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 (NO 3 − ) 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 (NO 2 − ), nitrous oxide (N 2 O), or ammonium (NH 4 + ). To identify the factors controlling the relative accumulation of NO 2 − , N 2 O, and/or NH 4 + in denitrifying woodchip bioreactors, porewater samples were collected over two operational years from a denitrifying woodchip bioreactor designed for removing NO 3 − from mine water. Woodchip samples were collected at the end of the operational period. Changes in the abundances of functional genes involved in denitrification, N 2 O reduction, and dissimilatory NO 3 − reduction to NH 4 + were correlated with porewater chemistry and temperature. Temporal changes in the abundance of the denitrification gene nirS were significantly correlated with increases in porewater N 2 O concentrations and indicated the preferential selection of incomplete denitrifying pathways ending with N 2 O. Temperature and the total organic carbon/NO 3 − ratio were strongly correlated with NH 4 + concentrations and inversely correlated with the ratio between denitrification genes and the genes indicative of ammonification (Σ nir / nrfA ), suggesting an environmental control on NO 3 − 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 N 2 O emissions with time from the denitrifying woodchip bioreactor.