Name: Dissulfurirhabdus thermomarina SH388
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 132569

Type strain:

Species: Dissulfurirhabdus thermomarina

Strain Designation: SH388

Culture col. no.: DSM 100025, VKM B-2960

Strain history: <- G. Slobodkina, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; SH388 <- G. Slobodkina {2014}

NCBI tax ID(s): 1765737 (species)

SI-ID 397082

DSM 100025

Special Collections

Section

Dissulfurirhabdus thermomarina SH388 is an anaerobe, lithoautotroph, Gram-negative bacterium that was isolated from water and sediment from a shallow, submarine hydrothermal vent.

Gram-negative
motile
rod-shaped
anaerobe
lithoautotroph
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	[Deltaproteobacteria, not assigned to order]
	Family	"Dissulfurirhabdaceae"
	Genus	*Dissulfurirhabdus*
	Species	**Dissulfurirhabdus thermomarina**
	Full Scientific Name (LPSN)	Dissulfurirhabdus thermomarina Slobodkina et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43947]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %98.619

[Ref.: #43947]	Cell length	1.0-2.5 µm

[Ref.: #43947]	Cell width	0.2-0.4 µm

[Ref.: #43947]	Cell shape	rod-shaped

[Ref.: #43947]	Motility	yes

[Ref.: #43947]	Flagellum arrangement	polar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #24358]

Culture medium

THERMOSULFURIMONAS MEDIUM (DSMZ Medium 1210a)

[Ref.: #24358]

Culture medium growth

[Ref.: #24358]

Culture medium link

Medium recipe at MediaDive

[Ref.: #24358]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #24358]	growth	50 °C
[Ref.: #43947]	growth	25-58 °C
[Ref.: #43947]	optimum	50 °C

	pH	Kind of pH		pH
[Ref.: #43947]			optimum	6.0-6.5
[Ref.: #43947]			growth	5.0-7.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43947]

Oxygen tolerance

anaerobe

[Ref.: #43947]

Nutrition type

lithoautotroph

[Ref.: #43947]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43947]		NaCl		growth	0.5-4	%(w/v)
[Ref.: #43947]		NaCl		optimum	2.0-2.5	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43947]	elemental sulfur ChEBI	-	oxidation
[Ref.: #43947]	elemental sulfur ChEBI	+	growth
[Ref.: #43947]	ferrihydrite	-	reduction
[Ref.: #43947]	nitrate ChEBI	-	reduction
[Ref.: #43947]	sulfate ChEBI	-	reduction
[Ref.: #43947]	sulfite ChEBI	+	growth

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

[Ref.: #24358]	Sample type/isolated from	water and sediment from a shallow, submarine hydrothermal vent
[Ref.: #24358]	Geographic location (country and/or sea, region)	Kurils, offshore Kunashir Island (44° 29.469' N 146° 06.247' E)
[Ref.: #24358]	Country	Russia
[Ref.: #24358]	Country ISO 3 Code	RUS
[Ref.: #24358]	Continent	Asia
[Ref.: #24358]	Geographic location	44.4833°/146.1000°

[Ref.: #43947]	Sample type/isolated from	mixed sample of sand, hydrothermal fluid (thermal water and dissolved gases) and seawater collected at a shallow, submarine hydrothermal vent, Kunashir Island, Kurils, Russia
[Ref.: #43947]	Geographic location (country and/or sea, region)	Kunashir Island, Kurils
[Ref.: #43947]	Country	Russia
[Ref.: #43947]	Country ISO 3 Code	RUS
[Ref.: #43947]	Continent	Asia
[Ref.: #43947]	Geographic location	44.4911°/146.1040°
[Ref.: #43947]	Enrichment culture	bicarbonate-buffered liquid medium
[Ref.: #43947]	Enrichment culture composition	0.33 g NH 4 Cl, 0.33 g KCl, 0.33 g CaCl2.6H2O, 0.33g KH2PO4, 18.0 g NaCl, 4.33 g MgCl2.6H2O, 2.0 g NaHCO3, 1 ml trace element solution, 1 ml vitamin solution, pH of 6.5–6.8
[Ref.: #43947]	Enrichment culture duration	15 days
[Ref.: #43947]	Enrichment culture temperature	50 ̊C
* marker position based on {}

Isolation sources categories

#Condition	#Thermophilic (>45°C)	-
#Environmental	#Aquatic	#Hydrothermal vent
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KU051627 (>99% sequence identity) for Dissulfurirhabdus thermomarina subclade from Microbeatlas

Aquatic Samples	19
Soil Samples	1
Animal Samples
Plant Samples
Total Samples	20

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

[Ref.: #24358]

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.: #24358]	Dissulfurirhabdus thermomarina strain SH388 16S ribosomal RNA gene, partial sequence	KU051627	1521	GenBank ENA	1765737 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Dissulfurirhabdus thermomarina SH388	GCA_012979235	contig	GenBank ENA	1765737 tax ID	*
[Ref.: #66792]	Dissulfurirhabdus thermomarina DSM 100025	GCA_010499435	contig	GenBank ENA	1765737 tax ID	*
[Ref.: #66792]	Dissulfurirhabdus thermomarina strain DSM 100025	1765737.4	wgs	PATRIC	1765737 tax ID	*

[Ref.: #24358]

GC-content

64.6 mol%

thermal denaturation, midpoint method (Tm)

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: Dissulfurirhabdus thermomarina strain DSM 100025 PATRIC: 1765737.5
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Dissulfurirhabdus thermomarina strain DSM 100025 PATRIC: 1765737.4
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	98.619	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	86.84	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	88.816	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	83.23	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	yes	60.387	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	77.991	yes

Availability in culture collections External links

[Ref.: #24358]

Culture collection no.

DSM 100025, VKM B-2960

[Ref.: #90886]

SI-ID 397082

Literature:

	Title	Authors	Journal	DOI	Year
Phylogeny	Genomic sequence analysis of Dissulfurirhabdus thermomarina SH388 and proposed reassignment to Dissulfurirhabdaceae fam. nov.	Ward LM, Bertran E, Johnston DT	Microb Genom	10.1099/mgen.0.000390	2020	*
Phylogeny	Dissulfurirhabdus thermomarina gen. nov., sp. nov., a thermophilic, autotrophic, sulfite-reducing and disproportionating deltaproteobacterium isolated from a shallow-sea hydrothermal vent.	Slobodkina GB, Kolganova TV, Kopitsyn DS, Viryasov MB, Bonch-Osmolovskaya EA, Slobodkin AI	Int J Syst Evol Microbiol	10.1099/ijsem.0.001083	2016	*
	Genomic Characterization and Environmental Distribution of a Thermophilic Anaerobe Dissulfurirhabdus thermomarina SH388(T) Involved in Disproportionation of Sulfur Compounds in Shallow Sea Hydrothermal Vents.	Allioux M, Yvenou S, Slobodkina G, Slobodkin A, Shao Z, Jebbar M, Alain K	Microorganisms	10.3390/microorganisms8081132	2020	*

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 )

#24358

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100025

#43947

Galina B. Slobodkina, Tatyana V. Kolganova, Dmitry S. Kopitsyn, Mikhail B. Viryasov, Elizaveta A. Bonch-Osmolovskaya, Alexander I. Slobodkin: Dissulfurirhabdus thermomarina gen. nov., sp. nov., a thermophilic, autotrophic, sulfite-reducing and disproportionating deltaproteobacterium isolated from a shallow-sea hydrothermal vent. IJSEM 66: 2515 - 2519 2016 ( DOI 10.1099/ijsem.0.001083 , PubMed 27082267 )

#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) .

#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 )

#90886

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-ID397082.1 )

* These data were automatically processed and therefore are not curated

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Dissulfurirhabdus thermomarina strain DSM 100025

Dissulfurirhabdus thermomarina strain DSM 100025

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