Strain identifier

BacDive ID: 295

Type strain: Yes

Species: Tolumonas osonensis

Strain history: <- R. S. Tanner, Dept. Botany and Microbiol., Univ. Oklahoma, USA; OCF 7

NCBI tax ID(s): 675874 (species)

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General

@ref: 16569

BacDive-ID: 295

DSM-Number: 22975

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, rod-shaped

description: Tolumonas osonensis DSM 22975 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from anoxic freshwater sediment.

NCBI tax id

  • NCBI tax id: 675874
  • Matching level: species

strain history

  • @ref: 16569
  • history: <- R. S. Tanner, Dept. Botany and Microbiol., Univ. Oklahoma, USA; OCF 7

doi: 10.13145/bacdive295.20230509.8.1

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 osonensis
  • full scientific name: Tolumonas osonensis Caldwell et al. 2011

@ref: 16569

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Aeromonadales

family: Aeromonadaceae

genus: Tolumonas

species: Tolumonas osonensis

full scientific name: Tolumonas osonensis Caldwell et al. 2011

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23265negative2.4-3.6 µm0.9 µmrod-shapedno
69480negative99.993

multimedia

  • @ref: 16569
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_22975.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 16569
  • name: REACTIVATION WITH LIQUID MEDIUM (DSMZ Medium 535b)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/535b
  • composition: Name: REACTIVATION WITH LIQUID MEDIUM (DSMZ Medium 535b) Composition: Trypticase soy broth 30.0 g/l Casein peptone 17.0 g/l Agar 15.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l K2HPO4 2.5 g/l D(+)-Glucose 2.5 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16569positivegrowth28mesophilic
23265positivegrowth15-37
23265positiveoptimum22psychrophilic

culture pH

@refabilitytypepHPH range
23265positivegrowth5.5-8.5alkaliphile
23265positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 23265
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.997

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2326530089acetate-growth
2326515963ribitol-growth
2326522599arabinose-growth
2326517750betaine-growth
2326528885butanol-growth
2326517968butyrate-growth
23265casamino acids-growth
2326516236ethanol-growth
2326515740formate-growth
2326517754glycerol-growth
2326529805glycolate-growth
2326517268myo-inositol-growth
2326524996lactate-growth
2326525115malate-growth
2326517790methanol-growth
23265peptone-growth
2326528831propanol-growth
2326517272propionate-growth
2326528017starch-growth
2326530031succinate-growth
2326518139trimethylamine-growth
2326518222xylose-growth
2326562968cellulose-hydrolysis
2326517029chitin-hydrolysis
232655291gelatin-hydrolysis
2326528017starch-hydrolysis
2326517632nitrate-reduction
2326516189sulfate-reduction
23265yeast extract-required for growth
2326517925alpha-D-glucose+aerobic catabolization
2326517057cellobiose+aerobic catabolization
2326515824D-fructose+aerobic catabolization
2326512936D-galactose+aerobic catabolization
2326516899D-mannitol+aerobic catabolization
2326516024D-mannose+aerobic catabolization
2326527605D-psicose+aerobic catabolization
2326517924D-sorbitol+aerobic catabolization
2326528066gentiobiose+aerobic catabolization
2326530849L-arabinose+aerobic catabolization
2326517716lactose+aerobic catabolization
232656359lactulose+aerobic catabolization
2326517306maltose+aerobic catabolization
2326528053melibiose+aerobic catabolization
23265320055methyl beta-D-glucopyranoside+aerobic catabolization
23265506227N-acetylglucosamine+aerobic catabolization
2326516634raffinose+aerobic catabolization
2326517992sucrose+aerobic catabolization
2326527082trehalose+aerobic catabolization
2326532528turanose+aerobic catabolization
2326537684mannose+fermentation
2326516634raffinose+fermentation
2326527613amygdalin+growth
2326517057cellobiose+growth
232654853esculin+growth
2326528757fructose+growth
2326529806fumarate+growth
2326528260galactose+growth
2326517234glucose+growth
2326528087glycogen+growth
2326515443inulin+growth
2326517716lactose+growth
2326517306maltose+growth
2326529864mannitol+growth
2326537684mannose+growth
232656731melezitose+growth
2326528053melibiose+growth
23265506227N-acetylglucosamine+growth
2326515361pyruvate+growth
2326516634raffinose+growth
2326533942ribose+growth
2326517814salicin+growth
2326530911sorbitol+growth
2326517992sucrose+growth
2326527082trehalose+growth
2326532528turanose+growth
23265yeast extract+growth
2326516199urea+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
2326517578tolueneno
2326535581indoleno

enzymes

@refvalueactivityec
23265Acid phosphatase+/-3.1.3.2
23265alanine arylamidase+3.4.11.2
23265alkaline phosphatase-3.1.3.1
23265Alkaline phosphatase+/-3.1.3.1
23265alpha-arabinosidase-3.2.1.55
23265alpha-chymotrypsin-3.4.21.1
23265alpha-fucosidase-3.2.1.51
23265alpha-galactosidase+3.2.1.22
23265alpha-galactosidase+/-3.2.1.22
23265alpha-glucosidase+3.2.1.20
23265alpha-glucosidase+/-3.2.1.20
23265alpha-mannosidase-3.2.1.24
23265arginine dihydrolase-3.5.3.6
23265beta-galactosidase-3.2.1.23
23265beta-galactosidase+3.2.1.23
23265beta-glucoronidase-3.2.1.31
23265beta-glucosidase+3.2.1.21
23265beta-glucuronidase-3.2.1.31
23265catalase+1.11.1.6
23265cystine arylamidase-3.4.11.3
23265cytochrome oxidase-1.9.3.1
23265esterase (C 4)+/-
23265esterase lipase (C 8)+/-
23265glutamate decarboxylase-4.1.1.15
23265glutamyl-glutamate arylamidase-
23265glycin arylamidase+
23265L-arginine arylamidase+
23265leucine arylamidase+3.4.11.1
23265leucine arylamidase-3.4.11.1
23265leucyl glycin arylamidase-3.4.11.1
23265lipase (C 14)-
23265N-acetyl-beta-glucosaminidase-3.2.1.52
23265naphthol-AS-BI-phosphohydrolase+/-
23265phenylalanine deaminase-4.3.1.5
23265proline-arylamidase-3.4.11.5
23265pyroglutamic acid arylamidase-
23265serine arylamidase+
23265trypsin-3.4.21.4
23265tyrosine arylamidase-
23265urease-3.5.1.5
23265valine arylamidase-

Isolation, sampling and environmental information

isolation

  • @ref: 16569
  • sample type: anoxic freshwater sediment
  • geographic location: Texas, Corpus Christi, Oso Creek (27° 43' N 97° 32' W)
  • country: USA
  • origin.country: USA
  • continent: North America
  • latitude: 27.7167
  • longitude: -97.5333

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Freshwater
#Environmental#Aquatic#Sediment
#Condition#Anoxic (anaerobic)

Safety information

risk assessment

  • @ref: 16569
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16569
  • description: Tolumonas osonensis strain OCF 7 16S ribosomal RNA gene, partial sequence
  • accession: GU370947
  • length: 1516
  • database: ena
  • NCBI tax ID: 675874

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Tolumonas osonensis DSM 22975GCA_014202415scaffoldncbi675874
66792Tolumonas osonensis strain DSM 22975675874.3wgspatric675874
66792Tolumonas osonensis DSM 229752861511751draftimg675874

GC content

@refGC-contentmethod
1656952high performance liquid chromatography (HPLC)
2326552.00high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno92yes
gram-positiveno98.189yes
anaerobicno94.166yes
aerobicno87.731yes
halophileno83.717no
spore-formingno95.973no
glucose-utilyes89.66yes
thermophileno98.485no
motileno88.008yes
glucose-fermentyes77.21no

External links

@ref: 16569

culture collection no.: DSM 22975, ATCC BAA 1908, OCF 7

straininfo link

  • @ref: 69977
  • straininfo: 402152

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21148672Tolumonas osonensis sp. nov., isolated from anoxic freshwater sediment, and emended description of the genus Tolumonas.Caldwell ME, Allen TD, Lawson PA, Tanner RSInt J Syst Evol Microbiol10.1099/ijs.0.023853-02010Aeromonadaceae/*classification/genetics/*isolation & purification/metabolism, Anaerobiosis, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Fresh Water/analysis/*microbiology, Geologic Sediments/analysis/*microbiology, Molecular Sequence Data, Oxygen/analysis/metabolism, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Metabolism23651598A new electrochemically active bacterium phylogenetically related to Tolumonas osonensis and power performance in MFCs.Luo J, Yang J, He H, Jin T, Zhou L, Wang M, Zhou MBioresour Technol10.1016/j.biortech.2013.04.03120131-Naphthylamine/analogs & derivatives/metabolism, Aeromonadaceae/drug effects/isolation & purification/*metabolism, Bioelectric Energy Sources/*microbiology, *Electricity, *Electrochemistry, Electrodes, Electron Transport/drug effects, Fatty Acids/metabolism, Fluorescence, Intracellular Space/drug effects/metabolism, *Phylogeny, Sodium Acetate/pharmacology, Ubiquinone/analogs & derivatives/metabolismPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16569Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22975)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22975
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
23265Matthew E. Caldwell, Toby D. Allen, Paul A. Lawson, Ralph S. Tanner10.1099/ijs.0.023853-0Tolumonas osonensis sp. nov., isolated from anoxic freshwater sediment, and emended description of the genus TolumonasIJSEM 61: 2659-2663 201121148672
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)
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
69977Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402152.1StrainInfo: A central database for resolving microbial strain identifiers