At the Okinawa Institute of Science and Technology (OIST), scientists from the Marine Genomics Unit, in collaboration with Japanese telecommunications company NTT Communications, identified for the first time the genera of mesophotic corals at using eDNA collected by underwater drones.
Their research was published in the journal Royal Society Open Science. Now, with the help of submersible robots, large-scale monitoring of coral eDNA can be carried out without resorting to direct observations during scuba diving or scientific snorkeling.
Mesophotic (“mid-light”) coral ecosystems are light-dependent tropical or subtropical habitats found at depths of 30 to 150 meters. They are unique because they support more native species than shallow-water coral ecosystems. Despite this, they are largely unexplored and further research is needed to understand their fundamental biology.
Researchers who study corals access these invertebrate reef builders through snorkeling and scuba diving, but these methods have limitations, particularly when identifying corals at deeper depths. Using the genetic material that organisms expel from their bodies into their environment (environmental DNA or eDNA), scientists can identify the types of corals and other organisms living in a particular habitat, providing a powerful tool for assessment of biodiversity.
Studying coral eDNA offers unique advantages. First, unlike fish, corals are stationary, eliminating any uncertainty about their location. Second, they constantly secrete mucus into the sea, providing plenty of coral eDNA for sampling. For this study, the researchers analyzed mitochondrial DNA, which is more abundant and of higher quality than nuclear DNA, improving the accuracy of their results.
Faster, easier monitoring of coral reefs
Japan’s mesophotic coral ecosystems (MCEs) are home to one of the greatest diversities of stony corals (Scleractinia) in the world, making them particularly important to researchers but difficult to monitor as they are often located at deeper depths . Additionally, to accurately monitor corals, scientists need skills in scuba diving and taxonomy, which can be difficult. Existing methods for monitoring MCEs therefore impose limitations on conducting in-depth investigations, and new methods are needed.
In October 2022, Professor Noriyuki Satoh, Head of the Marine Genomics Unit, was approached by Shinichiro Nagahama of NTT Communications who had learned of his research on coral eDNA methods. Nagahama suggested using his underwater drones to collect samples from deeper coral reefs to analyze eDNA. Professor Satoh then put forward the idea of using drones to conduct in-depth studies of mesophotic corals at greater depths.
Kerama National Park in Japan, about 30 km west of Okinawa Island, has some of the clearest waters in the Okinawa archipelago. Often referred to as Kerama blue, these waters provided an excellent opportunity for researchers to test this new sampling technique. They collected seawater samples, each measuring 0.5 liters, between 1 and 2 meters above the coral reefs (between 20 and 80 meters deep).
Sampling sites were chosen from 24 locations in six different areas around the picturesque Zamami Island. The next step was to submit these samples to coral metabarcoding analyses, which use scleractinian-specific genetic markers to identify the different coral genera present in each sample.
Using the results of the eDNA analysis, the researchers were able to identify the corals to the genus level. The presence and absence of certain genera of hard corals shown by this method indicate that the reefs around the Kerama Islands had different compositions of hard corals depending on location and depth. For example, the genus Acropora had the highest ratios at 11 sites, indicating that these corals are common on the reefs of Zamami Island.
The researchers also found that the proportion of Acropora eDNA was higher on shallow reefs and upper slope crests, while the proportion of the genus Porites increased on mesophotic sites. Regarding depth, Acropora was easily detected on shallow reefs (≤15 meters), while other genera were more frequently found on deeper reefs (>20 meters).
To study corals using eDNA metabarcoding methods, deeper sequencing of the mitochondrial genomes of stony corals is needed, and this study suggests that it may be possible to more effectively monitor mesophotic corals at the generic level using eDNA collected by underwater drones.
Collaborative innovation to come
NTT Communications has developed a new version of the original drone used for this study. In response to a request from Professor Satoh, an additional sampler was added so that two samples could be collected during a single dive. In addition, the length of the cable between the controller and the drone has been extended from 150 meters to 300 meters and the battery is now replaceable, so that researchers can continue their investigative work for a whole day.
Professor Satoh is currently working with two mesophotic coral specialists from 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 new and improved drones. He hopes to revolutionize the way coral studies are conducted. Currently, surveys are limited to very small locations, but with the help of these advanced underwater drones, scientists can expand their research from the shallowest regions to depths of 60 meters and beyond.
“My ideal study would include the full spectrum of coral reefs, from shallow waters to mesophotic zones, and even sandy depths. These machines provide an excellent method for conducting broader eDNA monitoring studies,” said Dr. he declared.
More information:
Koki Nishitsuji et al, Possible monitoring of mesophotic scleractinian corals using an underwater mini-ROV to sample coral eDNA, Royal Society Open Science (2024). DOI: 10.1098/rsos.221586
Provided by Okinawa Institute of Science and Technology
Quote: Diving deeper into our oceans: Underwater drones open new doors to global coral reef research (February 15, 2024) retrieved February 15, 2024 from
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