Solidesulfovibrio magneticus (DSM 13731, JCM 12223, RS-1)

Name: Solidesulfovibrio magneticus (DSM 13731, JCM 12223, RS-1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 4140

Type strain

Strain Designation RS-1

Culture col. no. DSM 13731 JCM 12223 RS-1

NCBI tax ID(s) 184917

Special Collections DSMZ JCM

History DSMZ <- T. Matsunaga, Tokyo University of Agriculture and Technology, Japan; RS-1 <- T. Sakaguchi and T. Matsunaga {1993}

Links

Solidesulfovibrio magneticus RS-1 is an anaerobe bacterium that was isolated from freshwater sulfide-rich mud.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 44239

ATCC 700980,DSM 13731,KCTC 12949,JCM 12223

@ref 20215

Last LPSN update 2026-05-29 08:25:52

Domain Bacteria

Phylum Thermodesulfobacteriota

Class Desulfovibrionia

Order Desulfovibrionales

Family Desulfovibrionaceae

Genus Solidesulfovibrio

Species Solidesulfovibrio magneticus

Full scientific name Solidesulfovibrio magneticus (Sakaguchi et al. 2002) Waite et al. 2020

Synonyms (1)

Desulfovibrio magneticus

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
5132	SOLIDESULFOVIBRIO MEDIUM (DSMZ Medium 896)		Medium recipe at MediaDive	Name: SOLIDESULFOVIBRIO MEDIUM (DSMZ Medium 896) Composition: Na2-fumarate 0.575968 g/l Na-pyruvate 0.436941 g/l KH2PO4 0.19861 g/l NH4Cl 0.0595829 g/l L-Cysteine HCl x H2O 0.0496524 g/l MgSO4 x 7 H2O 0.0119166 g/l Nitrilotriacetic acid 0.00595829 g/l FeCl3 x 6 H2O 0.00536246 g/l NaCl 0.00397219 g/l (-)-Quinic acid 0.00377358 g/l MnSO4 x H2O 0.0019861 g/l CoSO4 x 7 H2O 0.000714995 g/l ZnSO4 x 7 H2O 0.000714995 g/l CaCl2 x 2 H2O 0.000397219 g/l FeSO4 x 7 H2O 0.000397219 g/l NiCl2 x 6 H2O 0.000119166 g/l Pyridoxine hydrochloride 9.93049e-05 g/l AlK(SO4)2 x 12 H2O 7.94439e-05 g/l (DL)-alpha-Lipoic acid 4.96524e-05 g/l p-Aminobenzoic acid 4.96524e-05 g/l Calcium D-(+)-pantothenate 4.96524e-05 g/l Nicotinic acid 4.96524e-05 g/l Riboflavin 4.96524e-05 g/l Thiamine HCl 4.96524e-05 g/l CuSO4 x 5 H2O 3.97219e-05 g/l H3BO3 3.97219e-05 g/l Na2MoO4 x 2 H2O 3.97219e-05 g/l Folic acid 1.9861e-05 g/l Biotin 1.9861e-05 g/l Na2WO4 x 2 H2O 1.58888e-06 g/l Na2SeO3 x 5 H2O 1.19166e-06 g/l Vitamin B12 9.93049e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
5132	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
5132	anaerobe
125439	obligate anaerobe	99.844

Spore formation

@ref	Spore formation	Confidence
125439		98.962

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Freshwater
#Environmental	#Terrestrial	#Mud (Sludge)
#Condition	#Sulfuric	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
5132	freshwater sulfide-rich mud	Wakayama	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence D43944 (>99% sequence identity) for Desulfovibrio from Microbeatlas

Aquatic Samples	2969
Soil Samples	453
Animal Samples	351
Plant Samples	438
Total Samples	4211

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5132	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1066v1 assembly for Solidesulfovibrio magneticus RS-1	complete	GCA_000010665	573370.3	644736352	573370	98.87

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
5132	Desulfovibrio magneticus gene for 16S rRNA	D43944	1540		573370

GC content

@ref	GC-content (mol%)	Method
5132	65.8	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1066v1 assembly for Solidesulfovibrio magneticus RS-1
NCBI: GCA_000010665

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	99.84	no
125439	gram_stain	BacteriaNetⓘ	negative	83.01	no
125439	motility	BacteriaNetⓘ	yes	49.65	no
125439	spore_formation	BacteriaNetⓘ	no	98.96	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Solidesulfovibrio magneticus RS-1 RS-1
NCBI: GCA_000010665.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	86.86	no
125438	anaerobic	anaerobicⓘ	yes	71.14	no
125438	aerobic	aerobicⓘ	no	83.87	yes
125438	spore-forming	spore-formingⓘ	no	78.94	no
125438	thermophilic	thermophileⓘ	no	87.30	yes
125438	flagellated	motile2+ⓘ	yes	70.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Isolation and cultivation of a novel sulfate-reducing magnetotactic bacterium belonging to the genus Desulfovibrio.	Shimoshige H, Kobayashi H, Shimamura S, Mizuki T, Inoue A, Maekawa T	PLoS One	10.1371/journal.pone.0248313	2021
Metabolism	Genome Editing Method for the Anaerobic Magnetotactic Bacterium Desulfovibrio magneticus RS-1.	Grant CR, Rahn-Lee L, LeGault KN, Komeili A	Appl Environ Microbiol	10.1128/AEM.01724-18	2018
Metabolism	Elongated magnetite nanoparticle formation from a solid ferrous precursor in a magnetotactic bacterium.	Baumgartner J, Menguy N, Gonzalez TP, Morin G, Widdrat M, Faivre D	J R Soc Interface	10.1098/rsif.2016.0665	2016
Phylogeny	MamA as a Model Protein for Structure-Based Insight into the Evolutionary Origins of Magnetotactic Bacteria.	Zeytuni N, Cronin S, Lefevre CT, Arnoux P, Baran D, Shtein Z, Davidov G, Zarivach R	PLoS One	10.1371/journal.pone.0130394	2015
	Magnetite Crystal Orientation in Magnetosome Chains.	Kornig A, Winklhofer M, Baumgartner J, Gonzalez TP, Fratzl P, Faivre D	Adv Funct Mater	10.1002/adfm.201303737	2014
Pathogenicity	Anisotropy of bullet-shaped magnetite nanoparticles in the magnetotactic bacteria Desulfovibrio magneticus sp. Strain RS-1.	Chariaou M, Rahn-Lee L, Kind J, Garcia-Rubio I, Komeili A, Gehring AU	Biophys J	10.1016/j.bpj.2015.01.007	2015
Metabolism	A genetic strategy for probing the functional diversity of magnetosome formation.	Rahn-Lee L, Byrne ME, Zhang M, Le Sage D, Glenn DR, Milbourne T, Walsworth RL, Vali H, Komeili A	PLoS Genet	10.1371/journal.pgen.1004811	2015
Metabolism	Desulfovibrio magneticus RS-1 contains an iron- and phosphorus-rich organelle distinct from its bullet-shaped magnetosomes.	Byrne ME, Ball DA, Guerquin-Kern JL, Rouiller I, Wu TD, Downing KH, Vali H, Komeili A	Proc Natl Acad Sci U S A	10.1073/pnas.1001290107	2010
Genetics	Whole genome sequence of Desulfovibrio magneticus strain RS-1 revealed common gene clusters in magnetotactic bacteria.	Nakazawa H, Arakaki A, Narita-Yamada S, Yashiro I, Jinno K, Aoki N, Tsuruyama A, Okamura Y, Tanikawa S, Fujita N, Takeyama H, Matsunaga T	Genome Res	10.1101/gr.088906.108	2009
Proteome	Proteomic analysis of irregular, bullet-shaped magnetosomes in the sulphate-reducing magnetotactic bacterium Desulfovibrio magneticus RS-1.	Matsunaga T, Nemoto M, Arakari A, Tanaka M	Proteomics	10.1002/pmic.200800881	2009
Enzymology	Cadmium recovery by a sulfate-reducing magnetotactic bacterium, Desulfovibrio magneticus RS-1, using magnetic separation.	Arakaki A, Takeyama H, Tanaka T, Matsunaga T	Appl Biochem Biotechnol	10.1385/abab:98-100:1-9:833	2002
Phylogeny	Desulfovibrio magneticus sp. nov., a novel sulfate-reducing bacterium that produces intracellular single-domain-sized magnetite particles.	Sakaguchi T, Arakaki A, Matsunaga T	Int J Syst Evol Microbiol	10.1099/00207713-52-1-215	2002
Phylogeny	Fundidesulfovibrio magnetotacticus sp. nov., a sulphate-reducing magnetotactic bacterium, isolated from sediments and freshwater of a pond.	Shimoshige H, Kobayashi H, Shimamura S, Miyazaki M, Maekawa T	Int J Syst Evol Microbiol	10.1099/ijsem.0.005516	2022

References

#5132	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 13731
#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 )
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

Content

About us

Solidesulfovibrio magneticus (DSM 13731, JCM 12223, RS-1)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000010665

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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