Strain identifier

BacDive ID: 5806

Type strain: Yes

Species: Geotalea toluenoxydans

Strain Designation: TMJ1

Strain history: R. U. Meckenstock TMJ1.

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

@ref: 8065

BacDive-ID: 5806

DSM-Number: 19350

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

description: Geotalea toluenoxydans TMJ1 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from sludge of a monitoring well at a tar-oil contaminated aquifer.

NCBI tax id

NCBI tax idMatching level
421624species
1294260strain

strain history

@refhistory
8065<- U. Kunapuli, GSF - German Res. Center Environmental Health, Neuherberg, Germany; TMJ1
67770R. U. Meckenstock TMJ1.

doi: 10.13145/bacdive5806.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Deltaproteobacteria
  • order: Desulfuromonadales
  • family: Geobacteraceae
  • genus: Geotalea
  • species: Geotalea toluenoxydans
  • full scientific name: Geotalea toluenoxydans (Kunapuli et al. 2010) Waite et al. 2020
  • synonyms

    • @ref: 20215
    • synonym: Geobacter toluenoxydans

@ref: 8065

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Desulfuromonadales

family: Geobacteraceae

genus: Geotalea

species: Geotalea toluenoxydans

full scientific name: Geotalea toluenoxydans (Kunapuli et al. 2010) Waite et al. 2020

strain designation: TMJ1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29004negative2.95 µm0.4 µmrod-shapedno
69480yes93.529
69480negative100

colony morphology

  • @ref: 8065
  • incubation period: 3-7 days

Culture and growth conditions

culture medium

  • @ref: 8065
  • name: GEOANAEROBACTER MEDIUM (DSMZ Medium 838)
  • growth: yes
  • link: https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium838.pdf

culture temp

@refgrowthtypetemperaturerange
8065positivegrowth30mesophilic
29004positivegrowth25-32mesophilic
29004positiveoptimum28.5mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepH
29004positivegrowth6.6-7.5
29004positiveoptimum6.8

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8065anaerobe
29004anaerobe
69480anaerobe98.266

spore formation

@refspore formationconfidence
29004no
69481no100
69480no99.975

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2900417272propionate+carbon source
2900415361pyruvate+carbon source

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8065sludge of a monitoring well at a tar-oil contaminated aquiferStuttgartGermanyDEUEurope
67770Sludge of a monitoring well at a tar-oil-contaminated aquiferStuttgartGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination#Oil (Fuel)
#Engineered#Industrial#Oil reservoir
#Environmental#Aquatic
#Environmental#Terrestrial#Mud (Sludge)

taxonmaps

  • @ref: 69479
  • File name: preview.99_7373.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15357;96_514;97_592;98_680;99_7373&stattab=map
  • Last taxonomy: Geobacter
  • 16S sequence: EU711072
  • Sequence Identity:
  • Total samples: 1260
  • soil counts: 714
  • aquatic counts: 505
  • animal counts: 11
  • plant counts: 30

Safety information

risk assessment

  • @ref: 8065
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8065
  • description: Geobacter toluenoxydans strain TMJ1 16S ribosomal RNA gene, partial sequence
  • accession: EU711072
  • length: 1440
  • database: ena
  • NCBI tax ID: 1294260

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Geobacter toluenoxydans JCM 157641294260.3wgspatric1294260
66792Geobacter toluenoxydans JCM 157642728369703draftimg1294260
67770Geotalea toluenoxydans JCM 15764GCA_001311985contigncbi1294260

GC content

@refGC-contentmethod
806554.4high performance liquid chromatography (HPLC)
2900454.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes70.315yes
gram-positiveno98.647yes
anaerobicyes97.574yes
aerobicno97.485yes
halophileno91.019no
spore-formingno91.288yes
glucose-utilno66.103no
flagellatedno88.017yes
thermophileno90.999yes
glucose-fermentno86.594no

External links

@ref: 8065

culture collection no.: DSM 19350, JCM 15764

straininfo link

  • @ref: 75285
  • straininfo: 405747

literature

  • topic: Phylogeny
  • Pubmed-ID: 19656942
  • title: Desulfitobacterium aromaticivorans sp. nov. and Geobacter toluenoxydans sp. nov., iron-reducing bacteria capable of anaerobic degradation of monoaromatic hydrocarbons.
  • authors: Kunapuli U, Jahn MK, Lueders T, Geyer R, Heipieper HJ, Meckenstock RU
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.003525-0
  • year: 2009
  • mesh: Betaproteobacteria/*classification/genetics/*isolation & purification/metabolism, Cellulose/*metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8065Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19350)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19350
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
29004Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2543728776041
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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
75285Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID405747.1StrainInfo: A central database for resolving microbial strain identifiers