Molecular techniques to assess fish diet and describe prey availability

Food webs are challenging to describe, particularly for generalist predators whose diet consists largely of taxonomically diverse invertebrates. To better understand predator-prey relationships for fish belonging to Salmonidae and Cottidae, I compared traditional morphological identification of prey with sequencing of individual items and next generation sequencing of fish stomach homogenates. I also used next generation sequencing to assess invertebrate biodiversity from environmental DNA samples – stream water, ethanol preservative from Surber samples and fish stomach homogenates. Morphological identification was often limited to the Order level but allowed for quantitative data. Genetic analysis provided substantially greater taxonomic resolution, with sequencing of stomach homogenates revealing a much more diverse diet in fish. Water samples detected terrestrial and aquatic invertebrate species and Surber ethanol revealed a similar invertebrate diversity as fish stomach homogenates. Fish, however, appeared to be generalist feeders and collectively accounted for the greatest number of unique taxa.