Comparison of oyster reef and oyster aquaculture communities using environmental DNA metabarcoding and Nanopore sequencing

Oyster reefs are widely accepted as enhancing biodiversity through habitat provisioning, the loss of which has resulted in decreased habitat for many marine taxa, including fisheries-relevant species. The rapid growth of the bivalve aquaculture industry has augmented oyster harvests, but the impacts of this industry on biodiversity and how associated communities compare to those of oyster reefs is unknown. Here, we compared the biological communities associated with intertidal oyster reefs and aquaculture in estuaries in eastern North Carolina, USA, across seasons to examine the biodiversity associated with small-scale oyster aquaculture sites using broad-spectrum metabarcoding of environmental DNA (eDNA) samples. We utilized Nanopore sequencing and aquatic eDNA analyses to non-invasively record biological communities at broad taxonomic scales. In total, we identified 250 families over the course of 8 mo, 129 of which were shared between the 2 site types. However, the overall community structure differed between oyster reefs and aquaculture, which was driven by vertebrate taxa only recorded at oyster reefs. Despite these differences, the taxonomic complexity and mobility of organisms found at aquaculture sites indicate that oyster aquaculture can support a stable, biodiverse, and complex community, including fisheries-relevant taxa. These findings suggest that oyster aquaculture could contribute towards furthering both ecological and economic objectives by incorporating ecosystem service goals into aquaculture design and management.