eDNA metabarcoding as a new surveillance approach for coastal Arctic biodiversity

Abstract

Because significant global changes are currently underway in the Arctic, creating a large‐scale standardized database for Arctic marine biodiversity is particularly pressing. This study evaluates the potential of aquatic environmental DNA (eDNA) metabarcoding to detect Arctic coastal biodiversity changes and characterizes the local spatio‐temporal distribution of eDNA in two locations. We extracted and amplified eDNA using two COI primer pairs from ~80 water samples that were collected across two Canadian Arctic ports, Churchill and Iqaluit, based on optimized sampling and preservation methods for remote regions surveys. Results demonstrate that aquatic eDNA surveys have the potential to document large‐scale Arctic biodiversity change by providing a rapid overview of coastal metazoan biodiversity, detecting nonindigenous species, and allowing sampling in both open water and under the ice cover by local northern‐based communities. We show that DNA sequences of ~50% of known Canadian Arctic species and potential invaders are currently present in public databases. A similar proportion of operational taxonomic units was identified at the species level with eDNA metabarcoding, for a total of 181 species identified at both sites. Despite the cold and well‐mixed coastal environment, species composition was vertically heterogeneous, in part due to river inflow in the estuarine ecosystem, and differed between the water column and tide pools. Thus, COI‐based eDNA metabarcoding may quickly improve large‐scale Arctic biomonitoring using eDNA, but we caution that aquatic eDNA sampling needs to be standardized over space and time to accurately evaluate community structure changes.

Comparing eDNA metabarcoding and species collection for documenting Arctic metazoan biodiversity

“…A total of 117 water samples were collected and filtered following the methods outlined in Lacoursière- Roussel et al (2018). A 250ml water sample was taken at each of the three depths (surface, mid-depth, and deep water [i.e., 50 cm from the bottom]) for each station and port using 5-L Niskin bottles.…”

“…DNA was extracted from filters following a QIA shredder and phenol/chloroform protocol (Lacoursière- Roussel et al, 2018). All PCR manipulations were done in a decontaminated UV hood.…”

“…Following Lacoursière- Roussel et al (2018), we used the forward mlCOIintF (Leray et al, 2013) and reverse jgHCO2198 (Geller, Meyer, Parker, & Hawk, 2013) (hereafter called COI1) and the forward LCO1490 (Folmer, Black, Hoeh, Lutz, & Vrijenhoek, 1994) and reverse ill_C_R (Shokralla et al, 2015) (hereafter called COI2). These have been shown to work well for detecting a wide variety of taxa including invertebrates and have reasonably comprehensive databases of reference sequences.…”

“…eDNA metabarcoding provides valuable information toward a broader view of the taxonomic diversity that may help in developing more rigorous conservation plans, particularly in the Arctic. The simplicity of the sampling protocol for coastal water makes the method easy to learn, which constitutes a major asset for remote regions such as the Arctic, where it can be easily incorporated into existing sampling or community-based monitoring programs (Lacoursière- Roussel et al, 2018). The simplicity of the sampling protocol for coastal water makes the method easy to learn, which constitutes a major asset for remote regions such as the Arctic, where it can be easily incorporated into existing sampling or community-based monitoring programs (Lacoursière- Roussel et al, 2018).…”

“…Analysis of eDNA with metabarcoding is a rapid method of biodiversity assessment that links taxonomy with high-throughput DNA sequencing (Ji et al, 2013) to provide a snapshot of local species composition without the need for sampling individual organisms. Recent studies in coastal marine ecosystems have demonstrated the feasibility of eDNA metabarcoding to document marine metazoan biodiversity in the Arctic Lacoursière-Roussel et al, 2018). Despite limited knowledge of eDNA ecology (i.e., origin, fate, state, and transport; Barnes & Turner, 2016;Lacoursière-Roussel & Deiner, in press), eDNA is increasingly being incorporated within monitoring toolboxes for a large variety of aquatic organisms and ecosystems (Deiner et al, 2017;Roussel, Paillisson, Tréguier, & Petit, 2015).…”