Validation of Environmental DNA for Estimating Proportional and Absolute Biomass

Abstract

Environmental DNA (eDNA) has significant potential to improve the efficiency of biological sampling and detect species that pose challenges for traditional sampling methods. However, a key obstacle in utilizing eDNA data for ecosystem management is uncertainty surrounding the ability to estimate abundance or biomass of multiple species simultaneously. In this study, we use experimental trials with known biomasses of multiple species to explore the feasibility of (1) estimating species proportions from eDNA metabarcoding data and (2) estimating absolute eDNA concentrations of multiple species by scaling metabarcoding proportions with eDNA concentrations of a single species obtained from qPCR. The focal species for this study were three gadid fishes that are key components of marine ecosystems in Alaska and vary in their distribution and habitat use: Walleye pollock (Gadus chalcogrammus), Pacific cod (Gadus macrocephalus), and Arctic cod (Boreogadus saida). After designing gadid-specific metabarcoding primers and accounting for PCR biases in the metabarcoding data, we found corrected read proportions closely approximated the true biomass proportions of species. Furthermore, we found strong positive relationships between absolute eDNA concentration and absolute biomass for Arctic cod and Pacific cod using quantitative metabarcoding data combined with estimates of Walleye pollock eDNA concentration derived from qPCR. These findings suggest that it is possible to accurately quantify species compositions and estimate metrics of biomass for gadids in real-world scenarios. Furthermore, this work provides a framework for developing primers and analytical approaches that can be applied to other species to improve the quantitative utility of eDNA.