Turning down the gas: what is the potential for microbial detection of methane leakage from soils?

Bott, Tom (2022) Turning down the gas: what is the potential for microbial detection of methane leakage from soils? PhD thesis, University of Nottingham.

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Methane is a potent greenhouse gas. Emissions from soils, wetlands and subsurface sources are therefore a concern when trying to understand greenhouse gas emission and fluxes in the environment. Soil microbial communities can act as a sink for methane, mitigating its release. The purpose of the thesis was to test if terrestrial natural gas flux could be detected using changes in the soil microbiology, focussing upon changes in the relative abundance of methanotrophs. Two methane mono-oxygenase genes were focussed upon, pmoA, mmoX and Methylocella spp. mmoX. To detect these genes PCR and qPCR assays for use with soil samples were developed using existing primer sets. Next-generation amplicon sequencing, of the 16S rRNA gene, was also used to better explore community changes.

Assays were developed and tested in laboratory incubated soils and field samples. Field work used these molecular tools to develop a method of surveying sites to attempt to identify hotspots of natural gas emission using microbial indicators. Four field sites were surveyed: the two sites with clear methane releases, Hardstoft One and La Fontaine Ardent, appeared to have related increases in the relative abundance of methanotrophs. Across all four field sites spatial separation of pmoA, mmoX and Methylocella spp. mmoX genes appeared to be occurring suggesting either habitat preferences, differing growth strategies, differing substrate preferences or a combination of these.

Within the laboratory, soils were incubated with a methane headspace to develop methanotrophic communities. A methane pulse was simulated in a long-term experiment to develop an understanding of how soil microbial communities are impacted by methane fluxes. Overall, increases in the relative abundance of pmoA were observed alongside an increase in methane oxidation rates; the increased relative abundance of pmoA remained the duration of the experiment but methane oxidation rates declined through time.

The role of methanotrophs in natural attenuation was also explored using contaminated land samples. This work aimed to explore the use of molecular techniques to investigate the relative abundance of methane mono-oxygenase genes in contaminated land sites. This hoped to assess the use of these in future studies exploring the natural attenuation of organic contaminants, with the aim of identifying future research directions. Problems with DNA recovery and amplification limited the scope of this work but highlighted potential avenues for future work.

Cumulatively the thesis demonstrates the ability of qPCR to survey methane oxidising microbial communities over scales of tens of metres. These methods have the potential to help detect and monitor methane emissions from former oil and gas fields or sites where methane emission is suspected, for example landfill sites. The thesis also develops the understanding of methanotrophic community dynamics in soils.

Item Type: Thesis (University of Nottingham only) (PhD)
Supervisors: Gregory, Simon
Shaw, George
Palumbo-Roe, Barbara
Crout, Neil
Keywords: Microbial detection, Methane leakage, Soil, Methane
Subjects: Q Science > QR Microbiology > QR100 Microbial ecology
Faculties/Schools: UK Campuses > Faculty of Science > School of Biosciences
Item ID: 71158
Depositing User: Bott, Thomas
Date Deposited: 31 Dec 2022 04:40
Last Modified: 31 Dec 2023 04:30
URI: https://eprints.nottingham.ac.uk/id/eprint/71158

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