Strain identifier
BacDive ID: 13828
Type strain: 
Species: Rhodobaca barguzinensis
Strain Designation: alga-05
Strain history: <- V. M. Gorlenko, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; alga-05 <- E. N. Boldareva
NCBI tax ID(s): 441209 (species)
version 8.1 (current version)
General
@ref: 8389
BacDive-ID: 13828
DSM-Number: 19920
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Rhodobaca barguzinensis alga-05 is an anaerobe, mesophilic bacterium that was isolated from thin bacterial mat from a soda lake.
NCBI tax id
- NCBI tax id: 441209
- Matching level: species
strain history
- @ref: 8389
- history: <- V. M. Gorlenko, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; alga-05 <- E. N. Boldareva
doi: 10.13145/bacdive13828.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Paracoccaceae
- genus: Rhodobaca
- species: Rhodobaca barguzinensis
- full scientific name: Rhodobaca barguzinensis Boldareva et al. 2009
synonyms
- @ref: 20215
- synonym: Rhodobaca bogoriensis subsp. barguzinensis
@ref: 8389
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Rhodobaca
species: Rhodobaca barguzinensis
full scientific name: Rhodobaca barguzinensis Boldareva et al. 2009
strain designation: alga-05
type strain: yes
Culture and growth conditions
culture medium
- @ref: 8389
- name: RHODOBACA BARGUZINENSIS MEDIUM (DSMZ Medium 1227)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1227
- composition: Name: RHODOBACA BARGUZINENSIS MEDIUM (DSMZ Medium 1227) Composition: NaCl 20.0 g/l Na2CO3 10.0 g/l NaHCO3 5.0 g/l Yeast extract 1.0 g/l Na2S2O3 x 5 H2O 1.0 g/l KH2PO4 0.5 g/l Na2SO4 0.5 g/l KCl 0.5 g/l NaNO3 0.4 g/l NH4Cl 0.4 g/l MgCl2 x 6 H2O 0.2 g/l CoCl2 x 6 H2O 0.0001998 g/l MnCl2 x 4 H2O 9.99001e-05 g/l ZnCl2 6.99301e-05 g/l H3BO3 5.99401e-05 g/l Na2MoO4 x 2 H2O 3.996e-05 g/l NiCl2 x 6 H2O 1.998e-05 g/l CuCl2 x 2 H2O 1.998e-05 g/l HCl Vitamin B12 Distilled water
culture temp
- @ref: 8389
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 8389
- oxygen tolerance: anaerobe
Isolation, sampling and environmental information
isolation
- @ref: 8389
- sample type: thin bacterial mat from a soda lake
- geographic location: East Siberia, Buryatia, Bargusin Valley
- country: Russia
- origin.country: RUS
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Lake (large) |
| #Environmental | #Microbial community | #Microbial mat |
| #Condition | #Alkaline |
taxonmaps
- @ref: 69479
- File name: preview.99_5064.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_2407;97_2929;98_3659;99_5064&stattab=map
- Last taxonomy: Rhodobaca
- 16S sequence: EF554833
- Sequence Identity:
- Total samples: 167
- soil counts: 20
- aquatic counts: 120
- animal counts: 24
- plant counts: 3
Safety information
risk assessment
- @ref: 8389
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 8389
- description: Rhodobaca barguzinensis strain VKM B-2406 16S ribosomal RNA gene, partial sequence
- accession: EF554833
- length: 1367
- database: ena
- NCBI tax ID: 441209
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Rhodobaca barguzinensis DSM 19920 | GCA_004365885 | scaffold | ncbi | 441209 |
| 66792 | Rhodobaca barguzinensis strain DSM 19920 | 441209.10 | wgs | patric | 441209 |
| 66792 | Rhodobaca barguzinensis DSM 19920 | 2593339286 | draft | img | 441209 |
GC content
- @ref: 8389
- GC-content: 59.8
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 57.575 | no |
| flagellated | no | 77.071 | no |
| gram-positive | no | 98.389 | no |
| anaerobic | no | 92.246 | yes |
| aerobic | yes | 76.173 | yes |
| halophile | yes | 66.621 | no |
| spore-forming | no | 94.823 | no |
| glucose-util | yes | 80.689 | no |
| thermophile | no | 95.86 | yes |
| glucose-ferment | no | 91.547 | no |
External links
@ref: 8389
culture collection no.: DSM 19920, VKM B-2406
straininfo link
- @ref: 83004
- straininfo: 408062
literature
| topic | Pubmed-ID | title | authors | journal | year | mesh | topic2 | DOI |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 18522327 | [Rhodobaca barguzinensis sp. nov., a new alkaliphilic purple nonsulfur bacterium isolated from a soda lake of the Barguzin Valley (Buryat Republic, eastern Siberia)]. | Boldareva EN, Akimov VN, Boichenko VA, Stadnichuk IN, Moskalenko AA, Makhneva ZK, Gorlenko VM | Mikrobiologiia | 2008 | Anaerobiosis, Bacteriochlorophyll A/isolation & purification, Carotenoids/isolation & purification, Culture Media, Fresh Water/microbiology, Geologic Sediments/microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhodobacter/chemistry/classification/cytology/*isolation & purification/physiology, Sequence Homology, Siberia, Sodium Chloride, *Water Microbiology | Enzymology | |
| Phylogeny | 26263629 | [Rhodobaculum claviforme gen. nov., sp. nov., a New Alkaliphilic Nonsulfur Purple Bacterium]. | Bryantseva IA, Gaisin VA, Gorlenko VM | Mikrobiologiia | 2015 | Aerobiosis, Anaerobiosis, Bacteriochlorophyll A/metabolism, Base Composition, Carotenoids/metabolism, DNA, Bacterial/*chemistry, *Genes, rRNA, Hydrogen-Ion Concentration, Intracellular Membranes/ultrastructure, Lakes/microbiology, Light, Light-Harvesting Protein Complexes/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/isolation & purification/metabolism/ultrastructure, Rhodospirillaceae/*classification/isolation & purification/metabolism/ultrastructure, Salt Tolerance, Siberia, *Water Microbiology, Xanthophylls/metabolism | Metabolism | |
| Genetics | 30022245 | The complete genome sequence of Rhodobaca barguzinensis alga05 (DSM 19920) documents its adaptation for life in soda lakes. | Kopejtka K, Tomasch J, Bunk B, Sproer C, Wagner-Dobler I, Koblizek M | Extremophiles | 2018 | Adaptation, Physiological, *Genome, Bacterial, Lakes/*microbiology, Molecular Sequence Annotation, Rhodobacteraceae/*genetics/physiology | 10.1007/s00792-018-1041-8 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 8389 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19920) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19920 | |||
| 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 | |||
| 83004 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID408062.1 | StrainInfo: A central database for resolving microbial strain identifiers |