Solving the methane mitigation mystery? Effect of compost application on the atmospheric methane uptake of agricultural soils

This thesis aimed to resolve the “methane mitigation mystery” by systematically investigating how compost application influences the atmospheric methane (CH₄) uptake of agricultural soils, and to elucidate the underlying microbial and physicochemical mechanisms. Given the urgent need to reduce methane emissions, and the limited capacity of intensively managed soils to function as methane sinks, this work explores compost as a potential climate-smart strategy to enhance methane mitigation by agricultural soils. A combination of field experiments and controlled laboratory studies demonstrated that agricultural soils consistently act as net sinks for atmospheric methane, but their uptake capacity is strongly modulated by management practices. While compost application did not yield consistent effects on methane fluxes under field conditions, laboratory incubations revealed a clear and significant enhancement of the agricultural soil’s methane oxidation potential following organic amendment. Soil aggregate stability emerged as a key regulator of greenhouse gas fluxes, with higher stability, which was improved by organic inputs and reduced tillage, associated with increased methane uptake but also elevated CO₂ and N₂O emissions, highlighting important trade-offs. At the microbial level, compost application unequivocally reshaped methane-cycling microbial communities, increasing total abundance while reducing diversity. Compost acted both as a vector for microbial inoculation and as a stimulant of indigenous populations. Although methanotrophs such as Methylocaldum sp. became dominant in organic-amended soils, enhanced methane uptake was primarily attributed to conventional soil methanotrophs, particularly type II methanotrophs Methylocystis sp. and Methylosinus sp. Also, different types of compost were analyzed on their intrinsic methane mitigation potential, with green compost performing best, and their indigenous methane-cycling microbial communities, which were dominated by Methylocaldum szegediense and Methanosarcina sp. Mechanistic investigations rejected several hypothesized drivers, including stimulation of in situ methanogenesis and enhanced hydrogen-mediated co-oxidation of atmospheric methane. Instead, the results support a model in which prior exposure to elevated methane concentrations enables methanotrophs to oxidize methane at atmospheric levels, consistent with a “flush-feeding” ecological strategy. Four distinct methanotrophic groups, Methylocaldum sp., Methylosinus sporium, Methylocystis sp./Methylosinus trichosporium, and members of the USCalpha cluster, were identified as methanotrophically active at (sub-)atmospheric methane concentrations. Overall, this thesis provides a mechanistic framework explaining how compost application can enhance atmospheric methane uptake in agricultural soils through interacting effects on soil structure and microbial ecology. The findings emphasize the potential of compost as a climate-smart agricultural strategy, while also highlighting the need to balance methane mitigation against other greenhouse gas emissions. They also demonstrate that compost application can enhance soil methane uptake as a climate-smart practice for farmers, while calling on policymakers and the composting industry to recognize and integrate soil methane mitigation into climate-smart agriculture through targeted policies.