Tropicibacter naphthalenivorans (DSM 19561, CECT 7648, JCM 14838)

Name: Tropicibacter naphthalenivorans (DSM 19561, CECT 7648, JCM 14838)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13842

Type strain

Strain Designation C02

Culture col. no. DSM 19561 CECT 7648 JCM 14838 C02

NCBI tax ID(s) 441103

Special Collections DSMZ JCM Literature strains

History <- Y. Kasai, Marine Biotechnol. Inst., Kamaishi, Japan; C02 <- T. U. Harwati Y. Kasai C02.

Links

Tropicibacter naphthalenivorans C02 is an aerobe, Gram-negative, motile bacterium that was isolated from Seawater.

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

Name and taxonomic classification

SI-ID 360723

DSM 19561,JCM 14838,CECT 7648

@ref 20215

Last LPSN update 2026-02-09 11:21:15

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Tropicibacter

Species Tropicibacter naphthalenivorans

Full scientific name Tropicibacter naphthalenivorans Harwati et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
32634	negative	2.25 µm	0.4 µm	rod-shaped
125438	negative					99.5

Pigmentation

32634

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
8176	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)
8176	positive	growth	37
32634	positive	growth	10-43
32634	positive	optimum	37
67770	positive	growth	37

Culture pH

@ref	Ability	Type	PH	PH range
32634	positive	optimum	7.6
32634	positive	growth	6.5-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

32634

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125438		91.164
125439		91.5

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32634	NaCl	positive	growth	01-15 %
32634	NaCl	positive	optimum	5 %

Observation

@ref	Observation
32634	aggregates in clumps
67770	quinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32634	30089 ChEBI	acetate	+	carbon source
32634	16449 ChEBI	alanine	+	carbon source
32634	22599 ChEBI	arabinose	+	carbon source
32634	35391 ChEBI	aspartate	+	carbon source
32634	17057 ChEBI	cellobiose	+	carbon source
32634	23652 ChEBI	dextrin	+	carbon source
32634	28757 ChEBI	fructose	+	carbon source
32634	17234 ChEBI	glucose	+	carbon source
32634	17596 ChEBI	inosine	+	carbon source
32634	17716 ChEBI	lactose	+	carbon source
32634	17306 ChEBI	maltose	+	carbon source
32634	37684 ChEBI	mannose	+	carbon source
32634	28053 ChEBI	melibiose	+	carbon source
32634	17632 ChEBI	nitrate	+	reduction
32634	26271 ChEBI	proline	+	carbon source
32634	26546 ChEBI	rhamnose	+	carbon source
32634	17822 ChEBI	serine	+	carbon source
32634	30911 ChEBI	sorbitol	+	carbon source
32634	30031 ChEBI	succinate	+	carbon source
32634	17992 ChEBI	sucrose	+	carbon source
32634	27082 ChEBI	trehalose	+	carbon source
32634	53426 ChEBI	tween 80	+	carbon source
32634	16704 ChEBI	uridine	+	carbon source
32634	17151 ChEBI	xylitol	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
32634	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
32634	35581 ChEBI	indole	+

Enzymes

@ref	Value	Activity	Ec
32634	acid phosphatase	+	3.1.3.2
32634	alpha-galactosidase	+	3.2.1.22
32634	cytochrome oxidase	+	1.9.3.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cyanate degradation	100	3 of 3
66794	ethanol fermentation	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	denitrification	100	2 of 2
66794	Entner Doudoroff pathway	100	10 of 10
66794	alginate biosynthesis	100	4 of 4
66794	CMP-KDO biosynthesis	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	valine metabolism	100	9 of 9
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	gluconeogenesis	100	8 of 8
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	palmitate biosynthesis	100	22 of 22
66794	ethylmalonyl-CoA pathway	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	octane oxidation	100	3 of 3
66794	methylglyoxal degradation	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	photosynthesis	92.86	13 of 14
66794	leucine metabolism	92.31	12 of 13
66794	phenylalanine metabolism	92.31	12 of 13
66794	threonine metabolism	90	9 of 10
66794	lipid A biosynthesis	88.89	8 of 9
66794	allantoin degradation	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	vitamin B12 metabolism	88.24	30 of 34
66794	ketogluconate metabolism	87.5	7 of 8
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	proline metabolism	81.82	9 of 11
66794	purine metabolism	80.85	76 of 94
66794	hydrogen production	80	4 of 5
66794	gallate degradation	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	pyrimidine metabolism	80	36 of 45
66794	alanine metabolism	79.31	23 of 29
66794	citric acid cycle	78.57	11 of 14
66794	tyrosine metabolism	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	heme metabolism	78.57	11 of 14
66794	4-hydroxymandelate degradation	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	tryptophan metabolism	76.32	29 of 38
66794	cyclohexanol degradation	75	3 of 4
66794	toluene degradation	75	3 of 4
66794	lactate fermentation	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	butanoate fermentation	75	3 of 4
66794	pentose phosphate pathway	72.73	8 of 11
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	degradation of pentoses	71.43	20 of 28
66794	glutathione metabolism	71.43	10 of 14
66794	propionate fermentation	70	7 of 10
66794	4-hydroxyphenylacetate degradation	70	7 of 10
66794	phenol degradation	70	14 of 20
66794	urea cycle	69.23	9 of 13
66794	sulfate reduction	69.23	9 of 13
66794	methionine metabolism	69.23	18 of 26
66794	non-pathway related	68.42	26 of 38
66794	oxidative phosphorylation	68.13	62 of 91
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	methane metabolism	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	3-phenylpropionate degradation	66.67	10 of 15
66794	d-mannose degradation	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	lysine metabolism	66.67	28 of 42
66794	arginine metabolism	66.67	16 of 24
66794	IAA biosynthesis	66.67	2 of 3
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	glycolysis	64.71	11 of 17
66794	degradation of sugar acids	64	16 of 25
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	vitamin B1 metabolism	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	myo-inositol biosynthesis	60	6 of 10
66794	lipoate biosynthesis	60	3 of 5
66794	histidine metabolism	58.62	17 of 29
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	propanol degradation	57.14	4 of 7
66794	androgen and estrogen metabolism	56.25	9 of 16
66794	nitrate assimilation	55.56	5 of 9
66794	lipid metabolism	54.84	17 of 31
66794	vitamin B6 metabolism	54.55	6 of 11
66794	phenylmercury acetate degradation	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	glycogen biosynthesis	50	2 of 4
66794	ribulose monophosphate pathway	50	1 of 2
66794	coenzyme M biosynthesis	50	5 of 10
66794	glycine metabolism	50	5 of 10
66794	biotin biosynthesis	50	2 of 4
66794	selenocysteine biosynthesis	50	3 of 6
66794	quinate degradation	50	1 of 2
66794	carnitine metabolism	50	4 of 8
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	ascorbate metabolism	45.45	10 of 22
66794	d-xylose degradation	45.45	5 of 11
66794	daunorubicin biosynthesis	44.44	4 of 9
66794	degradation of hexoses	44.44	8 of 18
66794	polyamine pathway	43.48	10 of 23
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	creatinine degradation	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	metabolism of disaccharids	36.36	4 of 11
66794	enterobactin biosynthesis	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	sulfoquinovose degradation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	carotenoid biosynthesis	31.82	7 of 22
66794	starch degradation	30	3 of 10
66794	chlorophyll metabolism	27.78	5 of 18
66794	methanogenesis from CO2	25	3 of 12
66794	catecholamine biosynthesis	25	1 of 4

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
8176	Seawater	Java, Semarang Port	Indonesia	IDN	Asia
67770	Seawater in Semarang Port	Java	Indonesia	IDN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB302370 (>99% sequence identity) for Tropicibacter naphthalenivorans subclade from Microbeatlas

Aquatic Samples	51
Soil Samples	2
Animal Samples
Plant Samples
Total Samples	53

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8176	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
67770	IMG-taxon 2622736506 annotated assembly for Tropicibacter naphthalenivorans DSM 19561	scaffold	GCA_900176475	441103.4	2622736506	441103	72.92
67770	Tr.naphthalenivorans_CECT7648_Spades_Prokka assembly for Tropicibacter naphthalenivorans CECT 7648	scaffold	GCA_001458375	441103.7	2713896963	441103	72.75

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
8176	Tropicibacter naphthalenivorans gene for 16S rRNA, partial sequence	AB302370	1363		441103

GC content

@ref	GC-content (mol%)	Method
8176	64.6	high performance liquid chromatography (HPLC)
32634	64.6

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Tropicibacter naphthalenivorans CECT 7648
NCBI: GCA_001458375

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	91.50	no
125439	motility	BacteriaNetⓘ	yes	51.70	no
125439	gram_stain	BacteriaNetⓘ	negative	85.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative aerobe	78.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Tropicibacter naphthalenivorans strain CECT 7648
PATRIC: 441103.7

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.50	no
125438	anaerobic	anaerobicⓘ	no	93.09	yes
125438	spore-forming	spore-formingⓘ	no	91.16	no
125438	aerobic	aerobicⓘ	yes	78.77	yes
125438	thermophilic	thermophileⓘ	no	94.51	yes
125438	flagellated	motile2+ⓘ	yes	70.73	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Characterization and genome sequence of N,N-dimethylformamide degradation in Paracoccus sulfuroxidans DM175A1-1 isolated from activated sludge of wastewater.	Zheng G, Su Y, Zhang W, Liu X, Shao L, Shen Z, Zhang D, Wang K, Miao Z.	Front Microbiol	10.3389/fmicb.2024.1419461	2024
Phylogeny	Tropicibacter naphthalenivorans gen. nov., sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from Semarang Port in Indonesia.	Harwati TU, Kasai Y, Kodama Y, Susilaningsih D, Watanabe K	Int J Syst Evol Microbiol	10.1099/ijs.0.65821-0	2009

References

#8176	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19561
#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 )
#28845	IJSEM 392 2009 ( DOI 10.1099/ijs.0.65821-0 , PubMed 19196784 )
#32634	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28845
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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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Tropicibacter naphthalenivorans (DSM 19561, CECT 7648, JCM 14838)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900176475

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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