Digging for DNA at depth: Rapid universal metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity across a depth gradient
MetadataShow full item record
Funding and Sponsorship
Background: Effective 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. Methods: We 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. Results: Using 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. Discussion: Overall, 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.
Showing items related by title, author, creator and subject.
eDNA metabarcoding survey reveals fine-scale coral reef community variation across a remote, tropical island ecosystemWest, K.M.; Stat, Michael ; Harvey, Euan ; Skepper, C.L.; Di Battista, Joey ; Richards, Zoe ; Travers, M.J.; Newman, Stephen ; Bunce, Michael (2020)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 ...
Environmental DNA can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystemsDi Battista, Joey ; Reimer, J.D.; Stat, Michael ; Masucci, G.D.; Biondi, P.; De Brauwer, Maarten; Wilkinson, S.P.; Chariton, A.A.; Bunce, Michael (2020)Loss of biodiversity from lower to upper trophic levels reduces overall productivity and stability of coastal ecosystems in our oceans, but rarely are these changes documented across both time and space. The characterisation ...
Large-scale eDNA metabarcoding survey reveals marine biogeographic break and transitions over tropical north-western AustraliaWest, Katrina ; Travers, M.J.; Stat, Michael ; Harvey, Euan ; Richards, Zoe ; Di Battista, Joey ; Newman, Stephen ; Harry, A.; Skepper, C.L.; Heydenrych, Matt ; Bunce, Michael (2021)Aim: Environmental DNA (eDNA) metabarcoding has demonstrated its applicability as a highly sensitive biomonitoring tool across small spatial and temporal scales in marine ecosystems. However, it has rarely been tested ...