Animal profiling of a surface water with amplicon sequencing mitochondrial DNA

Fecal contamination of surface water poses a potential risk to public and environmental health but can also impact the local economy and recreational activities. Determining its source could facilitate mitigation of contamination at the source. Fecal contamination can originate from several animals, particularly in areas where urban and agricultural activities overlap. We developed a molecular approach to detect the presence of mammals, fish, and birds by sequencing mitochondrial DNA (mtDNA) amplicons derived from environmental DNA. We monitored the outlet of a stream located in an agricultural area for 16 weeks to detect the presence of mammals, including humans, livestock, domestic and wild mammals, birds, and fish to assess the potential of multiple species of fecal contamination. Our approach could provide crucial information for farmers to mitigate fecal pollution generated by agricultural activities.