Using DNA Metabarcoding of Cloacal Swabs to Elucidate the Diets of Four Coastal Shark Species

The Atlantic sharpnose (Rhizoprionodon terraenovae), blacknose (Carcharhinus acronotus), blacktip (Carcharhinus limbatus), and bonnethead (Sphyrna tiburo) sharks are commonly encountered large mobile consumers found in the estuaries along the western North Atlantic coast. The bulk of the dietary data for these species has been coarsely recorded at a broad taxonomic level (e.g., “teleost fish”). Here, we used DNA metabarcoding of fecal DNA collected using non-lethal cloacal swabs to identify the species of prey contributing to the diets of these shark species and measure the degree of trophic overlap. Samples were collected from 24 Atlantic sharpnose, 33 blacknose, six blacktip, and 17 bonnethead sharks in the summer of 2020. Based on previous dietary research on these shark species, we targeted teleost fishes and crustaceans using two previously published primer sets. From the 80 sharks sampled off the coast of North Carolina, we identified 38 prey taxa, with 82% classified to the species level and all assigned to at least the genus and family levels. The most common prey taxa found in the diet of the bonnethead was Atlantic blue crab (Callinectes sapidus; 44.75%, based on percent of occurrence) followed by penaeid shrimp (Penaeus spp.; 24.41%), mantis shrimp (Squilla empusa; 20.34%), and spot (Leiostomus xanthurus; 4.75%). Atlantic sharpnose and blacknose sharks had the largest Levin’s niche overlap, with both species relying on the same two most frequently consumed prey taxa: penaeid shrimp (Atlantic sharpnose: 33.33%, percent of occurrence, and blacknose: 34.78%) and spot (Atlantic sharpnose: 32.70% and blacknose: 22.32%). Bonnetheads and blacktips had the least amount of overlap between all shark species, where blacktips primarily consumed menhaden (Brevoortia spp.; 58.62%) and penaeid shrimp (26.44%). Our findings highlight the value of DNA metabarcoding in refining our understanding of predator diets, moving beyond broad taxonomic classifications to identify species-level prey associations and trophic interactions. As coastal habitats undergo increasing alteration due to anthropogenic impacts, such information is crucial for fisheries management, helping to identify key prey dependencies and anticipate potential ecosystem shifts.