Strain identifier
BacDive ID: 17452
Type strain: 
Species: Dokdonella soli
Strain Designation: KIS28-6
Strain history: S.-W. Kwon KIS28-6.
NCBI tax ID(s): 529810 (species)
version 8.1 (current version)
General
@ref: 16570
BacDive-ID: 17452
DSM-Number: 23099
keywords: 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Dokdonella soli KIS28-6 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 529810
- Matching level: species
strain history
| @ref | history |
|---|---|
| 16570 | <- KACC <- H.-Y. Weon, Natl. Inst. Horticultural and Medicinal Crop Sci., RDA, Republic of Korea; KIS28-6 |
| 67770 | S.-W. Kwon KIS28-6. |
doi: 10.13145/bacdive17452.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Lysobacterales
- family: Rhodanobacteraceae
- genus: Dokdonella
- species: Dokdonella soli
- full scientific name: Dokdonella soli Yoo et al. 2009
@ref: 16570
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Xanthomonadales
family: Rhodanobacteraceae
genus: Dokdonella
species: Dokdonella soli
full scientific name: Dokdonella soli Yoo et al. 2009
strain designation: KIS28-6
type strain: yes
Morphology
cell morphology
- @ref: 29066
- gram stain: negative
- cell length: 2.95 µm
- cell width: 0.45 µm
- cell shape: rod-shaped
- motility: no
pigmentation
- @ref: 29066
- production: yes
Culture and growth conditions
culture medium
- @ref: 16570
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: 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
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 16570 | positive | growth | 30 | mesophilic |
| 29066 | positive | growth | 05-35 | |
| 29066 | positive | optimum | 30 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 29066 | positive | growth | 5.0-8.0 |
| 29066 | positive | optimum | 6.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 29066
- oxygen tolerance: aerobe
halophily
- @ref: 29066
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-1.0 %
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29066 | 22599 | arabinose | + | carbon source |
| 29066 | 5291 | gelatin | + | carbon source |
| 29066 | 17716 | lactose | + | carbon source |
| 29066 | 53426 | tween 80 | + | carbon source |
| 29066 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 29066 | acid phosphatase | + | 3.1.3.2 |
| 29066 | alkaline phosphatase | + | 3.1.3.1 |
| 29066 | catalase | + | 1.11.1.6 |
| 29066 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 16570 | soil | island in the Sea of Japan (East Sea), Ulleung (37° 30' N 130° 52' E) | Republic of Korea | KOR | Asia | 37.5 | 130.867 |
| 67770 | Soil | Ulleung | Republic of Korea | KOR | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Safety information
risk assessment
- @ref: 16570
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16570
- description: Dokdonella sp. KIS28-6 16S ribosomal RNA gene, partial sequence
- accession: EU685334
- length: 1450
- database: ena
- NCBI tax ID: 529810
GC content
| @ref | GC-content | method |
|---|---|---|
| 16570 | 73.0 | high performance liquid chromatography (HPLC) |
| 29066 | 73 | |
| 67770 | 73 | high performance liquid chromatography (HPLC) |
External links
@ref: 16570
culture collection no.: DSM 23099, JCM 15421, KACC 12741
straininfo link
- @ref: 86448
- straininfo: 404435
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19567557 | Dokdonella soli sp. nov., a gammaproteobacterium isolated from soil. | Yoo SH, Weon HY, Anandham R, Kim BY, Hong SB, Jeon YA, Koo BS, Kwon SW | Int J Syst Evol Microbiol | 10.1099/ijs.0.005348-0 | 2009 | Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pigments, Biological/biosynthesis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Xanthomonadaceae/chemistry/*classification/genetics/*isolation & purification | Genetics |
| Phylogeny | 22888192 | Dokdonella kunshanensis sp. nov., isolated from activated sludge, and emended description of the genus Dokdonella. | Li Y, Zhang J, Chen Q, Yang G, Cai S, He J, Zhou S, Li SP | Int J Syst Evol Microbiol | 10.1099/ijs.0.041798-0 | 2012 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Waste Disposal, Fluid, Waste Water/microbiology, Xanthomonadaceae/*classification/genetics/isolation & purification | Genetics |
| Phylogeny | 22888194 | Dokdonella immobilis sp. nov., isolated from a batch reactor for the treatment of triphenylmethane dye effluent. | Liu Y, Jin JH, Liu HC, Liu ZP | Int J Syst Evol Microbiol | 10.1099/ijs.0.042002-0 | 2012 | Bacterial Typing Techniques, Base Composition, Coloring Agents/metabolism, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Trityl Compounds/*metabolism, *Waste Disposal, Fluid, Xanthomonadaceae/*classification/genetics/isolation & purification/metabolism | Metabolism |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 16570 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23099) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23099 | |||
| 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 | |||
| 29066 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 25496 | 28776041 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 86448 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID404435.1 | StrainInfo: A central database for resolving microbial strain identifiers |