Can environmental DNA unlock the mysteries of biodiversity on coral reefs?

Bridging the gaps through environmental DNA: A review of critical considerations for interpreting the biodiversity data in coral reef ecosystems

Coral reefs, the rainforests of the sea, are vital hotspots for marine biodiversity. However, the persistent challenge of climate change directly threatens the delicate balance of coral reef ecosystems, impacting myriad species and critical ecosystem services. Therefore, this comprehensive review critically discusses the associated challenges in assessing and preserving coral reef diversity, emphasizing the need for novel biomonitoring techniques due to the elusive and cryptic nature of many reef organisms. The review focuses on environmental DNA (eDNA) analysis as a non-invasive tool for coral species monitoring at various ecological levels. The review highlights that using eDNA in coral reef monitoring requires careful consideration of multiple factors, such as strategic assay development, optimization, and marker selection, substrate selection, and sample volume, which are critical for maximizing the probability of species detection. Moreover, integrating environmental RNA (eRNA) provides additional insights into temporal aspects advancing the coral reef biodiversity research and conservation efforts.

Possible monitoring of mesophotic scleractinian corals using an underwater mini-ROV to sample coral eDNA

Mesophotic coral ecosystems (MCEs) are light-dependent tropical or subtropical communities occurring at depths of 30-150 m. Broader surveys of MCEs are needed to better understand stony corals, the keystone species of coral-reef ecosystems. While MCEs have been studied by professional SCUBA divers and with deep-sea robots, comprehensive surveys of MCEs are required. An eDNA metabarcoding method has recently been used to survey scleractinian corals in shallow reefs. We tested whether MCEs might be more comprehensively surveyed by collecting seawater samples using an underwater mini-remote operated vehicle (mini-ROV). Seawater was collected 1-2 m above reef tops at depths of 20-80 m at 24 sites in six locations around the Zamami Islands (Okinawa, Japan). Water samples were then subjected to coral-specific eDNA amplification. Metabarcoding analyses of amplicons showed that except for one site, coral-specific eDNA from approximately 0.5 l seawater samples was sufficient to identify genera. The proportion of Acropora eDNA was higher at shallow reefs and upper ridges of slopes, while the proportion of Porites increased at mesophotic sites. Although further technical improvements are required, this study suggests that it may be possible to monitor mesophotic corals to the generic level using eDNA collected using mini-ROVs.