Automated eDNA and eRNA profiling for biodiversity monitoring in marine and freshwater ecosystems.

Biodiversity monitoring is essential to measure the impacts of pollution, invasive species, and the longer-term effects of climate change. Automated samplers enable temporally flexible, remote collection of environmental DNA (eDNA), improving access to time-sensitive events. The Dartmouth Ocean Technologies (DOT) Preserving eDNA Sampler has proven effective in multi-month marine deployments, but further validation is needed across a broader range of habitats and water chemistries, and to establish its suitability for collection and assessment of environmental RNA (eRNA). In this study, we collected samples near the surface (1-1.5 m depth) of a brackish pond, a freshwater lake, and two marine harbours. We identified patterns of species turnover consistent with transitions among aquatic environments, including invasive species such as smallmouth bass and chain pickerel in the freshwater lake. Automated deployment in Halifax Harbour following a significant rainfall event detected nearly ten times as many probable fecal-associated bacteria by proportion at this site relative to Lunenburg Harbour. Preserved eRNA allowed the identification of taxa below the eDNA limit of detection. Our pilot study demonstrates the feasibility of using the DOT sampler for longer-term biomonitoring in a diverse range of aquatic habitats, yielding ecological insights that would not be attainable through manual sampling alone.