For full understanding of the microbial community in the wastewater treatment bioreactors, one of the feasible and effective ways is to investigate the massive genetic information contained in the activated sludge. In this study, high-throughput pyrosequencing was applied to analyze the 16S rRNA gene of bacteria in a laboratory-scale nitrification reactor and a full-scale wastewater treatment plant. In total, 27,458 and 26,906 effective sequence reads of the 16S rRNA gene were obtained from the Reactor and the wastewater treatment plant activated sludge samples respectively. The taxonomic complexities in the two samples were compared at phylum and genus levels. According to the pyrosequencing results, even for a laboratory-scale reactor as simple as that in this study, a small size clone library is far from enough to reflect the whole profile of the bacterial community. In addition, it was found that the commonly used informatics tool "RDP classifier" may drastically assign Nitrosomonas sequences into a wrong taxonomic unit resulting in underestimation of ammonia-oxidizing bacteria in the bioreactors. In this paper the reasons for this mistakenly assignment were analyzed and correction methods were proposed.
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