Name: Desulfotomaculum nigrificans DSM 574
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 11792

Type strain:

Species: Desulfotomaculum nigrificans

Culture col. no.: DSM 574, ATCC 19858, ATCC 19998, CIP 111238, NCIMB 8395, WDCM 00081, Delft 74

Strain history: <- F. Hollaus <- NCIB <- K.R. Butlin (Desulfovibrio desulfuricans) <- J. Senez <- R.L. Starkey, Delft 74

NCBI tax ID(s): 696369 (strain), 1565 (species)

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

Special Collections

DSMZ
CIP

Other strains from Desulfotomaculum nigrificans

Section

Desulfotomaculum nigrificans DSM 574 is an anaerobe, spore-forming bacterium of the family Peptococcaceae.

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	*Peptococcaceae*
	Genus	*Desulfotomaculum*
	Species	**Desulfotomaculum nigrificans**
	Full Scientific Name (LPSN)	Desulfotomaculum nigrificans (Werkman and Weaver 1927) Campbell and Postgate 1965 (Approved Lists 1980)

	Synonym	"Clostridium* nigrificans"*
	Synonym	Desulfotomaculum carboxydivorans

Information on morphological and physiological properties Morphology

Multimedia content

[Ref.: #66793]

Caption:

electron microscopic image

[Ref.: #66793]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #291]

Culture medium

DESULFOVIBRIO (POSTGATE) MEDIUM (DSMZ Medium 63)

[Ref.: #291]

Culture medium growth

[Ref.: #291]

Culture medium link

Medium recipe at MediaDive

[Ref.: #291]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #291]			growth	55 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #291]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %92.518

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

[Ref.: #291]	Geographic location (country and/or sea, region)	freshwater
[Ref.: #291]	Country	Netherlands
[Ref.: #291]	Country ISO 3 Code	NLD
[Ref.: #291]	Continent	Europe
* marker position based on {}

[Ref.: #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

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

[Ref.: #291]

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.: #291]	Desulfotomaculum nigrificans partial 16S rRNA gene, type strain NCIMB 8395T	HG005352	1521	GenBank ENA	1565 tax ID
[Ref.: #124043]	Desulfotomaculum nigrificans gene for 16S ribosomal RNA, partial sequence, strain: DSM574.	LC127105	1491	GenBank ENA	696369 tax ID	*
[Ref.: #20218]	Sulphate-reducing bacteria ATCC 19858 16S rRNA region	A30643	1346	GenBank ENA	77133 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Desulfotomaculum nigrificans DSM 574	GCA_000189755	contig	GenBank ENA	696369 tax ID	*
[Ref.: #66792]	Desulfotomaculum nigrificans DSM 574	696369.3	wgs	PATRIC	696369 tax ID	*
[Ref.: #66792]	Desulfotomaculum nigrificans DSM 574	2507262026	draft	JGI IMG/M	696369 tax ID	*

[Ref.: #291]

GC-content

46 mol%

sequence analysis

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Desulfotomaculum nigrificans DSM 574 DSM 574 NCBI: GCA_000189755.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	77	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Desulfotomaculum nigrificans DSM 574 DSM 574 NCBI: GCA_000189755.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	56.113	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	92.518	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	96.979	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	86.072	no
[Ref.: #69480]	thermophilic	thermophileⓘ	yes	50.973	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	70.563	no

Availability in culture collections External links

[Ref.: #291]

Culture collection no.

DSM 574, ATCC 19858, ATCC 19998, CIP 111238, NCIMB 8395, WDCM 00081, Delft 74

[Ref.: #81010]

SI-ID 92880

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#81010

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-ID92880.1 )

#124043

Dr. Isabel Schober, Dr. Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

* These data were automatically processed and therefore are not curated

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Desulfotomaculum nigrificans DSM 574 DSM 574

Desulfotomaculum nigrificans DSM 574 DSM 574

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