Monitoring mammals, birds and fish during summer 2022 at the outlet of an agricultural stream by mtDNA

Abstract

Fecal contamination of surface waters 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 the contamination. Fecal contamination can originate from several animals, particularly in areas where urban and agricultural activities overlap. In previous work, we developed a molecular approach to detect the presence of mammals, fish, and birds by sequencing mitochondrial DNA (mtDNA) amplicons derived from environmental DNA. In this report, 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. We were able to detect mtDNA sequences affiliated to at least 73 animal lineages. Sequences affiliated to fish were proportionally the most abundant, followed by those affiliated to mammals. We observed increases in bovine and human mtDNA sequences after episodes of high flow in the watershed, suggesting that soil runoff to surface waters carried organic matter (e.g., manure, feces, wastewater) from these animals. Our approach could provide crucial information for farmers to mitigate fecal pollution generated by agricultural activities.