Profiling Fecal Pollution in Rivers in Hanoi, Vietnam, using Host-specific Bacteroidales and crAssphage Markers

Abstract

Microbial source tracking (MST) based on host-specific fecal microorganisms is a powerful tool for identifying sources of fecal contamination. In Vietnam, fecal contamination caused by untreated domestic wastewater as well as wastewater from the livestock sector is a major issue for the water environment. In this study, samples from different rivers in Hanoi, Vietnam, were analyzed using quantitative PCR analysis for Bacteroidales markers specific to human (HF183), pig (Pig2Bac), and ruminant (BacR) feces and a bacteriophage marker specific to human feces (crAssphage). Water samples were collected from Nhue River, To Lich River, Kim Nguu River, Day River, Duong River, and Red River during August, September, and December 2019. Groundwater samples from areas near the Nhue River and Day River were also collected. Regarding the To Lich River and Kim Nguu River, only human-specific markers (HF183 and crAssphage) were detected, indicating that the primary source of fecal contamination of these rivers was human feces. In the Nhue River, pig- and ruminant-specific markers were detected, in addition to human-specific markers. Pollution from multiple fecal sources was therefore suspected in the Nhue River. In the Day River, the concentration of pig-and ruminant-specific markers was generally higher than that of human-specific markers. Since the concentration of HF183 and crAssphage in the Day River was lower than those in the other rivers, the contribution of animal feces could be relatively higher in the Day River. The concentration of fecal markers in the Duong River and Red River was much lower than that in the other rivers. MST was successfully applied to characterize sources of fecal pollution in different rivers in Hanoi. The profiling of fecal sources is informative when considering water quality remediation in rivers.