Thiopseudomonas denitrificans (DSM 28679, CCTCC M 2013362, KCTC 42076)

Name: Thiopseudomonas denitrificans (DSM 28679, CCTCC M 2013362, KCTC 42076)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130582

Type strain

Strain Designation X2

Culture col. no. DSM 28679 CCTCC M 2013362 KCTC 42076 X2

NCBI tax ID(s) 1501432

Special Collections DSMZ KCTC

History DSMZ <- W.-B. Tan, State Key Laboratory of Urban Waste Resource and Environment, Harbin Institute of Technology, Harbin, P.R. China; X2 KCTC <- Wen-Bo TAN, Harbin Inst. Technol, China

Links

Thiopseudomonas denitrificans X2 is an aerobe bacterium that was isolated from sludge of an anaerobic, denitrifying sulfide-removal bioreactor.

aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 26177

KCTC 42076

@ref 20215

Last LPSN update 2026-05-29 08:37:24

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Pseudomonadales

Family Pseudomonadaceae

Genus Thiopseudomonas

Species Thiopseudomonas denitrificans

Full scientific name Thiopseudomonas denitrificans Tan et al. 2015

Morphology

Cell morphology

@ref	Confidence	Gram stain
125439	90.025
125439	99.291	negative
125438	98.494	negative

Multimedia

@ref:	22133
multimedia content:	DSM_28679.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_28679.jpg
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
22133	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
22133	TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)	Medium recipe at MediaDive	Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
22133	PSEUDOMONAS AGAR F (DSMZ Medium 907)	Medium recipe at MediaDive	Name: PSEUDOMONAS AGAR F (DSMZ Medium 907) Composition: Agar 15.0 g/l Glycerol 10.0 g/l Proteose peptone 10.0 g/l Tryptone 10.0 g/l MgSO4 1.5 g/l K2HPO4 1.5 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
22133	positive	growth	28
67771	positive	growth	30

Physiology and metabolism

Oxygen tolerance

67771

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125438		92.663
125439		99.95

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	-	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68369	gelatinase	-		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	formaldehyde oxidation	100	3 of 3
66794	cyanate degradation	100	3 of 3
66794	L-lactaldehyde degradation	100	3 of 3
66794	biotin biosynthesis	100	4 of 4
66794	valine metabolism	100	9 of 9
66794	palmitate biosynthesis	100	22 of 22
66794	adipate degradation	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	teichoic acid biosynthesis	100	1 of 1
66794	ubiquinone biosynthesis	100	7 of 7
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	tetrahydrofolate metabolism	100	14 of 14
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	denitrification	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	chorismate metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	propanol degradation	85.71	6 of 7
66794	phenylalanine metabolism	84.62	11 of 13
66794	vitamin B6 metabolism	81.82	9 of 11
66794	methylglyoxal degradation	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	heme metabolism	78.57	11 of 14
66794	citric acid cycle	78.57	11 of 14
66794	NAD metabolism	77.78	14 of 18
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	glutamate and glutamine metabolism	75	21 of 28
66794	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	purine metabolism	72.34	68 of 94
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	propionate fermentation	70	7 of 10
66794	alanine metabolism	68.97	20 of 29
66794	d-mannose degradation	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	proline metabolism	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	lipid metabolism	61.29	19 of 31
66794	cysteine metabolism	61.11	11 of 18
66794	lipoate biosynthesis	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	pyrimidine metabolism	57.78	26 of 45
66794	methionine metabolism	57.69	15 of 26
66794	glutathione metabolism	57.14	8 of 14
66794	aspartate and asparagine metabolism	55.56	5 of 9
66794	non-pathway related	55.26	21 of 38
66794	histidine metabolism	55.17	16 of 29
66794	lysine metabolism	54.76	23 of 42
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	leucine metabolism	53.85	7 of 13
66794	oxidative phosphorylation	53.85	49 of 91
66794	tryptophan metabolism	52.63	20 of 38
66794	polyamine pathway	52.17	12 of 23
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	Entner Doudoroff pathway	50	5 of 10
66794	selenocysteine biosynthesis	50	3 of 6
66794	sulfopterin metabolism	50	2 of 4
66794	kanosamine biosynthesis II	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	ribulose monophosphate pathway	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	butanoate fermentation	50	2 of 4
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	sulfate reduction	46.15	6 of 13
66794	pentose phosphate pathway	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	tyrosine metabolism	42.86	6 of 14
66794	arginine metabolism	41.67	10 of 24
66794	glycine metabolism	40	4 of 10
66794	starch degradation	40	4 of 10
66794	glycine betaine biosynthesis	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	urea cycle	38.46	5 of 13
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	methane metabolism	33.33	1 of 3
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	ascorbate metabolism	31.82	7 of 22
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	degradation of pentoses	28.57	8 of 28
66794	degradation of hexoses	27.78	5 of 18
66794	arachidonic acid metabolism	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	phenol degradation	25	5 of 20
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	degradation of sugar alcohols	25	4 of 16
66794	toluene degradation	25	1 of 4

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
22133	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	+
22133	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	+	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Bioreactor	-
#Environmental	#Terrestrial	#Mud (Sludge)
#Condition	#Anoxic (anaerobic)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
22133	sludge of an anaerobic, denitrifying sulfide-removal bioreactor	Northeast of China	China	CHN	Asia
67771	From sludge		China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence KJ567598 (>99% sequence identity) for Thiopseudomonas denitrificans subclade from Microbeatlas

Aquatic Samples	558
Soil Samples	276
Animal Samples	771
Plant Samples	78
Total Samples	1683

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22133	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM436303v1 assembly for Thiopseudomonas denitrificans DSM 28679	scaffold	GCA_004363035	1501432.4	2770939502	1501432	66.19
66792	ASM286606v1 assembly for Thiopseudomonas denitrificans X2	scaffold	GCA_002866065	1501432.3		1501432	63.53

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22133	Thiopseudomonas denitrificans strain X2 16S ribosomal RNA gene, partial sequence	KJ567598	1505		1501432

GC content

@ref	GC-content (mol%)	Method
22133	59	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM436303v1 assembly for Thiopseudomonas denitrificans DSM 28679
NCBI: GCA_004363035

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	87.13	no
125439	gram_stain	BacteriaNetⓘ	negative	99.29	no
125439	motility	BacteriaNetⓘ	yes	90.03	no
125439	spore_formation	BacteriaNetⓘ	no	99.95	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Thiopseudomonas denitrificans DSM 28679
NCBI: GCA_004363035.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.49	no
125438	anaerobic	anaerobicⓘ	no	85.07	no
125438	aerobic	aerobicⓘ	yes	58.79	no
125438	spore-forming	spore-formingⓘ	no	92.66	no
125438	thermophilic	thermophileⓘ	no	96.92	yes
125438	flagellated	motile2+ⓘ	yes	76.96	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Comparative genomic analysis of an emerging Pseudomonadaceae member, Thiopseudomonas alkaliphila.	Burcham ZM.	Microbiol Spectr	10.1128/spectrum.04157-23	2024
Phylogeny	Thiopseudomonas denitrificans gen. nov., sp. nov., isolated from anaerobic activated sludge.	Tan WB, Jiang Z, Chen C, Yuan Y, Gao LF, Wang HF, Cheng J, Li WJ, Wang AJ	Int J Syst Evol Microbiol	10.1099/ijs.0.064634-0	2014

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 )
#22133	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28679
#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 )
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68369	Automatically annotated from API 20NE .
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#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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Thiopseudomonas denitrificans (DSM 28679, CCTCC M 2013362, KCTC 42076)

Name and taxonomic classification

Morphology

Cell morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004363035

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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