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Just a few meters beneath the clear, blue waters of Okinawa, reef-building corals known as Scleractinia have quietly lived for centuries. Slowly, layer by layer, they have constructed intricate, rigid structures made of calcium carbonate to form the vibrant coral reefs of today.

Now, researchers have developed a comprehensive system to identify the diversity of these hard corals using only a sample of surface seawater. This environmental DNA (eDNA) metabarcoding system can successfully detect 83 of the 85 genera of reef-building corals known in Japan, enabling their effective and high-precision monitoring.

Published in Galaxea, this new study is the result of a collaboration between the Okinawa Institute of Science and Technology (OIST), the Incorporated Foundation Okinawa Environment Science Center, the University of the Ryukyus, the Okinawa Churashima Foundation Institute, Miyazaki University, and Kyushu University.

From unreliable surveys to environmental DNA precision

For years, coral surveys were carried out by trained divers and snorkelers who visited each reef, identified coral species one by one, and returned regularly to record any changes—a process that is both time-consuming and often imprecise. "Moreover, distinguishing corals can be challenging, as their external features or morphology show little variation within a species," explained Professor Nori Satoh of OIST's Marine Genomics Unit and co-author of the study.

"A comprehensive survey using this method is not feasible, as divers are constrained by time and depth. They may be able to examine coral reefs spanning 10 to 20 meters, but surveying areas of 10 or even 100 kilometers is beyond their capacity," he added. While underwater video imaging has improved large-scale assessments, these conventional monitoring methods remain limited in scope.

The new method solves many of these limitations. Corals, like all living organisms, are continuously shedding their DNA into the environment. Their mucus, debris, and other excretory material floats in seawater. By collecting and analyzing this eDNA, researchers will now be able to detect and monitor important reef-building corals with better accuracy, efficiency, and cost-effectiveness. The system, known as Scleractinian Environmental DNA Metabarcoding (Scl-eDNA-M), will allow researchers to monitor coral diversity without ever having to enter the water.

Building a comprehensive coral database

In 2021, researchers from OIST and the University of Tokyo developed a new environmental DNA-based tool for detecting coral species. When they used it to identify the different genera of Japan's Scleractinia, they found that many of the known Scleractinia genera could not be identified due to gaps or inconsistencies in reference mitochondrial genome sequence libraries, which is required for comparison.

While an estimated 85 genera of reef-building stony corals inhabit Japanese waters, internationally recognized databases contained data for only about 60 genera, leaving roughly 25 genera undetected. This study addresses those deficiencies.

Researchers sequenced nearly two-thirds of Japan's known Scleractinia genera to establish a comprehensive coral detection system. Their findings revealed a previously unrecognized diversity across the Ryukyu Archipelago, an exceptional richness of reef-building corals along Okinawa's coastline. Many of these coral genera may have been overlooked in previous surveys.

This discovery suggests that Okinawa's coastline could be home to a far greater coral diversity than previously thought. In addition, the Scl-eDNA-M system is highly likely to cover the majority of Scleractinia genera found in the Pacific Ocean.

"We collected samples from Okinawa's main and surrounding islands. Using this system, we identified at least 70 coral genera found in these waters, revealing Okinawa's rich reef biodiversity, which had remained largely unknown until now. Additionally, our samples from Kerama, Miyako, and Kumejima highlight the region's ecological significance and its vital role in future coral reef conservation," explained Prof. Satoh.

An important step toward conservation

Coral reefs are among the most biodiverse ecosystems on Earth, covering 0.2% of the ocean but supporting over 30% of all marine species. Coral reefs also play a crucial role in protecting coastlines from storms and erosion, sustaining fisheries, and supporting millions of livelihoods worldwide. These ecosystems are facing severe threats. Rising ocean temperatures have caused widespread coral bleaching, leading to coral death and the disappearance of reefs.

To protect coral reefs, researchers must first understand them—identifying which coral species are present in each reef and tracking changes over time. Frequent, detailed monitoring is essential for conservation efforts, and this new system provides a powerful tool to make that possible.

"Corals can now be found at the entrance to Tokyo Bay—another sign of climate change reshaping marine ecosystems. Such shifts highlight the urgent need for accurate monitoring, and our newly developed system offers a powerful solution," said Prof. Satoh. Through it, researchers can detect Scleractinian coral genera across Japan. "We can track coral populations in Tokyo Bay, monitor their changes over time, and anticipate future shifts."

"We are now preparing to test this system beyond Japan—in locations such as Palau and Taiwan, with plans to expand to Hawaii as well," added Prof. Satoh. As this system is applied to new regions, it is expected to usher in a new era of coral reef conservation, especially at a time when the world's oceans need it most.