Integration of natural treatment systems (NTS) (WSP, wetlands etc.) with each other as well as with advanced unit processes (biofiltration) offers a second lease of life to NTS. Long-term full and pilot scale experience in South Africa and Thailand have shown that contrary to a common view, a low tech N-removal from municipal and light industrial wastewater is a reality for a developing community The high treatment efficiency is ascribed to interplay of N-related processes complementing each other. The present FISH-based (Fluorescence In Situ Hybridization) approach to microbial community structure is a pioneering effort in the field of NTS. It establishes interrelationships between major N-removing groups (aerobic and anaerobic ammonia oxidizers (ANAMMOX), denitrifiers) within integrated systems and links them to the high treatment performance. Seasonally fluctuating presence of the ANAMMOX bacteria (0–2.5% of total bacterial numbers) in the NTS (free surface flow wetland) is reported for the first time. Their numbers correlate with metabolically dependent ammonia-oxidizers (2.0–3.0%) but not with stable overall Planctomycetes population (4.5–5.1%). As a result of the flexible microbial structure the robust low cost removal down to TN <10 mg/L is routinely feasible at the loading rates ranging from 0.005 to 0.08 TN kg/m3/day.

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