Elucidating shark diets with DNA metabarcoding from cloacal swabs.

Affiliation

van Zinnicq Bergmann MPM(1)(2), Postaire BD(1), Gastrich K(1), Heithaus MR(1), Hoopes LA(3), Lyons K(3), Papastamatiou YP(1), Schneider EVC(4), Strickland BA(1), Talwar BS(1)(4), Chapman DD(1), Bakker J(1).
Author information:
(1)Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA.
(2)Bimini Biological Field Station Foundation, Bimini, The Bahamas.
(3)Georgia Aquarium, Atlanta, Georgia, USA.
(4)Exuma Sound Ecosystem Research Project, Cape Eleuthera Institute, Eleuthera, The Bahamas.

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.