Archive BacDiveID:10.13145/bacdive11553.20230509.8.1

Strain identifier

BacDive ID: 11553

Type strain:

Species: Paenibacillus naphthalenovorans

Strain Designation: PR-N1

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

NCBI tax ID(s): 162209 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 5246

BacDive-ID: 11553

DSM-Number: 14203

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

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

NCBI tax id

NCBI tax id: 162209
Matching level: species

strain history

@ref: 5246
history: <- M. M. Häggblom; PR-N1 <- L. L. Daane

doi: 10.13145/bacdive11553.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/bacillota
domain: Bacteria
phylum: Bacillota
class: Bacilli
order: Caryophanales
family: Paenibacillaceae
genus: Paenibacillus
species: Paenibacillus naphthalenovorans
full scientific name: Paenibacillus naphthalenovorans Daane et al. 2002

@ref: 5246

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus naphthalenovorans

full scientific name: Paenibacillus naphthalenovorans Daane et al. 2002

strain designation: PR-N1

type strain: yes

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
5246	CASO AGAR (MERCK 105458) (DSMZ Medium 220)	yes	https://mediadive.dsmz.de/medium/220	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)	yes	https://mediadive.dsmz.de/medium/457	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: 5246
growth: positive
type: growth
temperature: 30
range: mesophilic

Isolation, sampling and environmental information

isolation

@ref: 5246
sample type: rhizosphere of Spartina alterniflora
host species: Spartina alterniflora
geographic location: New Jersey
country: USA
origin.country: USA
continent: North America

isolation source categories

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

taxonmaps

@ref: 69479
File name: preview.99_331.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_231;97_253;98_282;99_331&stattab=map
Last taxonomy: Paenibacillus naphthalenovorans subclade
16S sequence: AF353681
Sequence Identity:
Total samples: 1774
soil counts: 723
aquatic counts: 379
animal counts: 515
plant counts: 157

Safety information

risk assessment

@ref: 5246
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 5246
description: Paenibacillus naphthalenovorans strain PR-N1 16S ribosomal RNA gene, partial sequence
accession: AF353681
length: 1551
database: ena
NCBI tax ID: 162209

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Paenibacillus naphthalenovorans PR-N1	GCA_900099895	contig	ncbi	162209
66792	Paenibacillus naphthalenovorans PR-N1	2675903031	draft	img	162209

GC content

@ref: 5246
GC-content: 47-52

External links

@ref: 5246

culture collection no.: DSM 14203, ATCC BAA 206

straininfo link

@ref: 80781
straininfo: 97606

literature

topic: Phylogeny
Pubmed-ID: 11837295
title: PAH-degradation by Paenibacillus spp. and description of Paenibacillus naphthalenovorans sp. nov., a naphthalene-degrading bacterium from the rhizosphere of salt marsh plants.
authors: Daane LL, Harjono I, Barns SM, Launen LA, Palleron NJ, Haggblom MM
journal: Int J Syst Evol Microbiol
DOI: 10.1099/00207713-52-1-131
year: 2002
mesh: Bacillaceae/*classification/growth & development/metabolism/ultrastructure, Biodegradation, Environmental, DNA, Ribosomal/analysis, Environmental Pollutants, Fatty Acids/analysis, Fresh Water/*microbiology, Geologic Sediments/*microbiology, Naphthalenes/metabolism, Nucleic Acid Hybridization, Phenanthrenes/metabolism, Phenotype, Phylogeny, Plant Roots/*microbiology, Polycyclic Aromatic Hydrocarbons/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
topic2: Metabolism

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
5246	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14203)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-14203
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	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		10.1093/nar/gkaa1025	BRENDA, the ELIXIR core data resource in 2021: new developments and updates	Nucleic Acids Res. 49: D498-D508 2020	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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
80781	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID97606.1	StrainInfo: A central database for resolving microbial strain identifiers