Detection of a cryptic terrestrial insect using novel eDNA collection techniques

Abstract

Sensitive detection techniques are key to inform management practices for invasive and pest species by identifying the pest species’ distribution or identifying the presence of biological control agents that may negate the need for chemical control. Environmental DNA (eDNA) can be detected to infer the presence of rare, cryptic, and invasive species. This study provides a method that expands the application of eDNA techniques within terrestrial systems. Our study is focused on a cryptic biological control agent of the pointed snail Cochlicella acuta, the fly parasitoid Sarcophaga villeneuveana, which remains within the snail shell for most of its lifecycle, making it difficult to detect. Three sites were sampled using traditional surveys and three types of eDNA sampling 1/ crushing live snails, 2/ water washing live snails, old snail shells or vegetation, and 3/ vacuuming live snails or vegetation. An assay was developed to amplify a 129 bp fragment of S. villeneuveana, with positive detections recorded in crushed snail samples, water washed live snail, water washed vegetation, and laboratory vacuumed vegetation. Presence of the endoparasitoid was validated by traditional survey techniques conducted at the same time, indicating that all techniques tested are comparable for detection of the parasitoid. The new technique which only requires a small vegetation sample from the field post‐harvest and a portable vacuum has great potential to be applied to other insects and environments, particularly cryptic species, pests, and biological control agents in crops.

Validation of a nutria (Myocastor coypus) environmental DNA assay highlights considerations for sampling methodology

“…Given our additional assay testing, sequencing from four regions in the United States, and results reported previously for nutria in Japan, we believe that our results are generalizable to other invaded regions. However, monitoring efforts for management in areas with unknown nutria presence should consider sequencing an amplicon from one or more positive eDNA samples to confirm amplification of the target, although the number of amplicons to sequence is likely to be context‐dependent (e.g., Campbell et al, 2022; Peixoto et al, 2021). Additionally, a pilot test should be conducted in regions of interest before relying on eDNA results including revalidation of the assay specificity and sensitivity with any changes in laboratory equipment or reagents (Klymus et al, 2020).…”

Environmental DNA Metabarcoding: A Novel Contrivance for Documenting Terrestrial Biodiversity

“…One of the fascinating opportunities offered by eDNA metabarcoding is the possibility of carrying out multi-taxa diversity surveys using the same sampling scheme and eDNA extracts [ 91 ]. Soil eDNA metabarcoding can be employed to detect eukaryotic diversities in retort to environmental fluctuations [ 31 ].…”

Metabarcoding advances agricultural invertebrate biomonitoring by enhancing resolution, increasing throughput, and facilitating network inference

“…While purpose-built vacuum samplers (e.g., 'DVAC') and modified leafblowers/vacuums are frequently deployed in invertebrate sampling studies (Hossain, Gurr and Wratten, 1999;Cherrill, 2015), this method is yet to be combined with metabarcoding for species identification to our knowledge. However, molecular methods have been applied to successfully identify eDNA collected with atypical vacuums for entomological studies, for the purpose of detecting parasitoid DNA from a pest snail species (Campbell et al, 2022) and pest beetle DNA (Trujillo-González et al, 2022). On the other hand, bulk samples collected by stationary suction traps have been identified with metabarcoding.…”