Changes in ammonia-oxidizing bacterial (AOB) population dynamics were examined in a new sponge-based trickling filter (TF) post-upflow anaerobic sludge blanket (UASB) reactor by denaturating gradient gel electrophoresis (DGGE), and these changes were linked to relevant components influencing nitrification (chemical oxygen demand (COD), nitrogen (N)). The sponge-based packing media caused strong concentration gradients along the TF, providing an ecological selection of AOB within the system. The organic loading rate (OLR) affected the population dynamics, and under higher OLR or low ammonium-nitrogen (NH4+-N) concentrations some AOB bands disappeared, but maintaining the overall community function for NH4+-N removal. The dominant bands present in the upper portions of the TF were closely related to Nitrosomonas europaea and distantly affiliated to Nitrosomonas eutropha, and thus were adapted to higher NH4+-N and organic matter concentrations. In the lower portions of the TF, the dominant bands were related to Nitrosomonas oligotropha, commonly found in environments with low levels of NH4+-N. From a technology point of view, changes in AOB structure at OLR around 0.40–0.60 kgCOD m−3 d−1 did not affect TF performance for NH4+-N removal, but AOB diversity may have been correlated with the noticeable stability of the sponge-based TF for NH4+-N removal at low OLR. This study is relevant because molecular biology was used to observe important features of a bioreactor, considering realistic operational conditions applied to UASB/sponge-based TF systems.

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