Efficacy of Edna-Based Metagenetic Approaches for En Mass Molecular Assessment of Fish and Amphibian Species Richness

Freshwater fauna are particularly sensitive to environmental change and disturbance. Management agencies frequently use fish and amphibian biodiversity as indicators of ecosystem health and a means to prioritize and assess management strategies.  Traditional aquatic bioassessment that relies on capture or observation of organisms via nets, traps, and electrofishing gear typically has low detection probabilities for rare species and can injure individuals of protected species.  Our objective was to determine if environmental DNA (eDNA) sampling and metagenetic analysis can be used to more accurately measure aquatic richness in species assemblages with differing community structures.  We manipulated the density and relative abundance of eight fish and one amphibian species in a replicated mesocosm experiment.  Environmental DNA was captured via filtered water samples and mitochondrial gene fragments were sequenced to measure species richness of each mesocosm.  Metagenetic analysis identified all nine species in all treatment replicates.  We discuss the relationship between sequencing read abundance and species biomass, the specificity of the metagenetic approach, and the effect of utilizing multiple genetic markers on species detection.  Our results illustrate the potential for application of eDNA-metagenetic approaches for improved estimation of species richness in natural environments.