Strain identifier
BacDive ID: 11764
Type strain: 
Species: Desulfitobacterium hafniense
Strain Designation: PCE-S
Strain history: <- H. Scholz-Muramatsu, Univ. Stuttgart, Institut für Siedlungswasserbau, Stuttgart, Germany; PCE-S <- S. Granzow {1995}
NCBI tax ID(s): 49338 (species)
version 8.1 (current version)
General
@ref: 5430
BacDive-ID: 11764
DSM-Number: 14645
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Desulfitobacterium hafniense PCE-S is an anaerobe, mesophilic bacterium that was isolated from soil from landfill site Eppelheim.
NCBI tax id
- NCBI tax id: 49338
- Matching level: species
strain history
- @ref: 5430
- history: <- H. Scholz-Muramatsu, Univ. Stuttgart, Institut für Siedlungswasserbau, Stuttgart, Germany; PCE-S <- S. Granzow {1995}
doi: 10.13145/bacdive11764.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Desulfitobacteriaceae
- genus: Desulfitobacterium
- species: Desulfitobacterium hafniense
- full scientific name: Desulfitobacterium hafniense Christiansen and Ahring 1996
synonyms
- @ref: 20215
- synonym: Desulfitobacterium frappieri
@ref: 5430
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Peptococcaceae
genus: Desulfitobacterium
species: Desulfitobacterium hafniense
full scientific name: Desulfitobacterium hafniense Christiansen and Ahring 1996 emend. Niggemyer et al. 2001
strain designation: PCE-S
type strain: no
Culture and growth conditions
culture medium
- @ref: 5430
- name: DESULFITOBACTERIUM (PCE II) MEDIUM (DSMZ Medium 1062)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1062
- composition: Name: DESULFITOBACTERIUM (PCE II) MEDIUM (DSMZ Medium 1062) Composition: Na2-fumarate 6.42928 g/l Na-pyruvate 4.45104 g/l Yeast extract 1.97824 g/l Na2CO3 1.48368 g/l KCl 0.49456 g/l MgCl2 x 6 H2O 0.395648 g/l NH4Cl 0.24728 g/l KH2PO4 0.197824 g/l MgSO4 x 7 H2O 0.0296736 g/l FeSO4 x 7 H2O 0.0217606 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 CaCl2 x 2 H2O 0.00098912 g/l Sodium resazurin 0.00049456 g/l NiCl2 x 6 H2O 0.000296736 g/l Pyridoxine hydrochloride 0.000296736 g/l Thiamine-HCl x 2 H2O 0.000197824 g/l AlK(SO4)2 x 12 H2O 0.000197824 g/l Nicotinic acid 0.000197824 g/l CuSO4 x 5 H2O 9.8912e-05 g/l Calcium pantothenate 9.8912e-05 g/l Vitamin B12 9.8912e-05 g/l Na2MoO4 x 2 H2O 9.8912e-05 g/l H3BO3 9.8912e-05 g/l p-Aminobenzoic acid 7.91296e-05 g/l D-(+)-biotin 1.97824e-05 g/l Na2WO4 x 2 H2O 3.95648e-06 g/l Na2SeO3 x 5 H2O 2.96736e-06 g/l Distilled water
culture temp
- @ref: 5430
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 5430
- oxygen tolerance: anaerobe
Isolation, sampling and environmental information
isolation
- @ref: 5430
- sample type: soil from landfill site Eppelheim
- geographic location: Baden-Württemberg, near Heidelberg
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Waste | #Landfill |
| #Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_831.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_99;96_501;97_574;98_660;99_831&stattab=map
- Last taxonomy: Desulfitobacterium hafniense subclade
- 16S sequence: AJ512772
- Sequence Identity:
- Total samples: 225
- soil counts: 129
- aquatic counts: 46
- animal counts: 39
- plant counts: 11
Safety information
risk assessment
- @ref: 5430
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 5430
- description: Desulfitobacterium sp. PCE-S partial 16S rRNA gene, strain PCE-S
- accession: AJ512772
- length: 1451
- database: ena
- NCBI tax ID: 211883
Genome sequences
- @ref: 66792
- description: Desulfitobacterium hafniense PCE-S
- accession: GCA_000944695
- assembly level: contig
- database: ncbi
- NCBI tax ID: 49338
GC content
- @ref: 5430
- GC-content: 47.3
- method: sequence analysis
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | yes | 88.088 | no |
| flagellated | no | 65.861 | no |
| gram-positive | no | 86.318 | no |
| anaerobic | yes | 97.458 | no |
| aerobic | no | 95.683 | yes |
| halophile | no | 93.999 | no |
| spore-forming | yes | 94.843 | no |
| glucose-util | yes | 59.283 | no |
| thermophile | no | 99.702 | yes |
| glucose-ferment | no | 77.963 | no |
External links
@ref: 5430
culture collection no.: DSM 14645
straininfo link
- @ref: 80982
- straininfo: 403899
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Enzymology | 12902251 | Characterization of the corrinoid iron-sulfur protein tetrachloroethene reductive dehalogenase of Dehalobacter restrictus. | Maillard J, Schumacher W, Vazquez F, Regeard C, Hagen WR, Holliger C | Appl Environ Microbiol | 10.1128/AEM.69.8.4628-4638.2003 | 2003 | Bacteria, Anaerobic/*enzymology, Catalysis, Electron Spin Resonance Spectroscopy, Iron-Sulfur Proteins/*metabolism, Oxidoreductases/genetics/isolation & purification/*metabolism | Metabolism |
| Metabolism | 14758469 | Phenyl methyl ethers: novel electron donors for respiratory growth of Desulfitobacterium hafniense and Desulfitobacterium sp. strain PCE-S. | Neumann A, Engelmann T, Schmitz R, Greiser Y, Orthaus A, Diekert G | Arch Microbiol | 10.1007/s00203-004-0651-y | 2004 | Anisoles/*metabolism, Desulfitobacterium/*growth & development/*metabolism, Electron Transport, Fumarates/*metabolism, Gallic Acid/*analogs & derivatives/metabolism, Hydrocarbons, Chlorinated/metabolism, Oxidation-Reduction, Oxidoreductases, O-Demethylating/metabolism, Phenylacetates/metabolism, Succinic Acid/metabolism, Vanillic Acid/metabolism | Enzymology |
| Enzymology | 15643941 | Isolation and characterization of Tn-Dha1, a transposon containing the tetrachloroethene reductive dehalogenase of Desulfitobacterium hafniense strain TCE1. | Maillard J, Regeard C, Holliger C | Environ Microbiol | 10.1111/j.1462-2920.2004.00671.x | 2005 | Base Sequence, DNA Transposable Elements/*genetics, DNA, Bacterial/analysis/isolation & purification, Desulfitobacterium/*enzymology/genetics, Molecular Sequence Data, Oxidoreductases/*chemistry/genetics/*metabolism, Promoter Regions, Genetic, Sequence Analysis, DNA | Phylogeny |
| Metabolism | 18607569 | Enzymes involved in the anoxic utilization of phenyl methyl ethers by Desulfitobacterium hafniense DCB2 and Desulfitobacterium hafniense PCE-S. | Kreher S, Schilhabel A, Diekert G | Arch Microbiol | 10.1007/s00203-008-0400-8 | 2008 | Anaerobiosis, Anisoles/*metabolism, Bacterial Proteins/*metabolism, Carbon Dioxide/metabolism, Desulfitobacterium/*enzymology/metabolism, Enzymes/*metabolism, Metabolic Networks and Pathways, Models, Biological | Enzymology |
| Metabolism | 19888999 | Reductive dehalogenation of brominated ethenes by Sulfurospirillum multivorans and Desulfitobacterium hafniense PCE-S. | Ye L, Schilhabel A, Bartram S, Boland W, Diekert G | Environ Microbiol | 10.1111/j.1462-2920.2009.02093.x | 2009 | Bacteria, Anaerobic/enzymology/metabolism, Desulfitobacterium/*enzymology/growth & development, Dichloroethylenes/metabolism, Energy Metabolism, Epsilonproteobacteria/*enzymology, Ethylenes/metabolism, Halogenation, Hydrocarbons, Brominated/*metabolism, Oxidoreductases/metabolism, Tetrachloroethylene/metabolism, Trichloroethylene/metabolism | Enzymology |
| Metabolism | 25734359 | Substrate hydrophobicity and cell composition influence the extent of rate limitation and masking of isotope fractionation during microbial reductive dehalogenation of chlorinated ethenes. | Renpenning J, Rapp I, Nijenhuis I | Environ Sci Technol | 10.1021/es506108j | 2015 | Bacteria/*metabolism, Carbon Isotopes/chemistry, Cell Extracts, Chemical Fractionation, Desulfitobacterium/metabolism, Epsilonproteobacteria/metabolism, Ethylenes/*chemistry/metabolism, Geobacter/metabolism, Halogenation, Hydrocarbons, Chlorinated/*chemistry/metabolism, Hydrophobic and Hydrophilic Interactions, Oxidoreductases/metabolism, Tetrachloroethylene/chemistry/metabolism, Trichloroethylene/chemistry/metabolism | Enzymology |
| Genetics | 26203328 | Draft genome sequence and characterization of Desulfitobacterium hafniense PCE-S. | Goris T, Hornung B, Kruse T, Reinhold A, Westermann M, Schaap PJ, Smidt H, Diekert G | Stand Genomic Sci | 10.1186/1944-3277-10-15 | 2015 | ||
| Metabolism | 28987410 | Variable dual carbon-bromine stable isotope fractionation during enzyme-catalyzed reductive dehalogenation of brominated ethenes. | Woods A, Kuntze K, Gelman F, Halicz L, Nijenhuis I | Chemosphere | 10.1016/j.chemosphere.2017.09.128 | 2017 | Biotransformation, Bromine/*chemistry, Carbon/*chemistry, Carbon Isotopes/chemistry, Catalysis, Chemical Fractionation, Desulfitobacterium/*metabolism, Ethylene Dibromide/*metabolism, *Halogenation | Enzymology |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 5430 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14645) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-14645 | |
| 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 | |
| 80982 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID403899.1 | StrainInfo: A central database for resolving microbial strain identifiers |