Strain identifier
BacDive ID: 133068
Type strain:
Species: Thermodesulfitimonas autotrophica
Strain Designation: SF97
Strain history: <- G. Slobodkina, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; SF97 <- G. Slobodkina {2014}
NCBI tax ID(s): 1894989 (species)
General
@ref: 24856
BacDive-ID: 133068
DSM-Number: 102936
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, chemolithoautotroph, thermophilic, Gram-positive, motile, rod-shaped
description: Thermodesulfitimonas autotrophica SF97 is an anaerobe, chemolithoautotroph, thermophilic bacterium that was isolated from water and sediment from a terrestrial hot spring.
NCBI tax id
- NCBI tax id: 1894989
- Matching level: species
strain history
- @ref: 24856
- history: <- G. Slobodkina, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; SF97 <- G. Slobodkina {2014}
doi: 10.13145/bacdive133068.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Thermoanaerobacterales
- family: Thermoanaerobacteraceae
- genus: Thermodesulfitimonas
- species: Thermodesulfitimonas autotrophica
- full scientific name: Thermodesulfitimonas autotrophica Slobodkina et al. 2017
@ref: 24856
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Thermoanaerobacterales
family: Thermoanaerobacteraceae
genus: Thermodesulfitimonas
species: Thermodesulfitimonas autotrophica
full scientific name: Thermodesulfitimonas autotrophica Slobodkina et al. 2017
strain designation: SF97
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
25213 | positive | 1.0-2.0 µm | 0.5-0.6 µm | rod-shaped | yes | |
69480 | yes | 92.243 | ||||
69480 | positive | 99.719 |
Culture and growth conditions
culture medium
- @ref: 24856
- name: THERMODESULFITIMONAS MEDIUM (DSMZ Medium 503e)
- growth: yes
- link: https://mediadive.dsmz.de/medium/503e
- composition: Name: THERMODESULFITIMONAS MEDIUM (DSMZ Medium 503e) Composition: NaCl 0.997012 g/l Na2SO3 0.598205 g/l Na2CO3 0.498504 g/l KCl 0.498504 g/l MgCl2 x 6 H2O 0.398804 g/l Na2S x 9 H2O 0.299103 g/l NH4Cl 0.249253 g/l KH2PO4 0.199401 g/l CaCl2 x 2 H2O 0.149551 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 Nicotinic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 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 Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Folic acid 1.99402e-05 g/l Biotin 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 | range | confidence |
---|---|---|---|---|---|
25213 | positive | growth | 45.0-72.0 | thermophilic | |
25213 | positive | optimum | 65 | thermophilic | |
24856 | positive | growth | 65 | thermophilic | |
69480 | thermophilic | 100 |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
25213 | positive | growth | 5.5-8.5 | alkaliphile |
25213 | positive | optimum | 6.0-6.5 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
25213 | anaerobe | |
69480 | anaerobe | 100 |
nutrition type
- @ref: 25213
- type: chemolithoautotroph
spore formation
@ref | spore formation | confidence |
---|---|---|
25213 | no | |
69481 | no | 100 |
69480 | yes | 99.574 |
halophily
@ref | salt | tested relation | concentration | growth |
---|---|---|---|---|
25213 | NaCl | optimum | 0 % | |
25213 | NaCl | growth | 0.0-0.5 %(w/v) | positive |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
25213 | 33403 | elemental sulfur | - | electron acceptor |
25213 | 17632 | nitrate | - | electron acceptor |
25213 | 16189 | sulfate | - | electron acceptor |
25213 | 16094 | thiosulfate | - | electron acceptor |
25213 | 17359 | sulfite | + | reduction |
25213 | 17359 | sulfite | + | electron acceptor |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude | enrichment culture | enrichment culture composition | enrichment culture duration | enrichment culture temperature |
---|---|---|---|---|---|---|---|---|---|---|---|
24856 | water and sediment from a terrestrial hot spring | Kunashir Island | Russia | RUS | Asia | ||||||
25213 | water and sediment from a terrestrial hot spring | Kunashir Island | Russia | RUS | Asia | 44.171 | 145.92 | anaerobically prepared, bicarbonate-buffered liquid medium | per litre of distilled water: 0.33 g NH4Cl, 0.33 g KCl, 0.33 g CaCl2.6H2O, 0.33 g KH2PO4 , 0.33 g MgCl2.6H2O,2.0 g NaHCO3 , 1 ml trace element solution [8] and 1 ml vitamin solution; 5 mM Sodium sulfite; 10 mmol Fe(III) lâ??1 | 5 days | 65 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Sediment |
#Environmental | #Aquatic | #Thermal spring |
#Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_46394.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_4592;96_21162;97_26381;98_33541;99_46394&stattab=map
- Last taxonomy: Thermodesulfitimonas autotrophica subclade
- 16S sequence: KX450231
- Sequence Identity:
- Total samples: 91
- soil counts: 16
- aquatic counts: 69
- animal counts: 6
Safety information
risk assessment
- @ref: 24856
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24856
- description: Thermodesulfitimonas autotrophica strain SF97 16S ribosomal RNA gene, partial sequence
- accession: KX450231
- length: 1427
- database: ena
- NCBI tax ID: 1894989
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Thermodesulfitimonas autotrophica DSM 102936 | GCA_003815015 | contig | ncbi | 1894989 |
66792 | Thermodesulfitimonas autotrophica strain DSM 102936 | 1894989.3 | wgs | patric | 1894989 |
66792 | Thermodesulfitimonas autotrophica DSM 102936 | 2786546166 | draft | img | 1894989 |
GC content
- @ref: 25213
- GC-content: 55.8
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 87.266 | yes |
gram-positive | no | 87.44 | no |
anaerobic | yes | 99.998 | yes |
aerobic | no | 98.557 | yes |
halophile | no | 96.086 | yes |
spore-forming | yes | 65.613 | yes |
glucose-util | yes | 73.533 | no |
flagellated | no | 95.816 | no |
thermophile | yes | 100 | yes |
glucose-ferment | no | 73.113 | no |
External links
@ref: 24856
culture collection no.: DSM 102936, VKM B-2961
straininfo link
- @ref: 91333
- straininfo: 405919
literature
- topic: Phylogeny
- Pubmed-ID: 28287372
- title: Thermodesulfitimonas autotrophica gen. nov., sp. nov., a thermophilic, obligate sulfite-reducing bacterium isolated from a terrestrial hot spring.
- authors: Slobodkina GB, Baslerov RV, Novikov AA, Bonch-Osmolovskaya EA, Slobodkin AI
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.001619
- year: 2017
Reference
@id | authors | title | doi/url | catalogue | journal | 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 | |||
24856 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-102936 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102936) | |||
25213 | G. B. B. Slobodkina, R. V.,Novikov, A. A.,Bonch-Osmolovskaya, E. A.,Slobodkin, A. I. | Thermodesulfitimonas autotrophica gen. nov., sp. nov., a thermophilic, obligate sulfite-reducing bacterium isolated from a terrestrial hot spring | 10.1099/ijsem.0.001619 | IJSEM 67: 301-305 2017 | 28287372 | |
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 | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | 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. | 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 | |||
91333 | 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-ID405919.1 |