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 evaluated species detected with metabarcoding using two eDNA collection methods (tree bark vs. soil sampling), and compared the performance of two detection methods (qPCR vs. metabarcoding) within a single species. 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 versus 8 non-arboreal species detected (mean: 2466 vs. 289 reads/sample). Soil samples revealed a generally similar composition, but a lower diversity, of mammal species. Detection rates for big brown bat were 3.4 × higher for qPCR over metabarcoding, illustrating the enhanced sensitivity of single-species approaches. Our results suggest that sampling eDNA from on and around trees could serve as a useful new monitoring tool for cryptic arboreal mammal communities globally.

Using surface environmental DNA to assess arthropod biodiversity within a forested ecosystem

“…Given the taxonomic flexibility of some primer sets, there is also the possibility of combining surveys for disparate taxa using the same methods. For example, given our findings, joint surveys for mammals and arthropods may be possible with the 16S marker (Table S4; see also Allen, Kwait, et al., 2023). More studies, ideally those involving data on both detection probability and cost, are needed to address questions related to comparative cost efficiency and effectiveness relative to conventional methods (e.g., Smart et al., 2016).…”

“…Environmental DNA metabarcoding can also circumvent sampling issues associated with visually or behaviorally cryptic species (e.g., mosquitos; Boerlijst et al., 2019) or habitats that are dangerous or expensive to visit (e.g., deep ocean ecosystems; Closek et al., 2019). These successes have spurred research into novel methods for eDNA biodiversity surveys of terrestrial habitats targeting diverse taxa such as insects (Macher et al., 2023; Roger et al., 2022; Thomsen & Sigsgaard, 2019), mammals (Allen, Kwait, et al., 2023; Leempoel et al., 2020), reptiles (Kyle et al., 2022), and birds (Ushio et al., 2018). As eDNA sampling approaches are increasingly considered for inclusion in regulatory frameworks (e.g., Environmental Impact Assessments; Hinz et al., 2022), the capabilities of eDNA metabarcoding‐based methods need to be well characterized, especially for terrestrial systems and speciose groups such as arthropods (Belle et al., 2019; Jinbo et al., 2011).…”

Maximizing Efficiency in SedaDNA Analysis: A Novel Extract Pooling Approach

“…Genomic material can be obtained from various environmental sources, including soil (Allen et al, 2023; Ariza et al, 2023), water (Antich et al, 2021; Blattner et al, 2021), or air (M. D. Johnson et al, 2021; Lynggaard et al, 2022). Hence, environmental DNA (eDNA) is a valuable tool for ecological surveys of species that are challenging to observe directly or in the absence of their remains.…”

Using eDNA for mammal inventories still needs naturalist expertise, a meta‐analysis

“…First, the eDNA group, using substrates from the animal's environment such as water (seawater, freshwater, Ficetola et al., 2008; Foote et al., 2012), soil (Andersen et al., 2012; Taberlet et al., 2012), sediments (McDonald et al., 2023; Ryan et al., 2022), and air through filters (Garrett et al., 2023; Lynggaard et al., 2022). Another type of substrate can be considered eDNA traps, as they allow DNA concentration due to their intrinsic properties, such as feces (Van Der Heyde et al., 2021; Walker et al., 2019, hair (Croose et al., 2023; Lee et al., 2016), saliva bait (Nichols et al., 2015; Piaggio et al., 2019); saltlicks (Ishige et al., 2017), vegetation (Allen et al., 2023; Van Der Heyde et al., 2021) and even spider webs (Gregorič et al., 2022). Finally, a third group of DNA originates from invertebrates—iDNA—that are ectoparasites of the targeted taxa and blood/fecal meals are used as DNA sources (Calvignac‐Spencer et al., 2013).…”