Digging for DNA at depth: rapid universal metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity across a depth gradient

Abstract

BackgroundEffective biodiversity monitoring is fundamental in tracking changes in ecosystems as it relates to commercial, recreational, and conservation interests. Current approaches to survey coral reef ecosystems center on the use of indicator species and repeat surveying at specific sites. However, such approaches are often limited by the narrow snapshot of total marine biodiversity that they describe and are thus hindered in their ability to contribute to holistic ecosystem-based monitoring. In tandem, environmental DNA (eDNA) and next-generation sequencing metabarcoding methods provide a new opportunity to rapidly assess the presence of a broad spectrum of eukaryotic organisms within our oceans, ranging from microbes to macrofauna.MethodsWe here investigate the potential for rapid universal metabarcoding surveys (RUMS) of eDNA in sediment samples to provide snapshots of eukaryotic subtropical biodiversity along a depth gradient at two coral reefs in Okinawa, Japan based on 18S rRNA.ResultsUsing 18S rRNA metabarcoding, we found that there were significant separations in eukaryotic community assemblages (at the family level) detected in sediments when compared across different depths ranging from 10 to 40 m (p = 0.001). Significant depth zonation was observed across operational taxonomic units assigned to the class Demospongiae (sponges), the most diverse class (contributing 81% of species) within the phylum Porifera; the oldest metazoan phylum on the planet. However, zonation was not observed across the class Anthozoa (i.e., anemones, stony corals, soft corals, and octocorals), suggesting that the former may serve as a better source of indicator species based on sampling over fine spatial scales and using this universal assay. Furthermore, despite their abundance on the examined coral reefs, we did not detect any octocoral DNA, which may be due to low cellular shedding rates, assay sensitivities, or primer biases.DiscussionOverall, our pilot study demonstrates the importance of exploring depth effects in eDNA and suggest that RUMS may be applied to provide a baseline of information on eukaryotic marine taxa at coastal sites of economic and conservation importance.

Comparing environmental metabarcoding and trawling survey of demersal fish communities in the Gulf of St. Lawrence, Canada

“…All of these species were benthic or demersal fish species that feed and live on the seafloor or close to the bottom or deeper than 250 m, suggesting that a fine‐scale sampling of eDNA may provide a biologically relevant and comprehensive characterization of fish with different depth profiles. The application of eDNA metabarcoding at finer temporal and spatial resolution compared to traditional biomonitoring has been demonstrated by a number of scientific works (e.g., Andruszkiewicz et al., 2017; DiBattista et al., 2019; Hanfling et al., 2016). We here confirmed the usefulness of eDNA metabarcoding to determine marine fish distribution in different water layers and to characterize fish communities’ composition, richness, and relative abundance at different depths that might be fruitful for marine biodiversity assessments.…”

Meta‐analysis shows that environmental DNA outperforms traditional surveys, but warrants better reporting standards

“…The application of eDNA for ecology and conservation research has increased at an exponential rate over the last 20 years (Jiang & Yang, 2017), with more than 50 papers published year on year since 2016 (Beng & Corlett, 2020), from eDNA use for the detection of zooplankton (Yang & Zhang, 2020) to large mammals (Hauger et al, 2020) and many taxa in between. Creative and diverse sample types, such as salt licks (Ishige et al, 2017), blood meal (Rodgers et al, 2017), snow tracks (Franklin et al, 2019), as well as more conventional sampling of water (Brys et al, 2020), sediment (DiBattista et al, 2019) and soil (Marquina et al, 2019), have been taken from all major types of habitats: terrestrial (Abrams et al, 2019), marine (Closeket al, 2019), estuarine (Siegenthaler et al, 2019), lentic (Parsley et al, 2020), and lotic (Takahara et al, 2019).…”

Vertical stratification of environmental DNA in the open ocean captures ecological patterns and behavior of deep‐sea fishes

“…Although eDNA vertical structuring has been reported from inshore sediment samples (DiBattista et al 2019) and in lakes (Littlefair et al 2021), to date and to the best of our knowledge, no study has assessed whether eDNA is vertically structured or mixed up along the water column in the open ocean, which is crucial to evaluate the potential of eDNA to assess diversity and behavior of deep-sea fish communities. Here, we have applied eDNA metabarcoding to eight vertical profiles (up to 2000 m depth) collected during day and night-time along the continental slope of the Bay of Biscay.…”