Strain identifier
BacDive ID: 132530
Type strain: 
Species: Magnetospirillum marisnigri
Strain Designation: SP-1
Strain history: <- M. Dziuba, RAS, Centre Bioengineering, Russia <- M. Dziuba {2012}
NCBI tax ID(s): 1285242 (species)
version 8.1 (current version)
General
@ref: 24319
BacDive-ID: 132530
DSM-Number: 29006
keywords: genome sequence, 16S sequence, Bacteria, microaerophile, non-halophilic, motile, spiral-shaped
description: Magnetospirillum marisnigri SP-1 is a microaerophile, non-halophilic, motile bacterium that was isolated from freshwater sediment from a river.
NCBI tax id
- NCBI tax id: 1285242
- Matching level: species
strain history
- @ref: 24319
- history: <- M. Dziuba, RAS, Centre Bioengineering, Russia <- M. Dziuba {2012}
doi: 10.13145/bacdive132530.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodospirillales
- family: Rhodospirillaceae
- genus: Magnetospirillum
- species: Magnetospirillum marisnigri
- full scientific name: Magnetospirillum marisnigri Dziuba et al. 2016
synonyms
- @ref: 20215
- synonym: Paramagnetospirillum marisnigri
@ref: 24319
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodospirillales
family: Rhodospirillaceae
genus: Magnetospirillum
species: Magnetospirillum marisnigri
full scientific name: Magnetospirillum marisnigri Dziuba et al. 2016
strain designation: SP-1
type strain: yes
Morphology
cell morphology
| @ref | cell length | cell width | cell shape | motility | flagellum arrangement | confidence | gram stain |
|---|---|---|---|---|---|---|---|
| 43653 | 2.5-4 µm | 0.3-0.4 µm | spiral-shaped | yes | lophotrichous | ||
| 69480 | yes | 92.826 | |||||
| 69480 | 99.999 | negative |
Culture and growth conditions
culture medium
- @ref: 24319
- name: MAGNETOSPIRILLUM MEDIUM (DSMZ Medium 380)
- growth: yes
- link: https://mediadive.dsmz.de/medium/380
- composition: Name: MAGNETOSPIRILLUM MEDIUM (DSMZ Medium 380) Composition: Agar 1.3 g/l (optional) KH2PO4 0.68 g/l L(+)-Tartaric acid 0.37 g/l Succinic acid 0.37 g/l NaNO3 0.12 g/l Yeast extract 0.1 g/l Na-thioglycolate 0.05 g/l Na-acetate 0.05 g/l MgSO4 x 7 H2O 0.015 g/l FeCl3 x 6 H2O 0.009 g/l Nitrilotriacetic acid 0.0075 g/l NaCl 0.005 g/l Quinic acid 0.0038 g/l MnSO4 x H2O 0.0025 g/l CoSO4 x 7 H2O 0.0009 g/l ZnSO4 x 7 H2O 0.0009 g/l FeSO4 x 7 H2O 0.0005 g/l Sodium resazurin 0.0005 g/l CaCl2 x 2 H2O 0.0005 g/l Pyridoxine hydrochloride 0.0003 g/l Thiamine-HCl x 2 H2O 0.0002 g/l Nicotinic acid 0.0002 g/l NiCl2 x 6 H2O 0.00015 g/l AlK(SO4)2 x 12 H2O 0.0001 g/l Calcium pantothenate 0.0001 g/l Vitamin B12 0.0001 g/l p-Aminobenzoic acid 8e-05 g/l CuSO4 x 5 H2O 5e-05 g/l Na2MoO4 x 2 H2O 5e-05 g/l H3BO3 5e-05 g/l D-(+)-biotin 2e-05 g/l Na2WO4 x 2 H2O 2e-06 g/l Na2SeO3 x 5 H2O 1.5e-06 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 43653 | positive | growth | 18-42 | |
| 43653 | positive | optimum | 28-30 | mesophilic |
| 24319 | positive | growth | 28 | mesophilic |
culture pH
- @ref: 43653
- ability: positive
- type: optimum
- pH: 6.5-6.8
Physiology and metabolism
oxygen tolerance
- @ref: 43653
- oxygen tolerance: microaerophile
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.902 |
halophily
- @ref: 43653
- halophily level: non-halophilic
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-0.1 %(w/v)
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 43653 | 16947 | citrate | - | assimilation |
| 43653 | 17968 | butyrate | + | growth |
| 43653 | 17272 | propionate | + | growth |
| 43653 | 30929 | tartrate | + | growth |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 43653 | cytochrome oxidase | - | 1.9.3.1 |
| 43653 | catalase | - | 1.11.1.6 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 24319 | freshwater sediment from a river | Black Sea Coast, Krasnodar region, area of Gelendzhik, Pshada river | Russia | RUS | Europe | 44.3893 | 38.3363 |
| 43653 | Sediments of the Pshada river, near the coast of the Black Sea | Krasnodar region | Russia | RUS | Europe | 44.389 | 38.336 |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Freshwater |
| #Environmental | #Aquatic | #River (Creek) |
| #Environmental | #Aquatic | #Sediment |
| #Environmental | #Terrestrial | #Coast |
taxonmaps
- @ref: 69479
- File name: preview.99_6476.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_215;96_782;97_911;98_1068;99_6476&stattab=map
- Last taxonomy: Magnetospirillum marisnigri
- 16S sequence: KC252630
- Sequence Identity:
- Total samples: 306
- soil counts: 25
- aquatic counts: 242
- animal counts: 11
- plant counts: 28
Safety information
risk assessment
- @ref: 24319
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24319
- description: Magnetospirillum marisnigri strain SP-1 16S ribosomal RNA gene, complete sequence
- accession: KC252630
- length: 1443
- database: ena
- NCBI tax ID: 1285242
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Magnetospirillum marisnigri SP-1 | GCA_001650715 | scaffold | ncbi | 1285242 |
| 66792 | Magnetospirillum marisnigri SP-1 | 2791355011 | draft | img | 1285242 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 43653 | 63 | thermal denaturation, midpoint method (Tm) |
| 24319 | 63.0 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | yes | 81.345 | yes |
| gram-positive | no | 99.321 | no |
| anaerobic | no | 86.633 | yes |
| halophile | no | 96.374 | yes |
| spore-forming | no | 88.063 | no |
| glucose-util | yes | 50.762 | no |
| motile | yes | 87.243 | yes |
| aerobic | no | 94.515 | yes |
| thermophile | no | 95.38 | no |
| glucose-ferment | no | 89.521 | no |
External links
@ref: 24319
culture collection no.: DSM 29006, VKM B-2938
straininfo link
- @ref: 90856
- straininfo: 407912
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 26921147 | Magnetospirillum caucaseum sp. nov., Magnetospirillum marisnigri sp. nov. and Magnetospirillum moscoviense sp. nov., freshwater magnetotactic bacteria isolated from three distinct geographical locations in European Russia. | Dziuba M, Koziaeva V, Grouzdev D, Burganskaya E, Baslerov R, Kolganova T, Chernyadyev A, Osipov G, Andrianova E, Gorlenko V, Kuznetsov B | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000994 | 2016 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Geologic Sediments/*microbiology, Magnetosomes, Magnetospirillum/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Russia, Sequence Analysis, DNA | Transcriptome |
| Genetics | 27516508 | Draft Genome Sequences of Two Magnetotactic Bacteria, Magnetospirillum moscoviense BB-1 and Magnetospirillum marisnigri SP-1. | Koziaeva VV, Dziuba MV, Ivanov TM, Kuznetsov BB, Skryabin KG, Grouzdev DS | Genome Announc | 10.1128/genomeA.00814-16 | 2016 |
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 | |||
| 24319 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-29006 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29006) | |||
| 43653 | Marina Dziuba, Veronika Koziaeva, Denis Grouzdev, Ekaterina Burganskaya, Roman Baslerov, Tatjana Kolganova, Alexander Chernyadyev, Georgy Osipov, Ekaterina Andrianova, Vladimir Gorlenko, Boris Kuznetsov | Magnetospirillum caucaseum sp. nov., Magnetospirillum marisnigri sp. nov. and Magnetospirillum moscoviense sp. nov., freshwater magnetotactic bacteria isolated from three distinct geographical locations in European Russia | 10.1099/ijsem.0.000994 | IJSEM 66: 2069-2077 2016 | 26921147 | |
| 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 | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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 | |||
| 90856 | 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-ID407912.1 |