Passive Sampling of Urban Runoff Solids to Capture Environmental DNA for the Detection of Rodents in Urban Spaces.

Abstract

In urban environments, runoff may contain environmental DNA (eDNA) from nuisance animals, but its potential has not been investigated. Conventional eDNA methods, such as water sampling, may not be applicable to the detection of nuisance animals in urban areas due to the scarcity of target eDNA attributable to the sporadic contact of the animals with water sources, and the limited volume of samples collected may lead to false negative results. Given these limitations, this study aimed to develop a passive sampling method for the collection of runoff solids for the detection of rodents (mouse and rat) in urban areas using eDNA. The developed sampling method successfully collected 0.3-16.7 g dry weight of runoff solids per sampling event. Collected runoff samples contained 8.0-58.1 μg total DNA/g dry weight sample and were characterized by the presence of PCR inhibitors. Following the removal of these inhibitors, mouse eDNA was detected (albeit below the limit of quantification) using a designed species-specific assay. The results of this study demonstrate that runoff solids are a viable eDNA source for the detection of animals in urban environments. However, further work is required to improve the quantification of target DNA. Nevertheless, the developed methodology may provide new and important information on the ecology of animals in urban spaces that can be incorporated into the management of nuisance animals in urban areas. SUMMARY: A passive sampling scheme was successfully designed and captured 0.3-16.7 g dry weight of urban runoff solids in two sites in an urban space. Collected solids contain 8.0-58.1 μg/g of eDNA, which also contain PCR inhibitors which must be removed prior to qPCR. Mouse DNA was detected in six out of 19 samples, but the detections were below the determined quantification limit. This new passive sampling scheme can be applied for terrestrial animal detection in urban spaces to potentially track hidden animals.