A kind of gel beads loaded with iron–carbon powder (Fe–C), Zoogloea sp. L2, and riboflavin (VB2) were prepared through cross–linking of sodium alginate (SA) to establish an immobilized bioreactor. The optimal ratio of SA beads was adjusted by orthogonal experiment. The change of oxidation–reduction potential (ORP) and the concentration of Fe2+ and Fe3+ showed that the addition of VB2 as a redox mediator can promote denitrification. Under the optimal conditions (carbon to nitrogen (C/N) ratio = 2.0, pH = 7.0, and hydraulic retention time (HRT) = 8 h), the nitrate removal efficiency (NRE) of bioreactor reached 98.48% (1.99 mg L–1h−1). Furthermore, Fourier transform infrared spectrometer (FTIR), Fluorescence excitation–emission matrix (EEM), X–ray diffraction (XRD), and gas chromatography (GC) analysis revealed that the immobilization and denitrification of the immobilized bioreactor were excellent. High throughput sequencing also showed that Zoogloea played a vital role in nitrate removal.
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