Strain identifier
BacDive ID: 11830
Type strain: 
Species: Desulfofundulus thermosubterraneus
Strain Designation: RL50JIII
Strain history: DSM 16057 <-- A. Kaksonen RL50JIII.
NCBI tax ID(s): 1121432 (strain), 348840 (species)
version 9.2 (current version)
General
@ref: 6246
BacDive-ID: 11830
DSM-Number: 16057
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic
description: Desulfofundulus thermosubterraneus RL50JIII is an anaerobe, thermophilic bacterium that was isolated from geothermally active underground mine.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 348840 | species |
| 1121432 | strain |
strain history
| @ref | history |
|---|---|
| 6246 | <- A. H. Kaksonen, Tampere Univ. Technol., Finland; RL50JIII <- A. H. Kaksonen {2002} |
| 67770 | DSM 16057 <-- A. Kaksonen RL50JIII. |
doi: 10.13145/bacdive11830.20241212.9.2
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Peptococcaceae
- genus: Desulfofundulus
- species: Desulfofundulus thermosubterraneus
- full scientific name: Desulfofundulus thermosubterraneus (Kaksonen et al. 2006) Watanabe et al. 2018
synonyms
- @ref: 20215
- synonym: Desulfotomaculum thermosubterraneum
@ref: 6246
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Peptococcaceae
genus: Desulfofundulus
species: Desulfofundulus thermosubterraneus
full scientific name: Desulfofundulus thermosubterraneus (Kaksonen et al. 2006) Watanabe et al. 2018
strain designation: RL50JIII
type strain: yes
Culture and growth conditions
culture medium
- @ref: 6246
- name: DESULFOVIBRIO (MV) MEDIUM (DSMZ Medium 641)
- growth: yes
- link: https://mediadive.dsmz.de/medium/641
- composition: 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 | growth | type | temperature |
|---|---|---|---|
| 6246 | positive | growth | 60 |
| 67770 | positive | growth | 60 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 6246 | anaerobe | |
| 69480 | anaerobe | 91.546 |
observation
- @ref: 67770
- observation: quinones: MK-7
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 6246 | geothermally active underground mine | Hokkaido, Toyoha mine | Japan | JPN | Asia |
| 67770 | Geothermally active underground mine | Japan | JPN | Asia |
isolation source categories
- Cat1: #Engineered
- Cat2: #Other
- Cat3: #Mine
Safety information
risk assessment
- @ref: 6246
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6246
- description: Desulfotomaculum thermosubterraneum strain RL50JIII 16S ribosomal RNA gene, partial sequence
- accession: DQ208688
- length: 1505
- database: nuccore
- NCBI tax ID: 1121432
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Desulfotomaculum thermosubterraneum DSM 16057 | 1121432.3 | wgs | patric | 1121432 |
| 66792 | Desulfofundulus thermosubterraneus DSM 16057 | 2585428086 | draft | img | 1121432 |
| 67770 | Desulfofundulus thermosubterraneus DSM 16057 | GCA_900142025 | scaffold | ncbi | 1121432 |
GC content
- @ref: 67770
- GC-content: 54.5
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 77 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 59.952 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 91.546 | yes |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 81.152 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 95.513 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | yes | 75.713 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 66.651 | no |
External links
@ref: 6246
culture collection no.: DSM 16057, JCM 13837
straininfo link
- @ref: 81049
- straininfo: 297186
literature
- topic: Metabolism
- Pubmed-ID: 17082399
- title: Desulfotomaculum thermosubterraneum sp. nov., a thermophilic sulfate-reducer isolated from an underground mine located in a geothermally active area.
- authors: Kaksonen AH, Spring S, Schumann P, Kroppenstedt RM, Puhakka JA
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.64439-0
- year: 2006
- mesh: Alanine/metabolism, Alcohols/metabolism, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, Carboxylic Acids/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Desulfotomaculum/*classification/cytology/*isolation & purification/physiology, Fatty Acids/analysis, Genes, rRNA, Growth Inhibitors/pharmacology, Hydrogen/metabolism, Hydrogen-Ion Concentration, Japan, Lactic Acid/metabolism, *Mining, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Phylogeny, Pyruvic Acid/metabolism, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/pharmacology, *Soil Microbiology, Sulfates/*metabolism, Sulfites/metabolism, Sulfur/metabolism, Temperature
- topic2: Phylogeny
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 6246 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16057) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16057 | |
| 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) | |
| 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) | |
| 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 | |
| 81049 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297186.1 | StrainInfo: A central database for resolving microbial strain identifiers |