Alicycliphilus denitrificans (DSM 14773, CIP 107495, CCUG 64014)

Name: Alicycliphilus denitrificans (DSM 14773, CIP 107495, CCUG 64014)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2906

Type strain

Strain Designation K601

Culture col. no. DSM 14773 CIP 107495 CCUG 64014 K601

NCBI tax ID(s) 596154 179636

Special Collections DSMZ CCUG CIP

History DSMZ <- G. Fuchs; K601 CIP <- 2002, DSMZ <- G. Fuchs: strain K601

Links

Alicycliphilus denitrificans K601 is an aerobe, Gram-negative, motile bacterium that was isolated from anaerobic sewage sludge.

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

Name and taxonomic classification

SI-ID 100492

CIP 107495,DSM 14773,CCUG 64014

@ref 20215

Last LPSN update 2026-05-29 08:25:34

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Comamonadaceae

Genus Alicycliphilus

Species Alicycliphilus denitrificans

Full scientific name Alicycliphilus denitrificans Mechichi et al. 2003

BacDive ID	Other strains from **Alicycliphilus denitrificans** (2)	Type strain
2907	A. denitrificans BC, DSM 18852, JCM 14587
2924	A. denitrificans JS100, DSM 6838, CCM 7239

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
118891	negative	rod-shaped
125439	negative		98.707
125438	negative		97

Pigmentation

@ref	Production	Name
118891		Pyocyanin

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
5533	R2A MEDIUM (DSMZ Medium 830)	Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
5533	MINERAL MEDIUM PH 7.25 (DSMZ Medium 465)	Medium recipe at MediaDive	Name: MINERAL MEDIUM PH 7.25 (DSMZ Medium 465; with strain-specific modifications) Composition: Na2HPO4 x 2 H2O 3.5 g/l KH2PO4 1.0 g/l (NH4)2SO4 0.5 g/l None 0.1 g/l MgCl2 x 6 H2O 0.1 g/l Ca(NO3)2 x 4 H2O 0.05 g/l Na2-EDTA 0.0005 g/l H3BO3 0.0003 g/l FeSO4 x 7 H2O 0.0002 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Distilled water
5533	THAUERA AROMATICA MEDIUM (DSMZ Medium 586)	Medium recipe at MediaDive	Name: THAUERA AROMATICA MEDIUM (DSMZ Medium 586) Composition: K2HPO4 5.83251 g/l KNO3 1.97044 g/l KH2PO4 0.803941 g/l Na-benzoate 0.70936 g/l NH4Cl 0.522168 g/l MgSO4 x 7 H2O 0.197044 g/l CaCl2 x 2 H2O 0.0246305 g/l HCl 0.0246305 g/l FeCl2 x 4 H2O 0.0147783 g/l CoCl2 x 6 H2O 0.00187192 g/l MnCl2 x 4 H2O 0.000985222 g/l ZnCl2 0.000689655 g/l Na2MoO4 x 2 H2O 0.00035468 g/l p-Aminobenzoic acid 0.000246305 g/l alpha-lipoic acid 0.000246305 g/l Riboflavin 0.000246305 g/l Pantothenic acid 0.000246305 g/l Vitamin B12 0.000246305 g/l Thiamine-HCl x 2 H2O 0.000246305 g/l NiCl2 x 6 H2O 0.000236453 g/l Nicotine amide 0.000123153 g/l Nicotinic acid 0.000123153 g/l Folic acid 9.85222e-05 g/l Biotin 9.85222e-05 g/l H3BO3 5.91133e-05 g/l Pyridoxamine hydrochloride 4.92611e-05 g/l CuCl2 x 2 H2O 1.97044e-05 g/l Distilled water
34065	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118891	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
5533	positive	growth	28
34065	positive	growth	30
63060	positive	growth	30
118891	positive	growth	25-41
118891	negative	growth	5
118891	negative	growth	10

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
63060	aerobe
118891	obligate aerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.816
125438		90.345

Compound production

5533

Compoundhydratase and alcohol dehydrogenase, bifunctional molybdoenzyme

Halophily

@ref	Salt	Growth	Tested relation	Concentration
118891	NaCl	positive	growth	0-2 %
118891	NaCl		growth	4 %
118891	NaCl		growth	6 %
118891	NaCl		growth	8 %
118891	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
118891	16947 ChEBI	citrate	-	carbon source
118891	4853 ChEBI	esculin	-	hydrolysis
118891	17632 ChEBI	nitrate	+	reduction
118891	17632 ChEBI	nitrate	+	respiration
118891	16301 ChEBI	nitrite	+	reduction

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
118891	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
118891	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
118891	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
118891	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
118891	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
118891	caseinase	-	3.4.21.50
118891	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
118891	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
118891	gelatinase	-
118891	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
118891	lipase	-
68382	lipase (C 14)	-		from API zym
118891	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
118891	ornithine decarboxylase	-	4.1.1.17
118891	oxidase	+
118891	protease	-
68382	trypsin	-	3.4.21.4	from API zym
118891	tryptophan deaminase	-
118891	tween esterase	-
118891	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	denitrification	100	2 of 2
66794	cardiolipin biosynthesis	100	7 of 7
66794	ethylmalonyl-CoA pathway	100	5 of 5
66794	gallate degradation	100	5 of 5
66794	palmitate biosynthesis	100	22 of 22
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	valine metabolism	100	9 of 9
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	aerobactin biosynthesis	100	1 of 1
66794	taurine degradation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	lactate fermentation	100	4 of 4
66794	propanol degradation	100	7 of 7
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	ethanol fermentation	100	2 of 2
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	citric acid cycle	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	leucine metabolism	92.31	12 of 13
66794	propionate fermentation	90	9 of 10
66794	Entner Doudoroff pathway	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	phenol degradation	85	17 of 20
66794	vitamin B1 metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	purine metabolism	82.98	78 of 94
66794	proline metabolism	81.82	9 of 11
66794	3-chlorocatechol degradation	80	4 of 5
66794	methylglyoxal degradation	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	heme metabolism	78.57	11 of 14
66794	glutathione metabolism	78.57	11 of 14
66794	lysine metabolism	78.57	33 of 42
66794	allantoin degradation	77.78	7 of 9
66794	nitrate assimilation	77.78	7 of 9
66794	histidine metabolism	75.86	22 of 29
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	pentose phosphate pathway	72.73	8 of 11
66794	alanine metabolism	72.41	21 of 29
66794	tyrosine metabolism	71.43	10 of 14
66794	glycolysis	70.59	12 of 17
66794	urea cycle	69.23	9 of 13
66794	methionine metabolism	69.23	18 of 26
66794	lipid metabolism	67.74	21 of 31
66794	methane metabolism	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	octane oxidation	66.67	2 of 3
66794	4-hydroxymandelate degradation	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	pyrimidine metabolism	66.67	30 of 45
66794	tryptophan metabolism	65.79	25 of 38
66794	oxidative phosphorylation	64.84	59 of 91
66794	vitamin B6 metabolism	63.64	7 of 11
66794	ketogluconate metabolism	62.5	5 of 8
66794	arginine metabolism	62.5	15 of 24
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	cysteine metabolism	61.11	11 of 18
66794	vitamin K metabolism	60	3 of 5
66794	4-hydroxyphenylacetate degradation	60	6 of 10
66794	3-phenylpropionate degradation	60	9 of 15
66794	lipoate biosynthesis	60	3 of 5
66794	non-pathway related	57.89	22 of 38
66794	benzoyl-CoA degradation	57.14	4 of 7
66794	androgen and estrogen metabolism	56.25	9 of 16
66794	degradation of sugar alcohols	56.25	9 of 16
66794	degradation of sugar acids	56	14 of 25
66794	d-mannose degradation	55.56	5 of 9
66794	ribulose monophosphate pathway	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	toluene degradation	50	2 of 4
66794	myo-inositol biosynthesis	50	5 of 10
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	phenylmercury acetate degradation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	biotin biosynthesis	50	2 of 4
66794	glycogen biosynthesis	50	2 of 4
66794	quinate degradation	50	1 of 2
66794	degradation of hexoses	50	9 of 18
66794	vitamin B12 metabolism	47.06	16 of 34
66794	sulfate reduction	46.15	6 of 13
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	metabolism of disaccharids	45.45	5 of 11
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	arachidonate biosynthesis	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	polyamine pathway	39.13	9 of 23
66794	carotenoid biosynthesis	36.36	8 of 22
66794	ascorbate metabolism	36.36	8 of 22
66794	cholesterol biosynthesis	36.36	4 of 11
66794	bile acid biosynthesis, neutral pathway	35.29	6 of 17
66794	IAA biosynthesis	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	enterobactin biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	degradation of pentoses	32.14	9 of 28
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	cyclohexanol degradation	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	daunorubicin biosynthesis	22.22	2 of 9

Fatty acid profile

Metadata FA analysis

@ref

63060

Fatty acid	Percentage	ECL
C16:1 ω7c	40.7	15.819
C16:0	28.9	16
C18:1 ω7c /12t/9t	7.7	17.824
Unidentified	5.6	11.412
C17:0 CYCLO	5.3	16.888
C12:0	4.5	12
unk. 18.846/19:1 ω6c	2.4	18.846
Unidentified	1.5	16.29
C15:0	1.2	15
C15:0 ISO 3OH	0.9	16.135
11 methyl 18:1 ω7c	0.8	18.081
C14:0	0.6	14

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
118891	-	+	+	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
118891	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	+	-	+	-	-	-	+	+	+	+	-	-	-	-	+	+	+	+	+	-	+	-	-	+	+	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Waste	#Sewage sludge
#Condition	#Anoxic (anaerobic)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
5533	anaerobic sewage sludge	Konstanz	Germany	DEU	Europe
63060	Anaerobic sewage sludge	München	Germany	DEU	Europe
118891	Environment, Anaerobic sewage sludge		Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence AJ418042 (>99% sequence identity) for Alicycliphilus denitrificans subclade from Microbeatlas

Aquatic Samples	1420
Soil Samples	74
Animal Samples	282
Plant Samples	50
Total Samples	1826

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5533	1	Risk group (German classification) According to TRBA 466
118891	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM20464v1 assembly for Alicycliphilus denitrificans K601	complete	GCA_000204645	596154.3	650716008	596154	98.2

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
5533	Beta proteobacterium K601 16S rRNA gene, strain K601	AJ418042	1502		596154

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM20464v1 assembly for Alicycliphilus denitrificans K601
BV-BRC: 596154.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	89.55	no
125439	gram_stain	BacteriaNetⓘ	negative	98.71	no
125439	motility	BacteriaNetⓘ	yes	82.92	no
125439	spore_formation	BacteriaNetⓘ	no	99.82	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Alicycliphilus denitrificans K601 K601
NCBI: GCA_000204645.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.00	no
125438	anaerobic	anaerobicⓘ	no	96.00	yes
125438	aerobic	aerobicⓘ	yes	80.11	yes
125438	spore-forming	spore-formingⓘ	no	90.35	no
125438	thermophilic	thermophileⓘ	no	95.67	no
125438	flagellated	motile2+ⓘ	yes	84.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Metabolic mechanism of Cr(VI) pollution remediation by Alicycliphilus denitrificans Ylb10.	Wang Y, Zhou Z, Zhang W, Guo J, Li N, Zhang Y, Gong D, Lyu Y.	Sci Total Environ	10.1016/j.scitotenv.2023.169135	2024
	Granular activated carbon (GAC)-driven microbial electron shuttle boosts denitrification and mitigates N₂O in cold and carbon-limited biofilm system.	Yang X, Yao M, Li P, van der Hoek JP, Zhang L, Liu G.	Microbiome	10.1186/s40168-025-02161-3	2025
	Exploring the Functions of Efficient Canonical Denitrifying Bacteria as N₂O Sinks: Implications from ¹⁵N Tracer and Transcriptome Analyses.	Oba K, Suenaga T, Kuroiwa M, Riya S, Terada A.	Environ Sci Technol	10.1021/acs.est.2c02119	2022
	Rational design of a cyclohexanone dehydrogenase for enhanced alpha,beta-desaturation and substrate specificity.	Singh W, Brown NL, McCue HV, Marriott SR, Wilson RC, Perry J, Turkenburg JP, Dubey KD, Prior SH, Carnell AJ, Taylor EJ, Black GW.	Chem Sci	10.1039/d3sc04009g	2024
	Nitric oxide and nitrite removal by partial denitrifying hollow-fiber membrane biofilm reactor coupled with nitrous oxide generation as energy recovery.	Yu KH, Can F, Ergenekon P.	Environ Technol	10.1080/09593330.2021.1910348	2022
	Metagenomic analysis of blood microbiota alterations: insights into HIV progression and immune restoration.	Chen Y, Zhang R, Wen J, Zhao J, Zhang J.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1619059	2025
Genetics	Metagenomic Analysis of Surface Waters and Wastewater in the Colombian Andean Highlands: Implications for Health and Disease.	Urrea V, Paez-Triana L, Velasquez-Ortiz N, Camargo M, Patino LH, Vega L, Ballesteros N, Hidalgo-Troya A, Galeano LA, Ramirez JD, Munoz M.	Curr Microbiol	10.1007/s00284-024-04019-7	2025
	Longitudinal analysis of exposure to a low concentration of oxytetracycline on the zebrafish gut microbiome.	Kayani MUR, Yu K, Qiu Y, Yu X, Chen L, Huang L.	Front Microbiol	10.3389/fmicb.2022.985065	2022
Metabolism	Comprehensive evaluation of autohydrogenotrophic membrane biofilm reactor treating OTC-enriched water medium.	Celik A, Tunc MS, Hanay O, Taskan E, Hasar H.	Bioprocess Biosyst Eng	10.1007/s00449-018-1954-8	2018
	Groundwater chromate removal by autotrophic sulfur disproportionation.	Qiu YY, Xia J, Guo J, Gong X, Zhang L, Jiang F.	Environ Sci Ecotechnol	10.1016/j.ese.2024.100399	2024
Metabolism	Comparison of bacterial community characteristics between complete and shortcut denitrification systems for quinoline degradation.	Zhang X, Hua X, Yue X.	Appl Microbiol Biotechnol	10.1007/s00253-016-7949-y	2017
Pathogenicity	Effects of toxic organic flotation reagent (aniline aerofloat) on an A/O submerged membrane bioreactor (sMBR): Microbial community dynamics and performance.	Lin W, Sun S, Wu C, Xu P, Ye Z, Zhuang S.	Ecotoxicol Environ Saf	10.1016/j.ecoenv.2017.03.033	2017
Enzymology	Hydrogen-based membrane biofilm reactor for tetracycline removal: biodegradation, transformation products, and microbial community.	Taskan B, Hanay O, Taskan E, Erdem M, Hasar H.	Environ Sci Pollut Res Int	10.1007/s11356-016-7370-1	2016
Metabolism	Metabolic response of Alicycliphilus denitrificans strain BC toward electron acceptor variation.	Oosterkamp MJ, Boeren S, Plugge CM, Schaap PJ, Stams AJ.	Proteomics	10.1002/pmic.201200571	2013
Genetics	Microbial paracetamol degradation involves a high diversity of novel amidase enzyme candidates.	Rios-Miguel AB, Smith GJ, Cremers G, van Alen T, Jetten MSM, Op den Camp HJM, Welte CU.	Water Res X	10.1016/j.wroa.2022.100152	2022
Metabolism	Toluene biodegradation rates in unsaturated soil systems versus liquid batches and their relevance to field conditions.	Picone S, Grotenhuis T, van Gaans P, Valstar J, Langenhoff A, Rijnaarts H.	Appl Microbiol Biotechnol	10.1007/s00253-012-4480-7	2013
	Transformation of microflora during degradation of gaseous toluene in a biofilter detected using PCR-DGGE.	Okunishi S, Morita Y, Higuchi T, Maeda H, Nishi K.	J Air Waste Manag Assoc	10.1080/10962247.2012.672396	2012
Metabolism	Chlorate reduction capacity and characterisation of chlorate reducing bacteria communities in sediments of the rio Cruces wetland in southern Chile.	Schwarz AO, Urrutia H, Vidal JM, Perez N.	Water Res	10.1016/j.watres.2012.03.046	2012
	Electrochemical and Microbial Dissection of Electrified Biotrickling Filters.	Korth B, Pous N, Honig R, Haus P, Correa FB, Nunes da Rocha U, Puig S, Harnisch F.	Front Microbiol	10.3389/fmicb.2022.869474	2022
	Inoculation effect of Pseudomonas sp. TF716 on N₂O emissions during rhizoremediation of diesel-contaminated soil.	Kim JY, Cho KS.	Sci Rep	10.1038/s41598-022-17356-z	2022
	A cross-sectional study identifying disparities in serum metabolic profiles among hypertensive patients with ISH, IDH and SDH subtypes.	Shen Y, Wang P, Yang X, Chen M, Dong Y, Li J.	Front Cardiovasc Med	10.3389/fcvm.2023.1102754	2023
Genetics	Genomic Analysis of Carbapenem-Resistant Comamonas in Water Matrices: Implications for Public Health and Wastewater Treatments.	Hem S, Wyrsch ER, Drigo B, Baker DJ, Charles IG, Donner E, Jarocki VM, Djordjevic SP.	Appl Environ Microbiol	10.1128/aem.00646-22	2022
Metabolism	Nitrate-dependent degradation of acetone by Alicycliphilus and Paracoccus strains and comparison of acetone carboxylase enzymes.	Dullius CH, Chen CY, Schink B.	Appl Environ Microbiol	10.1128/aem.05385-11	2011
Enzymology	Michael hydratase alcohol dehydrogenase or just alcohol dehydrogenase?	Resch V, Jin J, Chen BS, Hanefeld U.	AMB Express	10.1186/s13568-014-0030-2	2014
	Inducible gene expression system by 3-hydroxypropionic acid.	Zhou S, Ainala SK, Seol E, Nguyen TT, Park S.	Biotechnol Biofuels	10.1186/s13068-015-0353-5	2015
Genetics	Genome analysis and physiological comparison of Alicycliphilus denitrificans strains BC and K601(T.).	Oosterkamp MJ, Veuskens T, Talarico Saia F, Weelink SA, Goodwin LA, Daligault HE, Bruce DC, Detter JC, Tapia R, Han CS, Land ML, Hauser LJ, Langenhoff AA, Gerritse J, van Berkel WJ, Pieper DH, Junca H, Smidt H, Schraa G, Davids M, Schaap PJ, Plugge CM, Stams AJ.	PLoS One	10.1371/journal.pone.0066971	2013
Genetics	A two-phase binning algorithm using l-mer frequency on groups of non-overlapping reads.	Vinh le V, Lang TV, Binh le T, Hoai TV.	Algorithms Mol Biol	10.1186/s13015-014-0030-4	2015
Metabolism	Heterologous expression of the gene for chlorite dismutase from Ideonella dechloratans is induced by an FNR-type transcription factor.	Rova M, Hellberg Lindqvist M, Goetelen T, Blomqvist S, Nilsson T.	Microbiologyopen	10.1002/mbo3.1049	2020
	Sierra Nevada sweep: metagenomic measurements of bioaerosols vertically distributed across the troposphere.	Jaing C, Thissen J, Morrison M, Dillon MB, Waters SM, Graham GT, Be NA, Nicoll P, Verma S, Caro T, Smith DJ.	Sci Rep	10.1038/s41598-020-69188-4	2020
	Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH.	Twing KI, Brazelton WJ, Kubo MD, Hyer AJ, Cardace D, Hoehler TM, McCollom TM, Schrenk MO.	Front Microbiol	10.3389/fmicb.2017.00308	2017
Phylogeny	Microbial communities associated with the co-metabolism of free cyanide and thiocyanate under alkaline conditions.	Mekuto L, Ntwampe SKO, Mudumbi JBN.	3 Biotech	10.1007/s13205-018-1124-3	2018
	Role of the horizontal gene exchange in evolution of pathogenic Mycobacteria.	Reva O, Korotetskiy I, Ilin A.	BMC Evol Biol	10.1186/1471-2148-15-s1-s2	2015
Enzymology	A newly discovered Bordetella species carries a transcriptionally active CRISPR-Cas with a small Cas9 endonuclease.	Ivanov YV, Shariat N, Register KB, Linz B, Rivera I, Hu K, Dudley EG, Harvill ET.	BMC Genomics	10.1186/s12864-015-2028-9	2015
Metabolism	Anaerobic and aerobic cleavage of the steroid core ring structure by Steroidobacter denitrificans.	Wang PH, Leu YL, Ismail W, Tang SL, Tsai CY, Chen HJ, Kao AT, Chiang YR.	J Lipid Res	10.1194/jlr.m034223	2013
Metabolism	Time-resolved analysis of a denitrifying bacterial community revealed a core microbiome responsible for the anaerobic degradation of quinoline.	Wang Y, Tian H, Huang F, Long W, Zhang Q, Wang J, Zhu Y, Wu X, Chen G, Zhao L, Bakken LR, Frostegard A, Zhang X.	Sci Rep	10.1038/s41598-017-15122-0	2017
	Complete nucleotide sequence and analysis of two conjugative broad host range plasmids from a marine microbial biofilm.	Norberg P, Bergstrom M, Hermansson M.	PLoS One	10.1371/journal.pone.0092321	2014
Genetics	Metagenomic Analysis of Hot Springs in Central India Reveals Hydrocarbon Degrading Thermophiles and Pathways Essential for Survival in Extreme Environments.	Saxena R, Dhakan DB, Mittal P, Waiker P, Chowdhury A, Ghatak A, Sharma VK.	Front Microbiol	10.3389/fmicb.2016.02123	2016
Proteome	Relationships Between Copper-Related Proteomes and Lifestyles in beta Proteobacteria.	Antoine R, Rivera-Millot A, Roy G, Jacob-Dubuisson F.	Front Microbiol	10.3389/fmicb.2019.02217	2019
Metabolism	Sodium lauryl ether sulfate (SLES) degradation by nitrate-reducing bacteria.	Paulo AMS, Aydin R, Dimitrov MR, Vreeling H, Cavaleiro AJ, Garcia-Encina PA, Stams AJM, Plugge CM.	Appl Microbiol Biotechnol	10.1007/s00253-017-8212-x	2017
Metabolism	Anaerobic benzene oxidation by Geobacter species.	Zhang T, Bain TS, Nevin KP, Barlett MA, Lovley DR.	Appl Environ Microbiol	10.1128/aem.02469-12	2012
Enzymology	Shotgun Metagenomic Profiles Have a High Capacity To Discriminate Samples of Activated Sludge According to Wastewater Type.	Ibarbalz FM, Orellana E, Figuerola EL, Erijman L.	Appl Environ Microbiol	10.1128/aem.00916-16	2016
Metabolism	Comparative genomics of two 'Candidatus Accumulibacter' clades performing biological phosphorus removal.	Flowers JJ, He S, Malfatti S, del Rio TG, Tringe SG, Hugenholtz P, McMahon KD.	ISME J	10.1038/ismej.2013.117	2013
Metabolism	An SOS Regulon under Control of a Noncanonical LexA-Binding Motif in the Betaproteobacteria.	Sanchez-Alberola N, Campoy S, Emerson D, Barbe J, Erill I.	J Bacteriol	10.1128/jb.00035-15	2015
Metabolism	The Perchlorate Reduction Genomic Island: Mechanisms and Pathways of Evolution by Horizontal Gene Transfer.	Melnyk RA, Coates JD.	BMC Genomics	10.1186/s12864-015-2011-5	2015
	High-throughput automated microfluidic sample preparation for accurate microbial genomics.	Kim S, De Jonghe J, Kulesa AB, Feldman D, Vatanen T, Bhattacharyya RP, Berdy B, Gomez J, Nolan J, Epstein S, Blainey PC.	Nat Commun	10.1038/ncomms13919	2017
Metabolism	Carbonylation as a key reaction in anaerobic acetone activation by Desulfococcus biacutus.	Gutierrez Acosta OB, Hardt N, Schink B.	Appl Environ Microbiol	10.1128/aem.02116-13	2013
Metabolism	Integrated multi-omics analyses reveal the biochemical mechanisms and phylogenetic relevance of anaerobic androgen biodegradation in the environment.	Yang FC, Chen YL, Tang SL, Yu CP, Wang PH, Ismail W, Wang CH, Ding JY, Yang CY, Yang CY, Chiang YR.	ISME J	10.1038/ismej.2015.255	2016
Metabolism	Anoxic androgen degradation by the denitrifying bacterium Sterolibacterium denitrificans via the 2,3-seco pathway.	Wang PH, Yu CP, Lee TH, Lin CW, Ismail W, Wey SP, Kuo AT, Chiang YR.	Appl Environ Microbiol	10.1128/aem.03880-13	2014
Metabolism	Characterization of the polyurethanolytic activity of two Alicycliphilus sp. strains able to degrade polyurethane and N-methylpyrrolidone.	Oceguera-Cervantes A, Carrillo-Garcia A, Lopez N, Bolanos-Nunez S, Cruz-Gomez MJ, Wacher C, Loza-Tavera H.	Appl Environ Microbiol	10.1128/aem.01230-07	2007
Pathogenicity	A new antibiotic kills pathogens without detectable resistance.	Ling LL, Schneider T, Peoples AJ, Spoering AL, Engels I, Conlon BP, Mueller A, Schaberle TF, Hughes DE, Epstein S, Jones M, Lazarides L, Steadman VA, Cohen DR, Felix CR, Fetterman KA, Millett WP, Nitti AG, Zullo AM, Chen C, Lewis K.	Nature	10.1038/nature14098	2015
Genetics	Dakarella massiliensis gen. nov., sp. nov., strain ND3^T: a new bacterial genus isolated from the female genital tract.	Dione N, Rathored J, Tomei E, Lagier JC, Khelaifia S, Robert C, Bretelle F, Raoult D, Fournier PE, Fenollar F.	New Microbes New Infect	10.1016/j.nmni.2017.05.003	2017
Phylogeny	Alicycliphilus denitrificans gen. nov., sp. nov., a cyclohexanol-degrading, nitrate-reducing beta-proteobacterium.	Mechichi T, Stackebrandt E, Fuchs G	Int J Syst Evol Microbiol	10.1099/ijs.0.02276-0	2003

References

#5533	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 14773
#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 )
#34065	; Curators of the CIP;
#63060	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 64014
#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 )
#68382	Automatically annotated from API zym .
#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 .
#118891	Collection of Institut Pasteur ; Curators of the CIP; CIP 107495
#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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Alicycliphilus denitrificans (DSM 14773, CIP 107495, CCUG 64014)

Name and taxonomic classification

Morphology

Cell morphology

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Culture and growth conditions

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Physiology and metabolism

Oxygen tolerance

Spore formation

Compound production

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Metabolite utilization

Antibiotic resistance

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API biotype100

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Genome browser: GCA_000204645

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