Archive BacDiveID:10.13145/bacdive132569.20230509.8.1

Strain identifier

BacDive ID: 132569

Type strain:

Species: Dissulfurirhabdus thermomarina

Strain Designation: SH388

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

NCBI tax ID(s): 1765737 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 24358

BacDive-ID: 132569

DSM-Number: 100025

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, lithoautotroph, Gram-negative, motile, rod-shaped

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

NCBI tax id

NCBI tax id: 1765737
Matching level: species

strain history

@ref: 24358
history: <- G. Slobodkina, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; SH388 <- G. Slobodkina {2014}

doi: 10.13145/bacdive132569.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Deltaproteobacteria
order: Deltaproteobacteria, not assigned to order
family: Dissulfurirhabdaceae
genus: Dissulfurirhabdus
species: Dissulfurirhabdus thermomarina
full scientific name: Dissulfurirhabdus thermomarina Slobodkina et al. 2016

@ref: 24358

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Deltaproteobacteria, not assigned to order

family: Dissulfurirhabdaceae

genus: Dissulfurirhabdus

species: Dissulfurirhabdus thermomarina

full scientific name: Dissulfurirhabdus thermomarina Slobodkina et al. 2016

strain designation: SH388

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	flagellum arrangement	confidence
43947	negative	1.0-2.5 µm	0.2-0.4 µm	rod-shaped	yes	polar
69480	negative						99.999

Culture and growth conditions

culture medium

@ref: 24358
name: THERMOSULFURIMONAS MEDIUM (DSMZ Medium 1210a)
growth: yes
link: https://mediadive.dsmz.de/medium/1210a
composition: Name: THERMOSULFURIMONAS MEDIUM (DSMZ Medium 1210a; with strain-specific modifications) Composition: NaCl 17.9462 g/l MgCl2 x 6 H2O 3.98804 g/l Na-acetate 1.49551 g/l Na2CO3 0.997009 g/l Na-pyruvate 0.498504 g/l (NH4)2SO4 0.498504 g/l Na2S2O5 0.498504 g/l KH2PO4 0.329013 g/l KCl 0.329013 g/l CaCl2 x 2 H2O 0.329013 g/l Yeast extract 0.199402 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Folic acid 1.99402e-05 g/l Biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water

culture temp

@ref	growth	type	temperature	range	confidence
43947	positive	growth	25-58
43947	positive	optimum	50	thermophilic
24358	positive	growth	50	thermophilic
69480				thermophilic	99.999

culture pH

@ref	ability	type	pH
43947	positive	growth	5.0-7.0
43947	positive	optimum	6.0-6.5

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
43947	anaerobe
69480	anaerobe	99.999

nutrition type

@ref: 43947
type: lithoautotroph

spore formation

@ref	spore formation	confidence
43947	no
69481	no	100
69480	no	99.977

halophily

@ref	salt	growth	tested relation	concentration
43947	NaCl	positive	growth	0.5-4 %(w/v)
43947	NaCl	positive	optimum	2.0-2.5 %(w/v)

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
43947	33403	elemental sulfur	-	oxidation
43947		ferrihydrite	-	reduction
43947	17632	nitrate	-	reduction
43947	16189	sulfate	-	reduction
43947	33403	elemental sulfur	+	growth
43947	17359	sulfite	+	growth

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent	latitude	longitude	enrichment culture	enrichment culture composition	enrichment culture duration	enrichment culture temperature
24358	water and sediment from a shallow, submarine hydrothermal vent	Kurils, offshore Kunashir Island (44° 29.469' N 146° 06.247' E)	Russia	RUS	Asia	44.4833	146.1
43947	mixed sample of sand, hydrothermal fluid (thermal water and dissolved gases) and seawater collected at a shallow, submarine hydrothermal vent, Kunashir Island, Kurils, Russia	Kunashir Island, Kurils	Russia	RUS	Asia	44.4911	146.104	bicarbonate-buffered liquid medium	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	15 days	50

isolation source categories

Cat1	Cat2	Cat3
#Condition	#Thermophilic (>45°C)
#Environmental	#Aquatic	#Hydrothermal vent
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

taxonmaps

@ref: 69479
File name: preview.99_40526.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_474;96_18897;97_23407;98_29566;99_40526&stattab=map
Last taxonomy: Dissulfurirhabdus thermomarina subclade
16S sequence: KU051627
Sequence Identity:
Total samples: 20
soil counts: 1
aquatic counts: 19

Safety information

risk assessment

@ref: 24358
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 24358
description: Dissulfurirhabdus thermomarina strain SH388 16S ribosomal RNA gene, partial sequence
accession: KU051627
length: 1521
database: ena
NCBI tax ID: 1765737

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Dissulfurirhabdus thermomarina SH388	GCA_012979235	contig	ncbi	1765737
66792	Dissulfurirhabdus thermomarina DSM 100025	GCA_010499435	contig	ncbi	1765737
66792	Dissulfurirhabdus thermomarina strain DSM 100025	1765737.4	wgs	patric	1765737

GC content

@ref: 24358
GC-content: 64.6
method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
motile	yes	86.857	yes
gram-positive	no	99.164	yes
anaerobic	yes	99.001	yes
aerobic	no	98.767	yes
halophile	no	67.837	no
spore-forming	no	95.275	yes
glucose-util	no	58.727	no
flagellated	no	88.126	no
thermophile	yes	99.317	yes
glucose-ferment	no	85.2	no

External links

@ref: 24358

culture collection no.: DSM 100025, VKM B-2960

straininfo link

@ref: 90886
straininfo: 397082

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	27082267	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	Autotrophic Processes, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Deltaproteobacteria/classification/genetics/isolation & purification, Fatty Acids/chemistry, Hydrothermal Vents/microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Russia, Seawater/microbiology, Sequence Analysis, DNA, Sulfites/metabolism, Sulfur/metabolism	Transcriptome
Phylogeny	32553052	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	Deltaproteobacteria/classification/genetics, Genome, Bacterial, High-Throughput Nucleotide Sequencing, Phylogeny, Whole Genome Sequencing/*methods	Genetics
	32727039	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

Reference

@id	authors	title	doi/url	catalogue	journal	pubmed
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	10.1099/ijsem.0.004332
24358	Curators of the DSMZ		https://www.dsmz.de/collection/catalogue/details/culture/DSM-100025	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (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	10.1099/ijsem.0.001083		IJSEM 66: 2515-2519 2016	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)	https://diaspora-project.de/progress.html#genomes
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	https://microbeatlas.org/
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)	https://diaspora-project.de/progress.html#genomes
69481	Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch	Predictions based on the model GenomeNet Sporulation v. 1	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	10.60712/SI-ID397082.1