Methyloprofundus sedimenti (DSM 29215, ATCC BAA-2619, WF1)

Name: Methyloprofundus sedimenti (DSM 29215, ATCC BAA-2619, WF1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140082

Type strain

Strain Designation WF1, whale fall 1

Culture col. no. DSM 29215 ATCC BAA-2619 WF1 whale fall 1

NCBI tax ID(s) 1420851

Special Collections DSMZ

History <- P. Tavormina, California Inst. Technology (Caltech), Pasadena, USA; ATCC BAA-2619

Links

Methyloprofundus sedimenti WF1 is a bacterium that was isolated from deep sea sediment.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 396425

ATCC BAA-2619,LMG 28393

@ref 20215

Last LPSN update 2026-02-09 11:33:31

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Methylococcales

Family Methylococcaceae

Genus Methyloprofundus

Species Methyloprofundus sedimenti

Full scientific name Methyloprofundus sedimenti Tavormina et al. 2015

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	98.1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
42689	METHYLOPROFUNDUS SEDIMENTI MEDIUM (DSMZ Medium 1567)		Medium recipe at MediaDive	Name: METHYLOPROFUNDUS SEDIMENTI MEDIUM (DSMZ Medium 1567) Composition: NaCl 19.8 g/l MgSO4 x 6 H2O 1.0 g/l KNO3 1.0 g/l Na2HPO4 x 12 H2O 0.716 g/l KH2PO4 0.26 g/l MgSO4 x 7 H2O 0.003 g/l Fe(III)-EDTA 0.00152 g/l Nitrilotriacetic acid 0.0015 g/l MnSO4 x H2O 0.0005 g/l ZnSO4 x 7 H2O 0.00018 g/l CoSO4 x 7 H2O 0.00018 g/l CaCl2 x 2 H2O 0.0001 g/l FeSO4 x 7 H2O 0.0001 g/l NiCl2 x 6 H2O 3e-05 g/l AlK(SO4)2 x 12 H2O 2e-05 g/l Pyridoxine hydrochloride 1e-05 g/l Na2MoO4 x 2 H2O 1e-05 g/l H3BO3 1e-05 g/l CuSO4 x 5 H2O 1e-05 g/l Lipoic acid 5e-06 g/l p-Aminobenzoic acid 5e-06 g/l D-Calcium pantothenate 5e-06 g/l Nicotinic acid 5e-06 g/l Riboflavin 5e-06 g/l Thiamine-HCl x 2 H2O 5e-06 g/l Folic acid 2e-06 g/l Biotin 2e-06 g/l Na2SeO3 x 5 H2O 3e-07 g/l Vitamin B12 1e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
42689	positive	growth	20

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98

Spore formation

@ref	Spore formation	Confidence
125439		97.5

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	biotin biosynthesis	100	4 of 4
66794	ribulose monophosphate pathway	100	2 of 2
66794	cyanate degradation	100	3 of 3
66794	cardiolipin biosynthesis	100	7 of 7
66794	methanofuran biosynthesis	100	5 of 5
66794	threonine metabolism	100	10 of 10
66794	adipate degradation	100	2 of 2
66794	octane oxidation	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	denitrification	100	2 of 2
66794	ubiquinone biosynthesis	100	7 of 7
66794	phenylalanine metabolism	92.31	12 of 13
66794	pentose phosphate pathway	90.91	10 of 11
66794	valine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	heme metabolism	85.71	12 of 14
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	vitamin B6 metabolism	81.82	9 of 11
66794	cholesterol biosynthesis	81.82	9 of 11
66794	peptidoglycan biosynthesis	80	12 of 15
66794	glycine betaine biosynthesis	80	4 of 5
66794	Entner Doudoroff pathway	80	8 of 10
66794	flavin biosynthesis	80	12 of 15
66794	serine metabolism	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	purine metabolism	77.66	73 of 94
66794	vitamin B1 metabolism	76.92	10 of 13
66794	alanine metabolism	75.86	22 of 29
66794	CMP-KDO biosynthesis	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	gluconeogenesis	75	6 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	vitamin B12 metabolism	73.53	25 of 34
66794	proline metabolism	72.73	8 of 11
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	starch degradation	70	7 of 10
66794	methionine metabolism	69.23	18 of 26
66794	leucine metabolism	69.23	9 of 13
66794	lipid metabolism	67.74	21 of 31
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	nitrate assimilation	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	histidine metabolism	65.52	19 of 29
66794	pyrimidine metabolism	64.44	29 of 45
66794	photosynthesis	64.29	9 of 14
66794	glutathione metabolism	64.29	9 of 14
66794	non-pathway related	63.16	24 of 38
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	sulfate reduction	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	lipoate biosynthesis	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	propanol degradation	57.14	4 of 7
66794	citric acid cycle	57.14	8 of 14
66794	aspartate and asparagine metabolism	55.56	5 of 9
66794	arginine metabolism	54.17	13 of 24
66794	oxidative phosphorylation	52.75	48 of 91
66794	tryptophan metabolism	52.63	20 of 38
66794	lysine metabolism	52.38	22 of 42
66794	polyamine pathway	52.17	12 of 23
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	phenylmercury acetate degradation	50	1 of 2
66794	methanogenesis from CO2	50	6 of 12
66794	propionate fermentation	50	5 of 10
66794	ethanol fermentation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	vitamin E metabolism	50	2 of 4
66794	butanoate fermentation	50	2 of 4
66794	glycolysis	47.06	8 of 17
66794	urea cycle	46.15	6 of 13
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	tyrosine metabolism	42.86	6 of 14
66794	arachidonate biosynthesis	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	3-phenylpropionate degradation	40	6 of 15
66794	metabolism of disaccharids	36.36	4 of 11
66794	degradation of pentoses	35.71	10 of 28
66794	enterobactin biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	degradation of hexoses	33.33	6 of 18
66794	pantothenate biosynthesis	33.33	2 of 6
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	coenzyme M biosynthesis	30	3 of 10
66794	arachidonic acid metabolism	27.78	5 of 18
66794	ascorbate metabolism	27.27	6 of 22
66794	d-xylose degradation	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	catecholamine biosynthesis	25	1 of 4
66794	phenol degradation	25	5 of 20
66794	carotenoid biosynthesis	22.73	5 of 22

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
42689	deep sea sediment	Monterey canyon off the coast of California (36.708° N 122.105° W; 1828 m below sea-level)	USA	USA	North America	36.708	-122.105 36.708/-122.105

Taxonmaps

69479

Global distribution of 16S sequence KF484906 (>99% sequence identity) for Methyloprofundus sedimenti subclade from Microbeatlas

Aquatic Samples	805
Soil Samples	96
Animal Samples	10
Plant Samples	8
Total Samples	919

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
42689	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	ASM207295v1 assembly for Methyloprofundus sedimenti WF1	contig	GCA_002072955	1420851.6	2785510765	1420851	73.9

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
42689	Methyloprofundus sedimenti strain WF1 16S ribosomal RNA gene, partial sequence	KF484906	1414		1420851

GC content

@ref	GC-content (mol%)	Method
42689	40.5	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Methyloprofundus sedimenti WF1
NCBI: GCA_002072955

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.50	no
125439	motility	BacteriaNetⓘ	yes	51.60	no
125439	gram_stain	BacteriaNetⓘ	negative	98.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker.	Knief C.	Front Microbiol	10.3389/fmicb.2015.01346	2015
Phylogeny	Methyloprofundus sedimenti gen. nov., sp. nov., an obligate methanotroph from ocean sediment belonging to the 'deep sea-1' clade of marine methanotrophs.	Tavormina PL, Hatzenpichler R, McGlynn S, Chadwick G, Dawson KS, Connon SA, Orphan VJ	Int J Syst Evol Microbiol	10.1099/ijs.0.062927-0	2014

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 )
#42689	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29215
#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 .
#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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Methyloprofundus sedimenti (DSM 29215, ATCC BAA-2619, WF1)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002072955

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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