Quantitative real-time PCR-based Microbial Source Tracking in the Miho River, Cheongju, South Korea

Abstract

Fecal contamination of river systems has become a global concern due to its adverse impact on human health and environment. Consumption of water contaminated with fecal components can lead to diseases such as cholera, diarrhoea, and hepatitis. Fecal pollution can be an outcome of a wide range of sources such as effluents from waste-water treatment plants (WWTP), sewer tank leaks, run-offs from agricultural lands or livestock farms. Therefore, it is essential to identify and track the sources responsible for fecal dissemination. Microbial source tracking methods have evolved immensely in the past few decades. These involve discrimination of the fecal sources based on host-specific genetic markers. In this study, we monitored Miho River which has been reported to be contaminated with fecal matter. Quantitative real-time PCR based microbial source tracking was applied to identify the sources with host-specific microbial markers. Furthermore, Illumina MiSeq sequencing was performed to analyse the taxonomical composition and distribution of microbial communities prior and after rainfall, and their association with fecal pollutants. Effect of rainfall was observed on the river samples along with the physicochemical parameters. Our results identified pig sources to be the highest contributor in fecal pollution, followed by cow. Humans showed relatively low copies/16SrRNA gene copies. Elevated levels of E.coli were observed in post-rainfall samples for all sites, indicating rainfall can facilitate dissemination of coliforms. Relative and differential abundance analysis of microbial communities was performed along with qPCR-based methods, to find and study associations between genera and source-specific pollutants. These insights can be used to develop new biological markers for source tracking.