Nitrate removal microbiology in woodchip bioreactors: A case-study with full-scale bioreactors treating aquaculture effluents.

Woodchip bioreactors are viable low-cost nitrate (NO) removal applications for treating agricultural and aquaculture discharges. The active microbial biofilms growing on woodchips are conducting nitrogen (N) removal, reducing NO while oxidizing the carbon (C) from woodchips. However, bioreactor age, and changes in the operating conditions or in the microbial community might affect the NO removal as well as potentially promote nitrous oxide (NO) production through either incomplete denitrification or dissimilatory NO reduction to ammonium (DNRA). Here, we combined stable isotope approach, amplicon sequencing, and captured metagenomics for studying the potential NO removal rates, and the abundance and community composition of microbes involved in N transformation processes in the three different full-scale woodchip bioreactors treating recirculating aquaculture system (RAS) effluents. We confirmed denitrification producing di‑nitrogen gas (N) to be the primary NO removal pathway, but found that 6% of NO could be released as NO under high NO concentrations and low amounts of bioavailable C, whereas DNRA rates tend to increase with the C amount. The abundance of denitrifiers was equally high between the studied bioreactors, yet the potential NO removal rates were linked to the denitrifying community diversity. The same core proteobacterial groups were driving the denitrification, while Bacteroidetes dominated the DNRA carrying microbes in all the three bioreactors studied. Altogether, our results suggest that woodchip bioreactors have a high genetic potential for NO removal through a highly abundant and diverse denitrifying community, but that the rates and dynamics between the NO removal pathways depend on the other factors (e.g., bioreactor design, operating conditions, and the amount of bioavailable C in relation to the incoming NO concentrations).