Name: Magnetospirillum marisnigri SP-1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 132530

Type strain:

Species: Magnetospirillum marisnigri

Strain Designation: SP-1

Culture col. no.: DSM 29006, VKM B-2938

Strain history: <- M. Dziuba, RAS, Centre Bioengineering, Russia <- M. Dziuba {2012}

NCBI tax ID(s): 1285242 (species)

SI-ID 407912

DSM 29006

Special Collections

Section

Magnetospirillum marisnigri SP-1 is a microaerophile, non-halophilic, motile bacterium that was isolated from freshwater sediment from a river.

motile
spiral-shaped
microaerophile
non-halophilic
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	*Alphaproteobacteria*
	Order	*Rhodospirillales*
	Family	*Rhodospirillaceae*
	Genus	*Magnetospirillum*
	Species	**Magnetospirillum marisnigri**
	Full Scientific Name (LPSN)	Magnetospirillum marisnigri Dziuba et al. 2016

Synonym

Paramagnetospirillum marisnigri

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %98.167

[Ref.: #43653]	Cell length	2.5-4 µm

[Ref.: #43653]	Cell width	0.3-0.4 µm

[Ref.: #43653]	Cell shape	spiral-shaped

[Ref.: #43653]	Motility	yes

[Ref.: #43653]	Flagellum arrangement	lophotrichous

Information on culture and growth conditions Culture and growth conditions

[Ref.: #24319]

Culture medium

MAGNETOSPIRILLUM MEDIUM (DSMZ Medium 380)

[Ref.: #24319]

Culture medium growth

[Ref.: #24319]

Culture medium link

Medium recipe at MediaDive

[Ref.: #24319]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #24319]	growth	28 °C
[Ref.: #43653]	growth	18-42 °C
[Ref.: #43653]	optimum	28-30 °C

	pH	Kind of pH		pH
[Ref.: #43653]			optimum	6.5-6.8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43653]

Oxygen tolerance

microaerophile

[Ref.: #69481]

Ability of spore formation

no Confidence in %100

[Ref.: #43653]

Halophily / tolerance level

non-halophilic

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43653]		NaCl		growth	0-0.1	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43653]	butyrate ChEBI	+	growth
[Ref.: #43653]	citrate ChEBI	-	assimilation
[Ref.: #43653]	propionate ChEBI	+	growth
[Ref.: #43653]	tartrate ChEBI	+	growth

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #43653]		catalase	-	1.11.1.6
[Ref.: #43653]		cytochrome oxidase	-	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	vitamin B12 metabolism	82.35	28 of 34
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	benzoyl-CoA degradation	71.43	5 of 7
[Ref.: #66794]	purine metabolism	70.21	66 of 94
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	70	7 of 10
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	lipid metabolism	64.52	20 of 31
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	tryptophan metabolism	60.53	23 of 38
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	pyrimidine metabolism	60	27 of 45
[Ref.: #66794]	lysine metabolism	59.52	25 of 42
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	oxidative phosphorylation	56.04	51 of 91
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	histidine metabolism	51.72	15 of 29
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	Entner Doudoroff pathway	50	5 of 10
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	sphingosine metabolism	50	3 of 6
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	starch degradation	50	5 of 10
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	cholesterol biosynthesis	45.45	5 of 11
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	phenol degradation	45	9 of 20
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	polyamine pathway	43.48	10 of 23
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	cellulose degradation	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	carotenoid biosynthesis	22.73	5 of 22
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #24319]	Sample type/isolated from	freshwater sediment from a river
[Ref.: #24319]	Geographic location (country and/or sea, region)	Black Sea Coast, Krasnodar region, area of Gelendzhik, Pshada river
[Ref.: #24319]	Country	Russia
[Ref.: #24319]	Country ISO 3 Code	RUS
[Ref.: #24319]	Continent	Europe
[Ref.: #24319]	Geographic location	44.3893°/38.3363°

[Ref.: #43653]	Sample type/isolated from	Sediments of the Pshada river, near the coast of the Black Sea
[Ref.: #43653]	Geographic location (country and/or sea, region)	Krasnodar region
[Ref.: #43653]	Country	Russia
[Ref.: #43653]	Country ISO 3 Code	RUS
[Ref.: #43653]	Continent	Europe
[Ref.: #43653]	Geographic location	44.3890°/38.3360°
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#River (Creek)
#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Coast

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KC252630 (>99% sequence identity) for Magnetospirillum marisnigri from Microbeatlas

Aquatic Samples	242
Soil Samples	25
Animal Samples	11
Plant Samples	28
Total Samples	306

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

[Ref.: #24319]

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.: #24319]	Paramagnetospirillum marisnigri strain SP-1 16S ribosomal RNA gene, complete sequence	KC252630	1443	GenBank ENA	1285242 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Magnetospirillum marisnigri SP-1	GCA_001650715	scaffold	GenBank ENA	1285242 tax ID	*
[Ref.: #66792]	Magnetospirillum marisnigri SP-1	2791355011	draft	JGI IMG/M	1285242 tax ID	*

[Ref.: #43653]	GC-content	63 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #24319]	GC-content	63.0 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: Magnetospirillum marisnigri SP-1 NCBI: GCA_001650715.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Magnetospirillum marisnigri SP-1 NCBI: GCA_001650715.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	98.167	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	67.873	no
[Ref.: #69480]	aerobic	aerobicⓘ	no	59.848	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	86.85	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	93.938	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	81.953	no

Availability in culture collections External links

[Ref.: #24319]

Culture collection no.

DSM 29006, VKM B-2938

[Ref.: #90856]

SI-ID 407912

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	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	*
Genetics	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	*

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 )

#24319

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; 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. IJSEM 66: 2069 - 2077 2016 ( DOI 10.1099/ijsem.0.000994 , PubMed 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) .

#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. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 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 .

#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 )

#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 . ( DOI 10.60712/SI-ID407912.1 )

* These data were automatically processed and therefore are not curated

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