Dethiosulfatarculus sandiegensis (DSM 100305, JCM 30857, SPR)

Name: Dethiosulfatarculus sandiegensis (DSM 100305, JCM 30857, SPR)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132452

Type strain

Strain Designation SPR

Culture col. no. DSM 100305 JCM 30857 SPR

NCBI tax ID(s) 1429043

Special Collections DSMZ JCM Literature strains

History <- I. Davidova, University of Oklahoma, Department of Botany and Microbiology, Norman, USA; SPR <- I. Davidova; {2011} I. Davidova; Dept. of Microbiol. & Plant Biol., Univ. of Oklahoma, USA; SPR.

Links

Dethiosulfatarculus sandiegensis SPR is an obligate anaerobe, chemoorganotroph, motile bacterium that forms circular colonies and was isolated from long-chain-paraffin-degrading consortium enriched from marine sediments.

motile vibrio-shaped colony-forming obligate anaerobe chemoorganotroph genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 404099

JCM 30857,DSM 100305

@ref 20215

Last LPSN update 2026-02-09 11:31:43

Domain Bacteria

Phylum Thermodesulfobacteriota

Class Desulfarculia

Order Desulfarculales

Family Desulfarculaceae

Genus Dethiosulfatarculus

Species Dethiosulfatarculus sandiegensis

Full scientific name Dethiosulfatarculus sandiegensis Davidova et al. 2016

Morphology

Cell morphology

@ref	Cell shape	Motility	Gram stain	Confidence
43713	vibrio-shaped
125439			negative	99.3

Colony morphology

@ref	Colony color	Colony shape	Incubation period	Medium used
43713	Opaque	circular	20 days	Basal reduced, sulfat-free, bicarbonate-buffered, seawater mineral medium

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
43713	Basal reduced, sulfat-free, bicarbonate-buffered, seawater mineral medium
24241	DESULFOBACTERIUM MEDIUM (DSMZ Medium 383)		Medium recipe at MediaDive	Name: DESULFOBACTERIUM MEDIUM (DSMZ Medium 383; with strain-specific modifications) Composition: NaCl 20.9372 g/l Na2SO4 2.99103 g/l MgCl2 x 6 H2O 2.99103 g/l Na-pyruvate 2.19342 g/l Na2CO3 0.997009 g/l KCl 0.498504 g/l Na2S x 9 H2O 0.398804 g/l NH4Cl 0.299103 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149551 g/l Yeast extract 0.0997009 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498504 g/l NaOH 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Riboflavin 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Folic acid 1.99402e-05 g/l Biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
24241	positive	growth	30
43713	positive	growth	15-45
43713	positive	optimum	30-37
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH
43713	positive	optimum	6-7.2
43713	positive	growth	5.8-8

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
43713	obligate anaerobe
125439	anaerobe	98.9

Nutrition type

43713

Typechemoorganotroph

Spore formation

@ref	Spore formation	Confidence
125439		98.3

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43713	NaCl	positive	minimum	10 g/L
43713	NaCl	positive	optimum	30-60 g/L

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43713	30089 ChEBI	acetate	-	electron donor
43713	33403 ChEBI	elemental sulfur	+	respiration
43713	15740 ChEBI	formate	-	electron donor
43713	17272 ChEBI	propionate	-	electron donor
43713	15361 ChEBI	pyruvate	+	electron donor
43713	26710 ChEBI	sodium chloride	+	required for growth
43713	16189 ChEBI	sulfate	-	electron acceptor
43713	16189 ChEBI	sulfate	-	reduction
43713	17359 ChEBI	sulfite	-	electron acceptor
43713	17359 ChEBI	sulfite	-	reduction
43713	16094 ChEBI	thiosulfate	+	electron acceptor

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	coenzyme A metabolism	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	methanofuran biosynthesis	100	5 of 5
66794	CMP-KDO biosynthesis	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	ribulose monophosphate pathway	100	2 of 2
66794	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	glycolate and glyoxylate degradation	100	6 of 6
66794	pentose phosphate pathway	100	11 of 11
66794	adipate degradation	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	benzoyl-CoA degradation	100	7 of 7
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	folate polyglutamylation	100	1 of 1
66794	ppGpp biosynthesis	100	4 of 4
66794	valine metabolism	100	9 of 9
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	biotin biosynthesis	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	threonine metabolism	90	9 of 10
66794	propionate fermentation	90	9 of 10
66794	serine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	87.5	7 of 8
66794	palmitate biosynthesis	86.36	19 of 22
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	propanol degradation	85.71	6 of 7
66794	phenylalanine metabolism	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	alanine metabolism	82.76	24 of 29
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	purine metabolism	81.91	77 of 94
66794	cellulose degradation	80	4 of 5
66794	lipoate biosynthesis	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	photosynthesis	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	nitrate assimilation	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	vitamin B12 metabolism	76.47	26 of 34
66794	degradation of aromatic, nitrogen containing compounds	75	9 of 12
66794	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	gluconeogenesis	75	6 of 8
66794	flavin biosynthesis	73.33	11 of 15
66794	methionine metabolism	73.08	19 of 26
66794	vitamin B6 metabolism	72.73	8 of 11
66794	proline metabolism	72.73	8 of 11
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	citric acid cycle	71.43	10 of 14
66794	pyrimidine metabolism	71.11	32 of 45
66794	glycolysis	70.59	12 of 17
66794	starch degradation	70	7 of 10
66794	cysteine metabolism	66.67	12 of 18
66794	methane metabolism	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	NAD metabolism	66.67	12 of 18
66794	lysine metabolism	66.67	28 of 42
66794	molybdenum cofactor biosynthesis	66.67	6 of 9
66794	oxidative phosphorylation	65.93	60 of 91
66794	tryptophan metabolism	65.79	25 of 38
66794	histidine metabolism	65.52	19 of 29
66794	polyamine pathway	65.22	15 of 23
66794	lipid metabolism	64.52	20 of 31
66794	heme metabolism	64.29	9 of 14
66794	non-pathway related	63.16	24 of 38
66794	urea cycle	61.54	8 of 13
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	glycogen metabolism	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	degradation of sugar alcohols	56.25	9 of 16
66794	sulfate reduction	53.85	7 of 13
66794	degradation of pentoses	53.57	15 of 28
66794	Entner Doudoroff pathway	50	5 of 10
66794	carnitine metabolism	50	4 of 8
66794	glutathione metabolism	50	7 of 14
66794	kanosamine biosynthesis II	50	1 of 2
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	lactate fermentation	50	2 of 4
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	denitrification	50	1 of 2
66794	coenzyme M biosynthesis	50	5 of 10
66794	selenocysteine biosynthesis	50	3 of 6
66794	phenylmercury acetate degradation	50	1 of 2
66794	vitamin E metabolism	50	2 of 4
66794	ketogluconate metabolism	50	4 of 8
66794	ethanol fermentation	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	arginine metabolism	50	12 of 24
66794	glycine metabolism	50	5 of 10
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	metabolism of disaccharids	45.45	5 of 11
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	allantoin degradation	44.44	4 of 9
66794	degradation of hexoses	44.44	8 of 18
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	methanogenesis from CO2	41.67	5 of 12
66794	vitamin K metabolism	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	phenylacetate degradation (aerobic)	40	2 of 5
66794	4-hydroxyphenylacetate degradation	40	4 of 10
66794	gallate degradation	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	d-xylose degradation	36.36	4 of 11
66794	tyrosine metabolism	35.71	5 of 14
66794	phenol degradation	35	7 of 20
66794	cyanate degradation	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	degradation of sugar acids	32	8 of 25
66794	ascorbate metabolism	31.82	7 of 22
66794	myo-inositol biosynthesis	30	3 of 10
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	toluene degradation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17
66794	chlorophyll metabolism	22.22	4 of 18

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Laboratory	#Lab enrichment
#Condition	#Anoxic (anaerobic)	-
#Engineered	#Industrial	-
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
24241	long-chain-paraffin-degrading consortium enriched from marine sediments	California, San Diego Bay	USA	USA	North America
43713	A methanogenic, long-chain-paraffin-degrading cosortium enriched from marine sediments of San Diego Bay	San Diego Bay, California	USA	USA	North America
67770	Methanogenic long-chain-paraffin-degrading consortium enriched from marine sediments of San Diego Bay

Taxonmaps

69479

Global distribution of 16S sequence KP868755 (>99% sequence identity) for Dethiosulfatarculus sandiegensis subclade from Microbeatlas

Aquatic Samples	463
Soil Samples	37
Animal Samples	96
Plant Samples	5
Total Samples	601

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24241	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM93193v2 assembly for Dethiosulfatarculus sandiegensis SPR	scaffold	GCA_000931935	1429043.4	2627853875	1429043	57.62

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24241	Dethiosulfatarculus sandiegensis strain SPR 16S ribosomal RNA gene, partial sequence	KP868755	1516		1429043

GC content

@ref	GC-content (mol%)	Method
43713	52.02
24241	52.02	sequence analysis
67770	52.02	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Dethiosulfatarculus sandiegensis SPR
NCBI: GCA_000931935

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.30	no
125439	motility	BacteriaNetⓘ	no	54.70	no
125439	gram_stain	BacteriaNetⓘ	negative	99.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	98.90	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Discovered by genomics: putative reductive dehalogenases with N-terminus transmembrane helixes.	Atashgahi S.	FEMS Microbiol Ecol	10.1093/femsec/fiz048	2019
	Identifying a key spot for electron mediator-interaction to tailor CO dehydrogenase's affinity.	Kim SM, Kang SH, Lee J, Heo Y, Poloniataki EG, Kang J, Yoon HJ, Kong SY, Yun Y, Kim H, Ryu J, Lee HH, Kim YH.	Nat Commun	10.1038/s41467-024-46909-1	2024
	Anaerobic degradation of organic carbon supports uncultured microbial populations in estuarine sediments.	Yu T, Wu W, Liang W, Wang Y, Hou J, Chen Y, Elvert M, Hinrichs KU, Wang F.	Microbiome	10.1186/s40168-023-01531-z	2023
Genetics	Single-Cell Genomics Reveals a Diverse Metabolic Potential of Uncultivated Desulfatiglans-Related Deltaproteobacteria Widely Distributed in Marine Sediment.	Jochum LM, Schreiber L, Marshall IPG, Jorgensen BB, Schramm A, Kjeldsen KU.	Front Microbiol	10.3389/fmicb.2018.02038	2018
Metabolism	A Heterodimeric Reduced-Ferredoxin-Dependent Methylenetetrahydrofolate Reductase from Syngas-Fermenting Clostridium ljungdahlii.	Yi J, Huang H, Liang J, Wang R, Liu Z, Li F, Wang S.	Microbiol Spectr	10.1128/spectrum.00958-21	2021
Phylogeny	Dethiosulfatarculus sandiegensis gen. nov., sp. nov., isolated from a methanogenic paraffin-degrading enrichment culture and emended description of the family Desulfarculaceae.	Davidova IA, Wawrik B, Callaghan AV, Duncan K, Marks CR, Suflita JM	Int J Syst Evol Microbiol	10.1099/ijsem.0.000864	2015

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 )
#24241	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100305
#43713	Irene A. Davidova, Boris Wawrik, Amy V. Callaghan, Kathleen Duncan, Christopher R. Marks, Joseph M. Suflita: Dethiosulfatarculus sandiegensis gen. nov., sp. nov., isolated from a methanogenic paraffin-degrading enrichment culture and emended description of the family Desulfarculaceae. IJSEM 66: 1242 - 1248 2016 ( DOI 10.1099/ijsem.0.000864 , PubMed 26704417 )
#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 .
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Dethiosulfatarculus sandiegensis (DSM 100305, JCM 30857, SPR)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Nutrition type

Spore formation

Halophily

Metabolite utilization

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000931935

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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