Stijn van den Bergh

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.

Agriculture is responsible for 30–50% of the yearly CO2, CH4, and N2O emissions. Soils have an important role in the production and consumption of these greenhouse gases (GHGs), with soil aggregates and the inhabiting microbes proposed to function as biogeochemical reactors, processing these gases. Here we studied, for the first time, the relationship between GHG fluxes and aggregate stability as determined via laser diffraction analysis (LDA) of agricultural soils, as well as the effect of sustainable agricultural management strategies thereon. Using the static chamber method, all soils were found to be sinks for CH4 and sources for CO2 and N2O. The application of organic amendments did not have a conclusive effect on soil GHG fluxes, but tilled soils emitted more CO2. LDA was a useful and improved method for assessing soil aggregate stability, as it allows for the determination of multiple classes of aggregates and their structural composition, thereby overcoming limitations of traditional wet sieving. Organic matter content was the main steering factor of aggregate stability. The presence of persistent stable aggregates and the disintegration coefficient of stable aggregates were improved in organic-amended and no-tilled soils. Predictive modelling showed that, especially in these soils, aggregate stability was a governing factor of GHG fluxes. Higher soil CH4 uptake rates were associated with higher aggregate stability, while CO2 and N2O emissions increased with higher aggregate stability. Altogether, it was shown that sustainable agricultural management strategies can be used to steer the soil's aggregate stability and, both consequently and outright, the soil GHG fluxes, thereby creating a potential to contribute to the mitigation of agricultural GHG emissions.

Conventional agricultural activity reduces the uptake of the potent greenhouse gas methane by agricultural soils. However, the recently observed improved methane uptake capacity of agricultural soils after compost application is promising but needs mechanistic understanding. In this study, the methane uptake potential and microbiomes involved in methane cycling were assessed in green compost and household-compost with and without pre-digestion. In bottle incubations of different composts with both high and near-atmospheric methane concentrations (∼10.000 & ∼10 ppmv, respectively), green compost showed the highest potential methane uptake rates (up to 305.19 ± 94.43 nmol h−1 g dw compost−1 and 25.19 ± 6.75 pmol h−1 g dw compost−1, respectively). 16S, pmoA and mcrA amplicon sequencing revealed that its methanotrophic and methanogenic communities were dominated by type Ib methanotrophs, and more specifically by Methylocaldum szegediense and other Methylocaldum species, and Methanosarcina species, respectively. Ordination analyses showed that the abundance of type Ib methanotrophic bacteria was the main steering factor of the intrinsic methane uptake rates of composts, whilst the ammonium content was the main limiting factor, being most apparent in household composts. These results emphasize the potential of compost to contribute to methane mitigation, providing added value to compost as a product for industrial, commercial, governmental and public interests relevant to waste management. Compost could serve as a vector for the introduction of active methanotrophic bacteria in agricultural soils, potentially improving the methane uptake potential of agricultural soils and contributing to global methane mitigation, which should be the focus of future research.

Process technologies, such as composting, anaerobic digestion, or lactic acid fermentation, greatly influence the resulting organic amendments (OAs) characteristics even when the same raw material is used. However, it is still unclear how these process technologies indirectly modify the effect of OAs on soil microbial activity and soil aggregation. To determine the effect of OA produced using pre-treatment technologies on the soil microbial activity and soil aggregation, we ran a soil column experiment in which we applied compost, digestate and lactic acid fermentation product made of the same model bio-waste. The results indicated that OAs produced under anaerobic conditions (fermented product and digestate) increased microbial activity, biomass, and soil micro- and macro-aggregation compared to compost and control treatments. Soil microbial activity strongly correlated to C, Ca, Mg, extracellular polymeric substances (EPS), fungal biomass, and macroaggregate formation (, ). Simultaneously, soil macroaggregate formation strongly correlated to water-extractable C, EPS, cation exchange capacity, K, Mg, Na, and bacterial biomass (, ). This study demonstrated that the effect of an organic substrate on soil properties can be modified towards desired effects using different pre-treatment technologies, suggesting the possibility of “engineer” OAs.