Name: Pseudodesulfovibrio hydrargyri BerOC1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158356

Type strain:

Species: Pseudodesulfovibrio hydrargyri

Strain Designation: BerOC1

Culture col. no.: DSM 103834, JCM 31820

Strain history: A. Ranchou-Peyruse; Univ. of Pau & Pays de l'Adour, France; BerOc1.

NCBI tax ID(s): 2125990 (species)

SI-ID 403299

DSM 103834

Section

Pseudodesulfovibrio hydrargyri BerOC1 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from brackish lagoon sediments.

Gram-negative
motile
vibrio-shaped
anaerobe
mesophilic
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	*Pseudodesulfovibrio*
	Species	**Pseudodesulfovibrio hydrargyri**
	Full Scientific Name (LPSN)	Pseudodesulfovibrio hydrargyri Ranchou-Peyruse et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #65548]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.838

[Ref.: #65548]	Cell length	2.8 µm

[Ref.: #65548]	Cell width	0.5 µm

[Ref.: #65548]	Cell shape	vibrio-shaped

[Ref.: #65548]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %97.036

[Ref.: #65548]	Colony color	white
[Ref.: #65548]	Cultivation medium used	anoxic medium

Information on culture and growth conditions Culture and growth conditions

[Ref.: #65032]

Culture medium

DESULFOSARCINA MEDIUM (BRACKISH WATER) (DSMZ Medium 198)

[Ref.: #65032]

Culture medium growth

[Ref.: #65032]

Culture medium link

Medium recipe at MediaDive

[Ref.: #65032]

Culture medium composition

expand / minimize

[Ref.: #65548]

Culture medium

anoxic medium

[Ref.: #65548]

Culture medium growth

		Temperature
[Ref.: #65032]	growth	30 °C
[Ref.: #65548]	growth	25-35 °C
[Ref.: #65548]	optimum	30 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #65032]	Temperature range	mesophilic
[Ref.: #65548]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #65548]			optimum	6.0-7.4

Information on physiology and metabolism Physiology and metabolism

[Ref.: #65548]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %98.651

[Ref.: #65548]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.907
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65548]		NaCl		growth	0.2-4	%(w/v)
[Ref.: #65548]		NaCl		optimum	1.5	%(w/v)

[Ref.: #65548]

Observation

methylation of inorganic mercury

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65548]	acetate ChEBI	-	growth
[Ref.: #65548]	acetone ChEBI	-	growth
[Ref.: #65548]	alanine ChEBI	-	growth
[Ref.: #65548]	arginine ChEBI	-	growth
[Ref.: #65548]	aspartate ChEBI	-	growth
[Ref.: #65548]	benzoate ChEBI	-	growth
[Ref.: #65548]	betaine ChEBI	-	growth
[Ref.: #65548]	butanol ChEBI	-	growth
[Ref.: #65548]	butyrate ChEBI	-	growth
[Ref.: #65548]	casamino acids	-	growth
[Ref.: #65548]	cellobiose ChEBI	-	growth
[Ref.: #65548]	choline ChEBI	-	growth
[Ref.: #65548]	citrate ChEBI	-	electron acceptor
[Ref.: #65548]	cysteine ChEBI	-	growth
[Ref.: #65548]	dihydrogen ChEBI	+	growth
[Ref.: #65548]	dimethyl sulfoxide ChEBI	+	reduction
[Ref.: #65548]	elemental sulfur ChEBI	-	electron acceptor
[Ref.: #65548]	ethanol ChEBI	+/-	growth
[Ref.: #65548]	formate ChEBI	-	growth
[Ref.: #65548]	fructose ChEBI	-	growth
[Ref.: #65548]	fumarate ChEBI	-	electron acceptor
[Ref.: #65548]	fumarate ChEBI	+	growth
[Ref.: #65548]	galactose ChEBI	-	growth
[Ref.: #65548]	gluconate ChEBI	-	growth
[Ref.: #65548]	glucose ChEBI	-	growth
[Ref.: #65548]	glutamate ChEBI	-	growth
[Ref.: #65548]	glycerol ChEBI	-	growth
[Ref.: #65548]	glycine ChEBI	-	growth
[Ref.: #65548]	glycolate ChEBI	-	growth
[Ref.: #65548]	hexadecanoate ChEBI	-	growth
[Ref.: #65548]	lactate ChEBI	+	growth
[Ref.: #65548]	lactose ChEBI	-	growth
[Ref.: #65548]	leucine ChEBI	-	growth
[Ref.: #65548]	malate ChEBI	-	growth
[Ref.: #65548]	mannose ChEBI	-	growth
[Ref.: #65548]	methanol ChEBI	-	growth
[Ref.: #65548]	methionine ChEBI	-	growth
[Ref.: #65548]	nitrate ChEBI	-	electron acceptor
[Ref.: #65548]	nitrite ChEBI	-	electron acceptor
[Ref.: #65548]	octadecanoate ChEBI	-	growth
[Ref.: #65548]	octanoate ChEBI	-	growth
[Ref.: #65548]	pentanol ChEBI	-	growth
[Ref.: #65548]	peptone	-	growth
[Ref.: #65548]	phenol ChEBI	-	growth
[Ref.: #65548]	propanol ChEBI	-	growth
[Ref.: #65548]	propionate ChEBI	-	growth
[Ref.: #65548]	pyruvate ChEBI	+	fermentation
[Ref.: #65548]	pyruvate ChEBI	+	growth
[Ref.: #65548]	ribose ChEBI	-	growth
[Ref.: #65548]	serine ChEBI	-	growth
[Ref.: #65548]	succinate ChEBI	-	growth
[Ref.: #65548]	sucrose ChEBI	-	growth
[Ref.: #65548]	sulfate ChEBI	+	reduction
[Ref.: #65548]	sulfite ChEBI	+	reduction
[Ref.: #65548]	tartrate ChEBI	-	growth
[Ref.: #65548]	thiosulfate ChEBI	+	reduction
[Ref.: #65548]	valerate ChEBI	-	growth
[Ref.: #65548]	valine ChEBI	-	growth
[Ref.: #65548]	yeast extract	-	growth
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #65548]		catalase	+	1.11.1.6

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

[Ref.: #65032]	Sample type/isolated from	brackish lagoon sediments
[Ref.: #65032]	Geographic location (country and/or sea, region)	Berre l'Etang
[Ref.: #65032]	Country	France
[Ref.: #65032]	Country ISO 3 Code	FRA
[Ref.: #65032]	Continent	Europe

[Ref.: #65548]	Sample type/isolated from	sediments of a brackish lagoon contaminated with petroleum hydrocarbons and heavy metals
[Ref.: #65548]	Sampling date	2004
[Ref.: #65548]	Geographic location (country and/or sea, region)	Etang de Berre
[Ref.: #65548]	Country	France
[Ref.: #65548]	Country ISO 3 Code	FRA
[Ref.: #65548]	Continent	Europe
[Ref.: #65548]	Enrichment culture	anoxic medium
[Ref.: #65548]	Enrichment culture composition	per litre: 0.25 g KH2PO4, 0.25 g K2HPO4, 0.5 g NH4Cl, 10 g NaCl, 0.05 g CaCl2 . 2H2O, 0.61 g MgCl2 . 6H2O, 2.86 g Na2SO4 , 0.4 ml Selenite-Tungstate solution, 1 ml SL10 trace element solution, 1 ml resazurin (0.1 %, w/v), 0.2 g Na2S . 9H2O, 2.5 g NaHCO3 , 1 ml filter-sterilized (0.22 µm) vitamins solution. The final pH was adjusted to 7 with an anoxic solution of 10 M NaOH.
[Ref.: #65548]	Enrichment culture duration	7 days
[Ref.: #65548]	Enrichment culture temperature	30 ̊C

[Ref.: #67770]	Sample type/isolated from	Brackish sediments contaminated with hydrocarbons and heavy metals in southeast France
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Brackish
#Engineered	#Contamination	#Heavy metal
#Engineered	#Contamination	#Oil (Fuel)
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

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

[Ref.: #65032]

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.: #65032]	Desulfovibrio sp. BerOc1 16S ribosomal RNA gene, partial sequence	EU137840	1434	ENA	2125990 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Pseudodesulfovibrio hydrargyri BerOc1	GCA_001874525	scaffold	GenBank	2125990 tax ID

[Ref.: #65032]	GC-content	62.6 mol%
[Ref.: #65548]	GC-content	62.6 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	62.6 mol%	genome sequence analysis

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: Pseudodesulfovibrio hydrargyri BerOc1 NCBI: GCA_001874525.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudodesulfovibrio hydrargyri BerOc1 NCBI: GCA_001874525.1
[Ref.: #69480]	flagellated	yes	64.523	no
[Ref.: #69480]	gram-positive	no	99.146	no
[Ref.: #69480]	anaerobic	yes	95.309	no
[Ref.: #69480]	aerobic	no	96.375	yes
[Ref.: #69480]	halophile	no	81.871	yes
[Ref.: #69480]	spore-forming	no	94.775	no
[Ref.: #69480]	thermophile	no	93.849	yes
[Ref.: #69480]	glucose-util	no	63.854	yes
[Ref.: #69480]	motile	yes	91.675	no
[Ref.: #69480]	glucose-ferment	no	82.205	no

Availability in culture collections External links

[Ref.: #65032]

Culture collection no.

DSM 103834, JCM 31820

[Ref.: #111161]

SI-ID 403299

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudodesulfovibrio hydrargyri sp. nov., a mercury-methylating bacterium isolated from a brackish sediment.	Ranchou-Peyruse M, Goni-Urriza M, Guignard M, Goas M, Ranchou-Peyruse A, Guyoneaud R	Int J Syst Evol Microbiol	10.1099/ijsem.0.002173	2018	*

References

#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 )

#65032

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103834

#65548

Magali Ranchou-Peyruse, Marisol Goñi-Urriza, Marion Guignard, Marjorie Goas, Anthony Ranchou-Peyruse and Rémy Guyoneaud: Pseudodesulfovibrio hydrargyri sp. nov., a mercury-methylating bacterium isolated from a brackish sediment. IJSEM 68: 1461 - 1466 2018 ( DOI 10.1099/ijsem.0.002173 , PubMed 29533171 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 )

#111161

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-ID403299.1 )

* These data were automatically processed and therefore are not curated

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Pseudodesulfovibrio hydrargyri BerOc1

Pseudodesulfovibrio hydrargyri BerOc1

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