Desulfotomaculum nigrificans (DSM 574, ATCC 19858, ATCC 19998)

Name: Desulfotomaculum nigrificans (DSM 574, ATCC 19858, ATCC 19998)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11792

Type strain

Culture col. no. DSM 574 ATCC 19858 ATCC 19998 CIP 111238 NCIMB 8395 2 more

NCBI tax ID(s) 696369 1565

Special Collections DSMZ CIP

Links

Desulfotomaculum nigrificans DSM 574 is an anaerobe, thermophilic prokaryote of the family Peptococcaceae.

anaerobe thermophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 92880

ATCC 19998,IFO 13698,NCIB 8395,ATCC 19858,DSM 574,NCIMB 8395,NBRC 13698,BCRC 14424,CCRC 14424,CCT 0902,VTT E-001654,CECT 8176

@ref 20215

Last LPSN update 2025-12-16 09:49:41

Domain Bacillati

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Peptococcaceae

Genus Desulfotomaculum

Species Desulfotomaculum nigrificans

Full scientific name Desulfotomaculum nigrificans (Werkman and Weaver 1927) Campbell and Postgate 1965 (Approved Lists 1980)

Synonyms (2)

"Clostridium nigrificans"
Desulfotomaculum carboxydivorans

BacDive ID	Other strains from **Desulfotomaculum nigrificans** (8)	Type strain
11793	D. nigrificans DSM 575, NCIMB 8706
11794	D. nigrificans Teddington Garden, DSM 7434, NCIMB 8351
11795	D. nigrificans Staines G, DSM 7435, NCIMB 8353
11796	D. nigrificans Aberdeen, DSM 7436, NCIMB 8354
11797	D. nigrificans Holland DT, DSM 7437, NCIMB 8355
11798	D. nigrificans DSM 7438, NCIMB 8788
11799	D. nigrificans 2133, DSM 7453, ATCC 7946, NCA 3750
11828	D. nigrificans CO-1-SRB, DSM 14880, VKM B-2319

Morphology

Multimedia

@ref:	66793
multimedia content:	EM_DSM_574_1.jpg
multimedia.multimedia content:	EM_DSM_574_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
291	DESULFOVIBRIO (POSTGATE) MEDIUM (DSMZ Medium 63)		Medium recipe at MediaDive	Name: DESULFOVIBRIO (POSTGATE) MEDIUM (DSMZ Medium 63) Composition: MgSO4 x 7 H2O 2.0 g/l Na-DL-lactate 2.0 g/l NH4Cl 1.0 g/l Yeast extract 1.0 g/l Na2SO4 1.0 g/l FeSO4 x 7 H2O 0.5 g/l K2HPO4 0.5 g/l CaCl2 x 2 H2O 0.1 g/l Na-thioglycolate 0.1 g/l Ascorbic acid 0.1 g/l Sodium resazurin 0.0005 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
291	positive	growth	55	thermophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
291	anaerobe
125438	anaerobe
125439	anaerobe

Isolation, sampling and environmental information

Isolation

@ref	Geographic location	Country	Country ISO 3 Code	Continent
291	freshwater	Netherlands	NLD	Europe

Taxonmaps

69479

Global distribution of 16S sequence HG005352 (>99% sequence identity) for Desulfotomaculum nigrificans subclade from Microbeatlas

Aquatic Samples	688
Soil Samples	516
Animal Samples	5582
Plant Samples	145
Total Samples	6931

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
291	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	ASM18975v3 assembly for Desulfotomaculum nigrificans DSM 574	scaffold	GCA_000189755	696369.3	2507262026	696369	76.43

Genome browser: GCA_000189755

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Sulphate-reducing bacteria ATCC 19858 16S rRNA region	A30643	1346	77133
291	Desulfotomaculum nigrificans partial 16S rRNA gene, type strain NCIMB 8395T	HG005352	1521	1565
124043	Desulfotomaculum nigrificans gene for 16S ribosomal RNA, partial sequence, strain: DSM574.	LC127105	1491	696369
124043	D.nigrificans 16S rRNA	X62176	1431	1565

GC content

@ref	GC-content (mol%)	Method
291	46	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Desulfotomaculum nigrificans DSM 574
NCBI: GCA_000189755

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	57.50	no
125439	motility	BacteriaNetⓘ	no	58.00	no
125439	gram_stain	BacteriaNetⓘ	positive	64.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	97.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Desulfotomaculum nigrificans DSM 574 DSM 574
NCBI: GCA_000189755.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	56.11	no
125438	anaerobic	anaerobicⓘ	yes	92.52	yes
125438	aerobic	aerobicⓘ	no	96.98	yes
125438	spore-forming	spore-formingⓘ	yes	86.07	no
125438	thermophilic	thermophileⓘ	yes	50.97	yes
125438	flagellated	motile2+ⓘ	yes	70.56	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Characterization of DsrD and its interaction with the DsrAB dissimilatory sulfite reductase.	Barbosa ACC, Venceslau SS, Ferreira D, Neukirchen S, Sousa FL, Melo MN, Pereira IAC.	Protein Sci	10.1002/pro.5222	2024
	Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans.	Visser M, Parshina SN, Alves JI, Sousa DZ, Pereira IA, Muyzer G, Kuever J, Lebedinsky AV, Koehorst JJ, Worm P, Plugge CM, Schaap PJ, Goodwin LA, Lapidus A, Kyrpides NC, Detter JC, Woyke T, Chain P, Davenport KW, Spring S, Rohde M, Klenk HP, Stams AJ.	Stand Genomic Sci	10.4056/sigs.4718645	2014
	Nested PCR-denaturing gradient gel electrophoresis approach to determine the diversity of sulfate-reducing bacteria in complex microbial communities.	Dar SA, Kuenen JG, Muyzer G.	Appl Environ Microbiol	10.1128/aem.71.5.2325-2330.2005	2005
Enzymology	PanG, a new ketopantoate reductase involved in pantothenate synthesis.	Miller CN, LoVullo ED, Kijek TM, Fuller JR, Brunton JC, Steele SP, Taft-Benz SA, Richardson AR, Kawula TH.	J Bacteriol	10.1128/jb.01740-12	2013
Metabolism	Identification and isolation of anaerobic, syntrophic phthalate isomer-degrading microbes from methanogenic sludges treating wastewater from terephthalate manufacturing.	Qiu YL, Sekiguchi Y, Imachi H, Kamagata Y, Tseng IC, Cheng SS, Ohashi A, Harada H.	Appl Environ Microbiol	10.1128/aem.70.3.1617-1626.2004	2004
	Development and testing of a DNA macroarray to assess nitrogenase (nifH) gene diversity.	Steward GF, Jenkins BD, Ward BB, Zehr JP.	Appl Environ Microbiol	10.1128/aem.70.3.1455-1465.2004	2004
	Distribution of thermophilic marine sulfate reducers in north sea oil field waters and oil reservoirs.	Nilsen RK, Beeder J, Thorstenson T, Torsvik T.	Appl Environ Microbiol	10.1128/aem.62.5.1793-1798.1996	1996
Metabolism	Cultivation and in situ detection of a thermophilic bacterium capable of oxidizing propionate in syntrophic association with hydrogenotrophic methanogens in a thermophilic methanogenic granular sludge.	Imachi H, Sekiguchi Y, Kamagata Y, Ohashi A, Harada H.	Appl Environ Microbiol	10.1128/aem.66.8.3608-3615.2000	2000
Metabolism	Comparative bioenergetics of sulfate reduction in Desulfovibrio and Desulfotomaculum spp.	Liu CL, Peck HD.	J Bacteriol	10.1128/jb.145.2.966-973.1981	1981
Enzymology	Distribution of thermophilic endospores in a temperate estuary indicate that dispersal history structures sediment microbial communities.	Bell E, Blake LI, Sherry A, Head IM, Hubert CRJ.	Environ Microbiol	10.1111/1462-2920.14056	2018
	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
Phylogeny	Desulfotomaculum carboxydivorans sp. nov., a novel sulfate-reducing bacterium capable of growth at 100% CO.	Parshina SN, Sipma J, Nakashimada Y, Henstra AM, Smidt H, Lysenko AM, Lens PNL, Lettinga G, Stams AJM	Int J Syst Evol Microbiol	10.1099/ijs.0.63780-0	2005

References

#291	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 574
#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) .
#66793	Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )
#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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Desulfotomaculum nigrificans (DSM 574, ATCC 19858, ATCC 19998)

Name and taxonomic classification

Morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Isolation, sampling and environmental information

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000189755

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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