Biological aerated filter (BAF) systems with internal reflux-coupled intermittent aeration enhance the removal of nitrogen pollutants from low-C/N ratio domestic sewage. Two experimental systems with the same specifications, a BAF system with internal reflux-coupled intermittent aeration (system A) and a traditional BAF system (system B) was constructed to explore the efficiency of nitrogen removal. Overall, the nitrification in system B was higher than that in system A due to the influence of aeration model. Conversely, the system A can use the alternating anoxic (DO<0.5 mg·L−1) and aerobic (DO around 1 mg·L−1) environment to obtain better Total Nitrogen (TN) removal rate of 21.56 mg·(kg·h)−1 in the bottom of 30–70 cm zone of the reactor by combining reflux nitrate with influent COD. This section had a low specific oxygen uptake rate but high triphenyl tetrazolium chloride-dehydrogenase activity, indicating that the system enhanced nitrogen removal by denitrification in this section. The 16 S rDNA high-throughput sequencing analysis showed that the diversity index of system A was higher than that of system B. The abundance of microorganisms involved in denitrification was higher in the 30–50 cm zone of system A, mainly in the phylum (10.63%) and the phylum Bacillus (32.05%), indicating that system A was used for denitrification through nitrate reflux and intermittent aeration.
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