Strain identifier
BacDive ID: 4140
Type strain: 
Species: Solidesulfovibrio magneticus
Strain Designation: RS-1
Strain history: <- T. Matsunaga, Tokyo University of Agriculture and Technology, Japan; RS-1 <- T. Sakaguchi and T. Matsunaga {1993}
NCBI tax ID(s): 184917 (species)
version 8.1 (current version)
General
@ref: 5132
BacDive-ID: 4140
DSM-Number: 13731
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Solidesulfovibrio magneticus RS-1 is an anaerobe, mesophilic bacterium that was isolated from freshwater sulfide-rich mud.
NCBI tax id
- NCBI tax id: 184917
- Matching level: species
strain history
- @ref: 5132
- history: <- T. Matsunaga, Tokyo University of Agriculture and Technology, Japan; RS-1 <- T. Sakaguchi and T. Matsunaga {1993}
doi: 10.13145/bacdive4140.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Desulfovibrionales
- family: Desulfovibrionaceae
- genus: Solidesulfovibrio
- species: Solidesulfovibrio magneticus
- full scientific name: Solidesulfovibrio magneticus (Sakaguchi et al. 2002) Waite et al. 2020
synonyms
- @ref: 20215
- synonym: Desulfovibrio magneticus
@ref: 5132
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Desulfovibrionales
family: Desulfovibrionaceae
genus: Solidesulfovibrio
species: Solidesulfovibrio magneticus
full scientific name: Solidesulfovibrio magneticus (Sakaguchi et al. 2002) Waite et al. 2020
strain designation: RS-1
type strain: yes
Culture and growth conditions
culture medium
- @ref: 5132
- name: DESULFOVIBRIO MAGNETICUS MEDIUM (DSMZ Medium 896)
- growth: yes
- link: https://mediadive.dsmz.de/medium/896
- composition: 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 FeCl3 x 6 H2O 0.00893744 g/l Nitrilotriacetic acid 0.00595829 g/l NaCl 0.00397219 g/l Quinic acid 0.00377358 g/l MnSO4 x H2O 0.0019861 g/l ZnSO4 x 7 H2O 0.000714995 g/l CoSO4 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 p-Aminobenzoic acid 4.96524e-05 g/l (DL)-alpha-Lipoic acid 4.96524e-05 g/l Thiamine HCl 4.96524e-05 g/l Riboflavin 4.96524e-05 g/l Nicotinic acid 4.96524e-05 g/l Calcium D-(+)-pantothenate 4.96524e-05 g/l Na2MoO4 x 2 H2O 3.97219e-05 g/l CuSO4 x 5 H2O 3.97219e-05 g/l H3BO3 3.97219e-05 g/l Biotin 1.9861e-05 g/l Folic acid 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: 5132
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 5132
- oxygen tolerance: anaerobe
Isolation, sampling and environmental information
isolation
- @ref: 5132
- sample type: freshwater sulfide-rich mud
- geographic location: Wakayama
- country: Japan
- origin.country: JPN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Freshwater |
| #Environmental | #Terrestrial | #Mud (Sludge) |
| #Condition | #Sulfuric |
taxonmaps
- @ref: 69479
- File name: preview.99_546.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_120;96_346;97_386;98_443;99_546&stattab=map
- Last taxonomy: Desulfovibrio
- 16S sequence: D43944
- Sequence Identity:
- Total samples: 4211
- soil counts: 453
- aquatic counts: 2969
- animal counts: 351
- plant counts: 438
Safety information
risk assessment
- @ref: 5132
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 5132
- description: Desulfovibrio magneticus gene for 16S rRNA
- accession: D43944
- length: 1540
- database: ena
- NCBI tax ID: 573370
Genome sequences
- @ref: 66792
- description: Solidesulfovibrio magneticus RS-1
- accession: GCA_000010665
- assembly level: complete
- database: ncbi
- NCBI tax ID: 573370
GC content
- @ref: 5132
- GC-content: 65.8
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | yes | 88.637 | no |
| flagellated | no | 72.738 | no |
| gram-positive | no | 98.321 | no |
| anaerobic | yes | 95.994 | yes |
| halophile | no | 89.395 | no |
| spore-forming | no | 91.744 | no |
| glucose-util | no | 50.524 | no |
| aerobic | no | 96.321 | no |
| thermophile | no | 93.494 | yes |
| glucose-ferment | no | 80.804 | no |
External links
@ref: 5132
culture collection no.: DSM 13731, JCM 12223
straininfo link
- @ref: 73643
- straininfo: 44239
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 11837306 | 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 | DNA, Ribosomal/analysis, Desulfovibrio/*classification/*metabolism/physiology, Fatty Acids/analysis, Ferrosoferric Oxide, Fresh Water/microbiology, Geologic Sediments/microbiology, Hydrogensulfite Reductase, Iron/*metabolism, Molecular Sequence Data, Oxidation-Reduction, Oxides/*metabolism, Oxidoreductases Acting on Sulfur Group Donors/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sulfates/*metabolism | Metabolism |
| Enzymology | 12018305 | 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 | Cadmium/*isolation & purification/*pharmacology, Calcium/pharmacology, Cell Fractionation, Culture Media, Desulfovibrio/drug effects/growth & development/*metabolism/ultrastructure, Kinetics, *Magnetics, Microscopy, Electron, Oxidation-Reduction, Sulfates/*metabolism | Cultivation |
| Proteome | 19579222 | 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 | Alphaproteobacteria/chemistry, Bacterial Proteins/*analysis/genetics, Chromatography, Liquid, Desulfovibrio/*chemistry/genetics, Magnetosomes/*chemistry/genetics, Magnetospirillum/chemistry, Membrane Proteins/*analysis/genetics, Proteome/*analysis/genetics, Tandem Mass Spectrometry | |
| Genetics | 19675025 | 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 | Desulfovibrio/*genetics/metabolism, Energy Metabolism/genetics, *Genes, Bacterial/physiology, *Genome, Bacterial, Genomics/methods, Magnetosomes/genetics, Magnetospirillum/*genetics/metabolism, *Multigene Family/physiology | Metabolism |
| Metabolism | 20566879 | 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 | Cryoelectron Microscopy, Crystallization, Cytoplasmic Granules/chemistry/*metabolism, Desulfovibrio/chemistry/*metabolism/ultrastructure, Electron Microscope Tomography, Ferrosoferric Oxide/chemistry, Iron/*metabolism, Magnetosomes/metabolism/ultrastructure, Microscopy, Electron, Transmission, Minerals/chemistry, Periplasm/metabolism/ultrastructure, Phosphorus/*metabolism | |
| Metabolism | 25569806 | 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 | Alleles, Desulfovibrio/*genetics/metabolism, Ferrosoferric Oxide/metabolism, Genomic Islands, Iron/metabolism, Magnetosomes/*genetics, Multigene Family, Mutation, Organelles/*genetics | |
| Pathogenicity | 25762338 | 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 | Anisotropy, Desulfovibrio/drug effects/*metabolism, Ferrosoferric Oxide/*pharmacology, Magnetic Fields, Magnetite Nanoparticles/*chemistry | Metabolism |
| 25866495 | 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 | |||
| Phylogeny | 26114501 | 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 | Bacterial Proteins/*chemistry/genetics, Crystallography, X-Ray, Desulfovibrio/*chemistry/genetics, *Evolution, Molecular, *Gene Transfer, Horizontal, *Phylogeny, Protein Structure, Tertiary, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics | |
| Metabolism | 27881802 | 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 | Desulfovibrio/*metabolism, Ferrosoferric Oxide/*metabolism, Iron/*metabolism, *Magnetite Nanoparticles, Sulfides/*metabolism | |
| Metabolism | 30194101 | 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 | Anaerobiosis, Desulfovibrio/*genetics/metabolism, Gene Editing/*methods, *Genome, Bacterial, Magnetosomes/genetics/metabolism, Mutagenesis, Plasmids/genetics/metabolism, Reverse Genetics/*methods | Genetics |
| Phylogeny | 33705469 | 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 | *Desulfovibrio/classification/genetics/isolation & purification/metabolism, Ferrosoferric Oxide/metabolism, Magnetite Nanoparticles, RNA, Bacterial/genetics/metabolism, RNA, Ribosomal, 16S/genetics/metabolism | Metabolism |
| Phylogeny | 36166368 | 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 | 1-Propanol, Bacterial Typing Techniques, Base Composition, Catalase/genetics, Cytochromes c/genetics, DNA, Bacterial/genetics, Ethanol, Fatty Acids/chemistry, Ferrosoferric Oxide, Formates, Fumarates, Hydrogensulfite Reductase/genetics, Iron, Lactates, Malates, Nucleotides, Peptones, Phylogeny, Ponds, Pyruvates, Quinic Acid, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride, Succinates, *Sulfates, *Tartrates, Thiosulfates, Vitamin K 2 | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 5132 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13731) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-13731 | |
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |
| 73643 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID44239.1 | StrainInfo: A central database for resolving microbial strain identifiers |