Sampling environmental DNA from trees and soil to detect cryptic arboreal mammals

Abstract

Environmental DNA (eDNA) approaches to monitoring biodiversity in terrestrial environments have largely focused on sampling water bodies, potentially limiting the geographic and taxonomic scope of eDNA investigations. We assessed the performance of two strictly terrestrial eDNA sampling approaches to detect arboreal mammals, a guild with many threatened and poorly studied taxa worldwide, within two central New Jersey (USA) woodlands. We compared detection rates between two eDNA collection methods (tree bark vs. soil sampling), and two detection methods (qPCR vs. metabarcoding). Our survey, which included 94 sampling events at 21 trees, detected 16 species of mammals, representing over 60% of the diversity expected in the area. More DNA was found for the 8 arboreal vs. 8 non-arboreal species detected (mean: 2466 vs. 289 reads / sample). Tree bark sampling showed 1.8-3.0x higher detection probability than soil sampling among the 5 most common species (overall effect size: β = 1.39, 95% CI: [0.85, 1.91]). Comparing detection methods for big brown bat revealed 3.4x higher detection rates for qPCR over metabarcoding, illustrating the enhanced sensitivity of single-species approaches. Our results suggest that sampling eDNA from trees could serve as a useful new monitoring tool for cryptic arboreal mammal communities globally.