A Miniaturized and Automated eDNA Sampler: Application to a Marine Environment

Environmental DNA (eDNA) analysis offers a time-and cost-efficient method to perform temporal and spatial observations of aquatic environments, providing a wealth of biodiversity data. Unfortunately, most protocols require manual collection of eDNA samples using highly skilled individuals to capture, filter and store the samples before they can be sent to a lab for analysis. Automated samplers exist to reduce this front-end collection burden, but they tend to be bulky and costly. Here we describe an eDNA sampler designed to be user-friendly and to automate the entire sample collection process. We describe and characterize our eDNA sampler, which offers multi-sample capture, preservation, and self cleaning to reduce cross contamination. DNA sequencing was performed on samples collected using the eDNA sampler as well as a traditional niskin bottle-based protocol at six stations in Bedford Basin, Nova Scotia, Canada. The two approaches showed similar algal and bacterial taxonomic compositions, demonstrating the ability of the eDNA sampler to generate results comparable to those obtained through gold-standard protocols.