Parasites are seldom considered essential components of biodiversity. They are often studied alongside microbial pathogens from the perspective of disease ecology. Cases where parasites become obvious include zoonotic spillover and outbreaks among host populations. In contrast, the loss of parasite biodiversity can go unnoticed. Parasites have permeating effects on behavior and mortality in host populations, and create unique trophic linkages between intermediate and definitive hosts. This project uses DNA metabarcoding to survey the parasite communities of fish in the Colorado River in Grand Canyon, as part of the collaborative effort to monitor this American landmark’s ecology. This 18s metabarcoding method complements traditional necropsies due to minimally invasive sample collection, efficient scaling, and more specific identification of microscopic parasites. We expect to observe differences in prevalence for key parasite groups both on an upstream-downstream gradient and between host species.
DNA was extracted from filtered water at 10 mainstem and 7 tributary sites spanning 450 river-kilometers, as well as feces of over 100 fish from the species Catostomus latipinnis (flannelmouth sucker), Oncorhynchus mykiss (rainbow trout), and the federally threatened Gila cypha (humpback chub). Our sequencing detected over 5000 unique taxa, including protists, algae, and invertebrates. Water samples from tributary streams had higher sequence richness than those from the Colorado river mainstem, or any fish species, supporting current models of dam-driven environmental homogenization and degradation in the mainstem. However, neither fish or mainstem water samples show richness increasing with distance from the dam. We identified 246 parasite taxa, the most prevalent being parasites of invertebrates (i.e. Gregarinia, Microsporidia), but also pathogenic fish parasites such as myxozoans and the Asian fish tapeworm Bothriocephalus acheilognathi. These results provide a baseline for monitoring parasite biodiversity and prevalence in fish host populations in Grand Canyon, especially with expansion to a multi-year monitoring effort.