While enabling economically viable use of poorly drained soils, artificial subsurface drainage has also been found to be a significant pathway for nutrient transfers from agricultural land to surface waters. Thus, mitigating the impacts of agriculture on surface water quality needs to address nutrient transfers via subsurface drainage. Woodchip bioreactors are a promising mitigation option as demonstrated under arable agriculture in the mid-west of the USA. However, research is needed to ascertain their efficiency in removing nutrients from very flashy drainage flows common in New Zealand (NZ) pastoral agriculture and any possible pollution swapping (e.g. reduction of leaching losses vs. greenhouse gas emissions). Accordingly, a lined 78-m3 woodchip bioreactor was constructed on a dairy farm in the Hauraki Plains (Waikato, NZ) with a drainage area of 0.65 ha. Rainfall, flow, hydrochemistry and dissolved gases in the inflow and outflow were monitored for two drainage seasons (part of 2017, 2018). Based on the nitrate-N fluxes, the estimated nitrate removal efficiency of the bioreactor was 99 and 48% in 2017 and 2018, respectively. The higher removal efficiency in 2017 could be attributed to two reasons. Firstly, the substantially longer hydraulic residence time (HRT) of the water in the bioreactor (mean = 21.1 days vs 4.7 days in 2018) provided more opportunity for microorganisms to reduce the nitrate. A strong positive relationship between HRT and removal efficiency was also observed within the 2018 drainage season. Secondly, denitrification was supported in 2017 by greater electron donor availability. Evidence of this was the higher mass of DOC discharge from the bioreactor (318 mg C L−1 of bioreactor volume vs 165 mg C L−1 in 2018). Removal rates in the bioreactor varied from 0.67–1.60 g N m−3 day−1 and were positively correlated with inflow nitrate loads. Pollution swapping was observed during the start-up phase of the bioreactor in both years (DOC, and DRP only in 2017) and during periods with very long HRTs (hydrogen sulphide (H2S) and methane (CH4) production). Substantially elevated discharges of DOC and DRP, as compared to inlet conditions, occurred during the initial start-up phase of the bioreactor in 2017 (3 to 3.5 pore volumes of the bioreactor), but only slightly elevated DOC and decreased DRP discharges were observed when drainage flow resumed at the start of the 2018 drainage season. Unexpectedly, cumulative DRP removal during the 2018 drainage season amounted to 89% of the DRP inflow into the bioreactor. Long HRTs (>5 days) enabled high nitrate removal efficiency (≥59%) and promoted complete reduction of nitrate to harmless dinitrogen gas but also promoted strongly reduced conditions, resulting in the production of H2S and CH4. On the other hand, short HRTs (<4 days) only allowed for moderate nitrate removal efficiency (≤43%) and constrained complete reduction of nitrate resulting in higher nitrous oxide concentrations in the outflow as compared to the inflow. Thus, nitrate removals above 50% were not able to be achieved without inducing H2S and CH4 generation. However, it may be achievable when the microbial community is provided with an additional source of readily available carbon during the critical periods when hydraulic flow and concomitant N load peaks occur.
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