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

Abstract

Environmental DNA (eDNA) metabarcoding, a technique for retrieving multispecies DNA from environmental samples, can detect a diverse array of marine species from filtered seawater samples. There is a growing potential to integrate eDNA alongside existing monitoring methods in order to establish or improve the assessment of species diversity. Remote island reefs are increasingly vulnerable to climate‐related threats and as such there is a pressing need for cost‐effective whole‐ecosystem surveying to baseline biodiversity, study assemblage changes and ultimately develop sustainable management plans. We investigated the utility of eDNA metabarcoding as a high‐resolution, multitrophic biomonitoring tool at the Cocos (Keeling) Islands, Australia (CKI)—a remote tropical coral reef atoll situated within the eastern Indian Ocean. Metabarcoding assays targeting the mitochondrial 16S rRNA and CO1 genes, as well as the 18S rRNA nuclear gene, were applied to 252 surface seawater samples collected from 42 sites within a 140 km2 area. Our assays successfully detected a wide range of bony fish and elasmobranchs (244 taxa), crustaceans (88), molluscs (37) and echinoderms (7). Assemblage composition varied significantly between sites, reflecting habitat partitioning across the island ecosystem and demonstrating the localisation of eDNA signals, despite extensive tidal and oceanic movements. In addition, we document putative new occurrence records for 46 taxa and compare the efficiency of our eDNA approach to visual survey techniques at CKI. Our study demonstrates the utility of a multimarker metabarcoding approach in capturing multitrophic biodiversity across an entire coral reef atoll and sets an important baseline for ongoing monitoring and management.

Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes

“…Our results align with those of West et al. (2020), who observed marked eDNA compositional differences between habitats in the Cocos Islands of Australia, and suggest that coastal eDNA can be localized in marine environments.…”

“…Nevertheless, the teleo primer did not recover some of the species that were recovered by the Vert01 primer (54 vs. 74 in Providencia and 39 vs. 64 in Gayraca), while the Vert01 primer did not recover a few species only found with the teleo primer (33 and 21 for Providencia and Gayraca, respectively). Hence, as this stage of primer development and testing, it appears that a multiprimer approach is required to capture of the entire diversity of a site (West et al., 2020). Moreover, because we found many Elasmobranchii with the teleo primer, a specialized primer for Elasmobranchii might not be needed and could be replaced by the more ubiquitous teleo primer.…”

“…Sequences are then taxonomically assigned using a genetic reference database, which provides an integrative inventory of species and composition in aquatic systems (Deiner et al., 2017; Harrison et al., 2019). A recent synthesis counted 54 papers on tropical eDNA, whereas only 15 focused on marine systems (Bakker et al., 2019; Huerlimann et al., 2020; Sigsgaard et al., 2019; West et al., 2020). Compared to freshwater systems, the marine environment has a larger water volume to fish biomass ratio, the movement of molecules in suspension is influenced by various currents, and reef systems can contain up to hundreds of species, which might challenge the detection of individual species (Collins et al., 2019; Hansen et al., 2018; Harrison et al., 2019).…”

Blind assessment of vertebrate taxonomic diversity across spatial scales by clustering environmental DNA metabarcoding sequences

“…While eDNA metabarcoding represents a promising tool for scaling-up biodiversity inventories (Berry et al 2019, Ruppert et al 2019, its strong dependence on genetic reference databases limits its application in many regions of the world, as well as for some taxonomic groups or some habitats (Weigand et al 2019). Indeed, even diverse yet well-studied ecosystems such as coral reefs do not have exhaustive genetic references for most lineages and the majority of commonly used primers in eDNA metabarcoding (DiBattista et al 2017, West et al 2020. Some reference-free tools exist, but their application remains mostly limited to unicellular or fungi organisms, with different aims and constraints compared to eDNA studies targeting vertebrates.…”

Development and evaluation of fish eDNA metabarcoding assays facilitate the detection of cryptic seahorse taxa (family: Syngnathidae)

“…Furthermore, by avoiding the need for visual observation, capture, and direct sampling (Goldberg et al, 2016), eDNA surveys frequently overcome some of the cost, time, biases, and at times invasive nature associated with traditional monitoring methods (Jeunen et al, 2019;Thomsen & Willerslev, 2015). eDNA metabarcoding surveys have been applied to a wide range of aquatic ecosystems, including: rivers Bylemans, Gleeson, Lintermans, et al, 2018); lakes (Fujii et al, 2019); open ocean (Truelove, Andruszkiewicz, & Block, 2019); coastal habitats (Andruszkiewicz et al, 2017;Koziol et al, 2019);and reefs (DiBattista et al, 2017;West et al, 2020)).…”