Methylocystis heyeri (DSM 16984, VKM B-2426, H2)

Name: Methylocystis heyeri (DSM 16984, VKM B-2426, H2)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7216

Type strain

Strain Designation H2

Culture col. no. DSM 16984 VKM B-2426 H2

NCBI tax ID(s) 391905

Special Collections DSMZ Literature strains

History <- S. N. Dedysh; H2

Links

Methylocystis heyeri H2 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from acidic Sphagnum peat bog lake.

Gram-negative rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 297264

DSM 16984,VKM B-2426

@ref 20215

Last LPSN update 2026-02-09 11:19:25

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Methylocystaceae

Genus Methylocystis

Species Methylocystis heyeri

Full scientific name Methylocystis heyeri Dedysh et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
31902	negative	2.7 µm	1 µm	rod-shaped
125438	negative					97.5

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
6591	MINERAL MEDIUM (DSMZ Medium 1007)		Medium recipe at MediaDive	Name: MINERAL MEDIUM (DSMZ Medium 1007) Composition: KNO3 0.25 g/l KH2PO4 0.1 g/l MgSO4 x 7 H2O 0.05 g/l CaCl2 x 2 H2O 0.01 g/l EDTA 0.005 g/l FeSO4 x 7 H2O 0.002 g/l CoCl2 x 6 H2O 0.0002 g/l CuCl2 x 5 H2O 0.0001 g/l ZnSO4 x 7 H2O 0.0001 g/l Na2MoO4 3e-05 g/l MnCl2 x 4 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
6591	positive	growth	20
31902	positive	growth	05-30
31902	positive	optimum	25

Culture pH

@ref	Ability	Type	PH
31902	positive	optimum	6
31902	positive	growth	4.4-7.5

Physiology and metabolism

Oxygen tolerance

31902

Oxygen toleranceaerobe

Spore formation

31902

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31902	NaCl	positive	growth	<0.5 %

Metabolite production

@ref	Chebi-ID	Metabolite	Production
31902	16183 ChEBI	methane

Enzymes

@ref	Value	Activity	Ec
31902	catalase	+	1.11.1.6
31902	cytochrome oxidase	+	1.9.3.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	suberin monomers biosynthesis	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	gluconeogenesis	100	8 of 8
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	acetate fermentation	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	coenzyme A metabolism	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ceramide biosynthesis	100	1 of 1
66794	adipate degradation	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	valine metabolism	100	9 of 9
66794	biotin biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	folate polyglutamylation	100	1 of 1
66794	ppGpp biosynthesis	100	4 of 4
66794	glycogen metabolism	100	5 of 5
66794	butanoate fermentation	100	4 of 4
66794	ethanol fermentation	100	2 of 2
66794	hydrogen production	100	5 of 5
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	cyanate degradation	100	3 of 3
66794	photosynthesis	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	threonine metabolism	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	tyrosine metabolism	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	leucine metabolism	84.62	11 of 13
66794	peptidoglycan biosynthesis	80	12 of 15
66794	flavin biosynthesis	80	12 of 15
66794	methanofuran biosynthesis	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	vitamin B12 metabolism	79.41	27 of 34
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	heme metabolism	78.57	11 of 14
66794	citric acid cycle	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	glycogen biosynthesis	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	proline metabolism	72.73	8 of 11
66794	pentose phosphate pathway	72.73	8 of 11
66794	glutathione metabolism	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	purine metabolism	70.21	66 of 94
66794	starch degradation	70	7 of 10
66794	propionate fermentation	70	7 of 10
66794	urea cycle	69.23	9 of 13
66794	vitamin B1 metabolism	69.23	9 of 13
66794	alanine metabolism	68.97	20 of 29
66794	nitrate assimilation	66.67	6 of 9
66794	methanogenesis from CO2	66.67	8 of 12
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	cysteine metabolism	66.67	12 of 18
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	acetoin degradation	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	methionine metabolism	65.38	17 of 26
66794	lipid metabolism	64.52	20 of 31
66794	vitamin B6 metabolism	63.64	7 of 11
66794	tryptophan metabolism	63.16	24 of 38
66794	non-pathway related	63.16	24 of 38
66794	arginine metabolism	62.5	15 of 24
66794	lysine metabolism	61.9	26 of 42
66794	sulfate reduction	61.54	8 of 13
66794	phosphatidylethanolamine bioynthesis	61.54	8 of 13
66794	glycine betaine biosynthesis	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	glycine metabolism	60	6 of 10
66794	pyrimidine metabolism	57.78	26 of 45
66794	degradation of sugar alcohols	56.25	9 of 16
66794	d-xylose degradation	54.55	6 of 11
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	oxidative phosphorylation	53.85	49 of 91
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	polyamine pathway	52.17	12 of 23
66794	Entner Doudoroff pathway	50	5 of 10
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	degradation of hexoses	50	9 of 18
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	denitrification	50	1 of 2
66794	CMP-KDO biosynthesis	50	2 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	quinate degradation	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	sphingosine metabolism	50	3 of 6
66794	catecholamine biosynthesis	50	2 of 4
66794	selenocysteine biosynthesis	50	3 of 6
66794	degradation of pentoses	50	14 of 28
66794	ascorbate metabolism	45.45	10 of 22
66794	metabolism of disaccharids	45.45	5 of 11
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	gallate degradation	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	elloramycin biosynthesis	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	cholesterol biosynthesis	36.36	4 of 11
66794	phenol degradation	35	7 of 20
66794	IAA biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	pantothenate biosynthesis	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	degradation of sugar acids	32	8 of 25
66794	carotenoid biosynthesis	31.82	7 of 22
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	toluene degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Lake (large)
#Environmental	#Terrestrial	#Wetland (Swamp)
#Host	#Plants	#Peat moss
#Condition	#Acidic	-

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
6591	acidic Sphagnum peat bog lake	Sphagnum	Teufelssee	Germany	DEU	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6591	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM480263v2 assembly for Methylocystis heyeri H2	complete	GCA_004802635	391905.6	2995287100	391905	91.73

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6591	Methylocystis heyeri partial 16S rRNA gene, type strain H2T	AM283543	1425		391905

GC content

6591

GC-content (mol%)61.5

Genome-based predictions

Predictions

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Methylocystis heyeri H2
NCBI: GCA_004802635.2

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.50	yes
125438	anaerobic	anaerobicⓘ	no	86.76	yes
125438	aerobic	aerobicⓘ	yes	77.06	yes
125438	spore-forming	spore-formingⓘ	no	86.54	yes
125438	thermophilic	thermophileⓘ	no	94.87	yes
125438	flagellated	motile2+ⓘ	no	56.67	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
	Key genes and microbial ecological clusters involved in organophosphate ester degradation in agricultural fields of a typical watershed in southwest China.	Cheng Y, Zheng X, Jiang Y, Xiao Q, Luo Q, Ding Y.	J Hazard Mater	10.1016/j.jhazmat.2025.138076	2025
Phylogeny	From genome to evolution: investigating type II methylotrophs using a pangenomic analysis.	Samanta D, Rauniyar S, Saxena P, Sani RK.	mSystems	10.1128/msystems.00248-24	2024
	Microbial community dynamics in two Central European peatlands affected by different nitrogen depositions.	Barta J, Santruckova H, Novak M, Cejkova B, Jackova I, Buzek F, Stepanova M, Curik J, Veselovsky F, Prechova E.	FEMS Microbiol Ecol	10.1093/femsec/fiaf056	2025
Metabolism	Facultative methanotrophs - diversity, genetics, molecular ecology and biotechnological potential: a mini-review.	Farhan Ul Haque M, Xu HJ, Murrell JC, Crombie A.	Microbiology (Reading)	10.1099/mic.0.000977	2020
	Cleaner anaerobic fermentation and greenhouse gas reduction of crop straw.	Du Z, Nakagawa A, Fang J, Ridwan R, Astuti WD, Sarwono KA, Sofyan A, Widyastuti Y, Cai Y.	Microbiol Spectr	10.1128/spectrum.00520-24	2024
	Comparative genomic analysis of Methylocystis sp. MJC1 as a platform strain for polyhydroxybutyrate biosynthesis.	Naizabekov S, Hyun SW, Na JG, Yoon S, Lee OK, Lee EY.	PLoS One	10.1371/journal.pone.0284846	2023
	A Novel Laboratory-Scale Mesocosm Setup to Study Methane Emission Mitigation by Sphagnum Mosses and Associated Methanotrophs.	Kox MAR, Smolders AJP, Speth DR, Lamers LPM, Op den Camp HJM, Jetten MSM, van Kessel MAHJ.	Front Microbiol	10.3389/fmicb.2021.651103	2021
	Acidophilic methanotrophs: Occurrence, diversity, and possible bioremediation applications.	Hwangbo M, Shao Y, Hatzinger PB, Chu KH.	Environ Microbiol Rep	10.1111/1758-2229.13156	2023
Genetics	Genomic Insights Into the Acid Adaptation of Novel Methanotrophs Enriched From Acidic Forest Soils.	Nguyen NL, Yu WJ, Gwak JH, Kim SJ, Park SJ, Herbold CW, Kim JG, Jung MY, Rhee SK.	Front Microbiol	10.3389/fmicb.2018.01982	2018
	The Microbiota of Recreational Freshwaters and the Implications for Environmental and Public Health.	Lee CS, Kim M, Lee C, Yu Z, Lee J.	Front Microbiol	10.3389/fmicb.2016.01826	2016
Metabolism	Heterotrophic N2-fixation contributes to nitrogen economy of a common wetland sedge, Schoenoplectus californicus.	Rejmankova E, Sirova D, Castle ST, Barta J, Carpenter H.	PLoS One	10.1371/journal.pone.0195570	2018
Phylogeny	Methylocystis heyeri sp. nov., a novel type II methanotrophic bacterium possessing 'signature' fatty acids of type I methanotrophs.	Dedysh SN, Belova SE, Bodelier PLE, Smirnova KV, Khmelenina VN, Chidthaisong A, Trotsenko YA, Liesack W, Dunfield PF	Int J Syst Evol Microbiol	10.1099/ijs.0.64623-0	2007

References

#6591	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16984
#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 )
#28160	IJSEM 472 2007 ( DOI 10.1099/ijs.0.64623-0 , PubMed 17329771 )
#31902	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28160
#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 )
#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 )
#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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Methylocystis heyeri (DSM 16984, VKM B-2426, H2)

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 production

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004802635

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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