Name: Methylovulum psychrotolerans DSM 100602
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 140162

Type strain:

Species: Methylovulum psychrotolerans

Culture col. no.: DSM 100602, LMG 29227, VKM B-3018, Sph 1

Strain history: <- S. N. Dedysh, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; Sph1 <- I. Y. Oshkin and S. E. Belova

NCBI tax ID(s): 1704499 (species)

SI-ID 396495

LMG 29227, VKM B-3018, DSM 100602

Special Collections

Section

Methylovulum psychrotolerans DSM 100602 is an aerobe, Gram-negative, coccus-shaped bacterium that forms circular colonies and was isolated from cold methane seep in a floodplain.

coccus-shaped
colony-forming
Gram-negative
aerobe
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	*Gammaproteobacteria*
	Order	*Methylococcales*
	Family	*Methylococcaceae*
	Genus	*Methylovulum*
	Species	**Methylovulum psychrotolerans**
	Full Scientific Name (LPSN)	Methylovulum psychrotolerans Oshkin et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43960]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %98

[Ref.: #43960]	Cell length	3-5 µm

[Ref.: #43960]	Cell shape	coccus-shaped

[Ref.: #43960]	Motility	no

[Ref.: #43960]	Colony color	light pink
[Ref.: #43960]	Colony shape	circular
[Ref.: #43960]	Cultivation medium used	Nitrate mineral salts medium

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43960]

Culture medium

Nitrate mineral salts medium

[Ref.: #43960]

Culture medium growth

[Ref.: #42769]

Culture medium

METHYLOSARCINA QUISQUILLARUM AND M. FIBRATA MEDIUM (DSMZ Medium 921)

[Ref.: #42769]

Culture medium growth

[Ref.: #42769]

Culture medium link

Medium recipe at MediaDive

[Ref.: #42769]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #42769]	growth	25 °C
[Ref.: #43960]	growth	2-36 °C
[Ref.: #43960]	optimum	20-25 °C

	pH	Kind of pH		pH
[Ref.: #43960]			optimum	6.0-7.0
[Ref.: #43960]			growth	4.0-8.9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43960]

Oxygen tolerance

aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43960]		NaCl		optimum	0	%(w/v)

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43960]		methane ChEBI	+	required for growth
[Ref.: #43960]		methanol ChEBI	+	required for growth

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	methanofuran biosynthesis	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	pentose phosphate pathway	100	11 of 11
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[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]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	methionine metabolism	84.62	22 of 26
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	vitamin B12 metabolism	79.41	27 of 34
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	chorismate metabolism	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	75	9 of 12
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	peptidoglycan biosynthesis	73.33	11 of 15
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	purine metabolism	70.21	66 of 94
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	sulfate reduction	69.23	9 of 13
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	methanogenesis from CO2	66.67	8 of 12
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	nitrate assimilation	66.67	6 of 9
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	pyrimidine metabolism	64.44	29 of 45
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	oxidative phosphorylation	62.64	57 of 91
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	histidine metabolism	62.07	18 of 29
[Ref.: #66794]	alanine metabolism	62.07	18 of 29
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	lipid metabolism	54.84	17 of 31
[Ref.: #66794]	cholesterol biosynthesis	54.55	6 of 11
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	grixazone biosynthesis	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	arginine metabolism	50	12 of 24
[Ref.: #66794]	lysine metabolism	47.62	20 of 42
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	degradation of sugar alcohols	43.75	7 of 16
[Ref.: #66794]	polyamine pathway	43.48	10 of 23
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	chlorophyll metabolism	33.33	6 of 18
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[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]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		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.: #42769]	Sample type/isolated from	cold methane seep in a floodplain
[Ref.: #42769]	Geographic location (country and/or sea, region)	West Siberia, Irtysh basin, valley of the river Mukhrinskaya (60° 53.358' N 68° 42.486' E)
[Ref.: #42769]	Country	Russia
[Ref.: #42769]	Country ISO 3 Code	RUS
[Ref.: #42769]	Continent	Europe
[Ref.: #42769]	Geographic location	60.8893°/68.7081°

[Ref.: #43960]	Sample type/isolated from	mud suspensions from cold methane seeps in a floodplain of the river Mukhrinskaya, Irtysh basin, West Siberia
[Ref.: #43960]	Geographic location (country and/or sea, region)	river Mukhrinskaya, Irtysh basin, Siberia
[Ref.: #43960]	Country	Russia
[Ref.: #43960]	Country ISO 3 Code	RUS
[Ref.: #43960]	Continent	Asia
[Ref.: #43960]	Geographic location	60.8893°/68.7081°
[Ref.: #43960]	Enrichment culture	diluted nitrate mineral salts medium
[Ref.: #43960]	Enrichment culture composition	addition of 0.1 % trace elements stock solution containing EDTA 5 g/L, FeSO4.7H2O 2 g/L, ZnSO4.7H2O 0.1 g/L, MnCl2.4H2O 0.03 g/L, CoCl2.6H2O 0.2 g/L, CuCl2.5H2O 0.1 g/L, NiCl2.6H2O 0.02 g/L, Na2MoO4 g/L 0.03, pH 6.8.
[Ref.: #43960]	Enrichment culture temperature	20 ̊C
* marker position based on {}

Isolation sources categories

#Condition	#Anoxic (anaerobic)	-
#Environmental	#Terrestrial	#Mud (Sludge)
#Environmental	#Aquatic	#River (Creek)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KT381578 (>99% sequence identity) for Methylovulum psychrotolerans subclade from Microbeatlas

Aquatic Samples	439
Soil Samples	110
Animal Samples	46
Plant Samples	17
Total Samples	612

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

[Ref.: #42769]

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.: #42769]	Methylovulum psychrotolerans strain Sph1 16S ribosomal RNA gene, partial sequence	KT381578	1487	GenBank ENA	1704499 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Methylovulum psychrotolerans strain Sph1	1704499.7	wgs	PATRIC	1704499 tax ID	*

[Ref.: #43960]	GC-content	51.4-51.9 mol%
[Ref.: #42769]	GC-content	51.6 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 Diaspora project based on: Methylovulum psychrotolerans strain Sph1 PATRIC: 1704499.7
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	98	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	85.997	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	87.399	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	80.67	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	95.882	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	63.136	yes

Availability in culture collections External links

[Ref.: #42769]

Culture collection no.

DSM 100602, LMG 29227, VKM B-3018, Sph 1

[Ref.: #96539]

SI-ID 396495

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Description of 'Candidatus Methylocucumis oryzae', a novel Type I methanotroph with large cells and pale pink colour, isolated from an Indian rice field.	Pandit PS, Hoppert M, Rahalkar MC	Antonie Van Leeuwenhoek	10.1007/s10482-018-1136-3	2018	*
Phylogeny	Methylovulum psychrotolerans sp. nov., a cold-adapted methanotroph from low-temperature terrestrial environments, and emended description of the genus Methylovulum.	Oshkin IY, Belova SE, Danilova OV, Miroshnikov KK, Rijpstra WIC, Sinninghe Damste JS, Liesack W, Dedysh SN	Int J Syst Evol Microbiol	10.1099/ijsem.0.001046	2016	*
Genetics	Draft Genome Sequence of Methylovulum psychrotolerans Sph1(T), an Obligate Methanotroph from Low-Temperature Environments.	Oshkin IY, Miroshnikov KK, Belova SE, Korzhenkov AA, Toshchakov SV, Dedysh SN	Genome Announc	10.1128/genomeA.01488-17	2018	*
	A Silent Biosynthetic Gene Cluster from a Methanotrophic Bacterium Potentiates Discovery of a Substrate Promiscuous Proteusin Cyclodehydratase.	Nguyen NA, Cong Y, Hurrell RC, Arias N, Garg N, Puri AW, Schmidt EW, Agarwal V	ACS Chem Biol	10.1021/acschembio.2c00251	2022	*

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 )

#42769

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100602

#43960

Igor Y. Oshkin, Svetlana E. Belova, Olga V. Danilova, Kirill K. Miroshnikov, W. Irene C. Rijpstra, Jaap S. Sinninghe Damsté, Werner Liesack, Svetlana N. Dedysh: Methylovulum psychrotolerans sp. nov., a cold-adapted methanotroph from low-temperature terrestrial environments, and emended description of the genus Methylovulum. IJSEM 66: 2417 - 2423 2016 ( DOI 10.1099/ijsem.0.001046 , PubMed 27031985 )

#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) .

#96539

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-ID396495.1 )

* These data were automatically processed and therefore are not curated

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Methylovulum psychrotolerans strain Sph1

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