Strain identifier
BacDive ID: 130283
Type strain: 
Species: Desulfobulbus alkaliphilus
Strain Designation: APS1
Strain history: <- D. Y. Sorokin, Dept. Biotechnol., Delft Univ. Technol., Netherlands; APS1 <- D. Y. Sorokin {2010}
NCBI tax ID(s): 869814 (species)
version 9.1 (current version)
General
@ref: 21886
BacDive-ID: 130283
DSM-Number: 24258
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, Gram-negative, motile, rod-shaped
description: Desulfobulbus alkaliphilus APS1 is an anaerobe, Gram-negative, motile bacterium that was isolated from sediments from a hypersaline soda lake.
NCBI tax id
- NCBI tax id: 869814
- Matching level: species
strain history
- @ref: 21886
- history: <- D. Y. Sorokin, Dept. Biotechnol., Delft Univ. Technol., Netherlands; APS1 <- D. Y. Sorokin {2010}
doi: 10.13145/bacdive130283.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Desulfobacterales
- family: Desulfobulbaceae
- genus: Desulfobulbus
- species: Desulfobulbus alkaliphilus
- full scientific name: Desulfobulbus alkaliphilus Sorokin et al. 2012
@ref: 21886
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Desulfobacterales
family: Desulfobulbaceae
genus: Desulfobulbus
species: Desulfobulbus alkaliphilus
full scientific name: Desulfobulbus alkaliphilus Sorokin et al. 2012
strain designation: APS1
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 30132 | negative | 2.25 µm | 1.25 µm | rod-shaped | yes | |
| 69480 | negative | 96.589 |
colony morphology
- @ref: 21886
- incubation period: 8-14 days
Culture and growth conditions
culture medium
- @ref: 21886
- name: DESULFONATRONUM THIOAUTOTROPHICUM MEDIUM (DSMZ Medium 1166)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1166
- composition: Name: DESULFONATRONUM THIOAUTOTROPHICUM MEDIUM (DSMZ Medium 1166; with strain-specific modifications) Composition: Na2CO3 21.9342 g/l NaHCO3 7.97607 g/l NaCl 5.98205 g/l Na2S2O3 x 5 H2O 4.98504 g/l Na2SO4 2.79163 g/l Na-propionate 1.91426 g/l K2HPO4 0.997009 g/l Na2S x 9 H2O 0.239282 g/l MgCl2 x 6 H2O 0.199402 g/l NH4Cl 0.199402 g/l Yeast extract 0.0498504 g/l EDTA 0.00498504 g/l FeSO4 x 7 H2O 0.00219342 g/l NaOH 0.000498504 g/l CoCl2 x 6 H2O 0.000199402 g/l ZnSO4 x 7 H2O 9.97009e-05 g/l Pyridoxine hydrochloride 9.97009e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l MnCl2 x 4 H2O 2.99103e-05 g/l NiCl2 x 6 H2O 2.99103e-05 g/l Na2MoO4 x 2 H2O 2.99103e-05 g/l CuCl2 x 2 H2O 2.99103e-05 g/l H3BO3 2.99103e-05 g/l Biotin 1.99402e-05 g/l Folic acid 1.99402e-05 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 21886 | positive | growth | 30 |
| 30132 | positive | optimum | 33 |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 30132 | positive | growth | 8.2-10.2 | alkaliphile |
| 30132 | positive | optimum | 9.4 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 21886 | anaerobe |
| 30132 | anaerobe |
spore formation
- @ref: 69481
- spore formation: no
- confidence: 96
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 30132 | NaCl | positive | growth | 0.58-8.7 % |
| 30132 | NaCl | positive | optimum | 1.16 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30132 | 17272 | propionate | + | carbon source |
| 30132 | 15361 | pyruvate | + | carbon source |
Isolation, sampling and environmental information
isolation
- @ref: 21886
- sample type: sediments from a hypersaline soda lake
- geographic location: Altai, south-western Siberia, Kulunda Steppe
- country: Russia
- origin.country: RUS
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Lake (large) |
| #Environmental | #Aquatic | #Sediment |
| #Condition | #Saline | |
| #Condition | #Alkaline |
taxonmaps
- @ref: 69479
- File name: preview.99_160660.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_128;96_60479;97_78306;98_105751;99_160660&stattab=map
- Last taxonomy: Desulfobulbus alkaliphilus subclade
- 16S sequence: HM750216
- Sequence Identity:
- Total samples: 349
- soil counts: 26
- aquatic counts: 221
- animal counts: 14
- plant counts: 88
Safety information
risk assessment
- @ref: 21886
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21886
- description: Desulfobulbus alkaliphilus strain APS1 16S ribosomal RNA gene, partial sequence
- accession: HM750216
- length: 1500
- database: nuccore
- NCBI tax ID: 869814
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Desulfobulbus alkaliphilus DSM 24258 | GCA_016918545 | contig | ncbi | 869814 |
| 66792 | Desulfobulbus alkaliphilus strain DSM 24258 | 869814.3 | wgs | patric | 869814 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 21886 | 52.8 | thermal denaturation, midpoint method (Tm) |
| 30132 | 52.8 |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 96 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 96.589 | yes |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 79.856 | yes |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 76.151 | yes |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 83.992 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 83.301 | no |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 77.034 | no |
External links
@ref: 21886
culture collection no.: DSM 24258, UNIQEM U900
straininfo link
- @ref: 88818
- straininfo: 402108
literature
- topic: Phylogeny
- Pubmed-ID: 22039002
- title: Desulfonatronobacter acidivorans gen. nov., sp. nov. and Desulfobulbus alkaliphilus sp. nov., haloalkaliphilic heterotrophic sulfate-reducing bacteria from soda lakes.
- authors: Sorokin DY, Tourova TP, Panteleeva AN, Muyzer G
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.029777-0
- year: 2011
- mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Deltaproteobacteria/*classification/genetics/isolation & purification, Fatty Acids/analysis, Geologic Sediments/microbiology, Heterotrophic Processes, Lakes/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Russia, Sequence Analysis, DNA, Sulfur-Reducing Bacteria/*classification/genetics/isolation & purification
- topic2: Enzymology
Reference
| @id | authors | title | doi/url | catalogue | ID_cross_reference | 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 | |||
| 21886 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24258 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24258) | |||
| 30132 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 26483 | 28776041 | |
| 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 | |||
| 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 | |||
| 88818 | 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-ID402108.1 |