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Improved methane mitigation potential and modulated methane cycling microbial communities in arable soil by compost addition

Bergh, Stijn van den12; Chardon, Iris1; Meima-Franke, Marion1; Pérez, Germán1; Rocha, Gabriel1; Brenzinger, Kristof1; Korthals, Gerard2; Mayer, Jochen3; Cougnon, Mathias4; Reheul, Dirk5; Boer, Wietse de12; Bodelier, Paul1

Published Oct 31, 2025 on Dryad. https://doi.org/10.5061/dryad.dz08kps8h

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Abstract

The global atmospheric concentration of the potent greenhouse gas methane (CH4) is rising rapidly, and agriculture is responsible for 30-50% of the yearly CH4 emissions. To limit its global warming effects, strong and sustained reductions are needed. Sustainable agricultural management strategies, as the use of organic amendments like compost, have previously proven to have a potent CH4 mitigation effect in laboratory experiments. Here we investigated, using an extensive field study, the effect of organic amendments on the CH4 mitigation potential of agricultural soils and the CH4 cycling microbial communities. Organic-amended soils had higher potential CH4 uptake rates and an improved potential to oxidize CH4 to sub-atmospheric concentrations. Also, we showed for the first time that the methanotrophic and methanogenic microbial communities of arable soils were unequivocally altered after organic amendment application by increasing in size while getting less diverse. Compost-amended soils became dominated by the compost-originating methanotroph Methylocaldum szegediense and methanogen Methanosarcina horonobensis, replacing the indigenous methane cycling community members. However, multivariate analyses did not point out type Ib methanotrophs like M. szegediense as significant driving factors for the observed improved soil CH4 uptake potential. Conventional type IIa methanotrophs like Methylocystis sp. also had higher differential abundances in organic-amended soils and are speculated to be contributing to the improved CH4 uptake potential. Altogether, the results showed that compost serves as a vector for the introduction of CH4 cycling microbes and improves the soil’s CH4 uptake potential, which emphasizes the potential of organic fertilization with compost to contribute to CH4 mitigation in agricultural soils.