Strain identifier

BacDive ID: 294

Type strain: Yes

Species: Tolumonas auensis

Strain Designation: TA4

Strain history: <- C. Fischer, TA4

NCBI tax ID(s): 595494 (strain), 43948 (species)

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General

@ref: 3506

BacDive-ID: 294

DSM-Number: 9187

keywords: genome sequence, Bacteria, anaerobe, mesophilic, Gram-negative, rod-shaped

description: Tolumonas auensis TA4 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from freshwater mud.

NCBI tax id

NCBI tax idMatching level
595494strain
43948species

strain history

  • @ref: 3506
  • history: <- C. Fischer, TA4

doi: 10.13145/bacdive294.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Aeromonadales
  • family: Aeromonadaceae
  • genus: Tolumonas
  • species: Tolumonas auensis
  • full scientific name: Tolumonas auensis Fischer-Romero et al. 1996

@ref: 3506

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Aeromonadales

family: Aeromonadaceae

genus: Tolumonas

species: Tolumonas auensis

full scientific name: Tolumonas auensis Fischer-Romero et al. 1996

strain designation: TA4

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23264negative2.5-3.2 µm0.9-1.2 µmrod-shapedno
69480negative99.979

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3506R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
3506CLOSTRIDIUM (GV) MEDIUM (DSMZ Medium 500)yeshttps://mediadive.dsmz.de/medium/500Name: CLOSTRIDIUM (GV) MEDIUM (DSMZ Medium 500; with strain-specific modifications) Composition: NaHCO3 2.98507 g/l NaCl 2.23881 g/l D-Glucose 1.99005 g/l Yeast extract 0.995025 g/l NH4Cl 0.497512 g/l MgSO4 x 7 H2O 0.497512 g/l K2HPO4 0.348259 g/l Na2S x 9 H2O 0.298507 g/l L-Cysteine HCl x H2O 0.298507 g/l CaCl2 x 2 H2O 0.248756 g/l KH2PO4 0.228856 g/l HCl 0.00248756 g/l FeSO4 x 7 H2O 0.00199005 g/l FeCl2 x 4 H2O 0.00149254 g/l NaOH 0.000497512 g/l Sodium resazurin 0.000497512 g/l CoCl2 x 6 H2O 0.000189055 g/l MnCl2 x 4 H2O 9.95025e-05 g/l Pyridoxine hydrochloride 9.95025e-05 g/l ZnCl2 6.96517e-05 g/l p-Aminobenzoic acid 4.97512e-05 g/l (DL)-alpha-Lipoic acid 4.97512e-05 g/l Calcium D-(+)-pantothenate 4.97512e-05 g/l Nicotinic acid 4.97512e-05 g/l Riboflavin 4.97512e-05 g/l Thiamine HCl 4.97512e-05 g/l Na2MoO4 x 2 H2O 3.58209e-05 g/l NiCl2 x 6 H2O 2.38806e-05 g/l Folic acid 1.99005e-05 g/l Biotin 1.99005e-05 g/l H3BO3 5.97015e-06 g/l Na2WO4 x 2 H2O 3.9801e-06 g/l Na2SeO3 x 5 H2O 2.98507e-06 g/l CuCl2 x 2 H2O 1.99005e-06 g/l Vitamin B12 9.95025e-07 g/l Distilled water
3506NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
3506positivegrowth28mesophilic
23264positiveoptimum22psychrophilic

culture pH

  • @ref: 23264
  • ability: positive
  • type: optimum
  • pH: 7.2

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
3506anaerobe
23264aerobe
23264anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.984

compound production

@refcompound
3506toluene
3506phenol

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2326417521(-)-quinic acid+aerobic catabolization
23264309162-oxoglutarate+aerobic catabolization
23264167244-hydroxybutyrate+aerobic catabolization
2326430089acetate+aerobic catabolization
2326416383cis-aconitate+aerobic catabolization
2326415824D-fructose+aerobic catabolization
2326412936D-galactose+aerobic catabolization
2326418024D-galacturonic acid+aerobic catabolization
232648391D-gluconate+aerobic catabolization
2326417634D-glucose+aerobic catabolization
2326415748D-glucuronate+aerobic catabolization
2326432323glucuronamide+aerobic catabolization
2326417596inosine+aerobic catabolization
2326416977L-alanine+aerobic catabolization
2326430849L-arabinose+aerobic catabolization
2326417196L-asparagine+aerobic catabolization
2326429991L-aspartate+aerobic catabolization
2326429985L-glutamate+aerobic catabolization
2326415971L-histidine+aerobic catabolization
2326416857L-threonine+aerobic catabolization
2326424996lactate+aerobic catabolization
2326415792malonate+aerobic catabolization
2326415361pyruvate+aerobic catabolization
2326441865sebacic acid+aerobic catabolization
2326430031succinate+aerobic catabolization
2326453423tween 40+aerobic catabolization
2326453426tween 80+aerobic catabolization
2326427248urocanic acid+aerobic catabolization
2326417108D-arabinose+anaerobic catabolization
2326417057cellobiose+anaerobic catabolization
2326415824D-fructose+anaerobic catabolization
2326417634D-glucose+anaerobic catabolization
2326416899D-mannitol+anaerobic catabolization
2326416024D-mannose+anaerobic catabolization
232646731melezitose+anaerobic catabolization
2326416634raffinose+anaerobic catabolization
2326416988D-ribose+anaerobic catabolization
2326417924D-sorbitol+anaerobic catabolization
2326416551D-trehalose+anaerobic catabolization
2326428087glycogen+anaerobic catabolization
2326415443inulin+anaerobic catabolization
2326462345L-rhamnose+anaerobic catabolization
2326417306maltose+anaerobic catabolization
2326428053melibiose+anaerobic catabolization
2326417814salicin+anaerobic catabolization
2326417992sucrose+anaerobic catabolization

metabolite production

@refChebi-IDmetaboliteproduction
2326435581indoleno
2326416136hydrogen sulfideno
2326417578tolueneyes
2326415740formateyes
2326416236ethanolyes
2326430089acetateyes

enzymes

@refvalueactivityec
23264catalase+/-1.11.1.6
23264cytochrome oxidase-1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
3506freshwater mudLake AuSwitzerlandCHEEurope
23264anoxic sediment of a freshwater lake

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Freshwater
#Environmental#Terrestrial#Mud (Sludge)

Safety information

risk assessment

  • @ref: 3506
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Tolumonas auensis DSM 9187GCA_000023065completencbi595494
66792Tolumonas auensis DSM 9187595494.3completepatric595494
66792Tolumonas auensis TA 4, DSM 9187643692052completeimg595494

GC content

@refGC-contentmethod
350649.2high performance liquid chromatography (HPLC)
2326449.00high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno85.855no
flagellatedno92.526no
gram-positiveno98.219no
anaerobicno91.551no
aerobicno84.477no
halophileno87.694no
spore-formingno94.88no
thermophileno98.588yes
glucose-utilyes89.199no
glucose-fermentyes80.949no

External links

@ref: 3506

culture collection no.: DSM 9187

straininfo link

  • @ref: 69976
  • straininfo: 48591

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3506Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9187)https://www.dsmz.de/collection/catalogue/details/culture/DSM-9187
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
23264C. FISCHER-ROMERO, B. J. TINDALL, F. JüTTNER10.1099/00207713-46-1-183Tolumonas auensis gen. nov., sp. nov., a Toluene-Producing Bacterium from Anoxic Sediments of a Freshwater LakeIJSEM 46: 183-188 19968573493
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
69976Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID48591.1StrainInfo: A central database for resolving microbial strain identifiers