43238]	chloramphenicol ChEBI		yes	100	µg/mL
[Ref.: #43238]	elemental sulfur ChEBI	yes
[Ref.: #43238]	kanamycin ChEBI		yes	100	µg/mL

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	flavin biosynthesis	93.33	14 of 15
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	palmitate biosynthesis	86.36	19 of 22
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	creatinine degradation	80	4 of 5
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	lipoate biosynthesis	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	coenzyme A metabolism	75	3 of 4
[Ref.: #66794]	vitamin B12 metabolism	73.53	25 of 34
[Ref.: #66794]	d-xylose degradation	72.73	8 of 11
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	sulfate reduction	69.23	9 of 13
[Ref.: #66794]	purine metabolism	69.15	65 of 94
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	tryptophan metabolism	65.79	25 of 38
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	NAD metabolism	61.11	11 of 18
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	degradation of sugar acids	60	15 of 25
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	heme metabolism	57.14	8 of 14
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	carotenoid biosynthesis	54.55	12 of 22
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	degradation of pentoses	53.57	15 of 28
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	50	1 of 2
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	tetrahydrofolate metabolism	50	7 of 14
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	lysine metabolism	47.62	20 of 42
[Ref.: #66794]	oxidative phosphorylation	47.25	43 of 91
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	45.45	5 of 11
[Ref.: #66794]	4-hydroxymandelate degradation	44.44	4 of 9
[Ref.: #66794]	allantoin degradation	44.44	4 of 9
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	glutathione metabolism	42.86	6 of 14
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	histidine metabolism	41.38	12 of 29
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	isoprenoid biosynthesis	38.46	10 of 26
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	phenol degradation	35	7 of 20
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	cardiolipin biosynthesis	28.57	2 of 7
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	peptidoglycan biosynthesis	26.67	4 of 15
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	butanoate fermentation	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	23.53	4 of 17
[Ref.: #66794]	ascorbate metabolism	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.: #43238]	Sample type/isolated from	a terrestrial acidic hot spring
[Ref.: #43238]	Geographic location (country and/or sea, region)	Ohwaku-dani, Hakone, Japan
[Ref.: #43238]	Country	Japan
[Ref.: #43238]	Country ISO 3 Code	JPN
[Ref.: #43238]	Continent	Asia
[Ref.: #43238]	Geographic location	35.0000°/139.0000°

[Ref.: #67770]	Sample type/isolated from	Hot spring sample collected at a solfataric field
[Ref.: #67770]	Geographic location (country and/or sea, region)	Ohwaku-dani, Hakone
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Condition	#Acidic	-
#Condition	#Thermophilic (>45°C)	-
#Environmental	#Aquatic	#Thermal spring
#Environmental	#Terrestrial	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence LC061218 (>99% sequence identity) for Sulfodiicoccus acidiphilus subclade from Microbeatlas

Aquatic Samples	9
Soil Samples
Animal Samples
Plant Samples
Total Samples	9

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.: #43238]	16S rRNA gene sequences	LC061218	1438	ENA	1670455 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sulfodiicoccus acidiphilus JCM 31740	GCA_014648235	scaffold	GenBank	1670455 tax ID	*
[Ref.: #66792]	Sulfodiicoccus acidiphilus HS-1	GCA_003967175	complete	GenBank	1670455 tax ID	*
[Ref.: #66792]	Sulfodiicoccus acidiphilus HS-1	2788499800	complete	JGI IMG/M	1670455 tax ID	*
[Ref.: #66792]	Sulfodiicoccus acidiphilus strain JCM 31740	1670455.11	wgs	PATRIC	1670455 tax ID	*
[Ref.: #66792]	Sulfodiicoccus acidiphilus strain HS-1	1670455.8	complete	PATRIC	1670455 tax ID	*

[Ref.: #43238]	GC-content	52 mol%	genome sequence analysis
[Ref.: #67770]	GC-content	51.15 mol%	genome sequence analysis
[Ref.: #67770]	GC-content	52 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 GenomeNet Sporulation v. 1 based on: Sulfodiicoccus acidiphilus HS-1 NCBI: GCA_003967175.1
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sulfodiicoccus acidiphilus HS-1 NCBI: GCA_003967175.1
[Ref.: #69480]	motile	no	82.361	no
[Ref.: #69480]	flagellated	no	97.669	yes
[Ref.: #69480]	gram-positive	no	94.989	no
[Ref.: #69480]	anaerobic	yes	64.644	yes
[Ref.: #69480]	aerobic	no	66.556	yes
[Ref.: #69480]	halophile	no	75.433	no
[Ref.: #69480]	spore-forming	no	97.531	no
[Ref.: #69480]	thermophile	yes	100	yes
[Ref.: #69480]	glucose-util	yes	88.488	yes
[Ref.: #69480]	glucose-ferment	no	78.044	no

Availability in culture collections External links

[Ref.: #43238]

Culture collection no.

InaCC Ar79, JCM 31740

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Complete genome sequence of the Sulfodiicoccus acidiphilus strain HS-1(T), the first crenarchaeon that lacks polB3, isolated from an acidic hot spring in Ohwaku-dani, Hakone, Japan.	Sakai HD, Kurosawa N	BMC Res Notes	10.1186/s13104-019-4488-5	2019	*
Phylogeny	Sulfodiicoccus acidiphilus gen. nov., sp. nov., a sulfur-inhibited thermoacidophilic archaeon belonging to the order Sulfolobales isolated from a terrestrial acidic hot spring.	Sakai HD, Kurosawa N	Int J Syst Evol Microbiol	10.1099/ijsem.0.001881	2017	*

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 )

#43238

Hiroyuki D. Sakai and Norio Kurosawa: Sulfodiicoccus acidiphilus gen. nov., sp. nov., a sulfur-inhibited thermoacidophilic archaeon belonging to the order Sulfolobales isolated from a terrestrial acidic hot spring. IJSEM 67: 1880 - 1886 2017 ( DOI 10.1099/ijsem.0.001881 , PubMed 28629504 )

#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 )

* These data were automatically processed and therefore are not curated

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