Microbial controls on net production of nitrous oxide in a denitrifying woodchip bioreactor

Denitrifying woodchip bioreactors are potential low‐cost technologies for the removal of nitrate (NO3−) in water through denitrification. However, if environmental conditions do not support microbial communities performing complete denitrification, other N transformation processes will occur, resulting in the export of nitrite (NO2−), nitrous oxide (N2O), or ammonium (NH4+). To identify the factors controlling the relative accumulation of NO2−, N2O, and/or NH4+ in denitrifying woodchip bioreactors, porewater samples were collected over two operational years from a denitrifying woodchip bioreactor designed for removing NO3− from mine water. Woodchip samples were collected at the end of the operational period. Changes in the abundances of functional genes involved in denitrification, N2O reduction, and dissimilatory NO3− reduction to NH4+ were correlated with porewater chemistry and temperature. Temporal changes in the abundance of the denitrification gene nirS were significantly correlated with increases in porewater N2O concentrations and indicated the preferential selection of incomplete denitrifying pathways ending with N2O. Temperature and the total organic carbon/NO3− ratio were strongly correlated with NH4+ concentrations and inversely correlated with the ratio between denitrification genes and the genes indicative of ammonification (Σnir/nrfA), suggesting an environmental control on NO3− transformations. Overall, our results for a denitrifying woodchip bioreactor operated at hydraulic residence times of 1.0–2.6 d demonstrate the temporal development in the microbial community and indicate an increased potential for N2O emissions with time from the denitrifying woodchip bioreactor.