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 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, providing more comprehensive biodiversity inventories. Rigorous benchmarking of eDNA metabarcoding results improved ecological interpretation and confidence in species detections while providing archived genetic resources for future analyses. Well designed and validated eDNA metabarcoding approaches are ideally suited for biomonitoring applications that rely on the detection of species, including mapping invasive species fronts and endangered species habitats as well as tracking range shifts in response to climate change. Incorporating these considerations will enhance the utility and efficacy of eDNA metabarcoding for routine biomonitoring applications.

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See our collaborative work with the Natural History Museum of LA County, the Ports of Los Angeles and Long Beach, and the CaleDNA program here.

LA Times Coverage here.
KPCC Coverage here and here.
UCLA News Coverage here.

Long Beach-Los Angeles Port Complex biomonitoring surveys. Aerial photograph of the Long Beach-Long Angeles Port Complex, one of the world’s largest commercial ports (A). Results of a midwater trawl for fish biomonitoring within the Port complex (B). Field sampling of seawater for eDNA monitoring. The transferring of seawater from a Niskin into a sterile 1 L pouch is depicted (C). Common dolphins (Delphinus delphis) are one of the thousands of marine species that utilize the marine habitats of the Port complex (D). Photo Credits: (A) Port of Los Angeles, (B) Wood Environment and Infrastructure, Inc., (C) Janie Chen, and (D) Zachary Gold.