Detection of coral biodiversity in seawater samples

Researchers from the Okinawa Institute of Science and Technology (OIST) have developed a method to measure coral biodiversity by extracting environmental DNA (or eDNA) from liters of surface seawater collected from above coral reefs. It has been confirmed that the method works through observations made by scientific divers in the same areas of the ocean.

The research, which was conducted in collaboration with the Okinawa Prefecture Environmental Science Center and the University of Tokyo, is published in Proceedings of the Royal Society B: Biological Sciences. It paved the way for comprehensive, large-scale surveys of reef-building, and it removes reliance on direct observations made through scientific dives or snorkels.

“Beautiful corals in subtropical and tropical seas represent only 0.2% of the entire ocean,” said co-author Professor Nori Satoh, Principal Investigator in the Marine Genome Unit at OIST. “However, it is the most biodiverse area in the ocean, and is home to about 30% of all marine life. Reef-building corals play a major role in reef formation, but recent global warming and other factors have caused many corals to bleach. Coral reefs are at risk of disappearing.”

To preserve and protect coral reefs, it is important to first know what corals are on the reef and how the composition of the reef changes over time. Previously, the only way to effectively survey coral reefs was through divers and snorkelers observing the reefs directly and recording species and changes over time. This was time consuming, expensive and labor intensive. But researchers are now using DNA that organisms release into the environment, through skin, waste products, and mucus. By extracting eDNA from seawater and analyzing it, a clear picture of the organisms that live in that part of the ocean can be found, without having to enter the water.

Reef building corals, or hard corals, are vital parts of the reef. It is estimated that there are approximately 1,300 coral species in 236 genera worldwide. These corals release mucus into the surrounding seawater, which contains part of their DNA. In 2021, researchers from OIST and the University of Tokyo successfully developed tools to amplify and identify the DNA of 45 genera of corals.

Now, researchers have tested whether these tools are effective and accurate by conducting a large-scale survey of the ocean around Okinawa using the eDNA method and scientific divers. This involved direct visual observation by divers to determine the dominant coral genera and the collection of two or three one-liter bottles of surface seawater at each site. Seawater was filtered as quickly as possible to fix the environmental DNA trapped in the filters and the filters were returned to the OIST laboratory for analysis. Over a four-month period, from early September to late December 2021, 62 sites were surveyed from across the main island of Okinawa and two to four dominant coral genera were recorded in each reef.

“We found that eDNA analysis matches direct scientific observations with over 91% accuracy,” said OIST research scientist Dr. Koki Nishitsuji, first author of the paper. In fact, 41 of the 62 sites were identical. The eDNA method indicated the presence of five dominant coral genera across all 62 sites surveyed. What is more, the results of the environmental DNA method indicated the presence of corals that had not been recorded before. Along the coast. Okinawa.”

The eDNA method requires complex sequence information, and as a result, only 45 out of 236 genera can currently be detected. With more information, the effectiveness of the eDNA method will increase. Although more research is needed, the eDNA method may be able to indicate the presence of corals that are difficult to detect by direct observation.