One of the most valuable and accessible ecological information is often what a predator eats. Based on this information we can derive predator-prey relationships and use those to describe food chains, which provide the framework to understand how energy flows through an ecosystem. Comprehensive food web are used to interpret ecosystem functioning which is essential to develop effective management and conservation strategies.
Atlantic puffins (Fratercula arctica) and their main prey, Atlantic herring (Clupea harengus) represent a simple food web model system that has been studied extensively using conventional methods. Puffin chick diet is for example known from hundreds of hours of observing adults provisioning their chicks as part of long-term seabird research programs. As adult puffins forage at sea it is impossible to obtain any sufficient amount of guano containing identifiable components of their prey. Therefore, chick diet has been used as a best estimate for adult diet for birds, an assumption supported by similar levels of nitrogen isotopes in chick and adult blood. These results contradict common theories on optimal foraging which predict that adult puffins should feed their chicks a less diverse diet of high quality food while they feed on a more varied assortment of potentially lower quality prey.
DNA-based dietary analysis of fecal samples provides an opportunity to test the similarity between adult and chick diet. A new study uses multi-locus (16S and COI DNA Barcodes) next-generation sequencing of feces samples of Atlantic puffin chicks and adults, and the stomach contents of their main prey, Atlantic herring to investigate this simple food web. By investigating the diet of the major prey of puffins, the researchers tried to gain insight in the potential effect of secondary consumption. Many likely planktonic prey of herring were detected in feces from puffin adults and chicks, highlighting the impact secondary consumption may have on the interpretation of molecular dietary analysis.
This study represents the first simultaneous molecular investigation into the diet of multiple components of a food chain. Both puffin and herring diet were described with more diversity at a higher taxonomic resolution with our molecular approach compared to conventional methods, enhancing our knowledge of the biology of and interactions between these animals. The sensitivity of these techniques to detect the prey of prey is an important consideration for molecular scatology, particularly when de novo diet assembly with universal primers is concerned. We suggest that results of DNA-based diet studies be viewed from the perspective of a food chain, rather than simply diet, due to the effect of secondary consumption. Further, because of the considerable discrepancies in the types, coverage, and frequency of occurrence of prey taxa between markers, we recommend the use of multiple barcoding markers for taxon identification.
Another interesting find of the study was that both herring and puffins, previously considered to be part of a planktonic food web only, proved to be part also of inshore or intertidal food webs, as a number of benthic organisms showed up in the herring samples. Secondary consumers such as the puffin in this case can no longer be assumed to derive their energy and nutrients from planktonic production alone. No doubt this is a very important message for any management and conservation effort that is intended to preserve puffin habitat.