Name: Paucidesulfovibrio gracilis SRL6146
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 4149

Type strain:

Species: Paucidesulfovibrio gracilis

Strain Designation: SRL6146

Culture col. no.: DSM 16080, ATCC BAA-904

Strain history: <- M. Magot, Université de Pau et des Pays de l'Adour, IBEAS, Pau, France; SRL6146 <- M. Magot {1991}

NCBI tax ID(s): 1121449 (strain), 47158 (species)

SI-ID 134286

ATCC BAA-904, DSM 16080

Section

Paucidesulfovibrio gracilis SRL6146 is an anaerobe, moderately halophilic, mesophilic bacterium that was isolated from oil pipeline water.

rod-shaped
anaerobe
mesophilic
moderately halophilic
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	*Pseudomonadota*
	Class	*Deltaproteobacteria*
	Order	*Desulfovibrionales*
	Family	*Desulfovibrionaceae*
	Genus	*Paucidesulfovibrio*
	Species	**Paucidesulfovibrio gracilis**
	Full Scientific Name (LPSN)	Paucidesulfovibrio gracilis (Magot et al. 2004) Waite et al. 2020

Synonym

Desulfovibrio gracilis

Information on morphological and physiological properties Morphology

[Ref.: #23373]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.996

[Ref.: #23373]	Cell length	4.5-9.0 µm

[Ref.: #23373]	Cell width	0.3 µm

[Ref.: #23373]	Cell shape	curved-shaped
[Ref.: #23373]	Cell shape	rod-shaped
[Ref.: #23373]	Cell shape	vibrio-shaped

[Ref.: #23373]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %94.546

[Ref.: #23373]	Flagellum arrangement	polar

[Ref.: #23373]

Colony color

grey to dark grey

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6279]

Culture medium

DESULFOVIBRIO HALOPHILUS MEDIUM (DSMZ Medium 496)

[Ref.: #6279]

Culture medium growth

[Ref.: #6279]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6279]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #6279]	growth	37 °C
[Ref.: #23373]	growth	20-40 °C
[Ref.: #23373]	optimum	37-40 °C

[Ref.: #6279]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #23373]			optimum	6.8-7.2
[Ref.: #23373]			growth	5.4-8.4

Information on physiology and metabolism Physiology and metabolism

[Ref.: #6279]	Oxygen tolerance	anaerobe
[Ref.: #23373]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.999

[Ref.: #23373]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %98.806

[Ref.: #23373]

Halophily / tolerance level

moderately halophilic

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #23373]		NaCl		growth	20-120	g/L
[Ref.: #23373]		NaCl		optimum	50-60	g/L

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #23373]	cysteine ChEBI	-	fermentation
[Ref.: #23373]	elemental sulfur ChEBI	+	electron acceptor
[Ref.: #23373]	fructose ChEBI	-	fermentation
[Ref.: #23373]	fumarate ChEBI	-	fermentation
[Ref.: #23373]	fumarate ChEBI	+	electron acceptor
[Ref.: #23373]	glucose ChEBI	-	fermentation
[Ref.: #23373]	glycerol ChEBI	-	fermentation
[Ref.: #23373]	lactate ChEBI	-	fermentation
[Ref.: #23373]	lactate ChEBI	+	growth
[Ref.: #23373]	lactate ChEBI	+	oxidation
[Ref.: #23373]	malate ChEBI	-	fermentation
[Ref.: #23373]	nitrate ChEBI	-	electron acceptor
[Ref.: #23373]	pyruvate ChEBI	-	fermentation
[Ref.: #23373]	pyruvate ChEBI	+	growth
[Ref.: #23373]	succinate ChEBI	-	fermentation
[Ref.: #23373]	sulfate ChEBI	+	electron acceptor
[Ref.: #23373]	sulfite ChEBI	+	electron acceptor
[Ref.: #23373]	thiosulfate ChEBI	+	electron acceptor
	Only first 10 entries are displayed. Click here to see all.

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	acetoin degradation	100	3 of 3
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	chorismate metabolism	100	9 of 9
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	90.91	20 of 22
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	nitrate assimilation	77.78	7 of 9
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	purine metabolism	72.34	68 of 94
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	sulfate reduction	69.23	9 of 13
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	vitamin B12 metabolism	67.65	23 of 34
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	pyrimidine metabolism	64.44	29 of 45
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	alanine metabolism	62.07	18 of 29
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	starch degradation	60	6 of 10
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	oxidative phosphorylation	58.24	53 of 91
[Ref.: #66794]	serine metabolism	55.56	5 of 9
[Ref.: #66794]	vitamin B6 metabolism	54.55	6 of 11
[Ref.: #66794]	tryptophan metabolism	52.63	20 of 38
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	Entner Doudoroff pathway	50	5 of 10
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	denitrification	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	histidine metabolism	48.28	14 of 29
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	arginine metabolism	45.83	11 of 24
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	cysteine metabolism	44.44	8 of 18
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	lipid metabolism	41.94	13 of 31
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	degradation of pentoses	39.29	11 of 28
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	degradation of sugar alcohols	25	4 of 16
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	glutathione metabolism	21.43	3 of 14
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #6279]	Sample type/isolated from	oil pipeline water
[Ref.: #6279]	Geographic location (country and/or sea, region)	Emeraude oilfield
[Ref.: #6279]	Country	Republic of the Congo
[Ref.: #6279]	Country ISO 3 Code	COG
[Ref.: #6279]	Continent	Africa

[Ref.: #23373]	Sample type/isolated from	from oilfield production water collected at the E153 wellhead of Emeraude Oilfield
* marker position based on {}

Isolation sources categories

#Engineered	#Industrial	#Machines and devices
#Environmental	#Aquatic	-
#Engineered	#Industrial	#Engineered product
#Engineered	#Industrial	#Oil reservoir

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence U53464 (>99% sequence identity) for Desulfovibrio gracilis from Microbeatlas

Aquatic Samples	103
Soil Samples	13
Animal Samples	21
Plant Samples	1
Total Samples	138

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

[Ref.: #6279]

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.: #23373]	Desulfovibrio gracilis strain SEBR 6116 16S ribosomal RNA gene, complete sequence	U53464	1449	GenBank	47158 tax ID
[Ref.: #6279]	Zea mays cultivar PI221733 starch debranching enzyme I (sbe1) gene, upstream region	AY453464	339	ENA	4577 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Paucidesulfovibrio gracilis DSM 16080	GCA_900167125	contig	GenBank	1121449 tax ID	*
[Ref.: #66792]	Desulfovibrio gracilis DSM 16080 strain DSM 16080	1121449.4	wgs	PATRIC	1121449 tax ID	*
[Ref.: #66792]	Desulfovibrio gracilis DSM 16080	2568526008	draft	JGI IMG/M	1121449 tax ID	*

[Ref.: #6279]	GC-content	59 mol%	high performance liquid chromatography (HPLC)
[Ref.: #23368]	GC-content	59.0 mol%
[Ref.: #23368]	GC-content	62.4 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Desulfovibrio gracilis DSM 16080 strain DSM 16080 PATRIC: 1121449.4
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Desulfovibrio gracilis DSM 16080 strain DSM 16080 PATRIC: 1121449.4
[Ref.: #69480]	motile	yes	92.166	yes
[Ref.: #69480]	flagellated	yes	52.974	no
[Ref.: #69480]	gram-positive	no	99.527	yes
[Ref.: #69480]	anaerobic	yes	99.05	yes
[Ref.: #69480]	aerobic	no	98.695	yes
[Ref.: #69480]	halophile	yes	59.628	yes
[Ref.: #69480]	spore-forming	no	94.729	yes
[Ref.: #69480]	thermophile	no	69.159	no
[Ref.: #69480]	glucose-util	no	66.382	no
[Ref.: #69480]	glucose-ferment	no	90.186	yes

Availability in culture collections External links

[Ref.: #6279]

Culture collection no.

DSM 16080, ATCC BAA-904

[Ref.: #73650]

SI-ID 134286

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Desulfovibrio bastinii sp. nov. and Desulfovibrio gracilis sp. nov., moderately halophilic, sulfate-reducing bacteria isolated from deep subsurface oilfield water.	Magot M, Basso O, Tardy-Jacquenod C, Caumette P	Int J Syst Evol Microbiol	10.1099/ijs.0.02977-0	2004	*

References

#6279

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16080

#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 )

#23368

Nurettin Sahin, Akio Tani, Recep Kotan, Ivo Sedlácek, Kazuhide Kimbara, Abdurrahman U. Tamer: Pandoraea oxalativorans sp. nov., Pandoraea faecigallinarum sp. nov. and Pandoraea vervacti sp. nov., isolated from oxalate-enriched culture. IJSEM 61: 2247 - 2253 2011 ( DOI 10.1099/ijs.0.026138-0 , PubMed 20952546 )

#23373

Michel Magot, Odile Basso, Christèle Tardy-Jacquenod, Pierre Caumette: Desulfovibrio bastinii sp. nov. and Desulfovibrio gracilis sp. nov., moderately halophilic, sulfate-reducing bacteria isolated from deep subsurface oilfield water. IJSEM 54: 1693 - 1697 2004 ( DOI 10.1099/ijs.0.02977-0 , PubMed 15388730 )

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#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 )

#73650

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-ID134286.1 )

* These data were automatically processed and therefore are not curated

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Desulfovibrio gracilis DSM 16080 strain DSM 16080

Desulfovibrio gracilis DSM 16080 strain DSM 16080

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