Strain identifier
BacDive ID: 4291
Type strain: 
Species: Thioalkalivibrio thiocyanoxidans
Variant: Isotype of BacDive ID 4290
Strain history: D. Y. Sorokin ARh 2 (grown with thiocyanate).
NCBI tax ID(s): 152475 (species)
version 9.1 (current version)
General
@ref: 5080
BacDive-ID: 4291
DSM-Number: 13532
keywords: genome sequence, 16S sequence, Bacteria, Gram-negative
description: Thioalkalivibrio thiocyanoxidans DSM 13532 is a Gram-negative bacterium that was isolated from soda lake.
NCBI tax id
- NCBI tax id: 152475
- Matching level: species
strain history
| @ref | history |
|---|---|
| 5080 | <- D. Y. Sorokin; ARh 2 |
| 67770 | D. Y. Sorokin ARh 2 (grown with thiocyanate). |
doi: 10.13145/bacdive4291.20240916.9.1
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 thiocyanoxidans
- full scientific name: Thioalkalivibrio thiocyanoxidans corrig. Sorokin et al. 2002
synonyms
- @ref: 20215
- synonym: Thialkalivibrio thiocyanoxidans
@ref: 5080
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Chromatiales
family: Ectothiorhodospiraceae
genus: Thioalkalivibrio
species: Thioalkalivibrio thiocyanoxidans
full scientific name: Thioalkalivibrio thiocyanoxidans Sorokin et al. 2002
variant: Isotype of BacDive ID 4290
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99
Culture and growth conditions
culture medium
- @ref: 5080
- 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 | growth | type | temperature |
|---|---|---|---|
| 5080 | positive | growth | 30 |
| 67770 | positive | growth | 30 |
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: no
- confidence: 93.399
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent |
|---|---|---|---|---|
| 5080 | soda lake | Kenya | KEN | Africa |
| 67770 | Soda lake | Kenya | KEN | Africa |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Lake (large) |
| #Condition | #Alkaline |
Safety information
risk assessment
- @ref: 5080
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 5080 | Thioalkalivibrio sp. ARh 2 16S ribosomal RNA gene, partial sequence | AF302081 | 1394 | nuccore | 1279019 |
| 5080 | Thioalkalivibrio thiocyanoxidans strain DSM 13532 type 16S ribosomal RNA gene, partial sequence | MN461569 | 1525 | nuccore | 152475 |
Genome sequences
- @ref: 67770
- description: Thioalkalivibrio thiocyanoxidans ARh2
- accession: GCA_000385215
- assembly level: contig
- database: ncbi
- NCBI tax ID: 1279019
GC content
- @ref: 5080
- GC-content: 66.2
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 99 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 62.095 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 52.141 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 93.399 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 94.779 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 70.86 | no |
External links
@ref: 5080
culture collection no.: DSM 13532, JCM 11368, ARh 2, DSM 13542, ATCC BAA-720, JCM 11370
straininfo link
- @ref: 73784
- straininfo: 101025
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 11931180 | Thioalkalivibrio thiocyanoxidans sp. nov. and Thioalkalivibrio paradoxus sp. nov., novel alkaliphilic, obligately autotrophic, sulfur-oxidizing bacteria capable of growth on thiocyanate, from soda lakes. | Sorokin DY, Tourova TP, Lysenko AM, Mityushina LL, Kuenen JG | Int J Syst Evol Microbiol | 10.1099/00207713-52-2-657 | 2002 | DNA, Bacterial/chemistry, Egypt, Fresh Water/*microbiology, Gammaproteobacteria/*classification/genetics/physiology, Kenya, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S/chemistry, Siberia, Species Specificity, Sulfur/chemistry/*metabolism, Thiocyanates/*metabolism | Genetics |
| Genetics | 26512310 | Partial genome sequence of the haloalkaliphilic soda lake bacterium Thioalkalivibrio thiocyanoxidans ARh 2(T). | Berben T, Sorokin DY, Ivanova N, Pati A, Kyrpides N, Goodwin LA, Woyke T, Muyzer G | Stand Genomic Sci | 10.1186/s40793-015-0078-x | 2015 | ||
| 29285524 | Analysis of the Genes Involved in Thiocyanate Oxidation during Growth in Continuous Culture of the Haloalkaliphilic Sulfur-Oxidizing Bacterium Thioalkalivibrio thiocyanoxidans ARh 2(T) Using Transcriptomics. | Berben T, Balkema C, Sorokin DY, Muyzer G | mSystems | 10.1128/mSystems.00102-17 | 2017 | |||
| Stress | 31333619 | Transcriptomic Analysis of Two Thioalkalivibrio Species Under Arsenite Stress Revealed a Potential Candidate Gene for an Alternative Arsenite Oxidation Pathway. | Ahn AC, Cavalca L, Colombo M, Schuurmans JM, Sorokin DY, Muyzer G | Front Microbiol | 10.3389/fmicb.2019.01514 | 2019 |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 5080 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13532) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-13532 | |
| 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 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
| 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) | |
| 73784 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID101025.1 | StrainInfo: A central database for resolving microbial strain identifiers |