Community assembly dynamics in a regulated stream: Insights from environmental DNA

Abstract

Degradation of freshwater habitats, including the alteration of natural flow regimes by impoundment, is a major threat to native fishes. When dam removal is not possible, management actions to recover natural flow regimes can benefit native species, but monitoring community responses is crucial to demonstrating efficacy. We used eDNA metabarcoding to quantify spatiotemporal trends in fish assemblages along the longitudinal profile of a regulated stream where a court-ratified framework uses environmental flows to support native fishes. At a subset of sites, we also evaluated concordance of eDNA results against concurrent surveys using long-term standardized fisheries monitoring techniques. From 59 eDNA samples collected over approximately 2 years, we detected 26 fish taxa, including 8 native species. Twenty-five taxa resolved to species level and one taxon could not be resolved between closely related species. Fish assemblages varied predictably along the longitudinal profile of the stream and by season (fall and spring). Diversity indices were higher at downstream sites and in fall, reflecting greater richness of warm-water non-native species. Evenness was similar among sites but shifts in species ranks suggests reordering processes drive spatiotemporal variation in assembly. Gradient forest analysis identified 13 species associated with spatiotemporal gradients, including both native and non-native species. Overall, eDNA results were concordant with conventional fisheries monitoring, but eDNA detected significantly greater species richness through increased detection of rare species. eDNA results align with long-term monitoring that demonstrated assemblage shifts in only upper stream reaches, and extends the insights into spatial responses, species reordering, and ecology of rare species. These findings demonstrate the value of eDNA as a complementary tool for understanding community assembly dynamics, including responses to stream rehabilitation and ecosystem management.