Assessing Biodiversity at Eastern Oyster ( Crassostrea virginica ) Aquaculture and Reef Sites Utilizing Real‐Time Monitoring and Environmental DNA in Rehoboth Bay, Delaware, USA

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Abstract
Eastern Oysters ( Crassostrea virginica ) are a keystone species and an important product of the commercial shellfish industry in Delaware. Oysters are known as “environmental engineers” that provide a structured habitat for the ecosystem, thus promoting biodiversity. In order to further investigate the role oysters play in increasing biodiversity, real‐time monitoring and environmental DNA (eDNA) were conducted at different sites around Rehoboth Bay, Delaware, USA. The sites include pilot artificial reefs, private aquaculture farms, and a control site without any oysters or habitat structure. Underwater GoPro Hero 3+ and 8 cameras were deployed every 2 weeks from June to October in 2022 and 2023. Cameras were deployed for approximately 2–3 h at a time, and upon retrieval, cameras were reviewed for any signs of aquatic life, and all documented species were identified and recorded for comparisons between sampling sites. Water samples were collected simultaneously for eDNA analysis to serve as a complementary method for species identification. DNA isolation and polymerase chain reaction (PCR) were performed to amplify gene sequences for targeted species. Using camera technology, 23 different animal species were recorded across the five study sites. The most abundant species included Spot ( Leiostomus xanthurus ), Atlantic Silverside ( Menidia menidia ), Atlantic Menhaden ( Brevoortia tyrannus ), Horseshoe Crab ( Limulus polyphemus ), Blue Crab ( Callinectes sapidus ), and Hermit Crabs ( Pagurus longicarpus ). The eDNA analysis also successfully detected these species, highlighting the effectiveness of eDNA as a tool for species monitoring. Notably, there was considerable overlap between species identified through both real‐time monitoring and eDNA methods. These findings contribute to ongoing oyster restoration initiatives and sustainable aquaculture practices in the Delaware Inland Bays (DIB), while also enhancing our understanding of complementary biodiversity monitoring techniques.
Funding Information
  • National Institute of Food and Agriculture (2016‐06642)

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