Scientists in Japan have developed a ground-breaking new environmental DNA (eDNA) ‘barcoding’ system that can successfully detect 83 out of the 85 types of reef-building corals across the region, taking effective monitoring abilities to a new level.

A few metres beneath the clear, blue waters of Okinawa these reef-building corals have lived quietly for centuries where, slowly – and layer by layer – they have constructed intricate structures made of calcium carbonate to form the vibrant coral reefs today.

For many years, surveying these coral reefs was the work of trained divers and snorkelers who visited each reef, identified coral species one-by-one, and returned regularly to record any changes. It was a process both time-consuming and all too often, imprecise.

Not only that, but distinguishing corals “can be challenging” said Professor Nori Satoh of Okinawa Institute of Science and Technology, the study’s co-author, “as their external features of morphology show little variation within a species.”

“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 metres, but surveying areas of 10 or even 100 kilometres is beyond their capacity,” he added. 

The Institute’s new method, therefore, solves many of these limitations. 

Corals – like most living organisms are continuously shedding their DNA into the environment. Their mucus, debris, and other excretory material floats in seawater. By collecting and analysing 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 (the species of coral) Environmental DNA Metabarcoding will allow researchers to monitor coral diversity without ever having to enter the water.

Researchers sequenced nearly two-thirds of Japan’s known Scleractinia genera to establish a comprehensive coral detection system. Along the way, they discovered previously unrecognised diversity across the Ryuku Archipelago, an exceptional richness of reef-building corals along Okinawa’s coastline. 

Many of these coral genera may have been previously overlooked, suggesting that Okinawa’s coastline could be home to a far greater coral diversity than previously thought.

“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,” said Professor Satoh. 

“Additionally, our samples from Kerama, Miyako, and Kumejima highlight the region’s ecological significance and its vital role in future coral reef conservation.”

Coral reefs are among the most biodiverse ecosystems on Earth, covering 0.2% of the ocean while 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, however, facing severe threats. Rising ocean temperatures have caused widespread coral bleaching in recent years, leading to coral death and the disappearance of reefs.

To protect them, researchers are on a mission to better 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 reshaping marine ecosystems. Such shifts highlight the urgent need for accurate monitoring, and our newly developed system offers a powerful solution,” said Professor Satoh. “We can track coral populations in Tokyo Bay, monitor their changes over time, and anticipate future shifts.”

The system is now being prepared for testing beyond Japan and in locations such as Palau and Taiwan with plans to extend to Hawaii in the near future. As it is applied to new regions, it is expected to usher in a new era of coral reef conservation at a time when the world’s ocean needs it the most.

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