Strain identifier

BacDive ID: 11765

Type strain: Yes

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)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 4028

BacDive-ID: 11765

DSM-Number: 10664

keywords: Gram-negative, mesophilic, spore-forming, anaerobe, Bacteria, 16S sequence, genome sequence, 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 idMatching level
272564strain
49338species

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}

doi: 10.13145/bacdive11765.20220920.7

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

@refnamegrowthlinkcomposition
4028DESULFITOBACTERIUM HAFNIENSE MEDIUM (DSMZ Medium 720)yeshttps://bacmedia.dsmz.de/medium/720Name: DESULFITOBACTERIUM HAFNIENSE MEDIUM (DSMZ Medium 720) Composition: NaHCO3 2.6 g/l Na-pyruvate 2.5 g/l Na2S2O3 x 5 H2O 1.25 g/l Yeast extract 1.0 g/l NH4Cl 1.0 g/l K2HPO4 x 3 H2O 0.4 g/l Na2S x 9 H2O 0.3 g/l MgCl2 x 6 H2O 0.1 g/l NaCl 0.1 g/l CaCl2 x 2 H2O 0.05 g/l Na2-EDTA x 2 H2O 0.0052 g/l FeCl2 x 4 H2O 0.0015 g/l NaOH 0.0005 g/l Sodium resazurin 0.0005 g/l CoCl2 x 6 H2O 0.00019 g/l Pyridoxine hydrochloride 0.0001 g/l MnCl2 x 4 H2O 0.0001 g/l ZnCl2 7e-05 g/l Thiamine HCl 5e-05 g/l Nicotinic acid 5e-05 g/l Calcium D-(+)-pantothenate 5e-05 g/l p-Aminobenzoic acid 5e-05 g/l Riboflavin 5e-05 g/l (±)-alpha-Lipoic acid 5e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l Folic acid 2e-05 g/l Biotin 2e-05 g/l H3BO3 6e-06 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Vitamin B12 1e-06 g/l Distilled water
43367BA Mediumyessupplemented with 40µM 2,4,6-trichlorphenol and 18.2mM pyruvate

culture temp

@refgrowthtypetemperaturerange
4028positivegrowth37mesophilic
43367positiveoptimum37mesophilic

culture pH

  • @ref: 43367
  • ability: positive
  • type: optimum
  • pH: 7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
4028anaerobe
43367obligate anaerobe

spore formation

  • @ref: 43367
  • spore description: terminal
  • type of spore: spore
  • spore formation: yes

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4336718050L-glutamine-growth
4336730089acetate-growth
4336716150benzoate-growth
4336717968butyrate-growth
4336717057cellobiose-growth
4336715824D-fructose-growth
4336712936D-galactose-growth
4336717634D-glucose-growth
4336716899D-mannitol-growth
4336716988D-ribose-growth
4336724996lactate-growth
433674853esculin-growth
4336729034ferric iron+reduction
4336715740formate-growth
4336733984fucose-growth
4336729806fumarate-growth
433675291gelatin-hydrolysis
4336717754glycerol-growth
4336715443inulin-growth
4336730849L-arabinose-growth
4336715971L-histidine-growth
4336717295L-phenylalanine-growth
4336762345L-rhamnose-growth
4336716857L-threonine-growth
4336717716lactose-growth
4336717306maltose-growth
4336737684mannose-growth
4336717632nitrate+reduction
4336717272propionate-growth
4336715361pyruvate+growth
4336716634raffinose-growth
4336717814salicin-growth
4336730911sorbitol-growth
4336728017starch-growth
4336717992sucrose-growth
4336716189sulfate-reduction
4336717359sulfite+reduction
4336716094thiosulfate+reduction
4336727082trehalose-growth
4336727897tryptophan+growth
4336718222xylose-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

@refsample typecountryorigin.countrycontinent
4028sewage sludgeDenmarkDNKEurope
43367municipal 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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Desulfitobacterium hafniense DCB-2 DCB-2GCA_000021925completencbi272564
66792Desulfitobacterium hafniense DCB-2272564.6completepatric272564
66792Desulfitobacterium hafniense DCB-2643348537completeimg272564

GC content

  • @ref: 4028
  • GC-content: 47
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 4028

culture collection no.: DSM 10664

straininfo link

  • @ref: 20218
  • passport: http://www.straininfo.net/strains/162104

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11722908Isolation and characterization of a novel As(V)-reducing bacterium: implications for arsenic mobilization and the genus Desulfitobacterium.Niggemyer A, Spring S, Stackebrandt E, Rosenzweig RFAppl Environ Microbiol10.1128/AEM.67.12.5568-5580.20012001Arsenates/*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, ChemicalMetabolism
Genetics11976746Evaluation 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 AArch Microbiol10.1007/s00203-001-0396-92002Acinetobacter/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 AcidEnzymology
Cultivation16541158Occurrence and expression of crdA and cprA5 encoding chloroaromatic reductive dehalogenases in Desulfitobacterium strains.Gauthier A, Beaudet R, Lepine F, Juteau P, Villemur RCan J Microbiol10.1139/w05-1112006Bacterial Proteins, Chlorophenols, Culture Media, DNA-Binding Proteins, Desulfitobacterium/enzymology/*genetics, Gene Expression Regulation, Bacterial, *Genes, Bacterial, Hydrolases/*genetics/metabolism, Repressor Proteins, Species SpecificityPhylogeny
Metabolism16911041The Desulfitobacterium genus.Villemur R, Lanthier M, Beaudet R, Lepine FFEMS Microbiol Rev10.1111/j.1574-6976.2006.00029.x2006Biodegradation, Environmental, Chlorine/metabolism, Desulfitobacterium/classification/*genetics/*metabolism, Genes, Bacterial, Genes, rRNA, Humic Substances, Hydrogen/metabolism, Metals/metabolism, Oxidation-Reduction, Phylogeny, Sulfites/metabolismPhylogeny
Phylogeny17496957Heterogeneity 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 RCan J Microbiol10.1139/w06-1112007DNA Transposable Elements/*genetics, Desulfitobacterium/classification/*genetics, In Situ Hybridization, Fluorescence, Molecular Sequence Data, Polymerase Chain Reaction, RNA, Ribosomal, 16S/*chemistry/classification/genetics, *Sequence Analysis, RNAGenetics
Metabolism19047736Divergent roles of CprK paralogues from Desulfitobacterium hafniense in activating gene expression.Gabor K, Hailesellasse Sene K, Smidt H, de Vos WM, van der Oost JMicrobiology (Reading)10.1099/mic.0.2008/021584-02008Amino 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/metabolismGenetics
Enzymology20870790Identification 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 RAppl Environ Microbiol10.1128/AEM.01362-102010Amino 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, TemperatureMetabolism
Metabolism20944207Structure 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 IAActa Crystallogr Sect F Struct Biol Cryst Commun10.1107/S17443091100075172010Amino 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, TertiaryGenetics
Enzymology20944230Structures 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 IAActa Crystallogr Sect F Struct Biol Cryst Commun10.1107/S17443091100201662010Aldehyde 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 FingersGenetics
Genetics22316246Genome 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 JMBMC Microbiol10.1186/1471-2180-12-212012Carbon 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, DNAMetabolism
Enzymology22522902Characterization of an O-demethylase of Desulfitobacterium hafniense DCB-2.Studenik S, Vogel M, Diekert GJ Bacteriol10.1128/JB.00146-122012Cloning, 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 SpecificityMetabolism
Metabolism23672517Corrinoid activation by a RACE protein: studies on the interaction of the proteins involved.Nguyen HD, Studenik S, Diekert GFEMS Microbiol Lett10.1111/1574-6968.121782013Acetobacterium/*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 SpecificityEnzymology
23705686Evaluation 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 KAMB Express10.1186/2191-0855-3-302013
Metabolism23897483Structure of the cobalamin-binding protein of a putative O-demethylase from Desulfitobacterium hafniense DCB-2.Sjuts H, Dunstan MS, Fisher K, Leys DActa Crystallogr D Biol Crystallogr10.1107/S09074449130113232013Base 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/metabolismEnzymology
Metabolism24814779Functional heterologous production of reductive dehalogenases from Desulfitobacterium hafniense strains.Mac Nelly A, Kai M, Svatos A, Diekert G, Schubert TAppl Environ Microbiol10.1128/AEM.00881-142014Allyl 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/metabolismEnzymology
Genetics26327380Structures of the methyltransferase component of Desulfitobacterium hafniense DCB-2 O-demethylase shed light on methyltetrahydrofolate formation.Sjuts H, Dunstan MS, Fisher K, Leys DActa Crystallogr D Biol Crystallogr10.1107/S13990047150130612015Amino Acid Sequence, Crystallography, X-Ray, Desulfitobacterium/*enzymology, Methyltransferases/*chemistry, Models, Molecular, Molecular Sequence Data, Protein Conformation, Sequence Homology, Amino Acid, Tetrahydrofolates/*chemical synthesisEnzymology
Enzymology30549216Guided 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 GMicrob Biotechnol10.1111/1751-7915.133392018Cobamides/*biosynthesis, Coenzymes/*biosynthesis, Desulfitobacterium/*enzymology, Enterobacteriaceae/*enzymology, Hydrolases/*metabolism, Vitamin B Complex/*biosynthesisBiotechnology
Metabolism32160390Flavodoxin hydroquinone provides electrons for the ATP-dependent reactivation of protein-bound corrinoid cofactors.Kissling L, Greiser Y, Durichen H, Studenik SFEBS J10.1111/febs.152902020Acetobacterium/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, SpectrophotometryEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4028Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10664)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10664
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
43367Nina Christiansen, Birgitte Kiaer Ahring10.1099/00207713-46-2-442Desulfitobacterium hafniense sp. nov., an Anaerobic, Reductively Dechlorinating BacteriumIJSB 45: 442-448 1996
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)