Strain identifier
BacDive ID: 140105
Type strain: 
Species: Aquabacterium olei
Strain Designation: NHI-1
Strain history: <- KACC <- Y. Kim, Ecology Laboratory, Kyonggi University, Suwon, Repubic of Korea; NHI-1
NCBI tax ID(s): 1296669 (species)
version 8.1 (current version)
General
@ref: 42712
BacDive-ID: 140105
DSM-Number: 105456
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile
description: Aquabacterium olei NHI-1 is a mesophilic, motile bacterium that was isolated from oil-contaminated soil.
NCBI tax id
- NCBI tax id: 1296669
- Matching level: species
strain history
- @ref: 42712
- history: <- KACC <- Y. Kim, Ecology Laboratory, Kyonggi University, Suwon, Repubic of Korea; NHI-1
doi: 10.13145/bacdive140105.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Comamonadaceae
- genus: Aquabacterium
- species: Aquabacterium olei
- full scientific name: Aquabacterium olei Pham et al. 2015
@ref: 42712
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Comamonadaceae
genus: Aquabacterium
species: Aquabacterium olei
full scientific name: Aquabacterium olei Pham et al. 2015
strain designation: NHI-1
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 95.299 | |
| 69480 | 99.992 | negative |
multimedia
- @ref: 42712
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_105456.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 42712
- 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: 42712
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.999 |
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 | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 42712 | + | - | - | - | + | - | - | - | + | - | - | + | - | - | - | - | - | + | + | - | + |
| 42712 | + | - | - | - | + | - | - | - | + | - | - | - | - | - | - | - | - | + | + | - | + |
Isolation, sampling and environmental information
isolation
- @ref: 42712
- sample type: oil-contaminated soil
- country: Republic of Korea
- origin.country: KOR
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Contamination | #Oil (Fuel) |
| #Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_22910.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_2647;97_14006;98_17267;99_22910&stattab=map
- Last taxonomy: Aquabacterium
- 16S sequence: KC424519
- Sequence Identity:
- Total samples: 940
- soil counts: 119
- aquatic counts: 164
- animal counts: 453
- plant counts: 204
Safety information
risk assessment
- @ref: 42712
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 42712
- description: Aquabacterium olei strain NHI-1 16S ribosomal RNA gene, partial sequence
- accession: KC424519
- length: 1463
- database: ena
- NCBI tax ID: 1296669
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Aquabacterium olei NBRC 110486 | GCA_003100395 | complete | ncbi | 1296669 |
| 66792 | Aquabacterium olei strain NBRC 110486 | 1296669.4 | complete | patric | 1296669 |
| 66792 | Aquabacterium olei NBRC 110486 | 2837173148 | complete | img | 1296669 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | yes | 74.906 | no |
| gram-positive | no | 98.706 | no |
| anaerobic | no | 97.046 | no |
| halophile | no | 97.139 | no |
| spore-forming | no | 95.417 | no |
| glucose-util | no | 52.63 | no |
| aerobic | yes | 84.776 | no |
| thermophile | no | 98.883 | yes |
| motile | yes | 89.938 | no |
| glucose-ferment | no | 90.994 | yes |
External links
@ref: 42712
culture collection no.: DSM 105456, KACC 18244, NBRC 110486, KEMB 9005-082
straininfo link
- @ref: 96513
- straininfo: 398218
literature
- topic: Phylogeny
- Pubmed-ID: 26297008
- title: Aquabacterium olei sp. nov., an oil-degrading bacterium isolated from oil-contaminated soil.
- authors: Pham VHT, Jeong SW, Kim J
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.000458
- year: 2015
- mesh: Bacterial Typing Techniques, Base Composition, Betaproteobacteria/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Petroleum Pollution, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants
- topic2: Genetics
Reference
| @id | authors | title | doi/url | catalogue | journal | pubmed |
|---|---|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |||
| 42712 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-105456 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 105456) | |||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
| 96513 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID398218.1 |