The use of traditional capture methods versus eDNA in detecting species richness of aquatic communities

Background/Question/Methods

Management of aquatic ecosystems requires the ability to identify species presence. This becomes increasingly difficult with low abundance species, such as threatened and endangered or recently introduced invasive species. Traditional capture methods can be intrusive to the organism, ineffective at capturing all present species, costly or limited by the body water type. We compare traditional capture methods with eDNA capture methods in an upper Midwestern pond and stream environment. We first filtered 250 ml water samples to capture environmental DNA (eDNA), or suspended particles containing DNA. Mitochondrial gene fragments were then amplified and sequenced with the Illumina Miseq platform, to uniquely identify all species within a body of water. To avoid sediment disturbance or contamination, only after filtered water samples were taken, were traditional capture methods deployed. A combination of fyke nets, seines, minnow traps and electroshock fishing techniques were utilized to characterize current species richness.

Results/Conclusions

Traditional methods identified 13 and 12 fish and amphibian species within the pond and stream, respectively. Metagenetic analysis of eDNA from the same pond and stream identified all species caught by traditional gears along with additional species, including some species known from historical capture records. Even when a species (i.e. golden shiner) was in low abundance (1 in 1000 fish) or present but not captured (i.e. visual sighting of common carp), genetic based approach could detect its presence. Overall, the eDNA method proves to be a more sensitive and effective tool with the added benefits of lowered handling stress on the fish and minimized time and cost associated with monitoring aquatic ecosystems. While our objective was to identify fish and amphibians, we also identified terrestrial, planktonic and bacterial taxa. The additional information of species allows for a more complete understanding of all organisms within the vicinity, both terrestrial and aquatic. Ultimately, eDNA promises to be a useful tool for managers to aid in monitoring and managing species.