Waterlogging effects on N₂O and N₂ emissions from a Stagnosol cultivated with Silphium perfoliatum and silage maize

European policy recommends that biomass production occur on marginal land, such as poorly draining Stagnosols. Compared to annual cropping, perennial crops may better mitigate N2O emissions at such sites, through more complete denitrification. To test that hypothesis, we compared N2 and N2O fluxes from the soils of a perennial crop (cup plant, Silphium perfoliatum L.) and an annual crop (silage maize, Zea mays L.). Intact soil columns (35 cm height, 14.4 cm diameter) were incubated for 37 days. The soils were fertilized with 60 or 120 kg N ha-1 and exposed to successive phases of waterlogging: free drainage, waterlogging of 1/3-, and waterlogging of 2/3- of the column. Source-specific N2O and N2 fluxes were measured using the 15 N gas flux method. Denitrification was higher in cup plant than maize soil and total N losses from denitrification were dominated by emissions from the third phase. Cup plant soil emitted 33.6?±?78.1 mg N m-2 and 95.8?±?64.4 mg N m-2 more N2O than maize soil in the low and high N treatments, respectively. The product ratio of denitrification (N2Oi?=?N2O/(N2?+?N2O)) increased with waterlogging in maize soil, while remaining stable in cup plant soil. Emissions from the top 10 cm dominated the N2Oi rather than N2 fluxes from the saturated soil. This study did not show N2O mitigation in cup plant soil, instead highlighting the complexity of plant-soil effects on denitrification. We clearly showed that the application of a general N2Oi for agricultural soils across annual and perennial cropping is not recommended.