Croceicoccus naphthovorans (DSM 102796, CGMCC 1.12805, NBRC 110381)

Name: Croceicoccus naphthovorans (DSM 102796, CGMCC 1.12805, NBRC 110381)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132207

Type strain

Strain Designation PQ-2

Culture col. no. DSM 102796 CGMCC 1.12805 NBRC 110381 PQ-2

NCBI tax ID(s) 1348774

Special Collections DSMZ

History <- NBRC <- Y. Zeng, Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Zhejiang University, Hangzhou, PR China

Links

Croceicoccus naphthovorans PQ-2 is a bacterium that was isolated from biofilm on a boat shell.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 404751

NBRC 110381,DSM 102796

@ref 20215

Last LPSN update 2026-02-09 11:31:39

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Erythrobacteraceae

Genus Croceicoccus

Species Croceicoccus naphthovorans

Full scientific name Croceicoccus naphthovorans Huang et al. 2015

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	97.433
125439	negative	98.5

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
23996	MINERAL MEDIUM WITH VITAMINS (DSMZ Medium 462)		Medium recipe at MediaDive	Name: MINERAL MEDIUM (BRUNNER) WITH VITAMINS (DSMZ Medium 462) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Casein peptone 15.0 g/l Peptone 5.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Meat extract 3.0 g/l Na2HPO4 2.44 g/l KH2PO4 1.52 g/l (NH4)2SO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l CaCl2 x 2 H2O 0.05 g/l EDTA 0.005 g/l FeSO4 x 7 H2O 0.002 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l Pyridoxamine 0.000125 g/l ZnSO4 x 7 H2O 0.0001 g/l Nicotinic acid 5e-05 g/l Vitamin B12 5e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l MnCl2 x 4 H2O 3e-05 g/l p-Aminobenzoate 2.5e-05 g/l Thiamine-HCl x 2 H2O 2.5e-05 g/l NiCl2 x 6 H2O 2e-05 g/l Calcium pantothenate 1.25e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Biotin 5e-06 g/l Distilled water
23996	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
23996	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	aerobe	96.7

Spore formation

@ref	Spore formation	Confidence
125438		91.278
125439		96

Compound production

23996

CompoundN acyl homoserine lactones

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	27689 ChEBI	decanoate	-	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	C4 and CAM-carbon fixation	100	8 of 8
66794	cardiolipin biosynthesis	100	7 of 7
66794	adipate degradation	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	valine metabolism	100	9 of 9
66794	quinate degradation	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	formaldehyde oxidation	100	3 of 3
66794	cyanate degradation	100	3 of 3
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	Entner Doudoroff pathway	90	9 of 10
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	citric acid cycle	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	phenylalanine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	proline metabolism	81.82	9 of 11
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	alanine metabolism	79.31	23 of 29
66794	purine metabolism	78.72	74 of 94
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	heme metabolism	78.57	11 of 14
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	vitamin B1 metabolism	76.92	10 of 13
66794	butanoate fermentation	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	lactate fermentation	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	pyrimidine metabolism	73.33	33 of 45
66794	3-phenylpropionate degradation	73.33	11 of 15
66794	peptidoglycan biosynthesis	73.33	11 of 15
66794	pentose phosphate pathway	72.73	8 of 11
66794	propanol degradation	71.43	5 of 7
66794	glutathione metabolism	71.43	10 of 14
66794	tyrosine metabolism	71.43	10 of 14
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	propionate fermentation	70	7 of 10
66794	phenol degradation	70	14 of 20
66794	acetoin degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	tryptophan metabolism	65.79	25 of 38
66794	methionine metabolism	65.38	17 of 26
66794	glycolysis	64.71	11 of 17
66794	lipid metabolism	64.52	20 of 31
66794	vitamin B6 metabolism	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	histidine metabolism	62.07	18 of 29
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	urea cycle	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	lipoate biosynthesis	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	lysine metabolism	57.14	24 of 42
66794	nitrate assimilation	55.56	5 of 9
66794	metabolism of disaccharids	54.55	6 of 11
66794	arginine metabolism	54.17	13 of 24
66794	sulfate reduction	53.85	7 of 13
66794	pantothenate biosynthesis	50	3 of 6
66794	ribulose monophosphate pathway	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	sulfopterin metabolism	50	2 of 4
66794	glycogen biosynthesis	50	2 of 4
66794	myo-inositol biosynthesis	50	5 of 10
66794	ketogluconate metabolism	50	4 of 8
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	oxidative phosphorylation	49.45	45 of 91
66794	lipid A biosynthesis	44.44	4 of 9
66794	vitamin B12 metabolism	44.12	15 of 34
66794	degradation of sugar alcohols	43.75	7 of 16
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	polyamine pathway	43.48	10 of 23
66794	vitamin K metabolism	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	glycine betaine biosynthesis	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	d-xylose degradation	36.36	4 of 11
66794	IAA biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	allantoin degradation	33.33	3 of 9
66794	enterobactin biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	degradation of hexoses	33.33	6 of 18
66794	degradation of pentoses	32.14	9 of 28
66794	ascorbate metabolism	31.82	7 of 22
66794	carotenoid biosynthesis	31.82	7 of 22
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	carnitine metabolism	25	2 of 8
66794	toluene degradation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	4-hydroxymandelate degradation	22.22	2 of 9

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
23996	+	-	-	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Environmental	#Biofilm

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
23996	biofilm on a boat shell	habour of Zhoushan island, Zhoushan Archipelago, Zhejiang Province	China	CHN	Asia	30.7293	122.489 30.7293/122.489

Taxonmaps

69479

Global distribution of 16S sequence KF145127 (>99% sequence identity) for Croceicoccus naphthovorans from Microbeatlas

Aquatic Samples	393
Soil Samples	921
Animal Samples	32
Plant Samples	286
Total Samples	1632

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
23996	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	ASM102870v1 assembly for Croceicoccus naphthovorans PQ-2	complete	GCA_001028705		2654588035	1348774	88.47
66792	ASM1419685v1 assembly for Croceicoccus naphthovorans DSM 102796	contig	GCA_014196855	1348774.9	2829998802	1348774	60.3

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
23996	Croceicoccus naphthovorans strain PQ-2 16S ribosomal RNA gene, partial sequence	KF145127	1356		1348774

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Croceicoccus naphthovorans strain PQ-2
PATRIC: 1348774.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.00	no
125439	motility	BacteriaNetⓘ	yes	65.10	no
125439	gram_stain	BacteriaNetⓘ	negative	98.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	96.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Croceicoccus naphthovorans PQ-2
NCBI: GCA_001028705.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.43	no
125438	anaerobic	anaerobicⓘ	no	93.56	no
125438	aerobic	aerobicⓘ	yes	89.60	no
125438	spore-forming	spore-formingⓘ	no	91.28	no
125438	thermophilic	thermophileⓘ	no	98.54	yes
125438	flagellated	motile2+ⓘ	no	63.26	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	The LuxI/LuxR-Type Quorum Sensing System Regulates Degradation of Polycyclic Aromatic Hydrocarbons via Two Mechanisms.	Yu Z, Hu Z, Xu Q, Zhang M, Yuan N, Liu J, Meng Q, Yin J	Int J Mol Sci	10.3390/ijms21155548	2020
Phylogeny	Croceicoccus bisphenolivorans sp. nov., a bisphenol A-degrading bacterium isolated from seawater.	Li J, Hu A, Lv M, Yu CP	Int J Syst Evol Microbiol	10.1099/ijsem.0.004658	2021
Phylogeny	Croceicoccus sediminis sp. nov., isolated from coastal sediment.	Huang Z, Zhang A, Lai Q, Yuan J	Int J Syst Evol Microbiol	10.1099/ijsem.0.003823	2020
Phylogeny	Croceicoccus pelagius sp. nov. and Croceicoccus mobilis sp. nov., isolated from marine environments.	Wu YH, Li GY, Jian SL, Cheng H, Huo YY, Wang CS, Shao ZZ, Xu XW	Int J Syst Evol Microbiol	10.1099/ijsem.0.001381	2016
Phylogeny	Croceicoccus naphthovorans sp. nov., a polycyclic aromatic hydrocarbons-degrading and acylhomoserine-lactone-producing bacterium isolated from marine biofilm, and emended description of the genus Croceicoccus.	Huang Y, Zeng Y, Feng H, Wu Y, Xu X	Int J Syst Evol Microbiol	10.1099/ijs.0.000132	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 )
#23996	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 102796
#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 )
#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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Croceicoccus naphthovorans (DSM 102796, CGMCC 1.12805, NBRC 110381)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Compound production

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_001028705

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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