The main objective of this study was to adapt molecular techniques for quantifying ammonia-oxidizing bacteria (AOB) in chloraminated systems, focusing on fluorescent in situ hybridization (FISH) and flow cytometry (FCM) and real-time polymerase chain reaction (PCR). The study also wanted to monitor AOB numbers. The real-time PCR assay developed in this study provides another tool for chloraminating utilities to monitor their systems for nitrification, targeted directly at the bacterial catalyst of this problem. The protocol represents a significant improvement over the traditional MPN method in terms of AOB quantitation and timeliness of results. Flushing and breakpoint chlorination were found to be ineffective in this study, but booster chloramination of a reservoir showed promising results at controlling AOB growth.
