Microbial Methane Oxidation and Community Dynamics in Southern Ontario Landfill Cover Soils

Abstract

Methane emissions from municipal solid waste landfills contribute to ~10% of global methane emissions, significantly contributing to climate change. Methanotrophic bacteria present in landfill cover soils (LCS) can mitigate these emissions by oxidizing methane. In capped landfills, surface methane emissions are often concentrated at highly emissive ‘hot spots’. The spatial distribution and overall levels of methane emissions vary over daily, seasonal, and multi-year timescales, driven by landfill age and meteorological factors. Methanotrophic community composition in LCS also varies spatially and temporally in response to methane emissions, soil moisture content, temperature, pH, and nutrient availability. The research presented in this thesis surveys community composition, methane flux, and soil chemistry across a decommissioned capped landfill cover over a total period of 8 years. The overall objectives were to assess how soil bacterial and archaeal communities changed in response to shifting methane dynamics, as well as the role of key physicochemical factors in driving changes in the relative abundances of methanotrophic taxa.

Surveying methane flux and soil methane concentrations at different sites across the landfill, I observed a long-term trend of disappearing methane at several former hot spots, concurrently with alterations to the landfill gas capture system that also saw two new hot spots emerge in a different area of the landfill. Active hot spots were lower in total nitrogen, NO3-, NO2-, and NH4+ relative to other sites, indicating that methanotrophy was likely N-limited in this landfill cover. Methane flux was significantly correlated with shifts in community composition, as were soil moisture content, pH, dissolved organic carbon, Ca2+, K+, Na+, and Cl-. Community profiling with 16S rRNA gene amplicon sequencing identified that active hot spots were dominated by methane oxidizing bacteria, especially by members of genera Methylobacter, Crenothrix, and Methylomicrobium, whereas sites without exposure to methane had much more diverse communities with methanotrophs constituting <1% of the community in all but one instance. Former hot spots, which experienced high methane emissions in 2020 that declined by 2022, saw an overall decline in total methanotroph relative abundance, but still maintained a higher relative abundance of methanotrophs than sites that had never been hot spots. Not all methanotrophic ASVs at these sites declined at the same rate, with some ASVs maintaining approximately the same relative abundance as during high methane efflux. Additionally, methane flux at the former hot spots was significantly more negative than at completely inactive sites, indicating oxidation of near-atmospheric concentrations of methane.

These findings indicate the potential for “persistent” methanotrophs which, following methane enrichment, can survive at high proportions of a soil microbial community for long periods of time when methane availability becomes reduced and/or infrequent. Methanotrophs which pursue this ecological strategy could be crucial to the mitigation of methane emissions from older landfills with lower background levels of methane but sporadic, more intense efflux events, and could be employed in strategic microbial amendments to LCS.