Genomics can help restore coral reefs in the Indian Ocean

Oliver Selmoni and Stéphane Joost from EPFL ENAC's Laboratory of Geographic Information Systems (LASIG) were contacted by the United Nations Development Programme (UNDP) after they took part in an environmental genomics research project with the ENTROPIE research unit at the French National Research Institute for Sustainable Development (IRD) in Nouméa, New Caledonia. Together with their New Caledonian partners, they are now acting as scientific consultants in a UNDP-led coral reef restoration project in Mauritius and Seychelles. Selmoni and Joost will combine their genomics know-how with insight from local scientists and marine conservation NGOs to identify corals that are able to withstand human and environmental pressure. These hardier species will then be used to restore damaged reefs.

When Selmoni joined the project in January of this year, he spent several days alongside scientists from the Mauritius Oceanography Institute, sharing environmental-genomics insight with those involved in day-to-day reef conservation. “Working out into the field with local experts was an incredible learning experience,” he says. “Without their knowledge, we wouldn’t have known where to find the right species, where to dive or how to avoid dangerous currents.”

After demonstrating genomics data-analysis methods and the associated software to the local scientists, Selmoni joined them on a dive campaign to collect corals from the reef before helping them analyze the samples. Having already worked on reefs in New Caledonia, he’s seen first-hand how conditions differ markedly from one location to the next. In Mauritius, for instance, the lagoons are so shallow that full scuba gear isn’t required for most dives – a simple snorkel mask is often all that’s needed. The local reefs are also home to different species. Mauritius is a popular tourist destination and has a high population density (1.2 million people in a country spanning just 2,040 km²), all of which places greater stress on the fragile lagoon ecosystem.

Out at sea, the team collected samples with methodical precision. Working from a boat, the scientists identified two flagship species (Acropora muricata and Pocillopora damicornis), entered the water, took photographs, and used a pair of tongs to collect a tiny sample of coral, taking care not to damage the reef. The samples were then stored in tubes for analysis. And, crucially, the sampled corals were labeled so that they can be retrieved in case their genomic analysis should reveal the presence genetic traits related to stress-tolerance.

Selmoni spent the early part of February in Seychelles, working with marine conservation NGOs. He also paid a visit to the University of Seychelles to examine possible equipment for a new molecular biology laboratory. The final leg of his journey took him back to Mauritius, where he gave a presentation on extracting genetic material from corals, before leaving behind the early-year heat and humidity of the Indian Ocean and returning to a sunny – albeit significantly colder – Switzerland. The samples were sent to Australia for sequencing. The results will be analyzed in October, when Selmoni will head back to the Indian Ocean to work once again with the local scientists.

Selmoni believes that collaboration and skills-sharing between these two island nations will prove essential to better coral reef conservation. “EPFL’s role in this joint project is to provide know-how in connecting geoenvironmental and genomics information, which is yet another tool in the fight against coral reef decline,” he says. A method called coral gardening – which entails growing coral colonies to restore reefs – is already in use in this part of the world. Using genomics to identify stress-resistant populations will help make this method more widespread and evidence-based. “Right now, the region is lacking the equipment and facilities needed to employ genomics-based conservation methods,” adds Selmoni, from EPFL’s School of Architecture, Civil and Environmental Engineering (ENAC). By the end of this year, the scientists in Mauritius and Seychelles will be in a position to continue their genetic analysis work well into the future and, crucially, without outside support.