Ecosystem-wide biodiversity with environmental DNA can inform management of Marine Protected Areas

Marine Protected Areas (MPAs) are managed regions that help ensure long-term conservation of natural resources and protect biodiversity, ecosystem services, and cultural values in the face of anthropogenic change. However, determining MPA effectiveness is often challenging due to lack of comprehensive baseline data and/or biases associated with traditional biodiversity survey methods. Environmental DNA (eDNA) represents a promising tool to overcome these challenges. Here, we used a suite of three metabarcoding targets – prokaryote-specific 16S, eukaryote-specific 18S, and vertebrate-specific 12S – to generate baseline data of all organisms from the smallest bacteria to the largest whales within Stellwagen Bank National Marine Sanctuary (SBNMS). Surface water, bottom water, and sediment from 40 sites revealed 3 archaeal, 46 bacterial, 22 protistan, and 17 metazoan phyla. Inclusion of the 12S primer dramatically increased the number of vertebrates found in the samples, including identification of marine mammals, sea birds, and 24 fish species. Detections of sand lance, a key forage species, also increased when comparing eDNA to visual survey results. Community composition differed significantly for all three targeted groups across the three sample types, as well as across different areas of the bank, demonstrating how eDNA can reveal complex biodiversity patterns even in a relatively similar ecosystem. This approach to assessing biodiversity within SBNMS provides more detailed results using simpler sample collection methods compared with traditional methods such as trawling, plankton tows, or visual surveys, exemplifying eDNA’s utility for MPA monitoring and management.