Elucidating shark diets with DNA metabarcoding from cloacal swabs

Abstract

Animal dietary information provides the foundation for understanding trophic relationships, which is essential for ecosystem management. Yet, in marine systems, high‐resolution diet reconstruction tools are currently under‐developed. This is particularly pertinent for large marine vertebrates, for which direct foraging behaviour is difficult or impossible to observe and, due to their conservation status, the collection of stomach contents at adequate sample sizes is frequently impossible. Consequently, the diets of many groups, such as sharks, have largely remained unresolved. To address this knowledge gap, we applied metabarcoding to prey DNA in faecal residues (fDNA) collected on cotton swabs from the inside of a shark's cloaca. We used a previously published primer set targeting a small section of the 12S rRNA mitochondrial gene to amplify teleost prey species DNA. We tested the utility of this method in a controlled feeding experiment with captive juvenile lemon sharks (Negaprion brevirostris) and on free‐ranging juvenile bull sharks (Carcharhinus leucas). In the captive trial, we successfully isolated and correctly identified teleost prey DNA without incurring environmental DNA contamination from the surrounding seawater. In the field, we were able to reconstruct high‐resolution teleost dietary information from juvenile C. leucas fDNA that was generally consistent with expectations based on published diet studies of this species. While further investigation is needed to validate the method for larger sharks and other species, it is expected to be broadly applicable to aquatic vertebrates and provides an opportunity to advance our understanding of trophic interactions in marine and freshwater systems.

Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward

“…For large fish, like sharks, collecting naturally defaecated faeces is feasible (e.g., by snorkelers; Meekan et al, 2009). Alternatively, DNA collected from cloacal swabs of sharks have effectively generated dietary information and the swabs are less prone to contamination by eDNA present in the surrounding water (van Zinnicq Bergmann et al, 2021). Species‐specific primers or general primers for taxonomic groups of interest can then be applied to elucidate the prey compositions of fish consumers.…”

Secondary predation constrains DNA-based diet reconstruction in two threatened shark species

“…The literature on the Russian-doll effect 39 in metabarcoding dietary studies is limited (reviewed in 27 , 38 ) but certainly deserves further attention (e.g. 54 ). We suggest that while the approach offers some utility in identifying unseen taxa, confirmation via visual identification and across sufficient replication (ideally from various sampling methods) is still required to comprehensively understand primary dietary preferences.…”

Elasmobranch microbiomes: emerging patterns and implications for host health and ecology

“…The major sources of microbes entering the fish GI tract are the surrounding water, parents, or food [12], with incoming microbes either becoming part of the resident community or passing through as transient members [12,43]. For example, in a study of yellow stingrays (Urobatis jamaicensis) in an aquarium, the microbiome of the cloaca (which contains fecal and GI residues [44]) differed significantly between rays that were wild-caught versus born in the aquarium, suggesting that initial microbial colonization may be driven by environmental parameters [45]. In certain teleost fishes, colonization involves specific bacteria, linked to variations on the egg surface [41].…”