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Facultative Methanotrophy at Natural Gas Seeps

One of the largest source of methane released to the atmosphere is geological methane, which arises from the thermogenic decomposition of fossil organic material to “natural gas”. Natural gas contains methane and substantial amounts (up to 50% in some cases) of other climate-active gaseous alkanes (ethane, propane and butane) which collectively influence atmospheric chemistry and cause climate change. Natural seepage of geological methane, (natural gas) occurs in wide ranging environments including terrestrial areas that overlay sedimentary organic carbon, deepsea hydrothermal vents, shallow marine methane seeps, soda lakes, hot springs and mud pots in volcanic regions of the Earth.


Although vast amounts of methane escape to the atmosphere, much more would escape if it were not for the activity of microbes that consume methane. Methane-consuming bacteria, methanotrophs, are crucial in mitigating emissions of methane as they oxidise most of the methane produced in soils and the subsurface before it reaches the atmosphere. Methanotrophs are usually obligate, i.e. grow only on methane and not on longer chain alkanes. Bacteria that grow on the other gaseous alkanes in natural gas such as propane have also been characterised, but they do not grow on methane.

One of the most exciting recent developments in the study of biological methane oxidation was the discovery of facultative methanotrophs of the genus Methylocella. Our lab discovered that that the facultative methanotroph Methylocella silvestris can grow on methane as well as other components of natural gas (ethane and propane), thus overturning the dogma that degradation of these gases was carried out by different groups of microbes (Crombie & Murrell 2014). The unique metabolic capability of Methylocella have profound implications for the biological consumption of natural gas in the environment.

Methylocella, being able to use most components of natural gas for growth, may have a competitive edge over less versatile obligate methanotrophs and propanotrophs in environments rich in natural gas. However, very little is known about the distribution of Methylocella in the environment. The aims of on-going projects in our lab are to improve molecular methods for detection of Methylocella in environmental samples, exploring the metabolic flexibility of these facultative methanotrophs at genetic and biomolecular levels, and to test the hypothesis that Methylocella-like facultative methanotrophs are prevalent in thermogenic, natural gas seep environments (Farhan Ul Haque et al. 2018, Rahman et al. 2011).

Selected Publications:

Ul Haque, M.F.,Hernández, M., Crombie, A.T. and Murrell, J.C. (2022) Identification of active gaseous alkane degraders at natural gas seeps. The ISME Journal, 16, 1705-1716.

Ul Haque, M., F., Xu, H.- J., Murrell, J.C. and Crombie, A.T. (2020). Facultative methanotrophs – diversity, genetics, molecular ecology and biotechnological potential; a mini-review. Microbiology, 166:894–908.

Bordel, S., Crombie, A.T., Muñoz, R. and Murrell, J.C. (2020). Genome scale metabolic model of the versatile methanotroph Methylocella silvestris. Microbial Cell Factories, 19:1-14

Farhan Ul Haque, M., Crombie, A.T. and Murrell, J.C. (2019) Active facultative methanotrophs at terrestrial natural gas seeps. Microbiome, 7, 1-17.


Farhan Ul Haque M, Crombie AT, Ensminger SA, Baciu C, Murrell JC: Facultative methanotrophs are abundant at terrestrial natural gas seeps. Microbiome. 2018; 6.

Crombie AT, Murrell JC: Trace-gas metabolic versatility of the facultative methanotroph Methylocella silvestris. Nature. 2014; 510:148

Patel NA, Crombie A, Slade SE, Thalassinos K, Hughes C, Connolly JB, Langridge J, Murrell JC, Scrivens JH: Comparison of one- and two-dimensional liquid chromatography approaches in the label-free quantitative analysis of Methylocella silvestris. J Proteome Res. 2012; 11:4755-4763.

Rahman MT, Crombie A, Chen Y, Stralis-Pavese N, Bodrossy L, Meir P, McNamara NP, Murrell JC: Environmental distribution and abundance of the facultative methanotroph Methylocella. The ISME J. 2011;5: 1061-1066.

Crombie A, Murrell JC: Development of a system for genetic manipulation of the facultative methanotroph Methylocella silvestris BL2. In Methods in Enzymology: Methods in Methane Metabolism, Vol 495, Pt B. Edited by Rosenzweig AC, Ragsdale SW; 2011: 119-133: Methods in Enzymology.

Rahman MT, Crombie A, Moussard H, Chen Y, Murrell JC: Acetate repression of methane oxidation by supplemental Methylocella silvestris in a peat soil microcosm. Appl Environ Microbiol. 2011; 77:4234-4236.

Chen Y, Crombie A, Rahman MT, Dedysh SN, Liesack W, Stott MB, Alam M, Theisen AR, Murrell JC, Dunfield PF: Complete genome sequence of the aerobic facultative methanotroph Methylocella silvestris BL2. J Bacteriol. 2010; 192:3840-3841.

Chen Y, Scanlan J, Song LJ, Crombie A, Rahman MT, Schafer H, Murrell JC: Gamma-glutamylmethylamide is an essential intermediate in the metabolism of methylamine by Methylocella silvestris. Appl Environ Microbiol. 2010; 76:4530-4537.

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