Desulfobacter hydrogenophilus (DSM 3380, ATCC 43915, AcRS1)

Name: Desulfobacter hydrogenophilus (DSM 3380, ATCC 43915, AcRS1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 3955

Type strain

Strain Designation AcRS1

Culture col. no. DSM 3380 ATCC 43915 AcRS1

NCBI tax ID(s) 2291

Special Collections DSMZ

Links

Desulfobacter hydrogenophilus AcRS1 is an anaerobe, mesophilic prokaryote that was isolated from marine mud.

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 42122

ATCC 43915,DSM 3380,CCUG 33216

@ref 20215

Last LPSN update 2025-12-16 09:47:41

Domain Pseudomonadati

Phylum Thermodesulfobacteriota

Class Desulfobacteria

Order Desulfobacterales

Family Desulfobacteraceae

Genus Desulfobacter

Species Desulfobacter hydrogenophilus

Full scientific name Desulfobacter hydrogenophilus Widdel 1988

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	94.752
125439	negative	99.9

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
1366	DESULFOBACTER CURVATUS MEDIUM (DSMZ Medium 195)		Medium recipe at MediaDive	Name: DESULFOBACTER CURVATUS MEDIUM (DSMZ Medium 195) Composition: NaCl 20.9372 g/l Na2SO4 2.99103 g/l MgCl2 x 6 H2O 2.99103 g/l Na-acetate x 3 H2O 2.49252 g/l Na2CO3 1.49551 g/l KCl 0.498504 g/l Na2S x 9 H2O 0.398804 g/l NH4Cl 0.299103 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149551 g/l HCl 0.00249252 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 Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Nicotinic 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

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
1366	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

1366

Oxygen toleranceanaerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.4

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Mud (Sludge)
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
1366	marine mud	Venice	Italy	ITA	Europe

Taxonmaps

69479

Global distribution of 16S sequence FR733673 (>99% sequence identity) for Desulfobacter hydrogenophilus subclade from Microbeatlas

Aquatic Samples	6
Soil Samples
Animal Samples
Plant Samples
Total Samples	6

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1366	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM431954v1 assembly for Desulfobacter hydrogenophilus AcRS1	chromosome	GCA_004319545	2291.6	2987086343	2291	86.59
66792	ASM326109v1 assembly for Desulfobacter hydrogenophilus DSM 3380	scaffold	GCA_003261095	2291.4	2890690344	2291	50.89
66792	ASM1049954v1 assembly for Desulfobacter hydrogenophilus DSM 3380	contig	GCA_010499545	2291.7	8001850917	2291

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	D.hydrogenophilus 16S ribosomal rRNA	M34412	1390	2291
1366	Desulfobacter hydrogenophilus partial 16S rRNA gene, type strain DSM3380T	FR733673	1549	2291
124043	Desulfobacter hydrogenophilus strain DSM 3380 16S ribosomal RNA gene, partial sequence.	MK782795	1549	2291
124043	Desulfobacter hydrogenophilus strain DSM 3380 16S ribosomal RNA gene, partial sequence.	MK782796	1549	2291

GC content

1366

GC-content (mol%)44.6

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Desulfobacter hydrogenophilus DSM 3380
NCBI: GCA_003261095

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.40	no
125439	motility	BacteriaNetⓘ	no	66.00	no
125439	gram_stain	BacteriaNetⓘ	negative	99.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	69.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Desulfobacter hydrogenophilus AcRS1
NCBI: GCA_004319545.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	94.75	no
125438	anaerobic	anaerobicⓘ	yes	78.69	yes
125438	aerobic	aerobicⓘ	no	79.62	yes
125438	spore-forming	spore-formingⓘ	no	84.05	no
125438	thermophilic	thermophileⓘ	no	90.38	yes
125438	flagellated	motile2+ⓘ	yes	78.68	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Application of denaturing high-performance liquid chromatography for monitoring sulfate-reducing bacteria in oil fields.	Priha O, Nyyssonen M, Bomberg M, Laitila A, Simell J, Kapanen A, Juvonen R.	Appl Environ Microbiol	10.1128/aem.01015-13	2013
Enzymology	Fractionation of Hydrogen Isotopes by Sulfate- and Nitrate-Reducing Bacteria.	Osburn MR, Dawson KS, Fogel ML, Sessions AL.	Front Microbiol	10.3389/fmicb.2016.01166	2016
Metabolism	Evidence for autotrophic CO2 fixation via the reductive tricarboxylic acid cycle by members of the epsilon subdivision of proteobacteria.	Hugler M, Wirsen CO, Fuchs G, Taylor CD, Sievert SM.	J Bacteriol	10.1128/jb.187.9.3020-3027.2005	2005
Metabolism	Transformation of tetrachloromethane to dichloromethane and carbon dioxide by Acetobacterium woodii.	Egli C, Tschan T, Scholtz R, Cook AM, Leisinger T.	Appl Environ Microbiol	10.1128/aem.54.11.2819-2824.1988	1988
	Reverse sample genome probing, a new technique for identification of bacteria in environmental samples by DNA hybridization, and its application to the identification of sulfate-reducing bacteria in oil field samples.	Voordouw G, Voordouw JK, Karkhoff-Schweizer RR, Fedorak PM, Westlake DW.	Appl Environ Microbiol	10.1128/aem.57.11.3070-3078.1991	1991
Metabolism	Presence of acetyl coenzyme A (CoA) carboxylase and propionyl-CoA carboxylase in autotrophic Crenarchaeota and indication for operation of a 3-hydroxypropionate cycle in autotrophic carbon fixation.	Menendez C, Bauer Z, Huber H, Gad'on N, Stetter KO, Fuchs G.	J Bacteriol	10.1128/jb.181.4.1088-1098.1999	1999
	Intracellular Campylobacter-like organism from ferrets and hamsters with proliferative bowel disease is a Desulfovibrio sp.	Fox JG, Dewhirst FE, Fraser GJ, Paster BJ, Shames B, Murphy JC.	J Clin Microbiol	10.1128/jcm.32.5.1229-1237.1994	1994
	Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations.	Amann RI, Binder BJ, Olson RJ, Chisholm SW, Devereux R, Stahl DA.	Appl Environ Microbiol	10.1128/aem.56.6.1919-1925.1990	1990
	Application of antisera raised against sulfate-reducing bacteria for indirect immunofluorescent detection of immunoreactive bacteria in sediment from the German Baltic Sea.	Lillebaek R.	Appl Environ Microbiol	10.1128/aem.61.9.3436-3442.1995	1995
Metabolism	Natural relationships among sulfate-reducing eubacteria.	Devereux R, Delaney M, Widdel F, Stahl DA.	J Bacteriol	10.1128/jb.171.12.6689-6695.1989	1989
Metabolism	Degradative capacities and 16S rRNA-targeted whole-cell hybridization of sulfate-reducing bacteria in an anaerobic enrichment culture utilizing alkylbenzenes from crude oil.	Rabus R, Fukui M, Wilkes H, Widdle F.	Appl Environ Microbiol	10.1128/aem.62.10.3605-3613.1996	1996
	Compilation of small ribosomal subunit RNA structures.	Neefs JM, Van de Peer Y, De Rijk P, Chapelle S, De Wachter R.	Nucleic Acids Res	10.1093/nar/21.13.3025	1993
Metabolism	Stable carbon isotope ratios of lipid biomarkers of sulfate-reducing bacteria.	Londry KL, Jahnke LL, Des Marais DJ.	Appl Environ Microbiol	10.1128/aem.70.2.745-751.2004	2004
Metabolism	Stable carbon isotope fractionation by sulfate-reducing bacteria.	Londry KL, Des Marais DJ.	Appl Environ Microbiol	10.1128/aem.69.5.2942-2949.2003	2003
Genetics	Draft Genome Sequence of Desulfobacter hydrogenophilus DSM 3380, a Psychrotolerant Sulfate-Reducing Bacterium.	Bertran E, Ward LM, Johnston DT	Microbiol Resour Announc	10.1128/MRA.00203-20	2020

References

#1366	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 3380
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#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) .
#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.: MicrobeAtlas 1.0 beta .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Desulfobacter hydrogenophilus (DSM 3380, ATCC 43915, AcRS1)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004319545

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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