Name: Desulfitobacterium hafniense DCB-2
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 11765

Type strain:

Species: Desulfitobacterium hafniense

Strain Designation: DCB-2

Culture col. no.: DSM 10664

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)

SI-ID 48855

DSM 10664, NCIMB 13714

Special Collections

Other strains from Desulfitobacterium hafniense

Section

Desulfitobacterium hafniense DCB-2 is an anaerobe, spore-forming, Gram-negative bacterium that was isolated from sewage sludge.

Gram-negative
motile
rod-shaped
spore-forming
anaerobe
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Desulfitobacteriaceae*
	Genus	*Desulfitobacterium*
	Species	**Desulfitobacterium hafniense**
	Full Scientific Name (LPSN)	Desulfitobacterium hafniense Christiansen and Ahring 1996

Synonym

Desulfitobacterium frappieri

Information on morphological and physiological properties Morphology

[Ref.: #43367]	Gram stain	negative

[Ref.: #43367]	Cell length	3.3-6 µm

[Ref.: #43367]	Cell width	0.6-0.7 µm

[Ref.: #43367]	Cell shape	rod-shaped

[Ref.: #43367]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #4028]

Culture medium

DESULFITOBACTERIUM HAFNIENSE MEDIUM (DSMZ Medium 720)

[Ref.: #4028]

Culture medium growth

[Ref.: #4028]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4028]

Culture medium composition

expand / minimize

[Ref.: #43367]

Culture medium

BA Medium

[Ref.: #43367]

Culture medium growth

[Ref.: #43367]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #4028]			growth	37 °C
[Ref.: #43367]			optimum	37 °C

	pH	Kind of pH		pH
[Ref.: #43367]			optimum	7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #4028]	Oxygen tolerance	anaerobe
[Ref.: #43367]	Oxygen tolerance	obligate anaerobe

[Ref.: #43367]	Spore description	terminal
[Ref.: #43367]	Type of spore	spore
[Ref.: #43367]	Ability of spore formation	yes

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43367]	acetate ChEBI	-	growth
[Ref.: #43367]	benzoate ChEBI	-	growth
[Ref.: #43367]	butyrate ChEBI	-	growth
[Ref.: #43367]	cellobiose ChEBI	-	growth
[Ref.: #43367]	D-fructose ChEBI	-	growth
[Ref.: #43367]	D-galactose ChEBI	-	growth
[Ref.: #43367]	D-glucose ChEBI	-	growth
[Ref.: #43367]	D-mannitol ChEBI	-	growth
[Ref.: #43367]	D-ribose ChEBI	-	growth
[Ref.: #43367]	esculin ChEBI	-	growth
[Ref.: #43367]	ferric iron ChEBI	+	reduction
[Ref.: #43367]	formate ChEBI	-	growth
[Ref.: #43367]	fucose ChEBI	-	growth
[Ref.: #43367]	fumarate ChEBI	-	growth
[Ref.: #43367]	gelatin ChEBI	-	hydrolysis
[Ref.: #43367]	glycerol ChEBI	-	growth
[Ref.: #43367]	inulin ChEBI	-	growth
[Ref.: #43367]	L-arabinose ChEBI	-	growth
[Ref.: #43367]	L-glutamine ChEBI	-	growth
[Ref.: #43367]	L-histidine ChEBI	-	growth
[Ref.: #43367]	L-phenylalanine ChEBI	-	growth
[Ref.: #43367]	L-rhamnose ChEBI	-	growth
[Ref.: #43367]	L-threonine ChEBI	-	growth
[Ref.: #43367]	lactate ChEBI	-	growth
[Ref.: #43367]	lactose ChEBI	-	growth
[Ref.: #43367]	maltose ChEBI	-	growth
[Ref.: #43367]	mannose ChEBI	-	growth
[Ref.: #43367]	nitrate ChEBI	+	reduction
[Ref.: #43367]	propionate ChEBI	-	growth
[Ref.: #43367]	pyruvate ChEBI	+	growth
[Ref.: #43367]	raffinose ChEBI	-	growth
[Ref.: #43367]	salicin ChEBI	-	growth
[Ref.: #43367]	sorbitol ChEBI	-	growth
[Ref.: #43367]	starch ChEBI	-	growth
[Ref.: #43367]	sucrose ChEBI	-	growth
[Ref.: #43367]	sulfate ChEBI	-	reduction
[Ref.: #43367]	sulfite ChEBI	+	reduction
[Ref.: #43367]	thiosulfate ChEBI	+	reduction
[Ref.: #43367]	trehalose ChEBI	-	growth
[Ref.: #43367]	tryptophan ChEBI	+	growth
[Ref.: #43367]	xylose ChEBI	-	growth
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43367]		indole ChEBI	yes

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #43367]		catalase	-	1.11.1.6

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #4028]	Sample type/isolated from	sewage sludge
[Ref.: #4028]	Country	Denmark
[Ref.: #4028]	Country ISO 3 Code	DNK
[Ref.: #4028]	Continent	Europe

[Ref.: #43367]	Sample type/isolated from	municipal sludge
* marker position based on {}

Isolation sources categories

#Engineered

#Waste

#Sewage sludge

What are isolation sources categories?

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #4028]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #4028]	D.hafniense 16S ribosomal RNA	X94975	1530	GenBank ENA	272564 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Desulfitobacterium hafniense DCB-2	GCA_000021925	complete	GenBank ENA	272564 tax ID	*
[Ref.: #66792]	Desulfitobacterium hafniense DCB-2	272564.6	complete	PATRIC	272564 tax ID	*
[Ref.: #66792]	Desulfitobacterium hafniense DCB-2	643348537	complete	JGI IMG/M	272564 tax ID	*

[Ref.: #4028]

GC-content

47 mol%

high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Desulfitobacterium hafniense DCB-2 DCB-2 NCBI: GCA_000021925.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	61.276	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	74.706	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	84.804	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	81.331	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	90.811	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	70.044	no

Availability in culture collections External links

[Ref.: #4028]

Culture collection no.

DSM 10664

[Ref.: #80983]

SI-ID 48855

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Metabolism	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	*
Enzymology	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	*
Genetics	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	*
Metabolism	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	*
Metabolism	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	*
Metabolism	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	*
Enzymology	Characterization of an O-demethylase of Desulfitobacterium hafniense DCB-2.	Studenik S, Vogel M, Diekert G	J Bacteriol	10.1128/JB.00146-12	2012	*
Genetics	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	*
Enzymology	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	*
Metabolism	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	*
Enzymology	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	*
Metabolism	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	*
Phylogeny	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	*
Metabolism	The Desulfitobacterium genus.	Villemur R, Lanthier M, Beaudet R, Lepine F	FEMS Microbiol Rev	10.1111/j.1574-6976.2006.00029.x	2006	*
Cultivation	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	*
Genetics	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	*
Phylogeny	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	*
Genetics	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	*
	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	*

References

#4028

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 10664

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#43367

Nina Christiansen, Birgitte Kiaer Ahring: Desulfitobacterium hafniense sp. nov., an Anaerobic, Reductively Dechlorinating Bacterium. IJSB 45: 442 - 448 1996 ( DOI 10.1099/00207713-46-2-442 )

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in 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.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID48855.1 )

* These data were automatically processed and therefore are not curated

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Desulfitobacterium hafniense DCB-2 DCB-2

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