Environmental DNA (eDNA) metabarcoding reveals strong discrimination among diverse marine habitats connected by water movement

Abstract

While in recent years environmental DNA (eDNA) metabarcoding surveys have shown great promise as an alternative monitoring method, the integration into existing marine monitoring programs may be confounded by the dispersal of the eDNA signal. Currents and tidal influences could transport eDNA over great distances, inducing false‐positive species detection, leading to inaccurate biodiversity assessments and, ultimately, mismanagement of marine environments. In this study, we determined the ability of eDNA metabarcoding surveys to distinguish localized signals obtained from four marine habitats within a small spatial scale (<5 km) subject to significant tidal and along‐shore water flow. Our eDNA metabarcoding survey detected 86 genera, within 77 families and across 11 phyla using three established metabarcoding assays targeting fish (16S rRNA gene), crustacean (16S rRNA gene) and eukaryotic (cytochrome oxidase subunit 1) diversity. Ordination and cluster analyses for both taxonomic and OTU data sets show distinct eDNA signals between the sampled habitats, suggesting dispersal of eDNA among habitats was limited. Individual taxa with strong habitat preferences displayed localized eDNA signals in accordance with their respective habitat, whereas taxa known to be less habitat‐specific generated more ubiquitous signals. Our data add to evidence that eDNA metabarcoding surveys in marine environments detect a broad range of taxa that are spatially discrete. Our work also highlights that refinement of assay choice is essential to realize the full potential of eDNA metabarcoding surveys in marine biodiversity monitoring programs.

Non‐specific amplification compromises environmental DNA metabarcoding with COI

“…Particularly important for regulatory applications, or where researchers wish to compare results over time or between studies, some degree of standardization is desirable (Hering et al, ). Our results – and those of previous studies using similar primer sets (Bakker et al, ; Jeunen et al, ; Lim et al, ; Macher et al, ; Singer et al, ; Stat et al, ; Yang et al, ) – show that environmental metabarcoding for restricted taxonomic groups using degenerate COI primers results in excessive volumes of ‘wasted’ sequencing effort. This co‐amplification of prokaryotic and non‐target eukaryotic DNAs and subsequent lack of specificity is due to the nature of mutation patterns in COI (Siddall et al, ).…”

“…Early eDNA metabarcoding studies targeting fishes used the cytochrome b gene (Minamoto, Yamanaka, Takahara, Honjo, & Kawabata, ; Thomsen, Kielgast, Iversen, Møller, et al, ; Thomsen, Kielgast, Iversen, Wiuf, et al, ), but more recent studies have used the 12S ribosomal rRNA locus (Hänfling et al, ; Kelly et al, ; Port et al, ; Stoeckle, Soboleva, & Charlop‐Powers, ; Ushio et al, ; Yamamoto et al, ), and also 16S rRNA (Berry et al, ; Bylemans, Gleeson, Hardy, & Furlan, ; Jeunen et al, ; Shaw et al, ; Stat et al, ). Various regions of 12S have been proposed as metabarcoding markers, including a ca.…”

eDNA metabarcoding survey reveals fine‐scale coral reef community variation across a remote, tropical island ecosystem

“…This indicates that eDNA signals from seawater are localised enough to discriminate between sites over small spatial scales and can provide a reproducible profile of their community composition. This data adds to a growing body of evidence that there is strong spatial fidelity in eDNA signals, attributed to dispersion and degradation in seawater (Jeunen et al, 2018; Koziol et al, 2018; Murakami et al, 2019; Stat et al, 2019).…”

Comparing eDNA metabarcoding and species collection for documenting Arctic metazoan biodiversity

“…Several studies have also revealed patterns of extensive eDNA dispersion over considerable distances within river systems (Deiner & Altermatt, 2014;Deiner, Fronhofer, Mächler, Walser, & Altermatt, 2016), which could influence community structure in estuarine settings such as the port of Churchill. In our study, the very cold Arctic waters may further contribute to reducing DNA degradation, thus providing more time for dispersion over larger distances compared to what has been previously reported at more temperate latitudes (Jeunen et al, 2019). This raises the hypothesis that spatial eDNA homogenization should be more important in the Arctic Ocean than more southern regions.…”