eDNA Metabarcoding- and Microscopic Analysis for Diet Determination in Waterfowl, a Comparative Study in Vejlerne, Denmark

Simple Summary eDNA metabarcoding is a relatively novel method for studying the diet of wild animals. This study compares eDNA metabarcoding with microscopy, in order to determine the diet of four species of waterfowl. In total, 56 plants were identified at the species level. The study concluded that the combination of morphological analysis and DNA metabarcoding can yield adequate information to address pertinent ecological inquiries.Abstract Understanding diets and structural food webs are keys to the apprehension of ecological communities, upon which conservation and management biology are based. The understanding of grazing and habitat choice for waterfowl is one of the most important topics for avian ecologists today and can, to some degree, be answered by dietary analysis. Droppings collected from four waterfowl, the Eurasian wigeon (Anas penelope), Greylag goose (Anser anser), pink-footed goose (Anser brachyrhynchus) and Barnacle goose (Branta leucopsis) in Vejlerne (Denmark), were analysed microscopically and through eDNA metabarcoding with the use of next generation sequencing (NGS) to accumulate knowledge about the diet of these waterfowl. In total, 120 dropping samples were microscopically analysed, of which the eDNA metabarcoding analysis was done on 79 samples. The prey items were identified according to the taxonomic level of species, and a qualitative method, frequency of occurrence (FO) and FO calculated as a percentage, was used in order to compare the results from the two methods. As neither of the methods was able to encompass all species discovered when combining the two methods, it was concluded in this study that the two methods can support each other in a dietary analysis of waterfowl, but not replace one another.

Automated summary

eDNA metabarcoding is a new method for studying the diet of wild animals. This study compared eDNA metabarcoding with microscopy to determine the diet of four species of waterfowl. It was found that combining morphological analysis and DNA metabarcoding can provide sufficient information for ecological inquiries.