Waterlogging effects on N 2 O and N 2 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 N 2 O emissions at such sites, through more complete denitrification. To test that hypothesis, we compared N 2 and N 2 O 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 N 2 O and N 2 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 N 2 O than maize soil in the low and high N treatments, respectively. The product ratio of denitrification (N 2 Oi = N 2 O/(N 2 + N 2 O)) increased with waterlogging in maize soil, while remaining stable in cup plant soil. Emissions from the top 10 cm dominated the N 2 Oi rather than N 2 fluxes from the saturated soil. This study did not show N 2 O mitigation in cup plant soil, instead highlighting the complexity of plant-soil effects on denitrification. We clearly showed that the application of a general N 2 Oi for agricultural soils across annual and perennial cropping is not recommended.