Strain identifier
BacDive ID: 5798
Type strain:
Species: Geobacter grbiciae
Strain Designation: TACP-2
Strain history: <- J. D. Coates, Southern Illinois University Carbondale, USA; TACP-2 <- J. D. Coates {1994}
NCBI tax ID(s): 155042 (species)
General
@ref: 4954
BacDive-ID: 5798
DSM-Number: 13689
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile
description: Geobacter grbiciae TACP-2 is an anaerobe, mesophilic, motile bacterium that was isolated from freshwater aquatic sediment.
NCBI tax id
- NCBI tax id: 155042
- Matching level: species
strain history
- @ref: 4954
- history: <- J. D. Coates, Southern Illinois University Carbondale, USA; TACP-2 <- J. D. Coates {1994}
doi: 10.13145/bacdive5798.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Desulfuromonadales
- family: Geobacteraceae
- genus: Geobacter
- species: Geobacter grbiciae
- full scientific name: Geobacter grbiciae Coates et al. 2001
@ref: 4954
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Desulfuromonadales
family: Geobacteraceae
genus: Geobacter
species: Geobacter grbiciae
full scientific name: Geobacter grbiciae Coates et al. 2001
strain designation: TACP-2
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | yes | 91.612 | |
69480 | 99.999 | negative |
colony morphology
- @ref: 4954
- incubation period: 3-7 days
Culture and growth conditions
culture medium
- @ref: 4954
- name: GEOBACTER MEDIUM (DSMZ Medium 579)
- growth: yes
- link: https://mediadive.dsmz.de/medium/579
- composition: Name: GEOBACTER MEDIUM (DSMZ Medium 579) Composition: Fe(III) citrate 13.5509 g/l Na-acetate 2.4728 g/l NaHCO3 2.4728 g/l NH4Cl 1.48368 g/l NaH2PO4 0.593472 g/l KCl 0.098912 g/l MgSO4 x 7 H2O 0.0296736 g/l Nitrilotriacetic acid 0.0148368 g/l NaCl 0.0098912 g/l MnSO4 x H2O 0.0049456 g/l CoSO4 x 7 H2O 0.00178042 g/l ZnSO4 x 7 H2O 0.00178042 g/l FeSO4 x 7 H2O 0.00098912 g/l CaCl2 x 2 H2O 0.00098912 g/l NiCl2 x 6 H2O 0.000296736 g/l Na2WO4 x 2 H2O 0.00024728 g/l AlK(SO4)2 x 12 H2O 0.000197824 g/l CuSO4 x 5 H2O 9.8912e-05 g/l H3BO3 9.8912e-05 g/l Na2MoO4 x 2 H2O 9.8912e-05 g/l Pyridoxine hydrochloride 9.8912e-05 g/l p-Aminobenzoic acid 4.9456e-05 g/l (DL)-alpha-Lipoic acid 4.9456e-05 g/l Calcium D-(+)-pantothenate 4.9456e-05 g/l Nicotinic acid 4.9456e-05 g/l Riboflavin 4.9456e-05 g/l Thiamine HCl 4.9456e-05 g/l Folic acid 1.97824e-05 g/l Biotin 1.97824e-05 g/l Na2SeO3 x 5 H2O 2.96736e-06 g/l Vitamin B12 9.8912e-07 g/l Distilled water
culture temp
- @ref: 4954
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
4954 | anaerobe | |
69480 | anaerobe | 97.395 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 92 |
69480 | no | 99.943 |
Isolation, sampling and environmental information
isolation
- @ref: 4954
- sample type: freshwater aquatic sediment
- geographic location: Virginia, Potomac River Estuary
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Freshwater |
#Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_4529.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15357;96_2263;97_2742;98_3405;99_4529&stattab=map
- Last taxonomy: Geobacter
- 16S sequence: AF335183
- Sequence Identity:
- Total samples: 695
- soil counts: 237
- aquatic counts: 409
- animal counts: 37
- plant counts: 12
Safety information
risk assessment
- @ref: 4954
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Geobacter grbicium strain TACP-2 16S ribosomal RNA gene, complete sequence | AF335182 | 1527 | ena | 155042 |
20218 | Geobacter sp. 16S ribosomal RNA gene, partial sequence | U46862 | 277 | ena | 46610 |
4954 | Geobacter grbicium strain TACP-5 16S ribosomal RNA gene, complete sequence | AF335183 | 1542 | ena | 155042 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Geobacter grbiciae DSM 13689 | GCA_018531165 | contig | ncbi | 155042 |
66792 | Geobacter grbiciae strain DSM 13689 | 155042.3 | wgs | patric | 155042 |
GC content
- @ref: 4954
- GC-content: 57.4
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 92 | no |
motile | yes | 84.376 | no |
gram-positive | no | 98.527 | no |
anaerobic | yes | 96.986 | yes |
aerobic | no | 95.058 | no |
halophile | no | 93.006 | no |
spore-forming | no | 90.841 | no |
thermophile | no | 94.484 | yes |
glucose-util | no | 60.245 | no |
flagellated | no | 76.895 | no |
glucose-ferment | no | 87.206 | no |
External links
@ref: 4954
culture collection no.: DSM 13689
straininfo link
- @ref: 75277
- straininfo: 126174
literature
- topic: Phylogeny
- Pubmed-ID: 11321104
- title: Geobacter hydrogenophilus, Geobacter chapellei and Geobacter grbiciae, three new, strictly anaerobic, dissimilatory Fe(III)-reducers.
- authors: Coates JD, Bhupathiraju VK, Achenbach LA, Mclnerney MJ, Lovley DR
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/00207713-51-2-581
- year: 2001
- mesh: Base Composition, Deltaproteobacteria/classification/isolation & purification/*metabolism, Ferric Compounds/*metabolism, Gram-Negative Anaerobic Straight, Curved, and Helical Rods/classification/isolation & purification/*metabolism, Hydrocarbons/metabolism, Iron/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidation-Reduction, RNA, Ribosomal, 16S/genetics
- topic2: Metabolism
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
4954 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13689) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-13689 | |||
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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
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) | |||
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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
75277 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID126174.1 | StrainInfo: A central database for resolving microbial strain identifiers |