An annual eDNA survey in a temperate estuary: similar fish assemblages supported by aquaculture gear and natural rock reefs

Acknowledgements This work was supported by the NOAA Fisheries Northeast Fisheries Science Center and the NOAA Fisheries Office of Aquaculture. Background Information Environmental DNA (eDNA) is increasingly being used as a non-invasive and highly sensitive technique for rapid biodiversity assessments, however, in coastal marine systems its application remains limited. We conducted an eDNA metabarcoding survey alongside video collection with GoPro cameras from May-September 2018 in nearshore Long Island Sound, Connecticut, USA. The goal of this work wass to compare the video collected by GoPro cameras to that of environmental DNA collected from water samples to assess community dynamics at off-bottom oyster aquaculture cage farms and a nearby, naturally occurring, rock reef. Shellfish aquaculture gear can support shelter oriented wild fish by providing structurally complex habitat (Mercaldo-Allen et al. 2021, Ferriss et al. 2021, Theuerkauf et al. 2021). A better understanding of the interactions of wild fish with shellfish farms can inform fisheries resource management through quantification of the potential benefits provided to fish by aquaculture gear (Mercaldo-Allen et al. 2024, Farrell et al. 2023, Ambrose and Munroe 2025).