Fishy Business—Assessing the Efficacy of Active and Passive eDNA to Describe the Fish Assemblage of a River in Southwestern Western Australia to Support Effective Monitoring

Worldwide, freshwater vertebrate populations are declining with increasing pressure on rivers due to numerous environmental and climatic threats. Environmental DNA (eDNA) could potentially provide a more efficient and non-invasive mechanism to monitor freshwater systems, either as a complement or in replacement to traditional methods to accurately assess species' distributions. Here, we utilize a hierarchical multispecies N-mixture model to compare three fish sampling methods: traditional fyke netting and active and passive environmental DNA sampling along a 30 km stretch of the Canning River in Western Australia. We used the fitted model to compare capture probabilities among sampling methods and reveal the sampling effort required to describe the species assemblage. Results indicated that while all methods could detect fish, combined eDNA methodologies detected one more fish species than those caught by fyke netting. In addition, active eDNA sampling produced the highest capture probabilities and more consistently described the entire fish assemblage at any given site. Fyke netting and passive eDNA did not show significant differences in their average capture probabilities, and both methods had lower abilities to capture individual species than active eDNA. Active eDNA also required fewer replicate samples to detect the expected observed richness, and fyke netting required the most replicates. Additionally, a hierarchical multispecies abundance model showed that active environmental DNA (eDNA) sampling is the most effective method for monitoring freshwater fish populations. This study contributes to our understanding of eDNA in aquatic systems and demonstrates that, at least under current conditions, active sampling is still the preferred method in freshwater systems with low flow compared to both passive sampling and fyke netting.