Strain identifier
BacDive ID: 5800
Type strain: 
Species: Geobacter hydrogenophilus
Strain Designation: H-2
Strain history: <- J. D. Coates, Southern Illinois University Carbondale, USA; H-2 <- J. D. Coates {1994}
NCBI tax ID(s): 40983 (species)
version 8.1 (current version)
General
@ref: 5116
BacDive-ID: 5800
DSM-Number: 13691
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile
description: Geobacter hydrogenophilus H-2 is an anaerobe, mesophilic, motile bacterium that was isolated from Petroleum-contaminated water table aquifer.
NCBI tax id
- NCBI tax id: 40983
- Matching level: species
strain history
- @ref: 5116
- history: <- J. D. Coates, Southern Illinois University Carbondale, USA; H-2 <- J. D. Coates {1994}
doi: 10.13145/bacdive5800.20230509.8.1
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 hydrogenophilus
- full scientific name: Geobacter hydrogenophilus Coates et al. 2001
@ref: 5116
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Desulfuromonadales
family: Geobacteraceae
genus: Geobacter
species: Geobacter hydrogenophilus
full scientific name: Geobacter hydrogenophilus Coates et al. 2001
strain designation: H-2
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 94.211 | |
| 69480 | 99.999 | negative |
colony morphology
- @ref: 5116
- incubation period: 3-7 days
Culture and growth conditions
culture medium
- @ref: 5116
- name: GEOBACTER SULFURREDUCENS MEDIUM (DSMZ Medium 826)
- growth: yes
- link: https://mediadive.dsmz.de/medium/826
- composition: Name: GEOBACTER SULFURREDUCENS MEDIUM (DSMZ Medium 826) Composition: Na2-fumarate 7.91296 g/l NaHCO3 2.4728 g/l NH4Cl 1.48368 g/l Na-acetate 0.811078 g/l Na2HPO4 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 ZnSO4 x 7 H2O 0.00178042 g/l CoSO4 x 7 H2O 0.00178042 g/l CaCl2 x 2 H2O 0.00098912 g/l FeSO4 x 7 H2O 0.00098912 g/l NiCl2 x 6 H2O 0.000296736 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 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 (DL)-alpha-Lipoic acid 4.9456e-05 g/l Folic acid 1.97824e-05 g/l Biotin 1.97824e-05 g/l Na2WO4 x 2 H2O 3.95648e-06 g/l Na2SeO3 x 5 H2O 2.96736e-06 g/l Vitamin B12 9.8912e-07 g/l Distilled water
culture temp
- @ref: 5116
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 5116 | anaerobe | |
| 69480 | anaerobe | 93.499 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.983 |
Isolation, sampling and environmental information
isolation
- @ref: 5116
- sample type: Petroleum-contaminated water table aquifer
- geographic location: South Carolina, Hanahan, Defense Fuel Supply Center
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
| Cat1 | Cat2 |
|---|---|
| #Engineered | #Contamination |
| #Environmental | #Aquatic |
taxonmaps
- @ref: 69479
- File name: preview.99_167828.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15357;96_2263;97_81348;98_110133;99_167828&stattab=map
- Last taxonomy: Geobacter hydrogenophilus subclade
- 16S sequence: U28173
- Sequence Identity:
- Total samples: 19
- soil counts: 1
- aquatic counts: 16
- animal counts: 1
- plant counts: 1
Safety information
risk assessment
- @ref: 5116
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 5116
- description: Geobacter hydrogenophilus 16S ribosomal RNA gene, partial sequence
- accession: U28173
- length: 1418
- database: ena
- NCBI tax ID: 40983
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Geobacter hydrogenophilus DSM 13691 | GCA_018501225 | contig | ncbi | 40983 |
| 66792 | Geobacter hydrogenophilus strain DSM 13691 | 40983.3 | wgs | patric | 40983 |
GC content
- @ref: 5116
- GC-content: 58.4
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| gram-positive | no | 98.274 | no |
| anaerobic | yes | 96.773 | yes |
| halophile | no | 92.479 | no |
| spore-forming | no | 87.851 | no |
| glucose-util | no | 60.623 | no |
| aerobic | no | 94.624 | yes |
| flagellated | no | 80.434 | no |
| motile | yes | 85.556 | no |
| thermophile | no | 96.937 | no |
| glucose-ferment | no | 89.173 | no |
External links
@ref: 5116
culture collection no.: DSM 13691
straininfo link
- @ref: 75279
- straininfo: 43065
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 5116 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13691) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-13691 | |
| 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 | |
| 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 | |
| 75279 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID43065.1 | StrainInfo: A central database for resolving microbial strain identifiers |