Strain identifier
BacDive ID: 2982
Type strain:
Species: Polaromonas naphthalenivorans
Strain Designation: CJ2
Strain history: <- E. L. Madsen; CJ2
NCBI tax ID(s): 216465 (species)
General
@ref: 6017
BacDive-ID: 2982
DSM-Number: 15660
keywords: genome sequence, 16S sequence, Bacteria, aerobe, chemoorganotroph, psychrophilic, Gram-negative, coccus-shaped, colony-forming
description: Polaromonas naphthalenivorans CJ2 is an aerobe, chemoorganotroph, psychrophilic bacterium that forms circular colonies and was isolated from coal-tar contaminated site.
NCBI tax id
- NCBI tax id: 216465
- Matching level: species
strain history
- @ref: 6017
- history: <- E. L. Madsen; CJ2
doi: 10.13145/bacdive2982.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Comamonadaceae
- genus: Polaromonas
- species: Polaromonas naphthalenivorans
- full scientific name: Polaromonas naphthalenivorans Jeon et al. 2004
@ref: 6017
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Comamonadaceae
genus: Polaromonas
species: Polaromonas naphthalenivorans
full scientific name: Polaromonas naphthalenivorans Jeon et al. 2004
strain designation: CJ2
type strain: yes
Morphology
cell morphology
- @ref: 23088
- gram stain: negative
- cell length: 1.0-4.0 µm
- cell shape: coccus-shaped
- motility: no
colony morphology
@ref | colony color | colony shape | medium used | incubation period |
---|---|---|---|---|
23088 | beige | circular | MSB-pyruvate medium | |
23088 | beige | circular | MSB-naphthalene medium | |
59113 | 4 days |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
6017 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water |
6017 | REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) | yes | https://mediadive.dsmz.de/medium/1a | Name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
23088 | MSB-naphthalene agar medium | yes | ||
23088 | MSB-naphthalene medium | yes | ||
23088 | MSB-pyruvate agar medium | yes | ||
23088 | MSB-pyruvate medium | yes |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6017 | positive | growth | 20 | psychrophilic |
23088 | no | growth | 30.0 | mesophilic |
23088 | positive | growth | 4.0-25.0 | |
23088 | positive | optimum | 20.0 | psychrophilic |
59113 | positive | growth | 20 | psychrophilic |
culture pH
- @ref: 23088
- ability: positive
- type: optimum
- pH: 7.0-7.5
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
23088 | aerobe |
59113 | aerobe |
nutrition type
- @ref: 23088
- type: chemoorganotroph
spore formation
- @ref: 23088
- spore formation: no
murein
- @ref: 23088
- murein short key: A31
- type: A1gamma m-Dpm-direct
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
23088 | 22599 | arabinose | - | builds gas from |
23088 | 17634 | D-glucose | - | builds gas from |
23088 | 29864 | mannitol | - | builds gas from |
23088 | 17992 | sucrose | - | builds gas from |
23088 | 27897 | tryptophan | - | energy source |
23088 | O-nitrophenyl-beta-D-galactopyranosid | - | hydrolysis | |
23088 | 22599 | arabinose | + | builds acid from |
23088 | 17634 | D-glucose | + | builds acid from |
23088 | 29864 | mannitol | + | builds acid from |
23088 | 17992 | sucrose | + | builds acid from |
23088 | 16947 | citrate | + | carbon source |
23088 | 28938 | ammonium | + | nitrogen source |
68369 | 25115 | malate | - | assimilation |
68369 | 17128 | adipate | - | assimilation |
68369 | 27689 | decanoate | - | assimilation |
68369 | 24265 | gluconate | - | assimilation |
68369 | 17306 | maltose | - | assimilation |
68369 | 59640 | N-acetylglucosamine | - | assimilation |
68369 | 16899 | D-mannitol | - | assimilation |
68369 | 16024 | D-mannose | - | assimilation |
68369 | 30849 | L-arabinose | - | assimilation |
68369 | 17634 | D-glucose | + | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 4853 | esculin | - | hydrolysis |
68369 | 16199 | urea | + | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | - | reduction |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
23088 | 35581 | indole | no |
23088 | 16136 | hydrogen sulfide | no |
23088 | 15688 | acetoin | no |
68369 | 35581 | indole | no |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test | citrate test |
---|---|---|---|---|---|
23088 | 15688 | acetoin | - | ||
23088 | 35581 | indole | - | ||
23088 | 16947 | citrate | + | ||
68369 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
23088 | arginine dihydrolase | + | 3.5.3.6 |
23088 | catalase | + | 1.11.1.6 |
23088 | cytochrome oxidase | + | 1.9.3.1 |
23088 | gelatinase | + | |
23088 | lysine decarboxylase | - | 4.1.1.18 |
23088 | ornithine decarboxylase | - | 4.1.1.17 |
23088 | tryptophan deaminase | - | 4.1.99.1 |
23088 | urease | - | 3.5.1.5 |
68369 | cytochrome oxidase | + | 1.9.3.1 |
68369 | gelatinase | - | |
68369 | beta-glucosidase | - | 3.2.1.21 |
68369 | urease | + | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
6017 | - | - | - | - | + | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | enrichment culture | enrichment culture composition | enrichment culture duration | enrichment culture temperature | isolation procedure |
---|---|---|---|---|---|---|---|---|---|---|
6017 | coal-tar contaminated site | New York | USA | USA | North America | |||||
23088 | coal-tar-contaminated freshwater sediment | South Glens Falls, New York | minimal salts base (MSB) agar medium | 0.2 % pyruvate (w/v), Luria-Bertani (LB) broth and oligotrophic medium PYGV | 30 days | 10.0 | incubated in the presence of naphthalene vapour as the sole carbon source | |||
59113 | Coal-tar contaminated site | USA | USA | North America |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Contamination | |
#Environmental | #Aquatic | #Freshwater |
#Environmental | #Terrestrial | #Geologic |
#Environmental | #Terrestrial | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_1546.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_884;97_1032;98_1221;99_1546&stattab=map
- Last taxonomy: Polaromonas
- 16S sequence: AY166684
- Sequence Identity:
- Total samples: 2817
- soil counts: 683
- aquatic counts: 1647
- animal counts: 380
- plant counts: 107
Safety information
risk assessment
- @ref: 6017
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6017
- description: Coccomonas naphthalovorans 16S ribosomal RNA gene, partial sequence
- accession: AY166684
- length: 1452
- database: ena
- NCBI tax ID: 365044
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Polaromonas naphthalenivorans CJ2 | GCA_000015505 | complete | ncbi | 365044 |
66792 | Polaromonas naphthalenivorans CJ2 | 365044.41 | plasmid | patric | 365044 |
66792 | Polaromonas naphthalenivorans CJ2 | 365044.36 | plasmid | patric | 365044 |
66792 | Polaromonas naphthalenivorans CJ2 | 365044.37 | plasmid | patric | 365044 |
66792 | Polaromonas naphthalenivorans CJ2 | 365044.42 | plasmid | patric | 365044 |
66792 | Polaromonas naphthalenivorans CJ2 | 365044.38 | plasmid | patric | 365044 |
66792 | Polaromonas naphthalenivorans CJ2 | 365044.39 | plasmid | patric | 365044 |
66792 | Polaromonas naphthalenivorans CJ2 | 365044.20 | complete | patric | 365044 |
66792 | Polaromonas naphthalenivorans CJ2 | 365044.43 | plasmid | patric | 365044 |
66792 | Polaromonas naphthalenivorans CJ2 | 365044.40 | plasmid | patric | 365044 |
66792 | Polaromonas naphthalenivorans CJ2 | 639633051 | complete | img | 365044 |
GC content
@ref | GC-content | method |
---|---|---|
6017 | 61.5 | |
23088 | 61.5 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 84.077 | yes |
flagellated | no | 87.575 | no |
gram-positive | no | 98.729 | yes |
anaerobic | no | 97.513 | yes |
halophile | no | 95.806 | no |
spore-forming | no | 94.021 | yes |
thermophile | no | 98.903 | no |
glucose-util | yes | 51.788 | no |
aerobic | yes | 77.328 | yes |
glucose-ferment | no | 90.859 | no |
External links
@ref: 6017
culture collection no.: DSM 15660, ATCC BAA 779, CCUG 51246
straininfo link
- @ref: 72504
- straininfo: 113601
literature
- topic: Phylogeny
- Pubmed-ID: 14742464
- title: Polaromonas naphthalenivorans sp. nov., a naphthalene-degrading bacterium from naphthalene-contaminated sediment.
- authors: Jeon CO, Park W, Ghiorse WC, Madsen EL
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.02636-0
- year: 2004
- mesh: Biodegradation, Environmental, Burkholderiaceae/*classification/isolation & purification/metabolism, Geologic Sediments/*microbiology, Industrial Waste, Molecular Sequence Data, Naphthalenes/*metabolism, Phospholipids/metabolism, Phylogeny
- topic2: Metabolism
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
6017 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15660) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15660 | |||
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 | |||
23088 | Che Ok Jeon,Woojun Park,William C. Ghiorse,Eugene L. Madsen | 10.1099/ijs.0.02636-0 | Polaromonas naphthalenivorans sp. nov., a naphthalene-degrading bacterium from naphthalene-contaminated sediment | IJSEM 54: 93-97 2004 | 14742464 | |
59113 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 51246) | https://www.ccug.se/strain?id=51246 | |||
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) | |||
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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
72504 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID113601.1 | StrainInfo: A central database for resolving microbial strain identifiers |