Sending scuba divers down to survey corals is time-consuming and expensive. In recent years, scientists have developed other methods to determine what kinds of corals are down there just by collecting water samples, sometimes right from the surface. These rely on analysis of the DNA that the corals secrete into the water.

Now, a team of marine scientists based in Japan, an archipelagic nation with a high level of coral biodiversity, has developed a system that can detect nearly all of the country’s 85 reef-building corals based on this free-floating genetic material in the environment, which scientists call environmental DNA, or eDNA. They released the results in a new study published in the journal Galaxea on May 22.

“It’s an incredible system that so far no one [else] can do,” study co-author Noriyuki Satoh, head of the marine genomics unit at the Okinawa Institute of Science and Technology (OIST), told Mongabay. Essentially, no other research group in the world has achieved the same level of detection accuracy and coverage for corals using eDNA as Satoh’s team.

eDNA research on corals can help scientists understand the changes wrought by global warming and marine pollution by providing coral identification data faster and in some cases more accurately. Satoh said OIST’s system can help save 10 or 20 experts from needing to work for a week or two on a diving survey in Japanese islands — and he and his team plan to expand it to other countries.

All organisms secrete DNA into the soil, air or water around them. Research designed to read these signals has blossomed over the last decade, including for corals. These are essential to study because of the key role they play in reef ecosystems — among the most biodiverse ecosystems on Earth. Corals are ideal for eDNA research because they release a lot of mucus into the water.

Scientists in Hawai‘i published a study in the journal Environmental DNA in 2019 showing that the concentration of coral eDNA in water samples closely matched the results from visual surveys. In other words, it’s possible not just to identify corals from water samples but also to roughly estimate their level of abundance.

This new field of coral research is developing at a critical juncture. Global coverage of living corals has declined by half since the 1950s, and a series of mass bleaching events have hit corals over the last three decades. Coral bleaching is a highly stressful event in which warming ocean waters trigger corals into expelling their symbiotic algae, the organisms that give them their rainbow of colors. The latest and most severe mass bleaching has been going on since early 2023 and has been “devastatingly lethal” for many of the world’s corals, according to a 2024 editorial in the journal Coral Reefs.

Japan’s waters have warmed faster than the global average over the last century. Corals can now be found at the entrance to Tokyo Bay, which could indicate recent coral expansion in the bay and is “another sign of climate change reshaping marine ecosystems,” Satoh said.

Satoh and his team first presented their method, which they call scleractinian environmental DNA metabarcoding, in a 2021 paper in the journal Frontiers in Marine Science. Researchers extract short segments of DNA from a water sample — the DNA is often a bit degraded, so it’s hard to get the long fragments one might find in tissue samples — and amplify the amount using polymerase chain reaction. They then analyze the DNA with the help of high-throughput sequencing to identify the unique sequences, often called DNA barcodes, of the various genera of reef-building corals (order Scleractinia) that are present.

The method can identify only down to the genus level, not the species level. It’s highly accurate, perhaps even more so than some visual observations, as coral features and morphology can be hard to distinguish, Satoh said. Samples can be extracted from surface water if the reef is no more than about 30 meters (98 feet) in depth, or with the help of an underwater robot in other cases, he said.

The method is broadly similar to that being used by coral eDNA research teams elsewhere, but Japan has an exceptional diversity of reef-building corals — 85 known genera — and Satoh’s team has now put together an especially comprehensive identification system using their method. Following the new study, they can identify 83 out of the 85 genera from water samples. However, 25 of the genera were lumped into groups of two or three genera as their sequences in the targeted gene region were identical, meaning further work will be required to refine the system. All 83 are shallow-water corals; the OIST researchers left the two other genera out of the study because of their rarity and depth.

“This system provides a powerful tool for comprehensive, eDNA-based survey of scleractinians in Japan,” the study says.

As with all eDNA work, the study involved comparing the DNA extracted from the water samples against existing genome records. In this case, the reference genomes were in a public database housed at the U.S. National Center for Biotechnology Information in Bethesda, Maryland. In the course of the study, Satoh and his colleagues also generated 22 sequences, adding them to that database, so that it now holds updated sequences for 83 reef-building coral genera from Japan, up from 61.

With all of this work completed, the system “now has the potential to actually be used in monitoring biodiversity around Japan; identifying where certain types of coral are in decline, or are in growth, to be able to inform conservation efforts,” OIST said in a statement to Mongabay.

Satoh said he has plans to test the system on reef-building corals in Palau, Taiwan and Hawai‘i.

Patrick Nichols, a marine ecologist at the University of Hawai‘i at Mānoa, who led the 2019 study and wasn’t involved with the new study, said this general type of metabarcoding should work “for other [non-scleractininan] corals and across other systems,” but added a lot of work remains to be done to get coral DNA sequences into public databases.

He praised OIST for doing that work on scleractinians in Japan, saying the institution has been “doing a lot of good work in recent years.”

“This is the sort of baseline we need in order to better understand what happens after bleaching … or any sort of change,” Nichols said.

Laurence Dugal, a research scientist for the government of Western Australia and an expert in eDNA biomonitoring, said the OIST study was “an important step forward in coral eDNA research” in a statement emailed to Mongabay.

“The authors have created a valuable global reference resource that will support future biodiversity monitoring with eDNA metabarcoding,” Dugal said.

Western Australia-based teams at Curtin University and the Australian Institute of Marine Science have been testing eDNA methods for offshore coral systems since 2019, Dugal said.

Banner image: Bleached coral. There have been four mass bleaching events in the last three decades, largely due to rising sea temperatures that cause corals to expel the symbiotic algae living in their tissue, a phenomenon known as bleaching. This photograph was taken near Nishidomari, Otsuki town, Kochi, Japan. Image courtesy of Takuma Mezaki.

Climate refugees? As the sea warms, corals thrive in Japan’s cool waters

Citations:

Hisata, K., Nagata, T., Kanai, M., Sinniger, F., Nagata, F., Suwa, M., … Satoh, N. (2025). An eDNA metabarcoding system for detecting scleractinian corals to the generic level along the Japanese coast. Galaxea, Journal of Coral Reef Studies, 27(1), 13-29. doi:10.3755/galaxea.g27d-5

Nichols, P. K., & Marko, P. B. (2019). Rapid assessment of coral cover from environmental DNA in Hawai‘i. Environmental DNA, 1(1), 40-53. doi:10.1002/edn3.8

Eddy, T. D., Lam, V. W., Reygondeau, G., Cisneros-Montemayor, A. M., Greer, K., Palomares, M. L. D., … Cheung, W. W. (2021). Global decline in capacity of coral reefs to provide ecosystem services. One Earth, 4(9), 1278-1285. doi:10.1016/j.oneear.2021.08.016

Reimer, J. D., Peixoto, R. S., Davies, S. W., Traylor-Knowles, N., Short, M. L., Cabral-Tena, R. A., … Voolstra, C. R. (2024). The fourth global coral bleaching event: Where do we go from here?. Coral Reefs, 43(4), 1121-1125. doi:10.1007/s00338-024-02504-w

Shinzato, C., Narisoko, H., Nishitsuji, K., Nagata, T., Satoh, N., & Inoue, J. (2021). Novel mitochondrial DNA markers for scleractinian corals and generic-level environmental DNA metabarcoding. Frontiers in Marine Science, 8, 758207. doi:10.3389/fmars.2021.758207

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