Combined use of eDNA metabarcoding and video surveillance for the assessment of fish biodiversity

Abstract

Monitoring communities of fish is important for the management and sustainability of fisheries and marine ecosystems. Baited remote underwater video systems (BRUVs) are among the most effective nondestructive techniques for sampling bony fishes and elasmobranchs (sharks, rays, and skates). However, BRUVs sample visually conspicuous biota; hence, some taxa are undersampled or not recorded at all. We compared the diversity of fishes characterized using BRUVs with diversity detected via environmental DNA (eDNA) metabarcoding. We sampled seawater and captured BRUVs imagery at 48 locales that included reef and seagrass beds inside and outside a marine reserve (Jurien Bay in Western Australia). Eighty-two fish genera from 13 orders were detected, and the community of fishes described using eDNA and BRUVs combined yielded >30% more generic richness than when either method was used alone. Rather than detecting a homogenous genetic signature, the eDNA assemblages mirrored the BRUVs' spatial explicitness; differentiation of taxa between seagrass and reef was clear despite the relatively small geographical scale of the study site (∼35 km² ). Taxa that were not sampled by one approach, due to limitations and biases intrinsic to the method, were often detected with the other. Therefore, using BRUVs and eDNA in concert provides a more holistic view of vertebrate marine communities across habitats. Both methods are noninvasive, which enhances their potential for widespread implementation in the surveillance of marine ecosystems.

Keywords: ADN ambiental; baited remote underwater video systems; elasmobranchs; elasmobranquios; environmental DNA; environmental genomics; genómica ambiental; manejo marino; marine management; sistemas remotos de video submarino con carnada.

Figure 1

Location of seawater and baited remote underwater video system samples collected in Jurien Bay, Western Australia (48 locales; 24 in reefs and 24 in seagrass beds). Locales are grouped into 16 sites (8 seagrass and 8 reef inside and outside the marine reserve).

Figure 2

Dendrogram of fish diversity detected from samples collected using baited remote underwater video systems (BRUVs), eDNA, and both methods at Jurien Bay in Western Australia. The inset shows the number of genera identified using BRUVs, eDNA, and both methods in combination.

Figure 3

Species accumulation curves for the number of fish genera detected at Jurien Bay in Western Australia with eDNA and baited remote underwater video systems (BRUVs) in seagrass beds and reefs (numbers in parentheses indicate total number of genera detected using eDNA, BRUVs, or both methods combined; percentages indicate the increase in taxa identified between BRUVs and both methods combined).

Figure 4

Results of canonical analysis of principle coordinates ordination plot showing the relationship of fish (genera) assemblages identified in each sample from Jurien Bay in Western Australia based on a Bray–Curtis similarity matrix for factors method (eDNA vs. BRUVs) and habitat (seagrass vs. reef).