Strain identifier

BacDive ID: 133068

Type strain: Yes

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)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refgram staincell lengthcell widthcell shapemotilityconfidence
25213positive1.0-2.0 µm0.5-0.6 µmrod-shapedyes
69480yes92.243
69480positive99.719

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

@refgrowthtypetemperaturerangeconfidence
25213positivegrowth45.0-72.0thermophilic
25213positiveoptimum65thermophilic
24856positivegrowth65thermophilic
69480thermophilic100

culture pH

@refabilitytypepHPH range
25213positivegrowth5.5-8.5alkaliphile
25213positiveoptimum6.0-6.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
25213anaerobe
69480anaerobe100

nutrition type

  • @ref: 25213
  • type: chemolithoautotroph

spore formation

@refspore formationconfidence
25213no
69481no100
69480yes99.574

halophily

@refsalttested relationconcentrationgrowth
25213NaCloptimum0 %
25213NaClgrowth0.0-0.5 %(w/v)positive

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2521333403elemental sulfur-electron acceptor
2521317632nitrate-electron acceptor
2521316189sulfate-electron acceptor
2521316094thiosulfate-electron acceptor
2521317359sulfite+reduction
2521317359sulfite+electron acceptor

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
24856water and sediment from a terrestrial hot springKunashir IslandRussiaRUSAsia
25213water and sediment from a terrestrial hot springKunashir IslandRussiaRUSAsia44.171145.92anaerobically prepared, bicarbonate-buffered liquid mediumper 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??15 days65

isolation source categories

Cat1Cat2Cat3
#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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thermodesulfitimonas autotrophica DSM 102936GCA_003815015contigncbi1894989
66792Thermodesulfitimonas autotrophica strain DSM 1029361894989.3wgspatric1894989
66792Thermodesulfitimonas autotrophica DSM 1029362786546166draftimg1894989

GC content

  • @ref: 25213
  • GC-content: 55.8
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes87.266yes
gram-positiveno87.44no
anaerobicyes99.998yes
aerobicno98.557yes
halophileno96.086yes
spore-formingyes65.613yes
glucose-utilyes73.533no
flagellatedno95.816no
thermophileyes100yes
glucose-fermentno73.113no

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

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
24856Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-102936Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102936)
25213G. 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 spring10.1099/ijsem.0.001619IJSEM 67: 301-305 201728287372
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
69479João 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 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions 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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91333Reimer, 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 identifiers10.60712/SI-ID405919.1