Author: Kyle Banwell
Freshwater ecosystems are among the most threatened globally, yet they are some of the most difficult to monitor effectively. This study explores how combining conventional netting strategies with molecular tools including environmental DNA (eDNA) metabarcoding and stomach content DNA (scDNA) quantitative-PCR (q-PCR) can improve fish community composition assessments in large lake ecosystems. Conventional netting methods are a hallmark of freshwater fish ecology due to its practical nature and comparatively lower technical requirements; however, it can show a bias to detect larger and/or more abundant species. The molecular genetic techniques provide an alternative; eDNA allows for broad detection of species within an ecosystem through the detection of their shed genetic material and scDNA enables the accurate identification of stomach contents, allowing researchers to objectively determine species presence; but generally only for small “prey” species. Results support that eDNA has greater detection sensitivity compared to conventional netting and scDNA. Interestingly, combining netting with scDNA closed this gap–in terms of the number of species detected–indicating the two methods–while biased– complemented each other. However, integration of all three consistently revealed greater species richness than any method alone across sampling sites, indicating unique method-specific detections. In addition, eDNA detection patterns varied significantly across species, driven primarily by species specific traits and proportional eDNA read abundance was positively correlated with independent abundance estimates. While multi-method detection approaches can be logistically challenging, these findings underscore their importance for freshwater fish community monitoring and highlight the complementary strengths of the various techniques. Researchers and fishery managers should invest in coordinated multi-method monitoring to create comprehensive data sets that will be of value to future research.