Bioremediation of Nitrate in Agricultural Drainage Ditches: Impacts of Low-Grade Weirs on Microbiomes and Nitrogen Cycle Gene Abundance

Abstract

Artificial drainage is essential for the success of modern agriculture, but it can also accelerate the movement of nutrients, especially nitrate, from soil to surrounding and downstream water bodies. Reduction of nitrate from agricultural drainage through the use of controlled drainage systems, such as ditches installed with low-grade weirs, has been shown to help reduce nutrient loading into watersheds. However, the effect of weir-installed ditch varies a lot, likely due to microbial structures and functions in the ditch. In this study, we analyzed the temporal and spatial dynamics of microbiomes in the weir-installed and uninstalled (control) ditches over two years by using the 16S rRNA gene amplicon sequencing and the high-throughput quantitative PCR targeting various N cycle-associated genes [the Nitrogen Cycle Evaluation (NiCE) chip]. The installation of the low-grade weir had a significant impact on the microbiome structure and the distribution of denitrifiers. Specifically, microbiome structures were different between the ditch inlets to the outlets. Denitrification functional genes were also more abundant in the inlet than in the other locations and in the channel installed with a low-grade weir. The ditch microbiomes sampled during high-flow seasons (i.e., spring and fall) exhibited greater similarity to each other than microbiomes sampled during low-flow seasons (i.e., summer). Taken together, this study indicates that the low-grade weirs have the potential to foster a more favorable environment for denitrifiers, resulting in an increase in the abundance of denitrification functional genes. These findings could offer valuable insights into system management and optimization strategies.