Physiology and Biochemistry of the Aerobic Methanotrophs

  • Valentina N. Khmelenina
  • J. Colin Murrell
  • Thomas J. Smith
  • Yuri A. TrotsenkoEmail author
Reference work entry
Part of the Handbook of Hydrocarbon and Lipid Microbiology book series (HHLM)


Methanotrophs are a widely distributed group of aerobic bacteria that use methane as their source of carbon and energy. They play key roles in the global carbon cycle, including controlling anthropogenic and natural emissions of the greenhouse gas methane. Methanotrophs oxidize methane using the unique enzyme methane monooxygenase which exists in two structurally and biochemically distinct forms. One form, the membrane-associated or particulate methane monooxygenase (pMMO), is found in most known methanotrophs and is located in the cytoplasmic membrane. Another form, the soluble methane monooxygenase (sMMO), is found in some methanotrophs and is located in the cytoplasm. Both forms of MMO can co-oxidize a range of hydrocarbons and chlorinated pollutants and hence are interesting with respect to the biotechnological potential of methanotrophs. Methanol is further oxidized to formaldehyde, formate, and CO2, by specific methylotrophic enzymes, while biomass is built from formaldehyde, formate, CO2, or a combination thereof via three cyclic biochemical pathways: the ribulose monophosphate (RuMP) cycle, the serine pathway, and the Calvin-Benson-Bassham (CBB) cycle. The availability of genome sequences of methanotrophs enables postgenomic studies to investigate the regulation of methane oxidation in the laboratory and in the environment by natural methanotrophs and in laboratory or industrial conditions by platform organisms. Recent studies have included synthetic biology approaches and in future may incorporate the design of new pathways.


Methane monooxygenases Environmental microbiology Global warming Bioremediation Single-cell protein 


  1. Anthony C, Williams P (2003) The structure and mechanism of methanol dehydrogenase. Biochim Biophys Acta 1647:8–23. Scholar
  2. Baani M, Liesack W (2008) Two isozymes of particulate methane monooxygenase with different methane oxidation kinetics are found in Methylocystis sp. strain SC2. Proc Natl Acad Sci USA 105:10203–10208. Scholar
  3. Balasubramanian R, Smith SM, Rawat S et al (2010) Oxidation of methane by a biological dicopper centre. Nature 465:115–119. Scholar
  4. Banerjee R, Proshlyakov Y, Lipscomb JD, Proshlyakov DA (2015) Structure of the key species in the enzymatic oxidation of methane to methanol. Nature 518:431–434. Scholar
  5. Bergmann DJ, Zahn JA, DiSpirito AA (1999) High-molecular-mass multi-c-heme cytochromes from Methylococcus capsulatus bath. J Bacteriol 181:991–997PubMedPubMedCentralGoogle Scholar
  6. Bogodar IW, Lin TS, Liao JC (2013) Synthetic non-oxidative glycolysis enables complete carbon conservation. Nature 502:693–697. Scholar
  7. Brazeau B, Lipscomb JD (2000) Kinetics and activation thermodynamics of methane monooxygenase compound Q formation and reaction with substrates. Biochemistry 39:13503–13515CrossRefGoogle Scholar
  8. But SY, Egorova SV, Khmelenina VN, Trotsenko YA (2017) Biochemical properties and phylogeny of hydroxypyruvate reductases from methanotrophic bacteria with different C1-assimilation pathways. Biochem Mosc 82:1295–1303. Scholar
  9. Chen Y, Crombie A, Rahman MT et al (2010a) Complete genome sequence of the aerobic facultative methanotroph Methylocella silvestris BL2. J Bacteriol 192:3840–3841. Scholar
  10. Chen Y, Scanlan J, Song L et al (2010b) γ-Glutamylmethylamide is an essential intermediate in the metabolism of methylamine by Methylocella silvestris. Appl Environ Microbiol 76:4530–4537. Scholar
  11. Chen Y, Patel NA, Crombie A et al (2011) Bacterial flavin-containing monooxygenase is trimethylamine monooxygenase. Proc Natl Acad Sci 108:17791–17796. Scholar
  12. Chistoserdova L (2011) Modularity of methylotrophy, revisited. Environ Microbiol 13:2603–2622. Scholar
  13. Chistoserdova L (2016) Lanthanides: new life metals? World J Microbiol Biotechnol 32:138. Scholar
  14. Chistoserdova L, Kalyuzhnaya MG, Lidstrom ME (2009) The expanding world of methylotrophic metabolism. Annu Rev Microbiol 63:477–499. Scholar
  15. Chu F, Lidstrom ME (2016) XoxF acts as the predominant methanol dehydrogenase in the type I methanotroph Methylomicrobium buryatense. J Bacteriol 198:1317–1325. Scholar
  16. Crombie AT, Murrell JC (2014) Trace-gas metabolic versatility of the facultative methanotroph Methylocella silvestris. Nature 510:148–151. Scholar
  17. Crowther GJ, Kosály G, Lidstrom ME (2008) Formate as the main branch point for methylotrophic metabolism in Methylobacterium extorquens AM1. J Bacteriol 190:5057–5062. Scholar
  18. Culpepper MA, Rosenzweig AC (2014) Structure and protein-protein interactions of methanol dehydrogenase from Methylococcus capsulatus (Bath). Biochemistry 53:6211–6219. Scholar
  19. Dassama LM, Kenney GE, Rosenzweig AC (2017) Methanobactins: from genome to function. Metallomics 9:7–20. Scholar
  20. De la Torre A, Metivier A, Chu F et al (2015) Genome-scale metabolic reconstructions and theoretical investigation of methane conversion in Methylomicrobium buryatense strain 5G(B1). Microb Cell Factories 14:188. Scholar
  21. Delmotte N, Knief C, Chaffron S et al (2009) Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc Natl Acad Sci USA 106:16428–11643. Scholar
  22. DiSpirito AA, Semrau JD, Murrell JC et al (2016) Methanobactin and the link between copper and bacterial methane oxidation. Microbiol Mol Biol Rev 80:387–409. Scholar
  23. Dunfield PF, Dedysh SN (2014) Methylocella: a gourmand among methanotrophs. Trends Microbiol 22:368–369. Scholar
  24. Dunfield PF, Yuryev A, Senin P et al (2007) Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia. Nature 450:879–882. Scholar
  25. Eshinimaev BT, Medvedkova KA, Khmelenina VN et al (2004) New thermophilic methanotrophs of the genus Methylocaldum. Microbiology (Moscow) 73:530–539CrossRefGoogle Scholar
  26. Eswayah AS, Smith TJ, Scheinost AC et al (2017) Microbial transformations of selenite by methane-oxidizing bacteria. Appl Microbiol Biotechnol 101:6713–6724. Scholar
  27. Ettwig KF, Butler MK, LePaslier D et al (2010) Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature 464:543–548. Scholar
  28. Ferenci T, Strøm T, Quayle JR (1974) Purification and properties of 3-hexulose phosphate synthase from Methylococcus capsulatus. Biochem J 144:477–486CrossRefGoogle Scholar
  29. Fru EC, Gray ND, McCann C et al (2011) Effects of copper mineralogy and methanobactin on cell growth and sMMO activity in Methylosinus trichosporium OB3b. Biosci Discuss 8:2887–2894Google Scholar
  30. Fu Y, Li Y, Lidstrom M (2017) The oxidative TCA cycle operates during methanotrophic growth of the Type I methanotroph Methylomicrobium buryatense 5GB1. Metab Eng 42:43–51. Scholar
  31. Gilman A, Laurens LM, Puri AW et al (2015) Bioreactor performance parameters for an industrially-promising methanotroph Methylomicrobium buryatense 5GB1. Microb Cell Fact 14:182. Scholar
  32. Gilman A, Fu Y, Hendershott M et al (2017) Oxygen-limited metabolism in the methanotroph Methylomicrobium buryatense 5GB1C. PeerJ 5:e3945. Scholar
  33. Han JI, Semrau JD (2000) Chloromethane stimulates growth of Methylomicrobium album BG8 on methanol. FEMS Microbiol Lett 187(1):77–81CrossRefGoogle Scholar
  34. Hanson RS, Hanson TE (1996) Methanotrophic bacteria. Microbiol Rev 60:439–471PubMedPubMedCentralGoogle Scholar
  35. Helm J, Wendlandt KD, Rogge G, Kappelmeyer U (2006) Characterizing a stable methane-utilizing mixed culture used in the synthesis of a high-quality biopolymer in an open system. J Appl Microbiol 101:387–395. Scholar
  36. Henard CA, Smith H, Dowe N et al (2016) Bioconversion of methane to lactate by an obligate methanotrophic bacterium. Sci Rep 6:21585. Scholar
  37. Islam T, Jensen S, Reigstad LJ (2008) Methane oxidation at 55°C and pH 2 by a thermoacidophilic bacterium belonging to the Verrucomicrobia phylum. Proc Natl Acad Sci USA 105:300–304. Scholar
  38. Jiang H, Chen Y, Jiang PX et al (2010) Methanotrophs: multifunctional bacteria with promising applications in environmental bioengineering. Biochem Eng J 49:277–288CrossRefGoogle Scholar
  39. Kalyuzhnaya MG (2016) Methane biocatalysis: selecting the right microbe. In: Trinh CA, Eckert Cong T (eds) Biotechnology for biofuel production and optimization. Elsevier, Amsterdam, pp 353–383CrossRefGoogle Scholar
  40. Kalyuzhnaya MG, Lidstrom ME (2005) QscR-mediated transcriptional activation of serine cycle genes in Methylobacterium extorquens AM1. J Bacteriol 187:7511–7517. Scholar
  41. Kalyuzhnaya MG, Yang S, Rozova ON et al (2013) Highly efficient methane biocatalysis revealed in a methanotrophic bacterium. Nat Commun 4:2785. Scholar
  42. Kalyuzhnaya MG, Pury AW, Lidstrom ME (2015) Metabolic engineering in methanotrophic bacteria. Metab Eng 29:142–152. Scholar
  43. Kao W-C, Chen Y-R, Yi EC (2004) Quantitative proteomic analysis of metabolic regulation by copper ions in Methylococcus capsulatus (Bath). J Biol Chem 279:51554–51560. Scholar
  44. Karlsen OA, Lillehaug JR, Jensen HB (2011) The copper responding surfaceome of Methylococcus capsulatus Bath. FEMS Microbiol Lett 23:97–104. Scholar
  45. Khadem AF, Pol A, Jetten MS, Op den Camp HJ (2010) Nitrogen fixation by the verrucomicrobial methanotroph ‘Methylacidiphilum fumariolicum’ SolV. Microbiology 156:1052–1059. Scholar
  46. Khadem AF, Pol A, Wieczorek A et al (2011) Autotrophic methanotrophy in Verrucomicrobia: Methylacidiphilum fumariolicum SolV uses the Calvin-Benson-Bassham cycle for carbon dioxide fixation. J Bacteriol 193:4438–4446. Scholar
  47. Khadem AF, Wieczorek AS, Pol A et al (2012) Draft genome sequence of the volcano-inhabiting thermoacidophilic methanotroph Methylacidiphilum fumariolicum strain SolV. J Bacteriol 194:3729–3730. Scholar
  48. Lawton TJ, Rosenzweig AC (2016) Biocatalysts for methane conversion: big progress on breaking a small substrate. Curr Opin Chem Biol 35:142–149. Scholar
  49. Lee S-K, Nesheim JC, Lipscomb JD (1993) Transient intermediates of the methane monooxygenase catalytic cycle. J Biol Chem 268:21569–21577PubMedGoogle Scholar
  50. Lee SJ, McCormick MS, Lippard SJ, Cho U-S (2013) Control of substrate access to the active site in methane monooxygenase. Nature 494:380–384. Scholar
  51. Levett I, Birkett G, Davies N et al (2016) Techno-economic assessment of Poly-3-Hydroxybutyrate (PHB) production from methane – the case for thermophilic bioprocessing. J Environ Chem Eng 4:3724–3733. Scholar
  52. Mattes TE, Nunn BL, Marshall KT et al (2013) Sulfur oxidizers dominate carbon fixation at a biogeochemical hot spot in the dark ocean. ISME J 7:2349–2360. Scholar
  53. McDonald IR, Bodrossy L, Chen Y, Murrell JC (2008) Molecular ecology techniques for the study of aerobic methanotrophs. Appl Environ Microbiol 74:1305–1315. Scholar
  54. Miroshnikov KK, Didriksen A, Naumoff DG et al (2017) Draft genome sequence of Methylocapsa palsarum NE2T, an obligate methanotroph from subarctic soil. Genome Announc 5:e00504-17. Scholar
  55. Moitinho-Silva L, Seridi L, Ryu T et al (2014) Revealing microbial functional activities in the Red Sea sponge Stylissa carteri by metatranscriptomics. Environ Microbiol 16:3683–3698. Scholar
  56. Murrell JC, Dalton H (1983) Nitrogen fixation in obligate methanotrophs. J Gen Microbiol 129:3481–3486Google Scholar
  57. Murrell JC, McDonald IR, Gilbert B (2000) Regulation of expression of methane monooxygenases by copper ions. Trends Microbiol 8:221–225. PMID:10785638CrossRefGoogle Scholar
  58. Ochsner AM, Christen M, Hemmerle L et al (2017) Transposon sequencing uncovers an essential regulatory function of phosphoribulokinase for methylotrophy. Curr Biol 27(17):2579–2588. Scholar
  59. Op den Camp HJM, Islam T, Stott MB et al (2009) Environmental, genomic and taxonomic perspectives on methanotrophic Verrucomicrobia. Environ Microbiol Rep 1:293–306. Scholar
  60. Oswald K, Graf JS, Littmann S et al (2017) Crenothrix are major methane consumers in stratified lakes. ISME J 11(9):2124–2140. Scholar
  61. Patel RN, Hou CT, Derelanko P, Felix A (1980) Purification and properties of a heme-containing aldehyde dehydrogenase from Methylosinus trichosporium. Arch Biochem Biophys 203:654–662CrossRefGoogle Scholar
  62. Pieja AJ, Rostkowski KH, Criddle CS (2011) Distribution and selection of poly-3-hydroxybutyrate production capacity in methanotrophic Proteobacteria. Microb Ecol 62:564–473. Scholar
  63. Pol A, Barends TR, Dietl A et al (2014) Rare earth metals are essential for methanotrophic life in volcanic mudpots. Environ Microbiol 16:255–264. Scholar
  64. Reshetnikov AS, Khmelenina VN, Mustakhimov II (2011) Diversity and phylogeny of the ectoine biosynthesis genes in aerobic, moderately halophilic methylotrophic bacteria. Extremophiles 15:653–666. Scholar
  65. Rosenzweig AC, Frederic CA, Lippard SJ, Nordlund P (1993) Crystal structure of a bacterial non-haem iron hydroxylase that catalyses the biological oxidation of methane. Nature 366: 537–543. Scholar
  66. Rozova ON, Khmelenina VN, Bocharova KA et al (2015a) Role of NAD+-dependent malate dehydrogenase in the metabolism of Methylobacterium alcaliphilum 20Z and Methylosinus trichosporium OB3b. Microorganisms 3:47–59CrossRefGoogle Scholar
  67. Rozova ON, Khmelenina VN, Gavletdinova JZ et al (2015b) Acetate kinase – an enzyme of the postulated phosphoketolase pathway in Methylomicrobium alcaliphilum 20Z. Ant Leeuw 108:965–974. Scholar
  68. Rozova ON, But SY, Khmelenina VN et al (2017) Characterization of two recombinant 3-hexulose 6-phosphate synthases from the halotolerant obligate methanotroph Methylomicrobium alcaliphilum 20Z. Biochem Mosc 82:176–185. Scholar
  69. Saville RM, Lee S, Regitsky DD et al (2014) Compositions and methods for biological production of lactate from C1 compounds using lactate dehydrogenase transformants, Patent WO2014205146A1Google Scholar
  70. Semrau JD, Jagadevan S, DiSpirito AA et al (2013) Methanobactin and MmoD work in concert to act as the “copper-switch” in methanotrophs. Environ Microbiol 15:3077–3086. Scholar
  71. Sharp CE, Smirnova AV, Kalyuzhnaya MG et al (2015) Draft genome sequence of the moderately halophilic methanotroph, Methylohalobius crimeensis strain 10Ki. Genome Announc 3.
  72. Shchukin VN, Khmelenina VN, Eshinimayev BT et al (2011) Primary characterization of dominant cell surface proteins of halotolerant methanotroph Methylomicrobium alcaliphilum 20Z. Microbiology (Moscow) 80:595–605CrossRefGoogle Scholar
  73. Sowell SM, Abraham PE, Shah M et al (2011) Environmental proteomics of microbial plankton in a highly productive coastal upwelling system. ISME J 5:856–865. Scholar
  74. Strong PJ, Xie S, Clarke WP (2015) Methane as a resource: can the methanotrophs add value? Environ Sci Technol 49:4001–4018. Scholar
  75. Strong PJ, Kalyuzhnaya M, Silverman J, Clarke WP (2016) A methanotroph-based biorefinery: potential scenarios for generating multiple products from a single fermentation. Bioresour Technol 215:314–323. Scholar
  76. Tavormina PL, Orphan VJ, Kalyuzhnaya MG et al (2011) A novel family of functional operons encoding methane/ammonia monooxygenase-related proteins in gammaproteobacterial methanotrophs. Environ Microbiol Rep 3:91–100. Scholar
  77. Torre A, Metivier A, Chu F et al (2015) Genome-scale metabolic reconstructions and theoretical investigation of methane conversion in Methylomicrobium buryatense strain 5G (B1). Microb Cell Fact 14:188. Scholar
  78. Trotsenko YA, Murrell JC (2008) Metabolic aspects of aerobic obligate methanotrophy. Adv Appl Microbiol 63:183–229. Scholar
  79. Van Teeseling MCF, Pol A, Harhangi HR et al (2014) Expanding the verrucomicrobial methanotrophic world: description of three novel species of Methylacidimicrobium gen. nov. Appl Environ Microbiol 80:6782–6791. Scholar
  80. Vekeman B, Kerckhof F-M, Cremers G et al (2016) New Methyloceanibacter diversity from North Sea sediments includes methanotroph containing solely the soluble methane monooxygenase. Environ Microbiol 18:4523–4536. Scholar
  81. Vita N, Platsaki S, Basle A et al (2015) A four-helix bundle stores copper for methane oxidation. Nature 525:140–143. Scholar
  82. Vorholt JA (2002) Cofactor-dependent pathways of formaldehyde oxidation in methylotrophic bacteria. Arch Microbiol 178:39–249. Scholar
  83. Vu HN, Subuyuj GA, Vijayakumar S et al (2016) Lanthanide-dependent regulation of methanol oxidation systems in Methylobacterium extorquens AM1 and their contribution to methanol growth. J Bacteriol 98:1250–1259. Scholar
  84. Wang W, Lippard SJ (2014) Diiron oxidation state control of substrate access to the active site of soluble methane monooxygenase mediated by the regulatory component. J Am Chem Soc 136:2244–2247. Scholar
  85. Zhu Y, Jameson E, Parslow RA et al (2014) Identification and characterization of trimethylamine N-oxide (TMAO) demethylase and TMAO permease in Methylocella silvestris BL2. Environ Microbiol 16:3318–3330. Scholar
  86. Zhu Y, Ksibe AZ, Schäfer H et al (2016) O2-independent demethylation of trimethylamine N-oxide by Tdm of Methylocella silvestris. FEBS J 283:3979–3993. Scholar
  87. Zuniga C, Morales M, Revah S (2013) Polyhydroxyalkanoates accumulation by Methylobacterium organophilum CZ-2 during methane degradation using citrate or propionate as cosubstrates. Bioresour Technol 130:686. Scholar

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© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Valentina N. Khmelenina
    • 1
  • J. Colin Murrell
    • 3
  • Thomas J. Smith
    • 2
  • Yuri A. Trotsenko
    • 1
    Email author
  1. 1.G.K. Skryabin Institute of Biochemistry and Physiology of MicroorganismsRussian Academy of SciencesPushchino/MoscowRussia
  2. 2.Biomolecular Sciences Research CentreSheffield Hallam UniversitySheffieldUK
  3. 3.School of Environmental SciencesUniversity of East Anglia, Norwich Research ParkNorwichUK

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