Desulfotomaculum nigrificans CO-1-SRB | DSM 14880, VKM B-2319 | BacDiveID:11828

Strain identifier

BacDive ID: 11828

Type strain:

Species: Desulfotomaculum nigrificans

Strain Designation: CO-1-SRB

Culture col. no.: DSM 14880, VKM B-2319

Strain history: <- S. N. Parshina, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; CO-1-SRB <- S. N. Parshina {2002}

NCBI tax ID(s): 1565 (species)

SI-ID 265599

DSM 14880, VKM B-2319

Other strains from Desulfotomaculum nigrificans

D. nigrificans DSM 574, ATCC 19858, ATCC 19998, ... (type strain)
D. nigrificans DSM 575, NCIMB 8706
D. nigrificans Teddington Garden, DSM 7434, NCIMB ...
D. nigrificans Staines G, DSM 7435, NCIMB 8353
D. nigrificans Aberdeen, DSM 7436, NCIMB 8354
D. nigrificans Holland DT, DSM 7437, NCIMB 8355
D. nigrificans DSM 7438, NCIMB 8788
D. nigrificans 2133, DSM 7453, ATCC 7946, NCA ...

Section

Desulfotomaculum nigrificans CO-1-SRB is an anaerobe, spore-forming, thermophilic bacterium that was isolated from sludge from an anaerobic bioreactor treating paper mill wastewater.

Gram-positive
motile
rod-shaped
spore-forming
anaerobe
thermophilic
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

[Ref.: #31544]	Gram stain	positive

[Ref.: #31544]	Cell length	10 µm

[Ref.: #31544]	Cell width	1 µm

[Ref.: #31544]	Cell shape	rod-shaped

[Ref.: #31544]	Motility	yes

[Ref.: #31544]	Flagellum arrangement	gliding

Pigment production

no

Multimedia content

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Information on culture and growth conditions Culture and growth conditions

Culture medium

DESULFOBULBUS SP. MEDIUM (FRESHWATER) (DSMZ Medium 194)

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #5596]			growth	55 °C
[Ref.: #31544]			growth	30-68 °C
[Ref.: #31544]			optimum	55 °C

[Ref.: #5596]	Temperature range	thermophilic
[Ref.: #31544]	Temperature range	thermophilic

	pH	Kind of pH		pH
[Ref.: #31544]			optimum	7
[Ref.: #31544]			growth	6.0-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #5596]	Oxygen tolerance	anaerobe
[Ref.: #31544]	Oxygen tolerance	anaerobe

Ability of spore formation

yes

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31544]		NaCl		growth	0-16	%
[Ref.: #31544]		NaCl		optimum	4	%

Observation

aggregates in clumps

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31544]		ethanol ChEBI	+	carbon source
[Ref.: #31544]		fructose ChEBI	+	carbon source
[Ref.: #31544]		glucose ChEBI	+	carbon source
[Ref.: #31544]		lactate ChEBI	+	carbon source
[Ref.: #31544]		pyruvate ChEBI	+	carbon source
[Ref.: #31544]		serine ChEBI	+	carbon source

	Metabolite production	Metabolite	Production
[Ref.: #31544]		hydrogen sulfide ChEBI	yes

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #31544]		alkaline phosphatase	+	3.1.3.1

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

[Ref.: #5596]	Sample type/isolated from	sludge from an anaerobic bioreactor treating paper mill wastewater
[Ref.: #5596]	Geographic location (country and/or sea, region)	Eerbeek, Industriewater Eerbeek BV
[Ref.: #5596]	Country	Netherlands
[Ref.: #5596]	Country ISO 3 Code	NLD
[Ref.: #5596]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Bioreactor	-
#Engineered	#Waste	#Industrial wastewater
#Environmental	#Terrestrial	#Mud (Sludge)
#Condition	#Anoxic (anaerobic)	-

What are isolation sources categories?

Global distribution of 16S sequence AY961415 (>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

Biosafety level

1

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.: #5596]	Desulfotomaculum carboxydivorans strain CO-1-SRB 16S ribosomal RNA gene, partial sequence	AY961415	1424	ENA	868595 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Desulfotomaculum nigrificans CO-1-SRB	GCA_000214435	complete	GenBank	868595 tax ID	*
[Ref.: #66792]	Desulfotomaculum carboxydivorans CO-1-SRB, DSM 14880	2505679104	complete	JGI IMG/M	868595 tax ID	*

GC-content

45.6 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Desulfotomaculum nigrificans CO-1-SRB CO-1-SRB NCBI: GCA_000214435.1
[Ref.: #69480]	motile	yes	86.244	no
[Ref.: #69480]	flagellated	no	91.714	yes
[Ref.: #69480]	gram-positive	no	87.989	no
[Ref.: #69480]	anaerobic	yes	99.364	no
[Ref.: #69480]	aerobic	no	97.028	no
[Ref.: #69480]	halophile	no	94.374	no
[Ref.: #69480]	spore-forming	yes	93.806	yes
[Ref.: #69480]	thermophile	yes	98.973	yes
[Ref.: #69480]	glucose-util	yes	86.798	yes
[Ref.: #69480]	glucose-ferment	no	74.493	no

Availability in culture collections External links

Culture collection no.

DSM 14880, VKM B-2319

SI-ID 265599

*

Literature:

	Title	Authors	Journal	DOI	Year
Metabolism	Engineering of vitamin prototrophy in Clostridium ljungdahlii and Clostridium autoethanogenum.	Annan FJ, Al-Sinawi B, Humphreys CM, Norman R, Winzer K, Kopke M, Simpson SD, Minton NP, Henstra AM	Appl Microbiol Biotechnol	10.1007/s00253-019-09763-6	2019	*
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	*
	Effect of Sulfate on Carbon Monoxide Conversion by a Thermophilic Syngas-Fermenting Culture Dominated by a Desulfofundulus Species.	Alves JI, Visser M, Arantes AL, Nijsse B, Plugge CM, Alves MM, Stams AJM, Sousa DZ	Front Microbiol	10.3389/fmicb.2020.588468	2020	*

References

#5596

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 14880

#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 )

#31544

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #27836 (see below)

#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) .

#81047

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-ID265599.1 )

#27836

IJSEM 2159 2005 ( DOI 10.1099/ijs.0.63780-0 , PubMed 16166725 )

* These data were automatically processed and therefore are not curated

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