Strain identifier
BacDive ID: 2907
Type strain: 
Species: Alicycliphilus denitrificans
Strain Designation: BC
Strain history: S. A. B. Weelink strain BC.
NCBI tax ID(s): 596153 (strain), 179636 (species)
version 9.3 (current version)
General
@ref: 7743
BacDive-ID: 2907
DSM-Number: 18852
keywords: genome sequence, Bacteria, aerobe, mesophilic, Gram-negative
description: Alicycliphilus denitrificans BC is an aerobe, mesophilic, Gram-negative bacterium that was isolated from samples from waste water treatment plant and benzene contaminated soil.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 596153 | strain |
| 179636 | species |
strain history
| @ref | history |
|---|---|
| 7743 | <- S. A. B. Weelink, Wageningen University; BC |
| 67770 | S. A. B. Weelink strain BC. |
doi: 10.13145/bacdive2907.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Comamonadaceae
- genus: Alicycliphilus
- species: Alicycliphilus denitrificans
- full scientific name: Alicycliphilus denitrificans Mechichi et al. 2003
@ref: 7743
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Comamonadaceae
genus: Alicycliphilus
species: Alicycliphilus denitrificans
full scientific name: Alicycliphilus denitrificans Mechichi et al. 2003
strain designation: BC
type strain: no
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 125438 | negative | 96.5 |
| 125439 | negative | 99.6 |
colony morphology
- @ref: 7743
- incubation period: 8-14 days
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 7743 | DECHLOROMONAS MEDIUM (DSMZ Medium 944a) | yes | https://mediadive.dsmz.de/medium/944a | Name: MEDIUM MODIFIED FOR DECHLOROMONAS SPP. (DSMZ Medium 944a; with strain-specific modifications) Composition: None 31.2 g/l NaHCO3 3.73 g/l NaClO3 1.06 g/l Na2HPO4 0.53 g/l NH4HCO3 0.44 g/l KH2PO4 0.41 g/l Na2SO4 0.2 g/l CaCl2 0.11 g/l MgCl2 0.1 g/l HCl 0.0025 g/l NaOH 0.002 g/l FeCl2 x 4 H2O 0.0015 g/l Resazurin 0.0005 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 g/l ZnCl2 7e-05 g/l Thiamine-HCl x 2 H2O 5e-05 g/l p-Aminobenzoic acid 5e-05 g/l alpha-lipoic acid 5e-05 g/l Riboflavin 5e-05 g/l Pantothenic acid 5e-05 g/l Vitamin B12 5e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l Nicotinic acid 2.5e-05 g/l Nicotine amide 2.5e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l Biotin 2e-05 g/l Folic acid 2e-05 g/l Na2WO4 x 2 H2O 1.6e-05 g/l Na2SeO3 x 5 H2O 1.2e-05 g/l Pyridoxamine hydrochloride 1e-05 g/l H3BO3 6e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Distilled water |
| 7743 | 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 |
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 7743 | positive | growth | 28 |
| 67770 | positive | growth | 30 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 7743 | aerobe |
| 7743 | anaerobe |
spore formation
- @ref: 125439
- spore formation: no
- confidence: 99.4
Isolation, sampling and environmental information
isolation
- @ref: 7743
- sample type: samples from waste water treatment plant and benzene contaminated soil
- geographic location: Wageningen
- country: Netherlands
- origin.country: NLD
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Contamination | |
| #Engineered | #Waste | #Water treatment plant |
| #Environmental | #Terrestrial | #Soil |
Safety information
risk assessment
- @ref: 7743
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Alicycliphilus denitrificans BC | GCA_000179015 | complete | ncbi | 596153 |
| 66792 | Alicycliphilus denitrificans BC | 596153.11 | plasmid | patric | 596153 |
| 66792 | Alicycliphilus denitrificans BC | 596153.4 | complete | patric | 596153 |
| 66792 | Alicycliphilus denitrificans BC | 596153.12 | plasmid | patric | 596153 |
| 66792 | Alicycliphilus denitrificans BC | 649633004 | complete | img | 596153 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 96.5 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 94.438 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 81.566 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 88.55 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 94.6 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 85.998 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 99.4 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 88.6 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 99.6 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 87.6 |
External links
@ref: 7743
culture collection no.: DSM 18852, JCM 14587
straininfo link
- @ref: 72430
- straininfo: 401132
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 7743 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18852) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18852 | |
| 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 | |
| 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) | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
| 72430 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID401132.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |