Strain identifier
BacDive ID: 160224
Type strain: 
Species: Desulfovibrio subterraneus
Strain Designation: HN2
Strain history: <- A. Ueno, Horonobe Research Institute for the Subsurface Environment (H-RISE), Horonobe-cho, Japan; HN2 <- S. Shimizu {2014}
NCBI tax ID(s): 2718620 (species)
version 8.1 (current version)
General
@ref: 67128
BacDive-ID: 160224
DSM-Number: 101010
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile
description: Desulfovibrio subterraneus HN2 is an anaerobe, mesophilic, motile bacterium that was isolated from groundwater from borehole in Horonobe Underground Research Laboratory, Japan Atomic Energy Agency..
NCBI tax id
- NCBI tax id: 2718620
- Matching level: species
strain history
- @ref: 67128
- history: <- A. Ueno, Horonobe Research Institute for the Subsurface Environment (H-RISE), Horonobe-cho, Japan; HN2 <- S. Shimizu {2014}
doi: 10.13145/bacdive160224.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Desulfovibrionales
- family: Desulfovibrionaceae
- genus: Desulfovibrio
- species: Desulfovibrio subterraneus
- full scientific name: Desulfovibrio subterraneus Ueno et al. 2021
synonyms
- @ref: 20215
- synonym: Psychrodesulfovibrio subterraneus
@ref: 67128
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Desulfovibrionales
family: Desulfovibrionaceae
genus: Desulfovibrio
species: Desulfovibrio subterraneus
full scientific name: Desulfovibrio subterraneus Ueno et al. 2021
strain designation: HN2
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 96.643 | |
| 69480 | 99.995 | negative |
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 67128 | DESULFOVIBRIO (POSTGATE) MEDIUM (DSMZ Medium 63) | yes | https://mediadive.dsmz.de/medium/63 | Name: DESULFOVIBRIO (POSTGATE) MEDIUM (DSMZ Medium 63) Composition: MgSO4 x 7 H2O 2.0 g/l Na-DL-lactate 2.0 g/l NH4Cl 1.0 g/l Yeast extract 1.0 g/l Na2SO4 1.0 g/l FeSO4 x 7 H2O 0.5 g/l K2HPO4 0.5 g/l CaCl2 x 2 H2O 0.1 g/l Na-thioglycolate 0.1 g/l Ascorbic acid 0.1 g/l Sodium resazurin 0.0005 g/l Distilled water |
| 67128 | DESULFOVIBRIO (MV) MEDIUM (DSMZ Medium 641) | yes | https://mediadive.dsmz.de/medium/641 | Name: DESULFOVIBRIO (MV) MEDIUM (DSMZ Medium 641) Composition: Na-DL-lactate 2.49252 g/l Na2SO4 1.99402 g/l NH4Cl 0.997009 g/l Yeast extract 0.997009 g/l Na2CO3 0.997009 g/l MgSO4 x 7 H2O 0.997009 g/l Na2S2O3 x 5 H2O 0.997009 g/l KH2PO4 0.498504 g/l Na2S x 9 H2O 0.0997009 g/l CaCl2 x 2 H2O 0.0997009 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Pyridoxine hydrochloride 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Riboflavin 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Biotin 1.99402e-05 g/l Folic acid 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water |
culture temp
- @ref: 67128
- growth: positive
- type: growth
- temperature: 35
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 69480
- oxygen tolerance: anaerobe
- confidence: 99.725
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69480 | no | 99.918 |
| 69481 | no | 100 |
Isolation, sampling and environmental information
isolation
- @ref: 67128
- sample type: groundwater from borehole in Horonobe Underground Research Laboratory, Japan Atomic Energy Agency.
- country: Japan
- origin.country: JPN
- continent: Asia
Sequence information
16S sequences
- @ref: 67128
- description: Desulfovibrio subterraneus HN2 gene for 16S rRNA, partial sequence
- accession: LC531930
- length: 1462
- database: ena
- NCBI tax ID: 2718620
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Desulfovibrio subterraneus HN2 | GCA_013340285 | scaffold | ncbi | 2718620 |
| 66792 | Desulfovibrio sp. HN2 | 2718620.3 | wgs | patric | 2718620 |
GC content
- @ref: 67128
- GC-content: 56.7
- method: sequence analysis
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 92.299 | no |
| flagellated | yes | 71.743 | no |
| gram-positive | no | 99.387 | no |
| anaerobic | yes | 98.689 | no |
| aerobic | no | 98.498 | no |
| halophile | no | 75.726 | no |
| spore-forming | no | 93.701 | no |
| glucose-util | yes | 53.538 | no |
| thermophile | no | 97.898 | no |
| glucose-ferment | no | 77.04 | no |
External links
@ref: 67128
culture collection no.: DSM 101010, NBRC 112213
straininfo link
- @ref: 112488
- straininfo: 408323
literature
- topic: Phylogeny
- Pubmed-ID: 33588983
- title: Desulfovibrio subterraneus sp. nov., a mesophilic sulfate-reducing deltaproteobacterium isolated from a deep siliceous mudstone formation.
- authors: Ueno A, Tamazawa S, Tamamura S, Murakami T, Kiyama T, Inomata H, Amano Y, Miyakawa K, Tamaki H, Naganuma T, Kaneko K
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.004683
- year: 2021
- mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Desulfovibrio/*classification/isolation & purification, Fatty Acids/chemistry, Groundwater/*microbiology, Japan, Oxidation-Reduction, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sulfates, Sulfites, Vitamin K 2/analogs & derivatives/chemistry
- topic2: Transcriptome
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 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 | |
| 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 | |
| 67128 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-101010 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 101010) | |
| 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 | |
| 112488 | 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-ID408323.1 |