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

Abstract

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.

Hidden in plain sight: The invasive macroalga Caulerpa prolifera evades detection by environmental DNA methods

“…This study calculated Sargassum horneri 's steady‐state concentration to be roughly 10 7 copies/g which placed it well within the range of previously recorded fish and invertebrates. We demonstrate here that because of its relatively high steady‐state concentration, and large biomass in the wild, S. horneri is an ideal candidate for environmental DNA detection as evidenced by previous detections via metabarcoding (Ely et al, 2021; Gold et al, 2022). Specifically, the use of this ddPCR assay in areas with low abundance before species establishment, environments of high turbidity and low visibility, locations that are difficult to dive in, and in ballast water of ships would allow for higher sensitivity monitoring and earlier intervention for this invasive species.…”

“…Previous work has highlighted the utility of eDNA as a complement to conventional survey techniques (Bohmann et al, 2014; Kelly et al, 2017). In the case of invasive species, eDNA can aid in early detection of areas of concern given the sensitivity of qPCR/ddPCR assays; however, there is always value for ‘boots on the ground’ confirmation, especially when there are significant management implications (Gold et al, 2022). A strong advantage of eDNA is the ability to reduce the complexity of the field logistics by narrowing the range of visual surveys and the time it would take to complete them.…”

Archived DNA reveals marine heatwave‐associated shifts in fish assemblages

“…Utilizing the dataset described in this manuscript in conjunction with mock communities, Gold, Shelton, et al (2022) demonstrate that rates of non-detection are a function of amplification efficiencies and underlying DNA concentration. These results highlight the future importance of not only modeling the deterministic PCR process as we have done here, but also modeling the stochastic subsampling process prior to amplification as both processes together drive observed biological signal (abundance of observed reads) and noise (the patterns of non-detections across technical replicates) in metabarcoding data sets (Gold, Shelton, et al, 2022;Gold, Wall, et al, 2022).…”

Comparison of traditional and molecular surveys of fish biodiversity in southern Te Wāhipounamu/Fiordland (Aotearoa/New Zealand)

“…We unite visual observations with the results of concurrent eDNA and BRUV surveys and information from OBIS (Ausubel, 1999). Without purposefully generated reference data for eDNA at hand for the surveyed region, we used a comprehensive public source of reference information, receiving data from many other initiatives, including 12S sequences (Collins et al., 2021; Pruesse et al., 2007), a currently frequently used fish primer set (e.g., see a recent evaluation in Zhu & Iwasaki, 2023), and relaxed taxonomic assignment parameters, to obtain the highest possible yield in identified eDNA species while minimizing missing assignments due to a limited search space (Gold et al., 2022). We did so at the cost of obtaining many less accurate eDNA assignments, which we inspected carefully, also due to shortcomings of taxonomic assignment algorithms (Garrido‐Sanz et al., 2022; Somervuo et al., 2017).…”