Biological nitrogen removal in a membrane separation bioreactor developed for on-site domestic wastewater treatment was investigated. The bioreactor employed hollow fiber membrane modules for solid–liquid separation so that the biomass could be completely retained within the system. Intermittent aeration was supplied with 90 minutes on and off cycle to achieve nitrification and denitrification reaction for nitrogen removal. High COD and nitrogen removal of more than 90% were achieved under a moderate temperature of 25 °C. As the temperature was stepwise decreased from 25 to 5 °C, COD removal in the system could be constantly maintained while nitrogen removal was deteriorated. Nevertheless, increasing aeration supply could enhance nitrification at low temperature with benefit from complete retention of nitrifying bacteria within the system by membrane separation. At low operating temperature range of 5 °C, nitrogen removal could be recovered to more than 85%. A mathematical model considering diffusion resistance of limiting substrate into the bio-particle is applied to describe nitrogen removal in a membrane separation bioreactor. The simulation suggested that limitation of the oxygen supply was the major cause of inhibition of nitrification during temperature decrease. Nevertheless, increasing aeration could promote oxygen diffusion into the bio-particle. Sufficient oxygen was supplied to the nitrifying bacteria and the nitrification could proceed. In the membrane separation bioreactor, biomass concentration under low temperature operation was allowed to increase by 2–3 times of that of moderate temperature to compensate for the loss of bacterial activities so that the temperature effect was masked.

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