Strain identifier
BacDive ID: 4286
Type strain: 
Species: Thioalkalivibrio denitrificans
Strain Designation: ALJD
Strain history: <- D. Y. Sorokin; ALJD
NCBI tax ID(s): 108003 (species)
version 9.1 (current version)
General
@ref: 5140
BacDive-ID: 4286
DSM-Number: 13742
keywords: genome sequence, 16S sequence, Bacteria, motile
description: Thioalkalivibrio denitrificans ALJD is a motile bacterium that was isolated from soda lake.
NCBI tax id
- NCBI tax id: 108003
- Matching level: species
strain history
- @ref: 5140
- history: <- D. Y. Sorokin; ALJD
doi: 10.13145/bacdive4286.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Chromatiales
- family: Ectothiorhodospiraceae
- genus: Thioalkalivibrio
- species: Thioalkalivibrio denitrificans
- full scientific name: Thioalkalivibrio denitrificans corrig. Sorokin et al. 2001
synonyms
- @ref: 20215
- synonym: Thialkalivibrio denitrificans
@ref: 5140
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Chromatiales
family: Ectothiorhodospiraceae
genus: Thioalkalivibrio
species: Thioalkalivibrio denitrificans
full scientific name: Thioalkalivibrio denitrificans Sorokin et al. 2001
strain designation: ALJD
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 98.494
Culture and growth conditions
culture medium
- @ref: 5140
- name: ALKALIPHILIC SULPHUR RESPIRING STRAINS MEDIUM (DSMZ Medium 925)
- growth: yes
- link: https://mediadive.dsmz.de/medium/925
- composition: Name: ALKALIPHILIC SULPHUR RESPIRING STRAINS MEDIUM (DSMZ Medium 925) Composition: Na2CO3 20.0 g/l NaHCO3 10.0 g/l NaCl 5.0 g/l K2HPO4 1.0 g/l MgCl2 x 6 H2O 0.2 g/l H3BO3 0.0006 g/l CoCl2 x 6 H2O 0.0004 g/l ZnSO4 x 7 H2O 0.0002 g/l Na2MoO4 x 2 H2O 6e-05 g/l MnCl2 x 4 H2O 6e-05 g/l NiCl2 x 6 H2O 4e-05 g/l CuCl2 x 2 H2O 2e-05 g/l EDTA 1e-05 g/l FeSO4 x 7 H2O 4e-06 g/l Distilled water
culture temp
- @ref: 5140
- growth: positive
- type: growth
- temperature: 30
Isolation, sampling and environmental information
isolation
- @ref: 5140
- sample type: soda lake
- country: Kenya
- origin.country: KEN
- continent: Africa
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Lake (large) |
| #Condition | #Alkaline |
taxonmaps
- @ref: 69479
- File name: preview.99_1061.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_56;96_121;97_128;98_143;99_1061&stattab=map
- Last taxonomy: Thioalkalivibrio denitrificans
- 16S sequence: AF126545
- Sequence Identity:
- Total samples: 204
- soil counts: 16
- aquatic counts: 178
- animal counts: 6
- plant counts: 4
Safety information
risk assessment
- @ref: 5140
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 5140
- description: Thioalcalovibrio denitrificans 16S ribosomal RNA gene, partial sequence
- accession: AF126545
- length: 1465
- database: nuccore
- NCBI tax ID: 108003
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Thioalkalivibrio denitrificans ALJD | GCA_002000365 | scaffold | ncbi | 108003 |
| 66792 | Thioalkalivibrio denitrificans ALJD | 2899100019 | draft | img | 108003 |
GC content
- @ref: 5140
- GC-content: 63.7
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 87 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 98.494 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 73.115 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 53.259 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 89.606 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 93.695 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 78.769 | no |
External links
@ref: 5140
culture collection no.: DSM 13742, NCCB 100001
straininfo link
- @ref: 73780
- straininfo: 101021
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 5140 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13742) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-13742 | |||
| 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) | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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 | |||
| 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 | |||
| 73780 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID101021.1 | StrainInfo: A central database for resolving microbial strain identifiers |