How to reduce NO3−-N from partial nitrification/Anammox (PN/Anammox) for low carbon emissions, thus achieve deep nitrogen removal, is a significant issue when applying PN/Anammox to treatment inorganic high-ammonia wastewater. This study designed a prepositioned double short-cut sulfur autotrophic denitrification (DSSADN) system integrated with PN/Anammox, achieving simultaneous sulfur recovery and complete autotrophic denitrification. It also examined the impact of reflux changes on the nitrogen and sulfur transformation characteristics in the coupled system when treating ammonia and sulfur-containing wastewater. Results indicate that the coupling of DSSADN zone (zone C1) enhanced TN removal by PN/Anammox, with the TN removal rate (TNRRT), TN removal efficiency (TNRET), and S2− removal rate reaching 0.54 kg/(m³·d), 95.1%, and 100%, respectively. The NO2−-N accumulation efficiency (NiAEC1) of DSSADN reached 87.1%, with ΔSO42--S consistently less than 11.8 mg/L, and the S0 accumulation efficiency (S0AEC1) reaching 82.4%. A small amount of O2 carried in the reflux can effectively reduce residual S2− in zone C1, preventing its entry into the PN/Anammox zone (zone C2) and mitigating its toxic effects on Anammox. However, O2 also increases the expression of soxB in zone C1, causing more S2− to be oxidized to SO42−, and reducing S0AEC1. When DOC1 was between 0.05 mg/L and 0.34 mg/L, nirK expression was significantly increased, and the abundance of related functional microorganisms changed, led to more NO3−-N being reduced to N2. When DOC1 exceeds 0.34 mg/L, it inhibits the denitrification process, leading to elevated NiAE. Therefore, when regulating reflux in DSSADN + PN/Anammox partitioned integrated coupling system, attention should be given to changes in DOC1, controlling it within 0.05 mg/L.
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