Ciliated protozoa have been widely used as water quality indicators because their main morphological characteristics are relatively simple to identify microscopically. The species and individual numbers in wastewater treatment systems are a consequence of the operational and environmental conditions of the process. The main objective of this research was to relate the effluent quality of a pilot aerated biofilter with the presence and relative abundance of ciliated protozoa when operated under different organic loading rates. The experimental work was done in a pilot aerated biofilter using 12 mm volcanic porous stones as filtering media and it was fed with municipal wastewater adjusting the experiments to 3 organic loading rates (3, 7, and 9 gCOD/m2·d). Temperature in the filter varied from 11 to 14°C during the experimental work. COD and BOD removal rates do not change significantly with the different organic loads. Nitrification improves inversely to the organic load and it does not show dependence on the slight temperature changes observed. Eighteen species were identified as typical residents in wastewater systems. Free swimming species prefer higher organic loads. Crawling and attached species did not show significant changes with the organic load. According to the saprobity index of Pantle and Buck, the system, independently of the organic load, presented typical α-mesosaprobe level.

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