Strain identifier
BacDive ID: 14175
Type strain: 
Species: Sphingobium chlorophenolicum
Strain Designation: ID 93-106, RA2
Strain history: <- H.J. Rehm <- ? <- P.M. Radehaus (Pseudomonas sp. RA 2)
NCBI tax ID(s): 46429 (species)
version 8.1 (current version)
General
@ref: 3342
BacDive-ID: 14175
DSM-Number: 8671
keywords: 16S sequence, Bacteria, mesophilic
description: Sphingobium chlorophenolicum ID 93-106 is a mesophilic bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 46429
- Matching level: species
strain history
- @ref: 3342
- history: <- H.J. Rehm <- ? <- P.M. Radehaus (Pseudomonas sp. RA 2)
doi: 10.13145/bacdive14175.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Sphingomonadales
- family: Sphingomonadaceae
- genus: Sphingobium
- species: Sphingobium chlorophenolicum
- full scientific name: Sphingobium chlorophenolicum (Nohynek et al. 1996) Takeuchi et al. 2001
synonyms
- @ref: 20215
- synonym: Sphingomonas chlorophenolica
@ref: 3342
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Sphingomonadaceae
genus: Sphingobium
species: Sphingobium chlorophenolicum
full scientific name: Sphingobium chlorophenolicum (Nohynek et al. 1996) Takeuchi et al. 2001
strain designation: ID 93-106, RA2
type strain: no
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 3342 | MINERAL MEDIUM WITH PCP (DSMZ Medium 465b) | yes | https://mediadive.dsmz.de/medium/465b | Name: MINERAL MEDIUM WITH PCP (DSMZ Medium 465b) Composition: Na2HPO4 x 2 H2O 3.15 g/l KH2PO4 0.9 g/l (NH4)2SO4 0.45 g/l Pentachlorophenol 0.1 g/l MgCl2 x 6 H2O 0.09 g/l Ca(NO3)2 x 4 H2O 0.045 g/l NaOH 0.039997 g/l EDTA 0.00045 g/l FeSO4 x 7 H2O 0.00018 g/l H3BO3 2.7e-05 g/l CoCl2 x 6 H2O 1.8e-05 g/l ZnSO4 x 7 H2O 9e-06 g/l Na2MoO4 x 2 H2O 2.7e-06 g/l MnCl2 x 4 H2O 2.7e-06 g/l NiCl2 x 6 H2O 1.8e-06 g/l CuCl2 x 2 H2O 9e-07 g/l Distilled water |
| 3342 | REACTIVATION WITH TRYPTONE SOYA BROTH (DSMZ Medium 220a) | yes | https://mediadive.dsmz.de/medium/220a | Name: REACTIVATION WITH TRYPTONE SOYA BROTH (DSMZ Medium 220a) Composition: Casein peptone 17.0 g/l Agar 15.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water |
culture temp
- @ref: 3342
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 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: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 3342 | - | - | - | - | - | + | - | + | - | - | - | - | - | - | - | - | - | - | - | - | + |
Isolation, sampling and environmental information
isolation
- @ref: 3342
- sample type: soil
- geographic location: Denver
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_38.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_32;97_33;98_36;99_38&stattab=map
- Last taxonomy: Sphingobium
- 16S sequence: X87164
- Sequence Identity:
- Total samples: 771
- soil counts: 53
- aquatic counts: 257
- animal counts: 442
- plant counts: 19
Safety information
risk assessment
- @ref: 3342
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 3342
- description: S.flava 16S rRNA gene, strain 'Pseudomonas' sp. RA2
- accession: X87164
- length: 1429
- database: ena
- NCBI tax ID: 46429
GC content
- @ref: 3342
- GC-content: 66.7
- method: high performance liquid chromatography (HPLC)
External links
@ref: 3342
culture collection no.: DSM 8671
straininfo link
- @ref: 83338
- straininfo: 48512
literature
- topic: Metabolism
- Pubmed-ID: 18555512
- title: Two-phase partitioning bioreactor for the biodegradation of high concentrations of pentachlorophenol using Sphingobium chlorophenolicum DSM 8671.
- authors: Zilouei H, Guieysse B, Mattiasson B
- journal: Chemosphere
- DOI: 10.1016/j.chemosphere.2008.04.035
- year: 2008
- mesh: Biodegradation, Environmental, Bioreactors/*microbiology, Kinetics, Pentachlorophenol/*metabolism, Sphingomonadaceae/growth & development/*metabolism
- topic2: Enzymology
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 3342 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8671) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-8671 | |
| 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 | |
| 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 | |
| 83338 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID48512.1 | StrainInfo: A central database for resolving microbial strain identifiers |