Paenibacillus naphthalenovorans (DSM 14203, ATCC BAA-206, PR-N1)

Name: Paenibacillus naphthalenovorans (DSM 14203, ATCC BAA-206, PR-N1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11553

Type strain

Strain Designation PR-N1

Culture col. no. DSM 14203 ATCC BAA-206 PR-N1

NCBI tax ID(s) 162209

Special Collections DSMZ

History DSMZ <- M. M. Häggblom; PR-N1 <- L. L. Daane

Links

Paenibacillus naphthalenovorans PR-N1 is a bacterium that was isolated from rhizosphere of Spartina alterniflora.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 97606

ATCC BAA-206,DSM 14203,BCRC 17352,CCRC 17352

@ref 20215

Last LPSN update 2026-05-29 08:27:35

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Paenibacillaceae

Genus Paenibacillus

Species Paenibacillus naphthalenovorans

Full scientific name Paenibacillus naphthalenovorans Daane et al. 2002

BacDive ID	Other strains from **Paenibacillus naphthalenovorans** (2)	Type strain
136597	P. naphthalenovorans CIP 102594
153516	P. naphthalenovorans CCUG 50012

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
5246	CASO AGAR (MERCK 105458) (DSMZ Medium 220)		Medium recipe at MediaDive	Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
5246	MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457)		Medium recipe at MediaDive	Name: MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457) Composition: 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 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

Culture temp

@ref	Growth	Type	Temperature (°C)
5246	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	facultative anaerobe	92.997

Spore formation

@ref	Spore formation	Confidence
125439		93.134

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	valine metabolism	100	9 of 9
66794	formaldehyde oxidation	100	3 of 3
66794	ethanol fermentation	100	2 of 2
66794	pentose phosphate pathway	100	11 of 11
66794	glycogen metabolism	100	5 of 5
66794	kanosamine biosynthesis II	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	threonine metabolism	100	10 of 10
66794	octane oxidation	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	propanol degradation	100	7 of 7
66794	L-lactaldehyde degradation	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	biotin biosynthesis	100	4 of 4
66794	butanoate fermentation	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	ribulose monophosphate pathway	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	taurine degradation	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	adipate degradation	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	methionine metabolism	92.31	24 of 26
66794	vitamin B1 metabolism	92.31	12 of 13
66794	Entner Doudoroff pathway	90	9 of 10
66794	serine metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	allantoin degradation	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	degradation of sugar alcohols	87.5	14 of 16
66794	isoleucine metabolism	87.5	7 of 8
66794	ketogluconate metabolism	87.5	7 of 8
66794	flavin biosynthesis	86.67	13 of 15
66794	photosynthesis	85.71	12 of 14
66794	citric acid cycle	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	phenol degradation	85	17 of 20
66794	phenylalanine metabolism	84.62	11 of 13
66794	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
66794	NAD metabolism	83.33	15 of 18
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	degradation of pentoses	82.14	23 of 28
66794	purine metabolism	81.91	77 of 94
66794	proline metabolism	81.82	9 of 11
66794	creatinine degradation	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	3-chlorocatechol degradation	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	4-hydroxyphenylacetate degradation	80	8 of 10
66794	3-phenylpropionate degradation	80	12 of 15
66794	gallate degradation	80	4 of 5
66794	vitamin B12 metabolism	79.41	27 of 34
66794	heme metabolism	78.57	11 of 14
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	non-pathway related	76.32	29 of 38
66794	pyrimidine metabolism	75.56	34 of 45
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	d-xylose degradation	72.73	8 of 11
66794	vitamin B6 metabolism	72.73	8 of 11
66794	alanine metabolism	72.41	21 of 29
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	oxidative phosphorylation	71.43	65 of 91
66794	coenzyme M biosynthesis	70	7 of 10
66794	propionate fermentation	70	7 of 10
66794	starch degradation	70	7 of 10
66794	urea cycle	69.23	9 of 13
66794	androgen and estrogen metabolism	68.75	11 of 16
66794	tryptophan metabolism	68.42	26 of 38
66794	4-hydroxymandelate degradation	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	arginine metabolism	66.67	16 of 24
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	degradation of sugar acids	64	16 of 25
66794	histidine metabolism	62.07	18 of 29
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	cysteine metabolism	61.11	11 of 18
66794	degradation of hexoses	61.11	11 of 18
66794	factor 420 biosynthesis	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	glycine betaine biosynthesis	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	glutathione metabolism	57.14	8 of 14
66794	lipid metabolism	54.84	17 of 31
66794	sulfate reduction	53.85	7 of 13
66794	pantothenate biosynthesis	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	lactate fermentation	50	2 of 4
66794	myo-inositol biosynthesis	50	5 of 10
66794	CMP-KDO biosynthesis	50	2 of 4
66794	lysine metabolism	50	21 of 42
66794	sphingosine metabolism	50	3 of 6
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	cholesterol biosynthesis	45.45	5 of 11
66794	lipid A biosynthesis	44.44	4 of 9
66794	nitrate assimilation	44.44	4 of 9
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	lipoate biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	ascorbate metabolism	36.36	8 of 22
66794	metabolism of disaccharids	36.36	4 of 11
66794	tyrosine metabolism	35.71	5 of 14
66794	polyamine pathway	34.78	8 of 23
66794	IAA biosynthesis	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	sulfoquinovose degradation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	carnitine metabolism	25	2 of 8
66794	vitamin E metabolism	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	chlorophyll metabolism	22.22	4 of 18

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
5246	rhizosphere of Spartina alterniflora	Spartina alterniflora	New Jersey	USA	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence AF353681 (>99% sequence identity) for Paenibacillus naphthalenovorans subclade from Microbeatlas

Aquatic Samples	379
Soil Samples	723
Animal Samples	515
Plant Samples	157
Total Samples	1774

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5246	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	IMG-taxon 2675903031 annotated assembly for Paenibacillus naphthalenovorans PR-N1	contig	GCA_900099895	162209.10	2675903031	162209	56.72

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
5246	Paenibacillus naphthalenovorans strain PR-N1 16S ribosomal RNA gene, partial sequence	AF353681	1551		162209

GC content

5246

GC-content (mol%)47-52

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2675903031 annotated assembly for Paenibacillus naphthalenovorans PR-N1
NCBI: GCA_900099895

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	variable	73.48	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	93.00	no
125439	motility	BacteriaNetⓘ	yes	88.20	no
125439	spore_formation	BacteriaNetⓘ	yes	93.13	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	PAH-degradation by Paenibacillus spp. and description of Paenibacillus naphthalenovorans sp. nov., a naphthalene-degrading bacterium from the rhizosphere of salt marsh plants.	Daane LL, Harjono I, Barns SM, Launen LA, Palleron NJ, Haggblom MM	Int J Syst Evol Microbiol	10.1099/00207713-52-1-131	2002

References

#5246	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 14203
#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) .
#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 )
#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 .
#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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Paenibacillus naphthalenovorans (DSM 14203, ATCC BAA-206, PR-N1)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900099895

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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