Planet Earth is currently experiencing its sixth major extinction event, which represents a major challenge in the field of biodiversity conservation for the 21st century. All conservation efforts rely on some form of monitoring survey, many of which are labor intensive. Traditionally, visual detection surveys have been used to characterize communities; however, these do not provide fine-scale resolution data required to make accurate management decisions. Environmental DNA (eDNA) is defined as the total DNA that originates from the feces, saliva, urine, and skin cells of an animal. Quantification of eDNA is a novel technique that can be used to detect threatened species. The utility of eDNA to characterize macrofauna communities has proven effective in aquatic environments. Currently, there is limited knowledge on the potential for terrestrial eDNA to be used as a tool in biodiversity conservation. The objectives of this project were to determine the utility of terrestrial eDNA for the detection of the Red-backed Salamander. More specifically the objectives were to, 1) determine if salamander eDNA could be detected in a terrestrial environment, feces, or skin swabs, 2) establish the limit of detection, 3) quantify eDNA degradation over time, 4) attempt to detect salamander eDNA in a mesocosm experiment.
Quantitative PCR (qPCR) was utilized for detection purposes. Salamander eDNA was positively detected in 100% of skin swabs, 66% of fecal samples, and 0% of natural soil samples. Salamander genomic DNA (gDNA) was detectable in all qPCR reactions when spiked into soil at 10, 5, and 1 ng/g soil. Only 33% of samples showed recoverable eDNA when spiked with 250 pg/g soil establishing the limit of detection of terrestrial salamander eDNA. To determine the rate of eDNA degradation in a terrestrial environment, gDNA was spiked into soil and detection success quantified over seven days. Salamander eDNA detection probability decreased over time, but eDNA was still amplifiable at day 7. Salamander eDNA was detected in 100% of samples at days 0, 1, and 2. Amplification success decreased from day 2 to 7 but was still detectible in 55%, 33%, 77%, 55%, and 66% of samples at days 3, 4, 5, 6, and 7, respectively. Salamander eDNA was detected in only two of 182 mesocosm soil samples over a 12 week sampling period (n=52 control samples; n=65 presence samples; n=65 eviction samples). Pending additional studies, these results indicate the limited efficacy of terrestrial eDNA for use in amphibian conservation.