The applicability of eDNA metabarcoding approaches for sessile benthic surveying in the Kimberley region, north‐western Australia

Abstract

The application of environmental DNA technologies is a promising new approach to rapidly audit biodiversity across large-scale, remote regions. Here, we examine the efficacy of a dual-assay eDNA metabarcoding approach for sessile benthic bioassessments in the turbid waters of the Lalang-garram marine parks, Kimberley, north-western Australia. We ask three principal questions: (1) "Is the eDNA released by sessile benthic taxa (i.e., hard and soft corals, sponges and tunicates) locally detectable?", (2) "What level of taxonomic resolution is afforded by eDNA metabarcoding using the ITS2 region?", and (3) "How well does eDNA metabarcoding compare to conventional benthic survey techniques?". We report that a dual-assay eDNA metabarcoding approach can detect approximately 70% of the local benthic taxa (i.e., at a species, genus level). It is, however, not as effective at the individual/population level, detecting only approximately 40% of unique amplicon sequence variant (ASV) signals released by an array of individual benthic organisms at the surveyed locations.In examining the efficacy and resolution of the applied ITS2 metabarcoding markers for bioassessments, we report large gaps in the variety of publicly available benthic ITS2 reference sequence data, limiting our ability to provide robust taxonomic assignments. These findings highlight the need to extend ITS2 databases for greater regional representation. Until this is adequately addressed, we recommend that investigating taxonomic assignments to a genus level is the most robust approach for benthic monitoring using eDNA. Lastly, we found eDNA metabarcoding and conventional belt transect surveys each detected numerous unique hard coral genera, indicating that a combined approach provides the most effective way to audit benthic biodiversity. This point notwithstanding, eDNA metabarcoding had the power to distinguish similar diversity trends between sites to that determined by the belt transect methodology, validating the application of eDNA metabarcoding as either a stand-alone, or complementary technique for assessing sessile benthic taxa.

Coral monitoring in northwest Australia with environmental DNA metabarcoding using a curated reference database for optimized detection

“…We presume that the similar taxonomic profiles across shallow depths may reflect coral mucus being constantly released (Wild et al, 2004b), often dominating suspended matter around reefs (Johannes, 1967; Marshall, 1968). The majority of this mucus usually dissolves in the water, but a fraction can form floating gel‐like mucus aggregates with positive buoyancy (Wild et al, 2004a). However, the residence time of this coral mucus (thus, eDNA) is thought to be low as aggregates trap particles and therefore decrease in buoyancy over time and sink (Wild et al, 2004a).…”

“…The majority of this mucus usually dissolves in the water, but a fraction can form floating gel‐like mucus aggregates with positive buoyancy (Wild et al, 2004a). However, the residence time of this coral mucus (thus, eDNA) is thought to be low as aggregates trap particles and therefore decrease in buoyancy over time and sink (Wild et al, 2004a). Due to this continuous cycle, sedimentation is estimated to occur within a few hours of release (Wild et al, 2004b).…”

Metabarcoding the marine environment: from single species to biogeographic patterns

“…Furthermore, BRUV and eDNA metabarcoding techniques detected distinct fish communities, with some species recovered only by a single method indicating that a combined approach is desired if the goal is to capture total community diversity in these intertidal habitats. West et al (2021) and Dugal et al (2021) focus on an important coral reef network in the Kimberley region of northwestern Australia. Specifically, they showed that eDNA metabarcoding of the ITS2 region resulted in high rates of detection at the species and genus level for the habitat building scleractinian corals (Dugal et al, 2021;West et al, 2021), as well as other benthic invertebrates such as sponges and tunicates (West et al, 2021).…”

“…West et al (2021) and Dugal et al (2021) focus on an important coral reef network in the Kimberley region of northwestern Australia. Specifically, they showed that eDNA metabarcoding of the ITS2 region resulted in high rates of detection at the species and genus level for the habitat building scleractinian corals (Dugal et al, 2021;West et al, 2021), as well as other benthic invertebrates such as sponges and tunicates (West et al, 2021).…”

“…Quantitative species data based on the concentration of eDNA in a sample, although fraught with issues, are an active area of research. West et al (2021) surveyed benthic communities such as corals, sponges, and tunicates on coral reefs in Australia using the ITS2 region. They found only a weak correlation between hard coral abundance, as determined by visual surveys and metabarcoding read counts, suggesting that in this system at least, relative read abundance from ITS2 is a poor proxy for estimating hard coral coverage.…”