The long-term effects of different combined organic–chemical fertilizer regimes on denitrifying communities remain unclear. In this study, we performed quantitative PCR and sequencing analyses to examine the abundance, diversity, and structure of two nir (nirK and nirS) denitrifying communities in response to five fertilization treatments, namely, no nitrogen (N) fertilizer (NF), chemical fertilizer (CF), pig manure + chemical fertilizer (PM), biogas slurry + chemical fertilizer (BF), and milk vetch + chemical fertilizer (GM). All N fertilizer...