Strain identifier
BacDive ID: 11765
Type strain:
Species: Desulfitobacterium hafniense
Strain Designation: DCB-2
Strain history: <- B. K. Ahring, Technical University of Denmark, Department of Environmental Science and Engineering, Lyngby, Denmark; DCB-2 <- D. Licht and T. Madsen {1992}
NCBI tax ID(s): 272564 (strain), 49338 (species)
General
@ref: 4028
BacDive-ID: 11765
DSM-Number: 10664
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, Gram-negative, motile, rod-shaped
description: Desulfitobacterium hafniense DCB-2 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from sewage sludge.
NCBI tax id
NCBI tax id | Matching level |
---|---|
49338 | species |
272564 | strain |
strain history
- @ref: 4028
- history: <- B. K. Ahring, Technical University of Denmark, Department of Environmental Science and Engineering, Lyngby, Denmark; DCB-2 <- D. Licht and T. Madsen {1992}
doi: 10.13145/bacdive11765.20230509.8.1
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: 4028
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: DCB-2
type strain: yes
Morphology
cell morphology
- @ref: 43367
- gram stain: negative
- cell length: 3.3-6 µm
- cell width: 0.6-0.7 µm
- cell shape: rod-shaped
- motility: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
4028 | DESULFITOBACTERIUM HAFNIENSE MEDIUM (DSMZ Medium 720) | yes | https://mediadive.dsmz.de/medium/720 | Name: DESULFITOBACTERIUM HAFNIENSE MEDIUM (DSMZ Medium 720) Composition: NaHCO3 2.59222 g/l Na-pyruvate 2.49252 g/l Na2S2O3 x 5 H2O 1.24626 g/l NH4Cl 0.997009 g/l Yeast extract 0.997009 g/l K2HPO4 x 3 H2O 0.398804 g/l Na2S x 9 H2O 0.299103 g/l MgCl2 x 6 H2O 0.0997009 g/l NaCl 0.0997009 g/l CaCl2 x 2 H2O 0.0498504 g/l Na2-EDTA x 2 H2O 0.00518445 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Pyridoxine hydrochloride 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Thiamine HCl 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Biotin 1.99402e-05 g/l Folic acid 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water |
43367 | BA Medium | yes | supplemented with 40µM 2,4,6-trichlorphenol and 18.2mM pyruvate |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
4028 | positive | growth | 37 | mesophilic |
43367 | positive | optimum | 37 | mesophilic |
culture pH
- @ref: 43367
- ability: positive
- type: optimum
- pH: 7
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
4028 | anaerobe |
43367 | obligate anaerobe |
spore formation
- @ref: 43367
- spore description: terminal
- type of spore: spore
- spore formation: yes
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43367 | 18050 | L-glutamine | - | growth |
43367 | 30089 | acetate | - | growth |
43367 | 16150 | benzoate | - | growth |
43367 | 17968 | butyrate | - | growth |
43367 | 17057 | cellobiose | - | growth |
43367 | 15824 | D-fructose | - | growth |
43367 | 12936 | D-galactose | - | growth |
43367 | 17634 | D-glucose | - | growth |
43367 | 16899 | D-mannitol | - | growth |
43367 | 16988 | D-ribose | - | growth |
43367 | 24996 | lactate | - | growth |
43367 | 4853 | esculin | - | growth |
43367 | 29034 | ferric iron | + | reduction |
43367 | 15740 | formate | - | growth |
43367 | 33984 | fucose | - | growth |
43367 | 29806 | fumarate | - | growth |
43367 | 5291 | gelatin | - | hydrolysis |
43367 | 17754 | glycerol | - | growth |
43367 | 15443 | inulin | - | growth |
43367 | 30849 | L-arabinose | - | growth |
43367 | 15971 | L-histidine | - | growth |
43367 | 17295 | L-phenylalanine | - | growth |
43367 | 62345 | L-rhamnose | - | growth |
43367 | 16857 | L-threonine | - | growth |
43367 | 17716 | lactose | - | growth |
43367 | 17306 | maltose | - | growth |
43367 | 37684 | mannose | - | growth |
43367 | 17632 | nitrate | + | reduction |
43367 | 17272 | propionate | - | growth |
43367 | 15361 | pyruvate | + | growth |
43367 | 16634 | raffinose | - | growth |
43367 | 17814 | salicin | - | growth |
43367 | 30911 | sorbitol | - | growth |
43367 | 28017 | starch | - | growth |
43367 | 17992 | sucrose | - | growth |
43367 | 16189 | sulfate | - | reduction |
43367 | 17359 | sulfite | + | reduction |
43367 | 16094 | thiosulfate | + | reduction |
43367 | 27082 | trehalose | - | growth |
43367 | 27897 | tryptophan | + | growth |
43367 | 18222 | xylose | - | growth |
metabolite production
- @ref: 43367
- Chebi-ID: 35581
- metabolite: indole
- production: yes
enzymes
- @ref: 43367
- value: catalase
- activity: -
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
4028 | sewage sludge | Denmark | DNK | Europe |
43367 | municipal sludge |
isolation source categories
- Cat1: #Engineered
- Cat2: #Waste
- Cat3: #Sewage sludge
Safety information
risk assessment
- @ref: 4028
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 4028
- description: D.hafniense 16S ribosomal RNA
- accession: X94975
- length: 1530
- database: ena
- NCBI tax ID: 272564
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Desulfitobacterium hafniense DCB-2 | GCA_000021925 | complete | ncbi | 272564 |
66792 | Desulfitobacterium hafniense DCB-2 | 272564.6 | complete | patric | 272564 |
66792 | Desulfitobacterium hafniense DCB-2 | 643348537 | complete | img | 272564 |
GC content
- @ref: 4028
- GC-content: 47
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 87.314 | yes |
flagellated | no | 69.928 | no |
gram-positive | no | 82.19 | yes |
anaerobic | yes | 97.928 | yes |
aerobic | no | 95.293 | yes |
halophile | no | 94.413 | no |
spore-forming | yes | 95.102 | no |
thermophile | no | 99.338 | yes |
glucose-util | yes | 58.152 | yes |
glucose-ferment | no | 77.941 | no |
External links
@ref: 4028
culture collection no.: DSM 10664
straininfo link
- @ref: 80983
- straininfo: 48855
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 11722908 | Isolation and characterization of a novel As(V)-reducing bacterium: implications for arsenic mobilization and the genus Desulfitobacterium. | Niggemyer A, Spring S, Stackebrandt E, Rosenzweig RF | Appl Environ Microbiol | 10.1128/AEM.67.12.5568-5580.2001 | 2001 | Arsenates/*metabolism, Arsenic/metabolism, Culture Media, DNA, Ribosomal/analysis, Formates/metabolism, Fresh Water/*microbiology, Gram-Positive Rods/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Water Pollution, Chemical | Metabolism |
Genetics | 11976746 | Evaluation of non-cyanobacterial genome sequences for occurrence of genes encoding proteins homologous to cyanophycin synthetase and cloning of an active cyanophycin synthetase from Acinetobacter sp. strain DSM 587. | Krehenbrink M, Oppermann-Sanio FB, Steinbuchel A | Arch Microbiol | 10.1007/s00203-001-0396-9 | 2002 | Acinetobacter/chemistry/classification/*enzymology/*genetics, Amino Acid Sequence, *Bacterial Proteins, Cloning, Molecular, Databases, Genetic, Escherichia coli/enzymology/genetics, Gene Expression, Genes, Bacterial/genetics, *Genome, Bacterial, Molecular Sequence Data, Open Reading Frames/genetics, Peptide Synthases/chemistry/*genetics, Phylogeny, Plant Proteins/isolation & purification/metabolism, Sequence Homology, Amino Acid | Enzymology |
Cultivation | 16541158 | Occurrence and expression of crdA and cprA5 encoding chloroaromatic reductive dehalogenases in Desulfitobacterium strains. | Gauthier A, Beaudet R, Lepine F, Juteau P, Villemur R | Can J Microbiol | 10.1139/w05-111 | 2006 | Bacterial Proteins, Chlorophenols, Culture Media, DNA-Binding Proteins, Desulfitobacterium/enzymology/*genetics, Gene Expression Regulation, Bacterial, *Genes, Bacterial, Hydrolases/*genetics/metabolism, Repressor Proteins, Species Specificity | Phylogeny |
Metabolism | 16911041 | The Desulfitobacterium genus. | Villemur R, Lanthier M, Beaudet R, Lepine F | FEMS Microbiol Rev | 10.1111/j.1574-6976.2006.00029.x | 2006 | Biodegradation, Environmental, Chlorine/metabolism, Desulfitobacterium/classification/*genetics/*metabolism, Genes, Bacterial, Genes, rRNA, Humic Substances, Hydrogen/metabolism, Metals/metabolism, Oxidation-Reduction, Phylogeny, Sulfites/metabolism | Phylogeny |
Phylogeny | 17496957 | Heterogeneity between 16S ribosomal RNA gene copies borne by one Desulfitobacterium strain is caused by different 100-200 bp insertions in the 5' region. | Villemur R, Constant P, Gauthier A, Shareck M, Beaudet R | Can J Microbiol | 10.1139/w06-111 | 2007 | DNA Transposable Elements/*genetics, Desulfitobacterium/classification/*genetics, In Situ Hybridization, Fluorescence, Molecular Sequence Data, Polymerase Chain Reaction, RNA, Ribosomal, 16S/*chemistry/classification/genetics, *Sequence Analysis, RNA | Genetics |
Metabolism | 19047736 | Divergent roles of CprK paralogues from Desulfitobacterium hafniense in activating gene expression. | Gabor K, Hailesellasse Sene K, Smidt H, de Vos WM, van der Oost J | Microbiology (Reading) | 10.1099/mic.0.2008/021584-0 | 2008 | Amino Acid Sequence, Bacterial Proteins/chemistry/*genetics/metabolism, Base Sequence, Cyclic AMP Receptor Protein/chemistry/*genetics/metabolism, Desulfitobacterium/genetics/*metabolism/physiology, Escherichia coli/genetics/metabolism, *Gene Expression Regulation, Bacterial, Iron-Sulfur Proteins/chemistry/*genetics/metabolism, Membrane Proteins/genetics/metabolism, Methyl-Accepting Chemotaxis Proteins, Molecular Sequence Data, Transcription Factors/chemistry/*genetics/metabolism | Genetics |
Enzymology | 20870790 | Identification and characterization of a novel CprA reductive dehalogenase specific to highly chlorinated phenols from Desulfitobacterium hafniense strain PCP-1. | Bisaillon A, Beaudet R, Lepine F, Deziel E, Villemur R | Appl Environ Microbiol | 10.1128/AEM.01362-10 | 2010 | Amino Acid Sequence, Cell Membrane/enzymology, Chlorophenols/*metabolism, Desulfitobacterium/*enzymology, Electrophoresis, Polyacrylamide Gel, Enzyme Stability, Hydrogen-Ion Concentration, Hydrolases/chemistry/*isolation & purification/*metabolism, Kinetics, Mass Spectrometry, Membrane Proteins/chemistry/isolation & purification/metabolism, Molecular Sequence Data, Molecular Weight, Substrate Specificity, Temperature | Metabolism |
Metabolism | 20944207 | Structure of the first representative of Pfam family PF04016 (DUF364) reveals enolase and Rossmann-like folds that combine to form a unique active site with a possible role in heavy-metal chelation. | Miller MD, Aravind L, Bakolitsa C, Rife CL, Carlton D, Abdubek P, Astakhova T, Axelrod HL, Chiu HJ, Clayton T, Deller MC, Duan L, Feuerhelm J, Grant JC, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Marciano D, McMullan D, Morse AT, Nigoghossian E, Okach L, Reyes R, van den Bedem H, Weekes D, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA | Acta Crystallogr Sect F Struct Biol Cryst Commun | 10.1107/S1744309110007517 | 2010 | Amino Acid Sequence, Bacterial Proteins/*chemistry/metabolism, Catalytic Domain, Crystallography, X-Ray, Desulfitobacterium/*chemistry/metabolism, Metals, Heavy/*chemistry/metabolism, Models, Molecular, Molecular Sequence Data, Phosphopyruvate Hydratase/*chemistry, Protein Binding, *Protein Folding, Protein Structure, Tertiary | Genetics |
Enzymology | 20944230 | Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved alpha+beta core domain and an auxiliary C-terminal treble-clef zinc finger. | Axelrod HL, Das D, Abdubek P, Astakhova T, Bakolitsa C, Carlton D, Chen C, Chiu HJ, Clayton T, Deller MC, Duan L, Ellrott K, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Lam WW, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA | Acta Crystallogr Sect F Struct Biol Cryst Commun | 10.1107/S1744309110020166 | 2010 | Aldehyde Oxidoreductases/*chemistry, Amino Acid Sequence, Crystallography, X-Ray, Desulfitobacterium/*enzymology, Methane/*biosynthesis, Models, Molecular, Molecular Sequence Data, Protein Structure, Secondary, Protein Structure, Tertiary, Structural Homology, Protein, *Zinc Fingers | Genetics |
Genetics | 22316246 | Genome sequence of Desulfitobacterium hafniense DCB-2, a Gram-positive anaerobe capable of dehalogenation and metal reduction. | Kim SH, Harzman C, Davis JK, Hutcheson R, Broderick JB, Marsh TL, Tiedje JM | BMC Microbiol | 10.1186/1471-2180-12-21 | 2012 | Carbon Dioxide/metabolism, DNA, Bacterial/*chemistry/*genetics, Desulfitobacterium/*genetics/metabolism, Genes, Bacterial, *Genome, Bacterial, Halogens/metabolism, Metabolic Networks and Pathways/genetics, Metals/metabolism, Molecular Sequence Data, Nitrogen Fixation, Organic Chemicals/metabolism, Oxidation-Reduction, Sequence Analysis, DNA | Metabolism |
Enzymology | 22522902 | Characterization of an O-demethylase of Desulfitobacterium hafniense DCB-2. | Studenik S, Vogel M, Diekert G | J Bacteriol | 10.1128/JB.00146-12 | 2012 | Cloning, Molecular, Corrinoids/metabolism, Desulfitobacterium/*enzymology/genetics, Escherichia coli/enzymology/genetics, Methyltransferases/chemistry/genetics/metabolism, Operon, *Oxidoreductases, O-Demethylating/chemistry/genetics/metabolism, Recombinant Proteins/genetics/metabolism, Substrate Specificity | Metabolism |
Metabolism | 23672517 | Corrinoid activation by a RACE protein: studies on the interaction of the proteins involved. | Nguyen HD, Studenik S, Diekert G | FEMS Microbiol Lett | 10.1111/1574-6968.12178 | 2013 | Acetobacterium/*enzymology/genetics/metabolism, Bacterial Proteins/genetics/*metabolism, Corrinoids/*metabolism, Enzyme Activation, Enzyme Activators/*metabolism, Methyltransferases/genetics/*metabolism, Oxidoreductases, O-Demethylating/genetics/metabolism, Protein Binding, Substrate Specificity | Enzymology |
23705686 | Evaluation of the inhibitory effects of chloroform on ortho-chlorophenol- and chloroethene-dechlorinating Desulfitobacterium strains. | Futagami T, Fukaki Y, Fujihara H, Takegawa K, Goto M, Furukawa K | AMB Express | 10.1186/2191-0855-3-30 | 2013 | |||
Metabolism | 23897483 | Structure of the cobalamin-binding protein of a putative O-demethylase from Desulfitobacterium hafniense DCB-2. | Sjuts H, Dunstan MS, Fisher K, Leys D | Acta Crystallogr D Biol Crystallogr | 10.1107/S0907444913011323 | 2013 | Base Sequence, Binding Sites, Cloning, Molecular, Crystallography, X-Ray, Desulfitobacterium/*chemistry/metabolism, Electron Spin Resonance Spectroscopy, Molecular Sequence Data, Oxidoreductases, O-Demethylating/chemistry/metabolism, Protein Conformation, Protein Structure, Tertiary, Spectrophotometry, Ultraviolet, Transcobalamins/*chemistry/genetics/*metabolism, Vitamin B 12/metabolism | Enzymology |
Metabolism | 24814779 | Functional heterologous production of reductive dehalogenases from Desulfitobacterium hafniense strains. | Mac Nelly A, Kai M, Svatos A, Diekert G, Schubert T | Appl Environ Microbiol | 10.1128/AEM.00881-14 | 2014 | Allyl Compounds/metabolism, Bacterial Proteins/genetics/*metabolism, Benzimidazoles/metabolism, Catalysis, Chlorophenols/metabolism, Cloning, Molecular, Cobamides/biosynthesis, Culture Media, DNA, Bacterial/genetics, Desulfitobacterium/*enzymology/genetics, Gammaproteobacteria/enzymology, Halogenation/*physiology, Hydrocarbons, Chlorinated, Hydroxocobalamin/metabolism, Oxidoreductases/genetics/*metabolism, Plasmids/genetics, Recombination, Genetic, Sequence Analysis, DNA, Trichloroethylene/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 | ||
Genetics | 26327380 | Structures of the methyltransferase component of Desulfitobacterium hafniense DCB-2 O-demethylase shed light on methyltetrahydrofolate formation. | Sjuts H, Dunstan MS, Fisher K, Leys D | Acta Crystallogr D Biol Crystallogr | 10.1107/S1399004715013061 | 2015 | Amino Acid Sequence, Crystallography, X-Ray, Desulfitobacterium/*enzymology, Methyltransferases/*chemistry, Models, Molecular, Molecular Sequence Data, Protein Conformation, Sequence Homology, Amino Acid, Tetrahydrofolates/*chemical synthesis | Enzymology |
Enzymology | 30549216 | Guided cobamide biosynthesis for heterologous production of reductive dehalogenases. | Schubert T, von Reuss SH, Kunze C, Paetz C, Kruse S, Brand-Schon P, Nelly AM, Nuske J, Diekert G | Microb Biotechnol | 10.1111/1751-7915.13339 | 2018 | Cobamides/*biosynthesis, Coenzymes/*biosynthesis, Desulfitobacterium/*enzymology, Enterobacteriaceae/*enzymology, Hydrolases/*metabolism, Vitamin B Complex/*biosynthesis | Biotechnology |
Metabolism | 32160390 | Flavodoxin hydroquinone provides electrons for the ATP-dependent reactivation of protein-bound corrinoid cofactors. | Kissling L, Greiser Y, Durichen H, Studenik S | FEBS J | 10.1111/febs.15290 | 2020 | Acetobacterium/genetics/metabolism, Adenosine Triphosphate/*metabolism, Bacterial Proteins/genetics/*metabolism, Corrinoids/*metabolism, Desulfitobacterium/genetics/metabolism, *Electrons, Flavodoxin/chemistry/*metabolism, Hydroquinones/chemistry/*metabolism, Oxidation-Reduction, Oxidoreductases/genetics/*metabolism, Spectrophotometry | Enzymology |
Reference
@id | authors | catalogue | doi/url | title | journal |
---|---|---|---|---|---|
4028 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10664) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-10664 | ||
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 | ||
43367 | Nina Christiansen, Birgitte Kiaer Ahring | 10.1099/00207713-46-2-442 | Desulfitobacterium hafniense sp. nov., an Anaerobic, Reductively Dechlorinating Bacterium | IJSB 45: 442-448 1996 | |
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) | ||
80983 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID48855.1 | StrainInfo: A central database for resolving microbial strain identifiers |