Alicycliphilus denitrificans (DSM 18852, BC, JCM 14587)

Name: Alicycliphilus denitrificans (DSM 18852, BC, JCM 14587)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2907

Type strain

Strain Designation BC

Culture col. no. DSM 18852 BC JCM 14587

NCBI tax ID(s) 596153 179636

Special Collections DSMZ JCM

History DSMZ <- S. A. B. Weelink, Wageningen University; BC JCM <-- S. A. B. Weelink strain BC.

Links

Alicycliphilus denitrificans BC is an aerobe bacterium that was isolated from samples from waste water treatment plant and benzene contaminated soil.

aerobe genome sequence Bacteria

Name and taxonomic classification

SI-ID 401132

DSM 18852

@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
2906	A. denitrificans K601, DSM 14773, CIP 107495, CCUG 64014 (type strain)
2924	A. denitrificans JS100, DSM 6838, CCM 7239

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	96.5
125439	negative	98.811

Colony morphology

7743

Incubation period8-14 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7743	DECHLOROMONAS MEDIUM (DSMZ Medium 944a)		Medium recipe at MediaDive	Name: MEDIUM MODIFIED FOR DECHLOROMONAS SPP. (DSMZ Medium 944a; with strain-specific modifications) Composition: None 31.2 g/l NaHCO3 3.73 g/l NaClO3 1.06 g/l Na2HPO4 0.53 g/l NH4HCO3 0.44 g/l KH2PO4 0.41 g/l Na2SO4 0.2 g/l CaCl2 0.11 g/l MgCl2 0.1 g/l HCl 0.0025 g/l NaOH 0.002 g/l FeCl2 x 4 H2O 0.0015 g/l Resazurin 0.0005 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 g/l ZnCl2 7e-05 g/l Thiamine-HCl x 2 H2O 5e-05 g/l p-Aminobenzoic acid 5e-05 g/l alpha-lipoic acid 5e-05 g/l Riboflavin 5e-05 g/l Pantothenic acid 5e-05 g/l Vitamin B12 5e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l Nicotinic acid 2.5e-05 g/l Nicotine amide 2.5e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l Biotin 2e-05 g/l Folic acid 2e-05 g/l Na2WO4 x 2 H2O 1.6e-05 g/l Na2SeO3 x 5 H2O 1.2e-05 g/l Pyridoxamine hydrochloride 1e-05 g/l H3BO3 6e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Distilled water
7743	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

Culture temp

@ref	Growth	Type	Temperature (°C)
7743	positive	growth	28
67770	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
7743	aerobe
7743	anaerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.852

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Contamination	-
#Engineered	#Waste	#Water treatment plant
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7743	samples from waste water treatment plant and benzene contaminated soil	Wageningen	Netherlands	NLD	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7743	1	Risk group (German 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	ASM17901v2 assembly for Alicycliphilus denitrificans BC	complete	GCA_000179015	596153.4	649633004	596153	98.2

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM17901v2 assembly for Alicycliphilus denitrificans BC
BV-BRC: 596153.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	87.57	no
125439	gram_stain	BacteriaNetⓘ	negative	98.81	no
125439	motility	BacteriaNetⓘ	yes	84.60	no
125439	spore_formation	BacteriaNetⓘ	no	99.85	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Alicycliphilus denitrificans BC BC
NCBI: GCA_000179015.2

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.50	no
125438	anaerobic	anaerobicⓘ	no	94.44	no
125438	aerobic	aerobicⓘ	yes	81.57	no
125438	spore-forming	spore-formingⓘ	no	88.55	no
125438	thermophilic	thermophileⓘ	no	94.60	yes
125438	flagellated	motile2+ⓘ	yes	86.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
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
Metabolism	Isolation and characterization of Alicycliphilus denitrificans strain BC, which grows on benzene with chlorate as the electron acceptor.	Weelink SA, Tan NC, ten Broeke H, van den Kieboom C, van Doesburg W, Langenhoff AA, Gerritse J, Junca H, Stams AJ.	Appl Environ Microbiol	10.1128/aem.00835-08	2008

References

#7743	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18852
#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 )
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 18852, BC, JCM 14587)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000179015

Genome-based predictions

Predictions

Literature

Literature

References

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