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.

Fig 1. Stations Sampled for eDNA metabarcoding analysis.

All are located within the Monterey Bay National Marine Sanctuary. See Table 1 for bottom depth of each station; green stations are on the shelf (<200 m water column depth) and blue stations are in a canyon (>200 m water column depth). Isobaths are labeled with water column depth in meters.

Fig 2. Percent of OTUs identified in 1, 2 or 3 of the biological replicates collected at each station/sampling depth.

Samples are labeled with station (i.e., 1F, 2F, etc.) followed by the sampling depth (i.e., 0 m, 20 m, 40 m). 3F-0 m and 5F-0 m are not shown because they do not have complete sets of three replicates after rarefying.

Fig 3. Families identified using eDNA metabarcoding in samples collected at stations on the continental shelf (water column depth < 200 m) and stations in a canyon (water column depth >200 m).

20 families were only found on the shelf, 2 were only found in a canyon, and 11 were found at both.

Fig 4. Families identified using eDNA metabarcoding in samples collected at surface and at subsurface (20/40 m).

6 families were only found when sampling at the surface of the water, 6 families were only found when sampling the subsurface (20/40 m), and 21 of 33 families were found both at surface and subsurface.