How shallow water table conditions affect N2O emissions and associated microbial abundances under different nitrogen fertilisations

•N2O emissions increased after fertilisation and remained elevated for 2–3 weeks.•Daily emissions were affected by water-filled pore space.•Size of nitrifying and denitrifying communities increased under high N fertilisation.•Shallow groundwater conditions appeared to reduce N2O emissions. Globally, agriculture is the largest source of nitrous oxide (N2O), a potent greenhouse gas (GHG). A recognised tool to prevent its loss from agricultural soils is the presence of a shallow water table. A four-year lysimeter experiment (2011–2014) was conducted in northeast Italy to investigate how water table levels affect N2O emissions after different N fertilisation techniques. Soil surface flux and groundwater-dissolved N2O were studied under free drainage and at two shallow water table levels (60 cm and 120 cm) and at two levels of N input (250 and 368 kg N ha−1 y−1), using dry manure in 2011 and 2012 and fresh manure in 2013 and 2014. DNA was extracted from soils and quantitative PCR (qPCR) was used to assess the size of nitrifying, denitrifying and N2-fixing bacterial communities. at three soil depths. The day after pre-seeding fertiliser incorporation, N2O emission started to be detected and continued for two-three weeks; brief measurable emissions also followed top–dressing fertilisation events. Cumulative N2O emission measured between 0.97 and 2.33 kg N2O-N ha−1 y−1, corresponding to emission factors from 0.4% to 1.1%. Manure fertilisation significantly affected the N dose only when applied as fresh manure. Water-filled pore space (WFPS) affected daily N2O emissions with a significant interaction with fertilisation level. The two N input levels showed differences only when WFPS was >40%, which revealed N availability as key to increased N2O emissions at high water content, supposedly by fostering anaerobic denitrification. No significant relationships were observed between peak N2O emissions and the values of the temperature or irrigation variables recorded during the experimental observation period. Groundwater dissolved N2O-N concentrations measured about 1.7 μg L−1 with some peak variability from nitrate leaching. Quantitative PCR assays demonstrated that shifts in microbial population that can be involved in oxidation processes and heterotrophic denitrification occurred in the soil, even though the contributions of the different N pathways on N2O emissions were indistinguishable. Indeed, both nitrifying and denitrifying genes were simultaneously promoted by