Wastewater irrigation mitigates the problem of water shortage but leads to the potential accumulation of pollutants and causes corresponding changes in denitrifying communities and denitrification, hence the potential ecological risk of long-term wastewater irrigation should not be overlooked. We investigated the relative contributions of different environmental factors to the abundance and diversity of denitrifying communities harboring nirK, nirS, and nosZ genes and the relative importance of these biotic and abiotic variables in potential denitrification activity (PDA) in soils with wastewater irrigation for around 25 years at a large watershed scale. Results showed that soil physicochemical properties, pollutants, including heavy metals and PAHs, and vegetation are the major factor groups influencing the abundance and structure of the three denitrifying communities and PDA. NirK-, nirS-, or nosZ-harboring denitrifiers responded in different manners to environmental changes, and were mainly influenced by substrate concentration, carbon source, or pollutants, respectively. The structure of the three denitrifying communities was more relevant to the environmental changes than their abundance. Conversely, the abundance, rather than diversity, was correlated with PDA. Pollutants and vegetation could affect PDA by both direct and indirect paths through soil physicochemical properties including pH, carbon and nitrogen sources, or through the abundance of denitrifying functional genes. The abundance of denitrifying functional genes is a valuable index that integrates potential activity and various environmental factors, and is therefore a good predictor of denitrification in the presence of environmental changes.
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