Date of Award


Publication Type

Master Thesis

Degree Name



Civil and Environmental Engineering


beach pollution, combined sewer overflow, culture-based method, disinfection, qPCR, UV


Rajesh Seth


Daniel Heath




Microbial contamination of beach water negatively affects public health and the nation’s economy. Combined sewer overflows (CSO) and sanitary sewer overflows (SSO) have repeatedly been identified as major threats to water quality. UV radiation can be used to reduce the risk of bacterial pollution. In order to quantify the efficacy of UV treatment in a timely manner, real-time quantitative polymerase chain reaction (qPCR) methods are analyzed in this thesis. First, a robust qPCR-based method was developed to quantify UV inactivation of E. coli. This method employed long amplicon qPCR with various gene targets in order to do a scan of DNA damage and determine suitable gene targets for reliable quantification. UV-induced DNA damage was found to be widespread through the genome of E. coli. Of all the gene targets, the cell division genes were found to be the most sensitive and therefore, would serve as good targets for detecting UV inactivation through qPCR. Next, the developed method was applied to simulated CSO samples. The qPCR method was found to have a linear correlation with the culture-based technique between the UV dose range of 0 – 20 mJ/cm2. Additionally, the UV disinfection kinetics were analyzed for all the samples. It was found that a single-strain pure E. coli culture was more susceptible to UV damage than E. coli found in wastewater. Overall, UV disinfection is an effective means of reducing microbial contamination, and qPCR is a good surrogate for quantifying UV inactivation as opposed to the time-consuming culturing methods.