Strain identifier
BacDive ID: 5792
Type strain: 
Species: Geobacter sulfurreducens
Strain Designation: PCA
Strain history: <- B. Schink, Universität Konstanz, Fakultät für Biologie, Konstanz, Germany <- D. R. Lovley, U.S. Geological Survey, Reston, USA <- Caccavo, F., Jr, University of Oklahoma, Norman, USA; PCA
NCBI tax ID(s): 35554 (species)
version 8.1 (current version)
General
@ref: 4609
BacDive-ID: 5792
DSM-Number: 12127
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Geobacter sulfurreducens PCA is an anaerobe, mesophilic bacterium that was isolated from ditch surface sediment.
NCBI tax id
- NCBI tax id: 35554
- Matching level: species
strain history
- @ref: 4609
- history: <- B. Schink, Universität Konstanz, Fakultät für Biologie, Konstanz, Germany <- D. R. Lovley, U.S. Geological Survey, Reston, USA <- Caccavo, F., Jr, University of Oklahoma, Norman, USA; PCA
doi: 10.13145/bacdive5792.20230509.8.1
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 sulfurreducens
- full scientific name: Geobacter sulfurreducens Caccavo et al. 1995
@ref: 4609
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Desulfuromonadales
family: Geobacteraceae
genus: Geobacter
species: Geobacter sulfurreducens subsp. sulfurreducens
full scientific name: Geobacter sulfurreducens subsp. sulfurreducens (Caccavo et al. 1995) Viulu et al. 2014
strain designation: PCA
type strain: yes
Morphology
colony morphology
- @ref: 4609
- incubation period: 3-7 days
Culture and growth conditions
culture medium
- @ref: 4609
- 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: 4609
- growth: positive
- type: growth
- temperature: 35
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 4609
- oxygen tolerance: anaerobe
Isolation, sampling and environmental information
isolation
- @ref: 4609
- sample type: ditch surface sediment
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Sediment
taxonmaps
- @ref: 69479
- File name: preview.99_2237.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15357;96_1009;97_1175;98_1405;99_2237&stattab=map
- Last taxonomy: Geobacter sulfurreducens
- 16S sequence: U13928
- Sequence Identity:
- Total samples: 3293
- soil counts: 1138
- aquatic counts: 1606
- animal counts: 458
- plant counts: 91
Safety information
risk assessment
- @ref: 4609
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 4609
- description: Geobacter sulfurreducens 16S ribosomal RNA, partial sequence
- accession: U13928
- length: 1408
- database: ena
- NCBI tax ID: 243231
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Geobacter sulfurreducens PCA | GCA_000007985 | complete | ncbi | 243231 |
| 66792 | Geobacter sulfurreducens PCA | 243231.5 | complete | patric | 243231 |
| 66792 | Geobacter sulfurreducens PCA | 637000120 | complete | img | 243231 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 4609 | 60 | sequence analysis |
| 4609 | 61.9 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | yes | 88.828 | no |
| flagellated | no | 58.419 | no |
| gram-positive | no | 98.909 | no |
| anaerobic | yes | 98.541 | yes |
| halophile | no | 91.083 | no |
| spore-forming | no | 89.541 | no |
| thermophile | no | 96.263 | no |
| glucose-util | no | 65.737 | no |
| aerobic | no | 95.364 | no |
| glucose-ferment | no | 82.87 | no |
External links
@ref: 4609
culture collection no.: DSM 12127, ATCC 51573
straininfo link
- @ref: 75271
- straininfo: 43055
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Enzymology | 22492459 | Simple absolute quantification method correcting for quantitative PCR efficiency variations for microbial community samples. | Brankatschk R, Bodenhausen N, Zeyer J, Burgmann H | Appl Environ Microbiol | 10.1128/AEM.07878-11 | 2012 | Bacterial Load/*methods/*standards, *Environmental Microbiology, Geobacter/isolation & purification, Nostoc commune/isolation & purification, Oxidoreductases/genetics, RNA, Ribosomal, 16S/genetics, Real-Time Polymerase Chain Reaction/*methods/*standards | Phylogeny |
| Phylogeny | 25052395 | Geobacter anodireducens sp. nov., an exoelectrogenic microbe in bioelectrochemical systems. | Sun D, Wang A, Cheng S, Yates M, Logan BE | Int J Syst Evol Microbiol | 10.1099/ijs.0.061598-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Ferric Compounds/*metabolism, Geobacter/*classification/genetics/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidation-Reduction, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Metabolism |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 4609 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12127) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-12127 | |
| 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 | |
| 75271 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID43055.1 | StrainInfo: A central database for resolving microbial strain identifiers |