Diving deeper into our oceans: Underwater drones open latest doors for global coral reef research

Mesophotic (‘middle-light’) coral ecosystems are light dependent tropical or subtropical habitats found at depths of 30 to 150 meters. They’re unique because they host more native species in comparison with shallow-water coral ecosystems. Despite this, they’re largely unexplored, and more research is required to grasp their basic biology.

Researchers studying corals access these invertebrate reef builders by snorkeling and scuba diving, but these methods have limitations, especially when identifying corals at deeper depths. Using genetic material that organisms shed from their bodies into their environment — environmental DNA or eDNA — scientists can discover varieties of corals and other organisms living in a specific habitat, providing a robust tool for biodiversity assessment.

Importantly, studying the eDNA of corals offers unique benefits. First, unlike fish, corals are stationary, eliminating uncertainties about their location. Second, they consistently secrete mucus into the ocean, providing loads of coral eDNA for sampling. For this study, the researchers analyzed mitochondrial DNA, which is more abundant and of upper quality in comparison with nuclear DNA, improving the accuracy of their findings. To learn more in regards to the coral eDNA metabarcording evaluation methods utilized in this study, see here.

Faster and easier monitoring of coral reefs

Mesophotic coral ecosystems (MCEs) in Japan have a few of the highest diversity of stony corals (Scleractinia) on the earth, making them particularly essential for researchers, but difficult to watch because they are sometimes positioned at deeper depths. Moreover, to accurately monitor corals, scientists require each scuba diving and taxonomy skills, which may be difficult. Existing methods for monitoring MCEs subsequently impose limitations on conducting thorough surveys, and latest methods are needed.

In October 2022, Prof. Noriyuki Satoh, leader of the Marine Genomics Unit, was approached by Mr. Shinichiro Nagahama of NTT Communications who had examine his research on coral eDNA methods. Mr. Nagahama suggested using their underwater drones to gather samples from deeper coral reefs for eDNA evaluation. Prof. Satoh then recommend the concept of using the drones to conduct extensive surveys of mesophotic corals at greater depths.

Kerama National Park in Japan, about 30 km west of Okinawa Island, boasts a few of the most transparent water within the Okinawa Archipelago. Sometimes called ‘Kerama blue’, these waters provided a wonderful opportunity for the researchers to check this latest sampling technique. They collected seawater samples — each measuring 0.5 liters — from 1 to 2 meters above the coral reefs (between 20 and 80 meters deep). The sampling sites were chosen across 24 locations inside 6 different areas across the picturesque Zamami Island. The subsequent step involved subjecting these samples to coral metabarcoding analyses, which uses Scleractinian-specific genetic markers to discover the various genera of corals present in each sample.

From the eDNA evaluation results, the researchers successfully identified corals on the genus level. The presence and absence of certain genera of stony corals shown by this method indicated that reefs across the Kerama Islands exhibited different compositions of stony corals depending on location and depth. For instance, the genus Acropora had the best ratios at 11 sites, indicating that these corals are common at Zamami Island reefs. The researchers also found that the proportion of Acropora eDNA was higher at shallow reefs and upper ridges of slopes, while the proportion of the genus Porites increased at mesophotic sites. Regarding depth, Acropora was readily detected at shallow reefs (≤15 meters), while other genera were more ceaselessly found at deeper reefs (>20 meters).

To review corals using eDNA metabarcoding methods, further sequencing of mitochondrial genomes of stony corals is required, and this study suggests that it might be possible to more efficiently monitor mesophotic corals on the generic level using eDNA collected by underwater drones.

Collaborative innovation ahead

NTT Communications has developed a new edition of the unique drone used for this study. In response to a request from Prof. Satoh, a further sampler was added in order that two samples may be collected during a single dive. Moreover, the cable length between the controller and drone was prolonged from 150 meters to 300 meters and the battery is now changeable, so researchers can proceed their survey work for a complete day.

Prof. Satoh is now working with two mesophotic coral specialists on the University of the Ryukyus, Dr. Frederick Singer and Dr. Saki Harii, to further test this method at study sites near Sesoko Island, using the brand new and improved drones. He hopes to revolutionize the way in which coral surveys are conducted. Currently, surveys are limited to very restricted spots, but with the assistance of those advanced underwater drones, scientists can extend their research from the shallowest regions to depths of 60 meters and beyond. “My ideal survey would come with your entire spectrum of the coral reef, from the shallow waters to the mesophotic zones, and even the sandy depths. These machines provide a wonderful method for conducting broader eDNA monitoring studies,” he remarked.