The overall goal of this study was to characterize and quantify ammonia-oxidizing bacteria (AOB) in four different full-scale sequence batch reactor (SBR) wastewater treatment plants. Also, this study focused on assessing the occurrence of the alternative ammonia-oxidizing microbes such as anammox (anaerobic ammonia oxidation) bacteria (AMX) and ammonia-oxidizing archaea (AOA) in these systems. Based on total AOB numbers and the estimated cell density in the mixed liquor samples, AOB constituted 0.3 - 1.8% of the total bacterial population in the four WWTPs. Based on clone library, Nitrosomonas ureae-like AOB were dominant in plant A and B, while plant C and D had Nitrosomonas nitrosa-like AOB as major AOB group. The four different AMX primer sets targeting AMX 16S rRNA gene produced PCR amplicons distantly related to Chlamydia and Planctomycetales group bacteria. However, it was not clear these groups of bacteria perform anammox reaction in the SBR plants. Also, molecular evidence of AOA was found in one of the SBR plants, with a sequence located in the deep branch of the sediment creanarchaeota group.
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