Assessing the Diet of the Elusive North American River Otter (Lontra canadensis) in Florida Using Faecal DNA Metabarcoding

North American river otters (Lontra canadensis) are semiaquatic mammals distributed throughout the North American continent. They are generalist carnivores with a high potential to affect community structure and dynamics. However, habitat degradation and ecosystem changes have the potential to impact their trophic interactions. Therefore, investigating their diet is critical to understand how anthropogenic disturbances can affect their ecological roles, particularly in the urbanised ecosystems in Florida, where such diet information is currently unavailable. Due to their elusive nature, direct observation of feeding events is a major challenge. Here, we have applied DNA metabarcoding of faecal matter (fDNA), opportunistically collected from river otters killed by road traffic in eastern Florida. Two mitochondrial markers were used to identify prey species' DNA—one for fish and one for vertebrates. A total of 23 unique exact sequence variants (ESVs) were identified, the majority belonging not only to teleosts but also to amphibians, reptiles, birds and mammals. The prey species identified are known dietary resources for river otters and the recovered dietary profiles provided independently by the fish and vertebrate assays were similar. Among the identified teleost prey, three fish species are considered invasive. Here, we show that when sufficient reference sequences are available, fDNA metabarcoding provides high prey species resolution. The collection and metabarcoding of faecal samples is particularly advantageous for scaling diet studies, both geographically and longitudinally, highlighting the potential of fDNA metabarcoding for the investigation of the diet of predators. This can provide foundational information on the organisation of ecological networks, which is vital for implementing successful ecosystem-based conservation management.