Strain identifier
BacDive ID: 5806
Type strain: 
Species: Geotalea toluenoxydans
Strain Designation: TMJ1
Strain history: R. U. Meckenstock TMJ1.
NCBI tax ID(s): 1294260 (strain), 421624 (species)
version 9.3 (current version)
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 id | Matching level |
|---|---|
| 421624 | species |
| 1294260 | strain |
strain history
| @ref | history |
|---|---|
| 8065 | <- U. Kunapuli, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany; TMJ1 |
| 67770 | R. U. Meckenstock TMJ1. |
doi: 10.13145/bacdive5806.20250331.9.3
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
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 29004 | negative | 2.95 µm | 0.4 µm | rod-shaped | no | |
| 125439 | negative | 98.4 | ||||
| 125438 | negative | 96.468 |
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
| @ref | growth | type | temperature |
|---|---|---|---|
| 8065 | positive | growth | 30 |
| 29004 | positive | growth | 25-32 |
| 29004 | positive | optimum | 28.5 |
| 67770 | positive | growth | 30 |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 29004 | positive | growth | 6.6-7.5 |
| 29004 | positive | optimum | 6.8 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 8065 | anaerobe |
| 29004 | anaerobe |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 29004 | no | |
| 125439 | no | 97.2 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29004 | 17272 | propionate | + | carbon source |
| 29004 | 15361 | pyruvate | + | carbon source |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 8065 | sludge of a monitoring well at a tar-oil contaminated aquifer | Stuttgart | Germany | DEU | Europe |
| 67770 | Sludge of a monitoring well at a tar-oil-contaminated aquifer | Stuttgart | Germany | DEU | Europe |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #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: nuccore
- NCBI tax ID: 1294260
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Geobacter toluenoxydans JCM 15764 | 1294260.3 | wgs | patric | 1294260 |
| 66792 | Geobacter toluenoxydans JCM 15764 | 2728369703 | draft | img | 1294260 |
| 67770 | Geotalea toluenoxydans JCM 15764 | GCA_001311985 | contig | ncbi | 1294260 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 8065 | 54.4 | high performance liquid chromatography (HPLC) |
| 29004 | 54.4 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 96.468 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 75.034 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 87.191 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 81.516 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 86.796 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 68.408 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 97.2 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 61.4 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 98.4 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | anaerobe | 84.7 |
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
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 8065 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19350) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19350 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 29004 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 25437 | 28776041 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 75285 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID405747.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |