Thiobacillus denitrificans (DSM 739, GP3)

Name: Thiobacillus denitrificans (DSM 739, GP3)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6141

Type strain

Strain Designation GP3

Culture col. no. DSM 739 GP3

NCBI tax ID(s) 36861

Special Collections DSMZ

History <- H. Hippe, GP3

Links

Thiobacillus denitrificans GP3 is a facultative anaerobe, mesophilic prokaryote that was isolated from pond water.

facultative anaerobe mesophilic 16S sequence

Name and taxonomic classification

SI-ID 47267

DSM 739

@ref 20215

Last LPSN update 2026-02-09 11:19:08

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Spirillales

Family Thiobacillaceae

Genus Thiobacillus

Species Thiobacillus denitrificans

Full scientific name Thiobacillus denitrificans (ex Beijerinck 1904) Kelly and Harrison 1989

Synonyms (1)

"Thiobacillus denitrificans"

BacDive ID	Other strains from **Thiobacillus denitrificans** (3)	Type strain
6143	T. denitrificans AB7, DSM 12475, ATCC 23644, JCM 3870, NCIMB ... (type strain)
6142	T. denitrificans RT, DSM 807, ATCC 29685
164863	T. denitrificans JCM 3869, ATCC 23642, BCRC 13020, NCIMB 9546

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
382	THIOBACILLUS DENITRIFICANS MEDIUM (DSMZ Medium 113)		Medium recipe at MediaDive	Name: THIOBACILLUS DENITRIFICANS MEDIUM (DSMZ Medium 113) Composition: Agar 14.9551 g/l (optional) Na2S2O3 x 5 H2O 4.98504 g/l KH2PO4 1.99402 g/l KNO3 1.99402 g/l NaHCO3 0.997009 g/l NH4Cl 0.997008 g/l MgSO4 x 7 H2O 0.797607 g/l FeSO4 x 7 H2O 0.00199402 g/l Na2-EDTA 0.000997009 g/l H3BO3 0.000598205 g/l CoCl2 x 6 H2O 0.000398804 g/l ZnSO4 x 7 H2O 0.000199402 g/l MnCl2 x 4 H2O 5.98205e-05 g/l Na2MoO4 x 2 H2O 5.98205e-05 g/l NiCl2 x 6 H2O 3.98804e-05 g/l CuCl2 x 2 H2O 1.99402e-05 g/l H2SO4 Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
382	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

382

Oxygen tolerancefacultative anaerobe

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	photosynthesis	100	14 of 14
66794	formaldehyde oxidation	100	3 of 3
66794	cardiolipin biosynthesis	100	7 of 7
66794	biotin biosynthesis	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	denitrification	100	2 of 2
66794	ubiquinone biosynthesis	100	7 of 7
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	lipid A biosynthesis	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	NAD metabolism	83.33	15 of 18
66794	pentose phosphate pathway	81.82	9 of 11
66794	hydrogen production	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	starch degradation	80	8 of 10
66794	threonine metabolism	80	8 of 10
66794	glycogen metabolism	80	4 of 5
66794	heme metabolism	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	d-mannose degradation	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	leucine metabolism	76.92	10 of 13
66794	vitamin B1 metabolism	76.92	10 of 13
66794	purine metabolism	75.53	71 of 94
66794	isoleucine metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	metabolism of disaccharids	72.73	8 of 11
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	Entner Doudoroff pathway	70	7 of 10
66794	acetoin degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	pyrimidine metabolism	66.67	30 of 45
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	glutathione metabolism	64.29	9 of 14
66794	citric acid cycle	64.29	9 of 14
66794	vitamin B6 metabolism	63.64	7 of 11
66794	proline metabolism	63.64	7 of 11
66794	ketogluconate metabolism	62.5	5 of 8
66794	gluconeogenesis	62.5	5 of 8
66794	flavin biosynthesis	60	9 of 15
66794	lipoate biosynthesis	60	3 of 5
66794	cellulose degradation	60	3 of 5
66794	alanine metabolism	58.62	17 of 29
66794	non-pathway related	57.89	22 of 38
66794	urea cycle	53.85	7 of 13
66794	lysine metabolism	52.38	22 of 42
66794	histidine metabolism	51.72	15 of 29
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	ethanol fermentation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	butanoate fermentation	50	2 of 4
66794	propionate fermentation	50	5 of 10
66794	degradation of sugar alcohols	50	8 of 16
66794	suberin monomers biosynthesis	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	phenylmercury acetate degradation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	arginine metabolism	50	12 of 24
66794	cysteine metabolism	50	9 of 18
66794	methionine metabolism	50	13 of 26
66794	tyrosine metabolism	50	7 of 14
66794	lipid metabolism	48.39	15 of 31
66794	sulfate reduction	46.15	6 of 13
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	oxidative phosphorylation	46.15	42 of 91
66794	cholesterol biosynthesis	45.45	5 of 11
66794	tryptophan metabolism	44.74	17 of 38
66794	nitrate assimilation	44.44	4 of 9
66794	vitamin B12 metabolism	41.18	14 of 34
66794	arachidonate biosynthesis	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	degradation of sugar acids	36	9 of 25
66794	degradation of pentoses	35.71	10 of 28
66794	polyamine pathway	34.78	8 of 23
66794	IAA biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	pantothenate biosynthesis	33.33	2 of 6
66794	degradation of hexoses	33.33	6 of 18
66794	sulfoquinovose degradation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	coenzyme M biosynthesis	30	3 of 10
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	d-xylose degradation	27.27	3 of 11
66794	ascorbate metabolism	27.27	6 of 22
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	vitamin E metabolism	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	androgen and estrogen metabolism	25	4 of 16
66794	carotenoid biosynthesis	22.73	5 of 22

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Pond (small)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
382	pond water	Göttingen	Germany	DEU	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
382	1	Risk group (German classification) According to TRBA 466

Sequence information

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Thiobacillus denitrificans strain DSM 739 16S ribosomal RNA gene, partial sequence	DQ407816	718		36861

Genome-based predictions

Literature

References

#382	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 739
#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 )
#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 )
#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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