Standard Methods for Sampling North American Freshwater Fishes, second edition

Chapter 19: Environmental DNA Sampling for Species Detection

Caren S. Goldberg, Taylor Wilcox, Alexis M. Janosik, and Robert Bajno

doi: https://doi.org/10.47886/9781934874769.ch19

The collection and analysis of environmental DNA (eDNA) from water samples to infer the presence of fish has been growing in application in recent years due to the benefits of increased sensitivity and reduced disturbance to both organism and habitat compared with traditional field methods (e.g., electrofishing, netting). Environmental DNA methodologies are currently most developed for inferring species presence using targeted quantitative PCR (qPCR) assays, which therefore is the focus of this chapter. This goal of detecting the presence of species is different from the goals of the other chapters of this book, which primarily focus on assessing biomass, demography, or community structure. Aquatic communities can also be characterized from eDNA samples using metabarcoding; at the time of writing, metabarcoding has not been as fully validated as targeted approaches and current methods may be less sensitive for detecting rare species (Simmons et al. 2015; Harper et al. 2018; Bylemans et al. 2019). Progress is being made on addressing these issues, and we hope that future versions of this chapter will include community assemblage analysis through metabarcoding, potentially using DNA sequence read counts to gather information on relative abundances (e.g., Skelton et al. 2023). Emerging applications of eDNA and related analyses also include estimating biomass and assessing reproductive status. Though in this chapter we focus on targeted species detection, samples collected and preserved under this protocol can be analyzed later with metabarcoding or other approaches to create a historical record of full community assemblages.