Toward a Quantitative Interpretation of Lake Fish Environmental DNA Metabarcoding Surveys: The Relative Importance of Sampling Strategies, Laboratory and Data Analyses Protocols
TL;DR
This first comparative study to determine the optimal strategies to move toward a quantitative interpretation of fish eDNA metabarcoding surveys is provided, showing that a spatially integrated sampling strategy and the use of internal standards to convert read counts to eDNA concentrations increases the probability of detecting positive correlations between eDNA concentrations and species' abundance and biomass estimates and increases model predictive performance.
Abstract
Analyses of environmental DNA (eDNA), that is, DNA obtained from environmental samples, has emerged as a highly promising tool for monitoring fish communities. While the ability to obtain quantitative estimates from eDNA metabarcoding surveys remains debatable; recent efforts have aimed to enhance the quantitative nature. Comparative studies assessing the impact of sampling strategies, refinements to molecular and data analyses protocols are, however, lacking. We compared two common sampling strategies (i.e., spatially integrated sampling vs. point sampling) in two natural lakes and six approaches designed to improve the quantitative interpretation of eDNA metabarcoding data. Metabarcoding estimates of eDNA concentrations were correlated against standard gillnet fishing estimates of species' abundance and biomass, absolute eDNA quantifications for five target species obtained through digital droplet PCR analyses, and the allometrically scaled abundance (i.e., correcting for the non‐linear relationship between eDNA production and body mass). Results showed that a spatially integrated sampling strategy and the use of internal standards to convert read counts to eDNA concentrations increases the probability of detecting positive correlations between eDNA concentrations and species' abundance and biomass estimates and increases model predictive performance. To our knowledge, we provide the first comparative study to determine the optimal strategies to move toward a quantitative interpretation of fish eDNA metabarcoding surveys. These findings are essential to pave the way for routine implementation of eDNA metabarcoding surveys.