Fecal source tracking and eDNA profiling in an urban creek following an extreme rain event

Zachery R. Staley,Thomas A. Edge,Josey Grabuski,Stephen J. Hill,Jun Dennis Chuong,Mehrdad Hajibabaei,Shadi Shokralla

doi:10.1038/s41598-018-32680-z

Abstract

Fecal contamination of recreational waters (i.e. lakes, rivers, beaches) poses an on-going problem for environmental and public health. Heavy rainfall can exacerbate existing problems with fecal contamination. As there could be variable sources of fecal contamination, identifying the source is critical for remediation efforts. This study utilized microbial source tracking (MST), chemical source tracking (CST) markers and environmental DNA (eDNA) metabarcoding to profile sampling areas and identify sources of fecal contamination in creek, stormwater outfall and beach sites in the Etobicoke Creek watershed (Toronto, ON). Water samples were collected before and immediately following an extreme rain event. MST and CST identified stormwater outfalls as an important source of human fecal contamination during dry and wet conditions. eDNA metabarcoding allowed for potential identification of additional sources of fecal contamination and provided additional evidence of human fecal contamination. The extreme rainfall event altered the eDNA profiles, causing creek and beach sites to reflect a greater diversity of mammal and bird eDNA sequences. The profiles provided by eDNA metabarcoding provide a proof of concept suggesting that eDNA metabarcoding can be a useful tool to complement MST and CST methods for profiling sources of fecal contamination and studying impacts of extreme rain events.

Highlights

Poor water quality within recreational waters is an on-going problem, especially in regions surrounding the Great Lakes designated as Areas of Concern (AOCs)
E. coli concentrations in creek and beach samples were significantly higher following the extreme rain event on July 9th (F2,23 = 38.27, P < 0.001 and F2,14 = 10.70, P = 0.002, respectively; Fig. 2A), no significant difference was observed for E. coli concentrations in outfall samples among sampling dates
This study found a significantly altered fecal pollution profile in an urban creek, associated stormwater outfalls, and an urban beach associated with an extreme rain event

Summary

Introduction

Poor water quality within recreational waters (i.e. any water body where swimming or water-related recreation occurs, such as lakes, rivers and beaches) is an on-going problem, especially in regions surrounding the Great Lakes designated as Areas of Concern (AOCs). Environmental DNA (eDNA) is the DNA extracted from environmental samples (e.g. water, soil) and it can provide biodiversity information through high throughput sequencing (HTS) analysis of marker genes such as species-specific DNA barcodes This eDNA metabarcoding approach has predominantly been utilized in ecology and evolutionary studies of community dynamics. EDNA metabarcoding could provide a more comprehensive indication of all potential sources of fecal contamination within a watershed, whereas qPCR-based methods will only allow for detection of targeted species. Several FST methods were applied and E. coli were quantified at creek and stormwater outfall sites in the Etobicoke Creek watershed and at Marie Curtis Beach in the Toronto and Region AOC (Fig. 1) These FST methods were used to compare water quality associated with an extreme rain event in Toronto in 2013 with two sampling dates leading up to this extreme event. We aimed to assess whether eDNA metabarcoding could provide additional information regarding other potential fecal pollution sources which MST and CST methods could not

Objectives

Methods

Results

Conclusion