Biomonitoring of marine vertebrates in Monterey Bay using eDNA metabarcoding

Abstract

Molecular analysis of environmental DNA (eDNA) can be used to assess vertebrate biodiversity in aquatic systems, but limited work has applied eDNA technologies to marine waters. Further, there is limited understanding of the spatial distribution of vertebrate eDNA in marine waters. Here, we use an eDNA metabarcoding approach to target and amplify a hypervariable region of the mitochondrial 12S rRNA gene to characterize vertebrate communities at 10 oceanographic stations spanning 45 km within the Monterey Bay National Marine Sanctuary (MBNMS). In this study, we collected three biological replicates of small volume water samples (1 L) at 2 depths at each of the 10 stations. We amplified fish mitochondrial DNA using a universal primer set. We obtained 5,644,299 high quality Illumina sequence reads from the environmental samples. The sequence reads were annotated to the lowest taxonomic assignment using a bioinformatics pipeline. The eDNA survey identified, to the lowest taxonomic rank, 7 families, 3 subfamilies, 10 genera, and 72 species of vertebrates at the study sites. These 92 distinct taxa come from 33 unique marine vertebrate families. We observed significantly different vertebrate community composition between sampling depths (0 m and 20/40 m deep) across all stations and significantly different communities at stations located on the continental shelf (<200 m bottom depth) versus in the deeper waters of the canyons of Monterey Bay (>200 m bottom depth). All but 1 family identified using eDNA metabarcoding is known to occur in MBNMS. The study informs the implementation of eDNA metabarcoding for vertebrate biomonitoring.

A rapid environmental DNA method for detecting white sharks in the open ocean

“…Our sequencing results reveal that average e ‐values and bit‐scores corresponding to MinIon sequencing reads at 97% is the same as that reported for studies using Illumina sequencing (Andruszkiewicz, Starks, et al, ; Kelly, Port, Yamahara, & Crowder, ; Miya et al, ), highlighting that a small number of accurate reads (e.g. 10–1,000, Figure a) can be produced in a 3.5‐hr MinIon sequencing run that are of high quality and similar confidence to that of Illumina sequencing.…”

The sceptical optimist: challenges and perspectives for the application of environmental DNA in marine fisheries

“…If physical transport, rather than local eDNA production, is the main factor responsible for eDNA distribution and abundance, particle transport would act to decouple inferences on presence/absence data from eDNA measurements and established observational surveys. However, both coastal (e.g., Andruszkiewicz et al., ; O'Donnell et al., ; Port et al., ; Thomsen et al., ; Yamamoto et al., ) and open ocean (Gargan et al., ; Sigsgaard et al., ; Thomsen et al., ) eDNA surveys report good concordance with established surveys in terms of local species detection. A study by Port et al.…”

Needle in a haystack? A comparison of eDNA metabarcoding and targeted qPCR for detection of the great crested newt (Triturus cristatus)

“…Similarly, sequencing of independent biological replicates, opposed to pseudoreplicates from a single water sample, may improve detection and minimise false negatives produced by eDNA metabarcoding (Andruszkiewicz et al, 2017;Bálint et al, 2017). Currently, 90 ml (6 × 15 ml sampled from 600 ml) water is sampled during T. cristatus eDNA survey, followed by ethanol precipitation (Biggs et al, 2015).…”

“…eDNA is retained by predators, discarded in feces, and transported by anthropogenic activity, combined with natural water currents and flow (Hänfling et al, 2016). In the laboratory, PCR-accumulated and sequencing error, including primer mismatch (Andersen et al, 2012) and "tag jumps" (Schnell, Bohmann, & Gilbert, 2015), can induce misassignment leading to false positives, crosscontamination between samples, or laboratory contamination (Andruszkiewicz et al, 2017).…”