Mesophotic coral ecosystems are home to some of the richest diversity of stony corals globally, making them a key focus for researchers. These ecosystems stand out because they support a greater number of native species compared to their shallow-water counterparts. However, monitoring these areas can be quite challenging due to their depths, which range from 30 to 150 metres. To effectively monitor these corals, scientists need to possess both scuba diving and taxonomy expertise, which can be demanding. As a result, current monitoring techniques have limitations that hinder comprehensive surveys, highlighting the need for new approaches.
But now an exciting solution has emerged: environmental DNA (eDNA) analysis using mini remotely-operated vehicles, or Mini-ROVs. By gathering and analysing the (eDNA) that corals naturally release into the water, researchers can now identify multiple species in these deeper habitats without needing direct observation. This advancement simplifies the study of biodiversity hotspots that were previously difficult to access.
At the Marine Genomics Unit of the Okinawa Institute of Science and Technology (OIST), along with partners from the University of the Ryukyus and NTT Communications, a strong system has been developed to monitor mesophotic coral ecosystems through the use of underwater robots and eDNA barcoding. This research has just been published in the journal Coral Reefs.
The team surveyed four monitoring sites in Shigeo Reef, located near the Motobu Peninsula in Okinawa, Japan. Two of the sites were around 35–45 metres deep (SR1 and SR2), while the other two were deeper, at approximately 54–59 metres (SR3 and SR4). A Mini-ROV was used to collect water samples from each location, with seawater gathered about 0.5–1 metres above the reef bottom and carefully preserved to safeguard any coral eDNA present. Scientists then examined mitochondrial DNA to determine various coral species. To enhance precision, they developed a specialised database that included complete mitochondrial genomes of corals. This resource facilitated the identification of eDNA sequences, enabling researchers to accurately recognise and analyse the coral genera found in their samples.
The analysis of eDNA, combined with observations from underwater robots, uncovered distinct coral communities at each research site. SR1 was abundant in several coral varieties, especially Acropora, Seriatopora, and Pachyseris, along with some Cycloseris and Galaxea. In contrast, SR2 was primarily characterised by Seriatopora corals, with a few Galaxea present.
At SR4, a diverse community was led by Alveopora, accompanied by various other coral species. Conversely, SR3 exhibited the least coral coverage, featuring only a handful of Lobophyllids and Cycloseris, despite its proximity to the more diverse SR4 site. These differing distributions made the sites perfect for evaluating the new DNA sampling method’s effectiveness.
Crucially, the findings from the eDNA metabarcoding analysis validated earlier observational data regarding coral species across all four sites. However, the technique does have its drawbacks. In certain instances, the eDNA analysis struggled to differentiate between closely related coral species, and the success rate of DNA sampling varied by location.
Nonetheless, this study marks a significant advancement in coral reef research. The capability to detect coral species through water samples, coupled with visual confirmation, offers scientists a valuable new method for monitoring the health and biodiversity of coral reefs in challenging-to-access areas.
