COS 239-4 - Exploring the potential for oyster aquaculture to remediate biodiversity loss in oyster reef habitats using non-destructive environmental DNA sampling

Abstract: Oyster populations have been a target for supplementation and restoration for decades due to their strong historical role in the ecology and economy of coastal areas. The rapid growth of aquaculture and its’ associated change in habitat structure may mimic benefits provided by historical oyster reefs and improve biodiversity provisioning in unstructured areas. If the positive impacts of aquaculture structure on provisioning oyster reef ecosystem services was understood, then there would be a more complete understanding of the state of these coastal ecosystems for ecological management. Addressing the often-limited resources of restoration managers to incorporate molecular methods into biodiversity studies, this study introduces a method to utilize third-generation Nanopore sequencing and aquatic environmental DNA (eDNA) analysis to non-invasively record biological communities associated with oyster aquaculture at a broad taxonomic scale. Over the course of nine months, water samples were collected biweekly from six bivalve aquaculture and oyster reef sites and processed for DNA extraction and amplification via the 18S, 12S, and COI markers. After sequencing, a total of 84 taxonomic families were captured at aquaculture sites and 69 families captured at oyster reefs. While each group had unique taxa associated with it, much of the biological community utilizing bivalve aquaculture did overlap with that of oyster reefs, including groups of fishes, ascidians, annelids and marine worms, and bryozoans. Classes unique to aquaculture included groups of waterfowl, anthozoans, and echinoderms. Here we show that a diverse biological community utilizes the structure provided by oyster aquaculture, many members of which are also found in present day oyster reefs. These findings indicate that thoughtful incorporation of aquaculture into ecosystem management plans could be used to relieve pressure from wild fisheries and contribute to providing ecosystem services.