Soil environmental DNA versus pitfall trapping for small mammal monitoring: qPCR assay development and pilot field evaluation

Small mammals are fundamental drivers of ecosystem processes, and they act as bioindicators of ecological integrity. Although their monitoring is crucial from a conservation perspective, conventional surveying devices such as pitfall traps are invasive and raise ethical concerns. A potential non-invasive alternative is the analysis of environmental DNA (eDNA) shed by small mammals in the environment. The first step in the adoption of eDNA-based monitoring is the design of species-specific, sensitive, and efficient quantitative PCR (qPCR) assays. Here, we developed and validated targeted qPCR assays for three Canadian small mammals: the smoky shrew ( Sorex fumeus Miller, 1895), the masked shrew ( Sorex cinereus Kerr, 1792), and the southern bog lemming ( Synaptomys cooperi Baird, 1858). We also conducted a pilot field study to compare small mammal detection rates from pitfall trap capture and eDNA analysis of soil samples. For the smoky shrew and the masked shrew, detection rates were low for both pitfall traps (6% and 16%, respectively) and eDNA (6% and 3%, respectively), while no capture or eDNA detection was made for the southern bog lemming, indicating that a greater sampling effort would be required to better compare the two methods. Additional studies are thus needed before eDNA can be adopted as a reliable method for monitoring small mammals.