This is the first study that examines the effect of operating conditions on fouling of Membrane Bio-Reactors (MBRs), which treat municipal wastewater in field conditions, with specific regard to the controlled development of filamentous microorganisms (or filaments). The novelty of the present work is extended to minimize the dissolved oxygen (DO) in recirculated activated sludge for improving the process of denitrification. For this purpose, two pilot-scale MBRs were constructed and operated in parallel: (i) Filament-MBR, where an attempt was made to regulate the growth of filaments by adjustment of DO, the Food-to-Microorganisms (F/M) ratio and temperature, and (ii) Control-MBR, where a gentle stirring tank was employed for the purpose of zeroing the DO in the recycled sludge. Results showed that low temperature (<15 °C) slightly increased the number of filaments in the Filament-MBR which, in turn, decreased the Trans-Membrane Pressure (TMP). As the Soluble Microbial Products (SMP) and the colloids are considered to be the basic foulants of membranes in MBR systems, specific attention was directed to keep their concentration at low values in the mixed liquor. The low F/M ratio in the aeration tanks which preceded the membrane tank was achieved to keep the SMP proteins and carbohydrates at very low values in the mixed liquor, i.e., less than 6 mg/L. Moreover, as a result of the low recirculation rate (2.6∙Qin), good aggregation of the produced excess sludge was achieved, and low concentration of colloids with a size ≤50 nm (nearly the membranes’ pore size used for filtration/separation) was measured, accounted for maximum 15% of the total colloids. Additionally, the increase in filamentous population at the Filament-MBR contributed to the further reduction of colloids in the mixed liquor at 7.9%, contributing beneficially to the reduction of TMP and of membrane fouling. The diminishing of DO in the recirculated sludge improved denitrification, and resulted in lower concentrations of Ν-NO3− and TN in the effluent of the Control-MBR. Furthermore, the recirculation rate of Qr = 2.6∙Qin, in comparison with Qr = 4.3∙Qin, resulted in improved performance regarding the removal of N-NH4+. Finally, high organics removal and ammonium nitrification was observed in the effluent of both pilots, since COD and Ν-ΝH4+ concentrations were generally in the range of 10–25 mg/L and <0.1 mg/L, respectively.
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