A manager’s guide to using eDNA metabarcoding in marine ecosystems

Environmental DNA (eDNA) metabarcoding is a powerful tool that can enhance marine ecosystem/biodiversity monitoring programs. Here we outline five important steps managers and researchers should consider when developing eDNA monitoring program: 1) select genes and primers to target focal taxa; 2) assemble or develop comprehensive barcode reference databases; 3) apply rigorous site occupancy based decontamination pipelines; 4) conduct pilot studies to define spatial and temporal variance of eDNA; and 5) archive samples, extracts, and raw sequence data. We demonstrate the importance of each of these considerations using a case study of eDNA metabarcoding in the Ports of Los Angeles and Long Beach. eDNA metabarcoding approaches detected 94.1% (16/17) of species observed in paired trawl surveys while identifying an additional 55 native fishes and provided more comprehensive biodiversity inventories. Rigorous benchmarking of eDNA metabarcoding results improved ecological interpretation and c...