Short‐Term Effects of Partial Substitution of Mineral Fertilisers With Compost and Biogas Slurry on Carbon Dioxide, Nitrous Oxide, and Nitrogen Emissions

ABSTRACT Compost and biogas slurry are increasingly used as organic fertilisers, but existing studies on their application on soil N 2 O emissions have been contradictory, studies on soil N 2 emissions are lacking, and the mechanism of microbial control of gaseous N loss is unclear. This study investigated the effects of partially replacing mineral fertilisers with compost (30%) and biogas slurry (50%) on CO 2 , N 2 O, and N 2 emissions, alongside soil nitrogen‐cycling microbial communities in no nitrogen application (LN) and 600 kg N ha −1 year −1 fertilisation (HN) soils from China's North China Plain. Through controlled incubation experiments, gas flux measurements, and metagenomic analysis, we found that in the first 5 days of fertilised treatments, N 2 O emissions accounted for 85.26% and 94.18%, while N 2 emissions accounted for 71.25% and 68.78% of total emissions under LN and HN, respectively. Organic substitutions reduced soil mineral nitrogen (‐N) content by limiting exogenous nitrogen input and suppressing native organic matter mineralisation, thereby decreasing pulse emissions of N 2 O, N 2 , and CO 2 . While both substitutions promoted complete denitrification, biogas slurry at 50% substitution significantly enhanced nitrifying microbe abundance ( Nitrosospira , Nitrospira ) and nitrification‐related functional genes ( AmoC and Hao ), increasing nitrification‐driven N 2 O emissions compared to compost. For sustainable management, high‐fertility soils benefit from partial substitution of mineral fertiliser with compost, whereas low‐fertility soils require substitution ratios of biogas slurry for mineral fertiliser to boost microbial activity. These findings provide critical insights for optimising organic substitution strategies to balance productivity and environmental sustainability in intensive agricultural systems.