Magnetospirillum marisnigri (DSM 29006, VKM B-2938, SP-1)

Name: Magnetospirillum marisnigri (DSM 29006, VKM B-2938, SP-1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132530

Type strain

Strain Designation SP-1

Culture col. no. DSM 29006 VKM B-2938 SP-1

NCBI tax ID(s) 1285242

Special Collections DSMZ Literature strains

Links

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

motile spiral-shaped microaerophile non-halophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 407912

DSM 29006

@ref 20215

Last LPSN update 2025-12-16 10:01:32

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodospirillales

Family Rhodospirillaceae

Genus Magnetospirillum

Species Magnetospirillum marisnigri

Full scientific name Magnetospirillum marisnigri Dziuba et al. 2016

Synonyms (1)

Paramagnetospirillum marisnigri

Morphology

Cell morphology

@ref	Cell length	Cell width	Cell shape	Flagellum arrangement	Gram stain	Confidence
43653	2.5-4 µm	0.3-0.4 µm	spiral-shaped	lophotrichous
125439					negative	97.6
125438					negative	98.167

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
24319	MAGNETOSPIRILLUM MEDIUM (DSMZ Medium 380)		Medium recipe at MediaDive	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 (°C)	Range
24319	positive	growth	28	mesophilic
43653	positive	growth	18-42
43653	positive	optimum	28-30	mesophilic

Culture pH

@ref	Ability	Type	PH
43653	positive	optimum	6.5-6.8

Physiology and metabolism

Oxygen tolerance

43653

Oxygen tolerancemicroaerophile

Spore formation

@ref	Spore formation	Confidence
125439		98.6

Halophily

@ref	Halophily level	Salt	Growth	Tested relation	Concentration
43653	non-halophilic	NaCl	positive	growth	0-0.1 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43653	17968 ChEBI	butyrate	+	growth
43653	16947 ChEBI	citrate	-	assimilation
43653	17272 ChEBI	propionate	+	growth
43653	30929 ChEBI	tartrate	+	growth

Enzymes

@ref	Value	Activity	Ec
43653	catalase	-	1.11.1.6
43653	cytochrome oxidase	-	1.9.3.1

Pathway annotation

Computationally determined by

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

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#River (Creek)
#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Coast

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	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 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 44.389/38.336

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24319	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM165071v1 assembly for Paramagnetospirillum marisnigri SP-1	scaffold	GCA_001650715	1285242.4	2791355011	1285242	52.73

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24319	Paramagnetospirillum marisnigri strain SP-1 16S ribosomal RNA gene, complete sequence	KC252630	1443		1285242

GC content

@ref	GC-content (mol%)	Method
43653	63	thermal denaturation, midpoint method (Tm)
24319	63.0	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Magnetospirillum marisnigri SP-1
NCBI: GCA_001650715

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.60	no
125439	motility	BacteriaNetⓘ	yes	73.50	no
125439	gram_stain	BacteriaNetⓘ	negative	97.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative aerobe	58.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Magnetospirillum marisnigri SP-1
NCBI: GCA_001650715.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.17	no
125438	anaerobic	anaerobicⓘ	no	67.87	no
125438	aerobic	aerobicⓘ	no	59.85	no
125438	spore-forming	spore-formingⓘ	no	86.85	no
125438	thermophilic	thermophileⓘ	no	93.94	yes
125438	flagellated	motile2+ⓘ	yes	81.95	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Evolutionary Rescue of an Environmental Pseudomonas otitidis in Response to Anthropogenic Perturbation.	Garcia-Ulloa MI, Escalante AE, Moreno-Letelier A, Eguiarte LE, Souza V.	Front Microbiol	10.3389/fmicb.2020.563885	2020
	Genome-centric resolution of novel microbial lineages in an excavated Centrosaurus dinosaur fossil bone from the Late Cretaceous of North America.	Liang R, Lau MCY, Saitta ET, Garvin ZK, Onstott TC.	Environ Microbiome	10.1186/s40793-020-00355-w	2020
Genetics	Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.	Hordt A, Lopez MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Goker M.	Front Microbiol	10.3389/fmicb.2020.00468	2020
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
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

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 .
#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 )

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Magnetospirillum marisnigri (DSM 29006, VKM B-2938, SP-1)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001650715

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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