Spatial and temporal variations in the microbiomes of agricultural drainage water treatment systems

Abstract

Artificial drainage is crucial for the success of modern agriculture. However, the extensive network of subsurface drainage installed under millions of hectares of agricultural soils in the upper Midwest of the U.S. and northern Europe transports a large amount of nutrients, particularly nitrate, to nearby water bodies. This contributes to the degradation of water quality across various freshwater and marine ecosystems. Bioremediation of nitrate through the use of denitrifying bioreactors and controlled drainage systems has been shown to help reduce nutrient loading into watersheds. Despite these efforts, the temporal and spatial dynamics of microbiomes in these systems remain poorly understood.In this study, we analyzed microbiomes from drainage ditches and woodchip bioreactors using bacterial 16S rRNA gene amplicon sequencing, fungal ITS2 gene amplicon sequencing, high-throughput quantitative PCR targeting various nitrogen (N) cycle-associated genes [the Nitrogen Cycle Evaluation (NiCE) chip], and microscopic visualization. We also examined the correlation between microbiome structure patterns, the abundance of nitrogen cycle-associated genes, and environmental parameters. The results revealed that the distribution of denitrifiers was heterogeneous within these systems and that microbiome composition significantly changed from inlets to outlets. One of the major challenges for treatment systems processing agricultural drainage is ensuring a sufficient carbon source for heterotrophic denitrification. Analysis of the fungal microbiome in woodchip bioreactors, based on the ITS2 gene amplicon sequencing, indicates that fungi continue to play a crucial role in breaking down complex lignocellulosic biomass into simpler carbon substrates, even in the oxygen-depleted, saturated environment. Enhancing conditions favorable to wood-degrading fungi could serve as an alternative to the addition of exogenous carbon, potentially improving denitrification efficiency, especially in low-temperature environments. Furthermore, cold-adapted N2-producing denitrifying bacteria were isolated from drainage ditches for future bioaugmentation efforts aimed at establishing a stable and efficient nitrate removing system with minimum emission of nitrous oxide (N2O) in cold climate regions such as Minnesota. This research offers valuable insights into system management and optimization strategies that could reduce maintenance costs and ensure long-term optimal performance.