Name: Polaromonas naphthalenivorans CJ2
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 2982

Type strain:

Species: Polaromonas naphthalenivorans

Strain Designation: CJ2

Culture col. no.: DSM 15660, ATCC BAA-779, CCUG 51246

Strain history: <- E. L. Madsen; CJ2

NCBI tax ID(s): 216465 (species)

SI-ID 113601

DSM 15660, ATCC BAA-779, CCUG 51246

Section

Polaromonas naphthalenivorans CJ2 is an aerobe, chemoorganotroph, psychrophilic bacterium that forms circular colonies and was isolated from coal-tar contaminated site.

coccus-shaped
colony-forming
Gram-negative
aerobe
chemoorganotroph
psychrophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Comamonadaceae*
	Genus	*Polaromonas*
	Species	**Polaromonas naphthalenivorans**
	Full Scientific Name (LPSN)	Polaromonas naphthalenivorans Jeon et al. 2004

Information on morphological and physiological properties Morphology

[Ref.: #23088]	Gram stain	negative

[Ref.: #23088]	Cell length	1.0-4.0 µm

[Ref.: #23088]	Cell shape	coccus-shaped

[Ref.: #23088]	Motility	no

[Ref.: #23088]	Colony color	beige
[Ref.: #23088]	Colony shape	circular
[Ref.: #23088]	Cultivation medium used	MSB-pyruvate medium

[Ref.: #23088]	Colony color	beige
[Ref.: #23088]	Colony shape	circular
[Ref.: #23088]	Cultivation medium used	MSB-naphthalene medium

[Ref.: #59113]	Incubation period	4 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6017]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #6017]

Culture medium composition

expand / minimize

[Ref.: #6017]

Culture medium

REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)

[Ref.: #6017]

Culture medium growth

[Ref.: #6017]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6017]

Culture medium composition

expand / minimize

[Ref.: #23088]

Culture medium

MSB-naphthalene agar medium

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Culture medium growth

[Ref.: #23088]

Culture medium

MSB-naphthalene medium

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Culture medium growth

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Culture medium

MSB-pyruvate agar medium

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Culture medium growth

[Ref.: #23088]

Culture medium

MSB-pyruvate medium

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Culture medium growth

	Kind of temperature		Temperature
[Ref.: #6017]		growth	20 °C
[Ref.: #23088]	no	growth	30.0 °C
[Ref.: #23088]		growth	4.0-25.0 °C
[Ref.: #23088]		optimum	20.0 °C
[Ref.: #59113]		growth	20 °C

[Ref.: #6017]	Temperature range	psychrophilic
[Ref.: #23088]	Temperature range	mesophilic
[Ref.: #23088]	Temperature range	psychrophilic
[Ref.: #59113]	Temperature range	psychrophilic

	pH	Kind of pH		pH
[Ref.: #23088]			optimum	7.0-7.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #23088]	Oxygen tolerance	aerobe
[Ref.: #59113]	Oxygen tolerance	aerobe

[Ref.: #23088]

Nutrition type

chemoorganotroph

[Ref.: #23088]

Ability of spore formation

[Ref.: #23088]	Murein short key	A31
[Ref.: #23088]	Murein types	A1gamma m-Dpm-direct

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #23088]	ammonium ChEBI	+	nitrogen source
[Ref.: #23088]	arabinose ChEBI	-	builds gas from
[Ref.: #23088]	arabinose ChEBI	+	builds acid from
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #23088]	citrate ChEBI	+	carbon source
[Ref.: #23088]	D-glucose ChEBI	-	builds gas from
[Ref.: #23088]	D-glucose ChEBI	+	builds acid from
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #23088]	mannitol ChEBI	-	builds gas from
[Ref.: #23088]	mannitol ChEBI	+	builds acid from
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #23088]	O-nitrophenyl-beta-D-galactopyranosid	-	hydrolysis
[Ref.: #23088]	sucrose ChEBI	-	builds gas from
[Ref.: #23088]	sucrose ChEBI	+	builds acid from
[Ref.: #23088]	tryptophan ChEBI	-	energy source
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	+	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #23088]	acetoin ChEBI	no
[Ref.: #23088]	hydrogen sulfide ChEBI	no
[Ref.: #23088]	indole ChEBI	no
[Ref.: #68369]	indole ChEBI	no	* from API 20NE

	Metabolite	Voges-Proskauer-test	Indole test	Citrate test
[Ref.: #23088]	acetoin ChEBI	-
[Ref.: #23088]	citrate ChEBI			+
[Ref.: #23088]	indole ChEBI		-
[Ref.: #68369]	indole ChEBI		-		* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #23088]	arginine dihydrolase	+	3.5.3.6
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE
[Ref.: #23088]	catalase	+	1.11.1.6
[Ref.: #23088]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #23088]	gelatinase	+
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #23088]	lysine decarboxylase	-	4.1.1.18
[Ref.: #23088]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #23088]	tryptophan deaminase	-	4.1.99.1
[Ref.: #23088]	urease	-	3.5.1.5
[Ref.: #68369]	urease	+	3.5.1.5	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

API® 20NE:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #6017]	25427	-	-	-	-	+	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	+

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #6017]	Sample type/isolated from	coal-tar contaminated site
[Ref.: #6017]	Geographic location (country and/or sea, region)	New York
[Ref.: #6017]	Country	USA
[Ref.: #6017]	Country ISO 3 Code	USA
[Ref.: #6017]	Continent	North America

[Ref.: #23088]	Sample type/isolated from	coal-tar-contaminated freshwater sediment
[Ref.: #23088]	Geographic location (country and/or sea, region)	South Glens Falls, New York
[Ref.: #23088]	Enrichment culture	minimal salts base (MSB) agar medium
[Ref.: #23088]	Enrichment culture composition	0.2 % pyruvate (w/v), Luria-Bertani (LB) broth and oligotrophic medium PYGV
[Ref.: #23088]	Enrichment culture duration	30 days
[Ref.: #23088]	Enrichment culture temperature	10.0 ̊C
[Ref.: #23088]	Isolation/enrichment procedure	incubated in the presence of naphthalene vapour as the sole carbon source

[Ref.: #59113]	Sample type/isolated from	Coal-tar contaminated site
[Ref.: #59113]	Country	USA
[Ref.: #59113]	Country ISO 3 Code	USA
[Ref.: #59113]	Continent	North America
* marker position based on {}

Isolation sources categories

#Engineered	#Contamination	-
#Environmental	#Aquatic	#Freshwater
#Environmental	#Terrestrial	#Geologic
#Environmental	#Terrestrial	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY166684 (>99% sequence identity) for Polaromonas from Microbeatlas

Aquatic Samples	1647
Soil Samples	683
Animal Samples	380
Plant Samples	107
Total Samples	2817

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #6017]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #6017]	Coccomonas naphthalovorans 16S ribosomal RNA gene, partial sequence	AY166684	1452	ENA	365044 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Polaromonas naphthalenivorans CJ2	639633051	complete	JGI IMG/M	365044 tax ID	*
[Ref.: #66792]	Polaromonas naphthalenivorans CJ2	365044.41	plasmid	PATRIC	365044 tax ID	*
[Ref.: #66792]	Polaromonas naphthalenivorans CJ2	365044.36	plasmid	PATRIC	365044 tax ID	*
[Ref.: #66792]	Polaromonas naphthalenivorans CJ2	365044.37	plasmid	PATRIC	365044 tax ID	*
[Ref.: #66792]	Polaromonas naphthalenivorans CJ2	365044.42	plasmid	PATRIC	365044 tax ID	*
[Ref.: #66792]	Polaromonas naphthalenivorans CJ2	365044.38	plasmid	PATRIC	365044 tax ID	*

[Ref.: #6017]	GC-content	61.5 mol%
[Ref.: #23088]	GC-content	61.5 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Polaromonas naphthalenivorans CJ2 CJ2 NCBI: GCA_000015505.1
[Ref.: #69480]	motile	no	84.077	yes
[Ref.: #69480]	flagellated	no	87.575	no
[Ref.: #69480]	gram-positive	no	98.729	yes
[Ref.: #69480]	anaerobic	no	97.513	yes
[Ref.: #69480]	halophile	no	95.806	no
[Ref.: #69480]	spore-forming	no	94.021	yes
[Ref.: #69480]	thermophile	no	98.903	no
[Ref.: #69480]	glucose-util	yes	51.788	no
[Ref.: #69480]	aerobic	yes	77.328	yes
[Ref.: #69480]	glucose-ferment	no	90.859	no

Availability in culture collections External links

[Ref.: #6017]

Culture collection no.

DSM 15660, ATCC BAA-779, CCUG 51246

[Ref.: #72504]

SI-ID 113601

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Polaromonas naphthalenivorans sp. nov., a naphthalene-degrading bacterium from naphthalene-contaminated sediment.	Jeon CO, Park W, Ghiorse WC, Madsen EL	Int J Syst Evol Microbiol	10.1099/ijs.0.02636-0	2004	*

References

#6017

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15660

#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 )

#23088

Che Ok Jeon,Woojun Park,William C. Ghiorse,Eugene L. Madsen: Polaromonas naphthalenivorans sp. nov., a naphthalene-degrading bacterium from naphthalene-contaminated sediment. IJSEM 54: 93 - 97 2004 ( DOI 10.1099/ijs.0.02636-0 , PubMed 14742464 )

#59113 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 51246

#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) .

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#72504

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID113601.1 )

* These data were automatically processed and therefore are not curated

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Polaromonas naphthalenivorans CJ2 CJ2

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