Name: Paenibacillus naphthalenovorans PR-N1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 11553

Type strain:

Species: Paenibacillus naphthalenovorans

Strain Designation: PR-N1

Culture col. no.: DSM 14203, ATCC BAA-206

Strain history: <- M. M. Häggblom; PR-N1 <- L. L. Daane

NCBI tax ID(s): 162209 (species)

SI-ID 97606

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

Special Collections

DSMZ

Other strains from Paenibacillus naphthalenovorans

Section

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

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	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Paenibacillaceae*
	Genus	*Paenibacillus*
	Species	**Paenibacillus naphthalenovorans**
	Full Scientific Name (LPSN)	Paenibacillus naphthalenovorans Daane et al. 2002

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5246]

Culture medium

CASO AGAR (MERCK 105458) (DSMZ Medium 220)

[Ref.: #5246]

Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #5246]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #5246]			growth	30 °C

Information on physiology and metabolism Physiology and metabolism

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

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

[Ref.: #5246]	Sample type/isolated from	rhizosphere of Spartina alterniflora
[Ref.: #5246]	Host species	Spartina alterniflora
[Ref.: #5246]	Geographic location (country and/or sea, region)	New Jersey
[Ref.: #5246]	Country	USA
[Ref.: #5246]	Country ISO 3 Code	USA
[Ref.: #5246]	Continent	North America
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #5246]

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.: #5246]	Paenibacillus naphthalenovorans strain PR-N1 16S ribosomal RNA gene, partial sequence	AF353681	1551	GenBank ENA	162209 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Paenibacillus naphthalenovorans PR-N1	GCA_900099895	contig	GenBank ENA	162209 tax ID	*
[Ref.: #66792]	Paenibacillus naphthalenovorans PR-N1	2675903031	draft	JGI IMG/M	162209 tax ID	*

[Ref.: #5246]

GC-content

47-52 mol%

Availability in culture collections External links

[Ref.: #5246]

Culture collection no.

DSM 14203, ATCC BAA-206

[Ref.: #80781]

SI-ID 97606

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 .

#80781

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-ID97606.1 )

* These data were automatically processed and therefore are not curated

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