Methylocystis bryophila (DSM 21852, VKM B-2545, H2s)

Name: Methylocystis bryophila (DSM 21852, VKM B-2545, H2s)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7219

Type strain

Strain Designation H2s

Culture col. no. DSM 21852 VKM B-2545 H2s

NCBI tax ID(s) 655015

Special Collections DSMZ Literature strains

History DSMZ <- S. N. Dedysh, Winogradski Inst. Microbiol., RAS, Moscow, Russia; H2s <- S. E. Belova and S. N. Dedysh

Links

Methylocystis bryophila H2s is an aerobe, Gram-negative, coccus-shaped bacterium that was isolated from Sphagnum peat, bank of a bog lake.

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

Name and taxonomic classification

SI-ID 403670

VKM B-2545,DSM 21852

@ref 20215

Last LPSN update 2026-05-29 08:26:35

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Methylocystaceae

Genus Methylocystis

Species Methylocystis bryophila

Full scientific name Methylocystis bryophila Belova et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
30743	negative	2.6 µm	1.15 µm	coccus-shaped
125439	negative					97.699

Pigmentation

30743

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15991	METHYLOCYSTIS MEDIUM (DSMZ Medium 1409)		Medium recipe at MediaDive	Name: METHYLOCYSTIS MEDIUM (DSMZ Medium 1409) Composition: KNO3 0.2 g/l KH2PO4 0.1 g/l MgSO4 x 7 H2O 0.05 g/l CaCl2 x 2 H2O 0.01 g/l NaCl 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 ZnSO4 x 7 H2O 0.0001 g/l CuCl2 x 5 H2O 0.0001 g/l Na2MoO4 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
15991	positive	growth	22
30743	positive	growth	08-37
30743	positive	optimum	27.5

Culture pH

@ref	Ability	Type	PH
30743	positive	optimum	6.25
30743	positive	growth	4.2-7.6

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
15991	aerobe
30743	aerobe
125439	obligate aerobe	97.652

Spore formation

@ref	Spore formation	Confidence
30743
125439		99.11

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30743	16449 ChEBI	alanine	+	carbon source
30743	22653 ChEBI	asparagine	+	carbon source
30743	29987 ChEBI	glutamate	+	carbon source
30743	26271 ChEBI	proline	+	carbon source
30743	17822 ChEBI	serine	+	carbon source

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	hydrogen production	100	5 of 5
66794	suberin monomers biosynthesis	100	2 of 2
66794	lactate fermentation	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	photosynthesis	100	14 of 14
66794	ceramide biosynthesis	100	1 of 1
66794	methylglyoxal degradation	100	5 of 5
66794	acetate fermentation	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	butanoate fermentation	100	4 of 4
66794	biotin biosynthesis	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	vitamin B12 metabolism	94.12	32 of 34
66794	phenylalanine metabolism	92.31	12 of 13
66794	pentose phosphate pathway	90.91	10 of 11
66794	threonine metabolism	90	9 of 10
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	flavin biosynthesis	86.67	13 of 15
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	tyrosine metabolism	85.71	12 of 14
66794	propanol degradation	85.71	6 of 7
66794	leucine metabolism	84.62	11 of 13
66794	peptidoglycan biosynthesis	80	12 of 15
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	methanofuran biosynthesis	80	4 of 5
66794	heme metabolism	78.57	11 of 14
66794	citric acid cycle	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	phosphatidylethanolamine bioynthesis	76.92	10 of 13
66794	sulfate reduction	76.92	10 of 13
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	cardiolipin biosynthesis	71.43	5 of 7
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	propionate fermentation	70	7 of 10
66794	purine metabolism	69.15	65 of 94
66794	histidine metabolism	68.97	20 of 29
66794	tryptophan metabolism	68.42	26 of 38
66794	non-pathway related	68.42	26 of 38
66794	lipid metabolism	67.74	21 of 31
66794	cyanate degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	methanogenesis from CO2	66.67	8 of 12
66794	nitrate assimilation	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	glutathione metabolism	64.29	9 of 14
66794	proline metabolism	63.64	7 of 11
66794	d-xylose degradation	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	cysteine metabolism	61.11	11 of 18
66794	Entner Doudoroff pathway	60	6 of 10
66794	glycine metabolism	60	6 of 10
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
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	degradation of sugar alcohols	56.25	9 of 16
66794	urea cycle	53.85	7 of 13
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	pyrimidine metabolism	53.33	24 of 45
66794	oxidative phosphorylation	52.75	48 of 91
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
66794	CMP-KDO biosynthesis	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	ribulose monophosphate pathway	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	quinate degradation	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	sphingosine metabolism	50	3 of 6
66794	starch degradation	50	5 of 10
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	metabolism of disaccharids	45.45	5 of 11
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	polyamine pathway	43.48	10 of 23
66794	degradation of pentoses	42.86	12 of 28
66794	3-chlorocatechol degradation	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	carnitine metabolism	37.5	3 of 8
66794	ascorbate metabolism	36.36	8 of 22
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	enterobactin biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	degradation of hexoses	33.33	6 of 18
66794	sulfoquinovose degradation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	degradation of sugar acids	32	8 of 25
66794	myo-inositol biosynthesis	30	3 of 10
66794	phenol degradation	30	6 of 20
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	arachidonic acid metabolism	27.78	5 of 18
66794	carotenoid biosynthesis	27.27	6 of 22
66794	cholesterol biosynthesis	27.27	3 of 11
66794	cyclohexanol degradation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17
66794	daunorubicin biosynthesis	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Peat moss

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
15991	Sphagnum peat, bank of a bog lake	Sphagnum	north eastern Germany, lake Teufelssee	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence FN422003 (>99% sequence identity) for Methylocystis bryophila subclade from Microbeatlas

Aquatic Samples	249
Soil Samples	210
Animal Samples	29
Plant Samples	12
Total Samples	500

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15991	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
124043	ASM2792544v1 assembly for Methylocystis bryophila DSM 21852	complete	GCA_027925445	655015.15	8117788544	655015	91.65

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15991	Methylocystis bryophila partial 16S rRNA gene, type strain H2sT	FN422003	1427		655015

GC content

@ref	GC-content (mol%)	Method
15991	62	thermal denaturation, midpoint method (Tm)
30743	62

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM2792544v1 assembly for Methylocystis bryophila DSM 21852
NCBI: GCA_027925445

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.65	no
125439	gram_stain	BacteriaNetⓘ	negative	97.70	no
125439	motility	BacteriaNetⓘ	no	67.01	no
125439	spore_formation	BacteriaNetⓘ	no	99.11	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Hydrogen Oxidation Benefits Alphaproteobacterial Methanotrophs Under Severe Methane Limitation.	Peterse IF, Pol A, Cremers G, Berben T, van Alen TA, Op den Camp HJM, Veraart AJ, Lucker S.	Environ Microbiol	10.1111/1462-2920.70163	2025
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
	Bentazone stress resistance in Methylocystis-Tetradesmus symbiosis: Biochemical and communicative exchanges.	Lu YZ, Di C, Sun J, Wang L, Li X, Zhu GC.	Bioresour Technol	10.1016/j.biortech.2025.133053	2025
Metabolism	Light-dependent enhancement of sulfadiazine detoxification and mineralization by non-photosynthetic methanotrophs.	Wang Y, Lu Y, Li X, Zhu G, Li N, Han J, Sun L, Yang Z, Zeng RJ.	Water Res	10.1016/j.watres.2022.118623	2022
	Mixotrophic Cultivation of Microalgae Using Biogas as the Substrate.	Li X, Lu Y, Li N, Wang Y, Yu R, Zhu G, Zeng RJ.	Environ Sci Technol	10.1021/acs.est.1c06831	2022
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
	Biomethanol Production from Methane by Immobilized Co-cultures of Methanotrophs.	Patel SKS, Gupta RK, Kumar V, Kondaveeti S, Kumar A, Das D, Kalia VC, Lee JK.	Indian J Microbiol	10.1007/s12088-020-00883-6	2020
	Effects of different proportions of organic substitution for mineral fertilizers on soil methanogenic and methanotrophic communities in paddy fields.	Yuan D, Dang K, Yin J, Liu H, Ma T, Liu J, Xiang X.	PeerJ	10.7717/peerj.19000	2025
	Biotransformation of methane into methanol by methanotrophs immobilized on coconut coir.	Patel SKS, Kalia VC, Joo JB, Kang YC, Lee JK.	Bioresour Technol	10.1016/j.biortech.2019.122433	2020
	Encapsulation of Methanotrophs within a Polymeric Matrix Containing Copper- and Iron-Based Nanoparticles to Enhance Methanol Production from a Simulated Biogas.	Patel SKS, Gupta RK, Kim IW, Lee JK.	Polymers (Basel)	10.3390/polym15183667	2023
	DSOF: A Rapid Method to Determine the Abundance of Microalgae and Methanotrophic Bacteria in Coculture Using a Combination of Differential Sedimentation, Optical Density, and Fluorescence.	Cartin-Caballero C, Collet C, Gapes D, Gostomski PA, Stott MB, Carere CR.	Bioengineering (Basel)	10.3390/bioengineering12091000	2025
	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	Unusual Genomic Traits Suggest Methylocystis bryophila S285 to Be Well Adapted for Life in Peatlands.	Han D, Dedysh SN, Liesack W.	Genome Biol Evol	10.1093/gbe/evy025	2018
Metabolism	Biological Methanol Production by a Type II Methanotroph Methylocystis bryophila.	Patel SK, Mardina P, Kim SY, Lee JK, Kim IW.	J Microbiol Biotechnol	10.4014/jmb.1601.01013	2016
	Biotransformation of Methane and Carbon Dioxide Into High-Value Products by Methanotrophs: Current State of Art and Future Prospects.	Sahoo KK, Goswami G, Das D.	Front Microbiol	10.3389/fmicb.2021.636486	2021
Phylogeny	Isolation of methanotrophic bacteria from termite gut.	Reuss J, Rachel R, Kampfer P, Rabenstein A, Kuver J, Droge S, Konig H.	Microbiol Res	10.1016/j.micres.2015.06.003	2015
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
	Biosynthesis of Lactobionic Acid in Whey-Containing Medium by Microencapsulated and Free Bacteria of Pseudomonas taetrolens.	Goderska K.	Indian J Microbiol	10.1007/s12088-021-00944-4	2021
	Grazing exclusion alters soil methane flux and methanotrophic and methanogenic communities in alpine meadows on the Qinghai-Tibet Plateau.	Wang S, Chen X, Li W, Gong W, Wang Z, Cao W.	Front Microbiol	10.3389/fmicb.2023.1293720	2023
	How methanotrophs respond to pH: A review of ecophysiology.	Yao X, Wang J, Hu B.	Front Microbiol	10.3389/fmicb.2022.1034164	2022
	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
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
Phylogeny	Methylocystis bryophila sp. nov., a facultatively methanotrophic bacterium from acidic Sphagnum peat, and emended description of the genus Methylocystis (ex Whittenbury et al. 1970) Bowman et al. 1993.	Belova SE, Kulichevskaya IS, Bodelier PLE, Dedysh SN	Int J Syst Evol Microbiol	10.1099/ijs.0.043505-0	2012

References

#15991	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21852
#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 )
#27074	IJSEM 1096 2013 ( DOI 10.1099/ijs.0.043505-0 , PubMed 22707532 )
#30743	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 #27074
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Methylocystis bryophila (DSM 21852, VKM B-2545, H2s)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_027925445

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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