In this study, simultaneous nitrification and autotrophic denitrification (SNAD) with either elemental sulfur or pyrite were investigated in fluidized bed reactors in mesophilic conditions. The reactor performance was evaluated at different ammonium (12–40 mg/L of NH4+-N), nitrate (35–45 mg/L of NO3−-N), and dissolved oxygen (DO) (0.1–1.5 mg/L) concentrations, with a hydraulic retention time of 12 h. The pyrite reactor supported the SNAD process with a maximum nitrogen removal efficiency of 139.5 mg/(L⸱d) when the DO concentration was in the range of 0.8–1.5 mg/L. This range, however, limited the denitrification efficiency of the reactor, which decreased from 90.0% ± 5.3% in phases II–V to 67.9% ± 7.2% in phases VI and VII. Sulfate precipitated as iron sulfate (FeSO4/Fe2(SO4)3) and sodium sulfate (Na2SO4) minerals during the experiment. The sulfur reactor did not respond well to nitrification with a low and unstable ammonium removal efficiency, while denitrification occurred with a nitrate removal efficiency of 97.8%. In the pyrite system, the nitrifying bacterium Nitrosomonas sp. was present, and its relative abundance increased from 0.1% to 1.1%, while the autotrophic denitrifying genera Terrimonas, Ferruginibacter, and Denitratimonas dominated the community. Thiobacillus, Sulfurovum, and Trichlorobacter were the most abundant genera in the sulfur reactor during the entire experiment.
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