Strain identifier
BacDive ID: 10512
Type strain: 
Species: Aquitalea denitrificans
Strain Designation: 5YN1-3
Strain history: <- S.-W. Kwon, KACC; 5YN1-3 <- H.-Y. Weon
NCBI tax ID(s): 519081 (species)
version 8.1 (current version)
General
@ref: 15617
BacDive-ID: 10512
DSM-Number: 21330
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Aquitalea denitrificans 5YN1-3 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 519081
- Matching level: species
strain history
- @ref: 15617
- history: <- S.-W. Kwon, KACC; 5YN1-3 <- H.-Y. Weon
doi: 10.13145/bacdive10512.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Neisseriales
- family: Chromobacteriaceae
- genus: Aquitalea
- species: Aquitalea denitrificans
- full scientific name: Aquitalea denitrificans Lee et al. 2009
@ref: 15617
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Neisseriales
family: Chromobacteriaceae
genus: Aquitalea
species: Aquitalea denitrificans
full scientific name: Aquitalea denitrificans Lee et al. 2009
strain designation: 5YN1-3
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 28968 | negative | 1.75 µm | 0.7 µm | rod-shaped | yes | |
| 69480 | yes | 97.719 | ||||
| 69480 | negative | 100 |
pigmentation
- @ref: 28968
- production: yes
Culture and growth conditions
culture medium
- @ref: 15617
- 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 |
|---|---|---|---|---|
| 15617 | positive | growth | 28 | mesophilic |
| 28968 | positive | growth | 10-40 | |
| 28968 | positive | optimum | 30 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 28968 | positive | growth | 7.5 | |
| 28968 | positive | optimum | 05-09 | alkaliphile |
Physiology and metabolism
oxygen tolerance
- @ref: 28968
- oxygen tolerance: facultative anaerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.998 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 28968 | NaCl | positive | growth | 0-1 % |
| 28968 | NaCl | positive | optimum | 0.5 % |
observation
- @ref: 28968
- observation: aggregates in clumps
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 28968 | 37054 | 3-hydroxybutyrate | + | carbon source |
| 28968 | 16449 | alanine | + | carbon source |
| 28968 | 27689 | decanoate | + | carbon source |
| 28968 | 17234 | glucose | + | carbon source |
| 28968 | 27570 | histidine | + | carbon source |
| 28968 | 24996 | lactate | + | carbon source |
| 28968 | 506227 | N-acetylglucosamine | + | carbon source |
| 28968 | 26271 | proline | + | carbon source |
| 28968 | 17272 | propionate | + | carbon source |
| 28968 | 33942 | ribose | + | carbon source |
| 28968 | 17822 | serine | + | carbon source |
| 28968 | 53426 | tween 80 | + | carbon source |
| 28968 | 31011 | valerate | + | carbon source |
| 28968 | 17632 | nitrate | + | reduction |
metabolite production
- @ref: 28968
- Chebi-ID: 35581
- metabolite: indole
- production: yes
metabolite tests
- @ref: 28968
- Chebi-ID: 35581
- metabolite: indole
- indole test: +
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 28968 | acid phosphatase | + | 3.1.3.2 |
| 28968 | catalase | + | 1.11.1.6 |
| 28968 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 15617
- sample type: soil
- country: Republic of Korea
- origin.country: KOR
- continent: Asia
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Safety information
risk assessment
- @ref: 15617
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 28968
- description: Aquitalea denitrificans strain 5YN1-3 16S ribosomal RNA gene, partial sequence
- accession: EU594330
- length: 1408
- database: nuccore
- NCBI tax ID: 519081
Genome sequences
- @ref: 66792
- description: Aquitalea denitrificans 5YN1-3
- accession: GCA_009856625
- assembly level: complete
- database: ncbi
- NCBI tax ID: 519081
GC content
- @ref: 28968
- GC-content: 64
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 93.838 | yes |
| flagellated | yes | 86.047 | no |
| gram-positive | no | 98.038 | yes |
| anaerobic | no | 97.633 | yes |
| aerobic | yes | 64.781 | yes |
| halophile | no | 94.485 | yes |
| spore-forming | no | 94.555 | no |
| glucose-util | yes | 92.314 | yes |
| thermophile | no | 98.779 | yes |
| glucose-ferment | no | 81.212 | no |
External links
@ref: 15617
culture collection no.: DSM 21330, KACC 12729
straininfo link
- @ref: 79789
- straininfo: 406192
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19406790 | Aquitalea denitrificans sp. nov., isolated from a Korean wetland. | Lee CM, Weon HY, Kim YJ, Son JA, Yoon SH, Koo BS, Kwon SW | Int J Syst Evol Microbiol | 10.1099/ijs.0.002840-0 | 2009 | Bacterial Typing Techniques, DNA, Bacterial/analysis/genetics, Fatty Acids/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Neisseriaceae/*classification/genetics/isolation & purification/physiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, *Wetlands | Genetics |
| Phylogeny | 32701427 | Craterilacuibacter sinensis gen. nov. sp. nov., isolated from a crater lake in China. | Liu ZX, Phurbu D, Liu HC, Zhou YG, Li AH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004353 | 2020 | Bacterial Typing Techniques, Base Composition, Betaproteobacteria/*classification/isolation & purification, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lakes/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
| Phylogeny | 32821034 | Aquitalea aquatilis sp. nov., isolated from Jungwon waterfall. | Ngo HTT, Kim H, Trinh H, Yi TH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004351 | 2020 | Bacterial Typing Techniques, Base Composition, Betaproteobacteria/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Fresh Water, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/chemistry, *Water Microbiology | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 15617 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21330) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21330 | |||
| 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 | |||
| 28968 | 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 | 25405 | 28776041 | |
| 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) | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 79789 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID406192.1 | StrainInfo: A central database for resolving microbial strain identifiers |