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Searching for ‘Super Reefs’ Ocean waters are becoming warmer and more acidic, threatening to harm coral reefs. But in the Rock Islands of Paulau in the western Pacific, scientists have found corals that can survive these conditions. (Lux Tonnerre, Creative Commons)

Searching for ‘Super Reefs’

Corals are threatened by changing ocean conditions


A newborn coral—shaped like a very tiny grain of rice—drifts through the open ocean. It gets one chance to choose a home where it might survive. After settling down, it never moves again. If it finds the right place, the young coral dives down and begins adding to an underwater metropolis pulsing with life. But will its new neighborhood continue to thrive or go downhill in the future?

Corals are superheroes in the oceans. Majestic reefs arise from the hard skeletons corals build around themselves. These can withstand centuries of being battered by waves, and they provide habitats for a spectacular array of fish and other critters. Inside their soft tissues, corals also offer protection for another inhabitant: algae. These microscopic plants use the sunlight streaming into the ocean to make food and share it with their coral hosts, trading dinner for shelter.

But like any superhero, corals have weaknesses. When ocean waters warm up, their algae die or are evicted from their coral homes. The algae give corals their vibrant color, so their departure leaves corals stark white—a process known as coral bleaching. Bleached corals may look like elegant marble sculptures, but they are starving. A few weeks of this too-strict diet can be fatal.

The villain in this story is carbon dioxide (CO2). Our fossil-fueled lifestyles release CO2 into atmosphere, where it serves as an insulating blanket warming our planet. The oceans have been absorbing the brunt of this excess heat, making coral bleaching more common.

CO2 also threatens corals in another way. It mixes into seawater, driving a domino chain of chemical reactions that changes the ocean’s pH (a measure of how acidic or basic a liquid is). As the ocean becomes more acidic (lower pH), a key molecule called carbonate becomes scarcer in seawater. Carbonate is what corals use to construct their skeletons, so as the ocean’s pH declines, building skeletons becomes more arduous.

In the past, when our newborn coral had found the perfect reef on which to settle, it might have grown for hundreds of years. Today, climate change is rapidly creating unfavorable conditions on once-ideal reefs.

Is there any hope?

A natural laboratory

The answer to that question lies in our ability to understand whether some corals could handle the increasingly adverse conditions of their oceanic home. We can find clues from corals that are already living in seawater with higher temperatures and/or lower pH, as well as corals that have survived past heat waves.

Anne Cohen, a scientist at Woods Hole Oceanographic Institution, has focused on doing exactly that. In partnership with other coral reef scientists, conservation organizations, and several coral reef island nations, she and scientists in her lab launched an initiative to find “Super Reefs”—coral reefs that can survive extreme conditions. They have explored corals from the Pacific coast of Panama, across the equatorial Pacific, and into the South China Sea and Micronesia.  In some places, they have discovered coral reefs that have survived heat waves and other reefs that thrive despite very warm or low-pH waters.

One of those places is the island country of Palau in the western Pacific Ocean—at once a tropical paradise and a fantastic natural laboratory. It has an extensive barrier reef offshore in the open ocean. Farther inland, south of Palau’s mainland, is an area known as the Rock Islands with hundreds of small islands, many distinctively umbrella-shaped, that are surrounded by vibrant coral reefs. 

In a collaboration with The Nature Conservancy, Cohen and her students discovered that Rock Islands reefs have waters that are much warmer and have lower pH than Palau’s open ocean reefs. Although these conditions should be stressful to corals, those in the Rock Islands are doing well.

They also found that Rock Island corals are less vulnerable to bleaching. During two successive global-scale bleaching events, corals in the Rock Islands experienced minimal bleaching, even though they were exposed to water temperatures much higher than other places that did bleach.

Closets in the skeletons

Because of the way corals grow, we can find out how a coral responded to heat in the past—even if there was no one there to see it—by extracting core samples of coral skeletons. Corals form their skeletons and grow upward and outward, adding floors and wings to their undersea castles. As they grow, they leave behind a detailed record in their skeleton—a diary, if you will. Learn to read it and it can reveal how the coral and the reef they live in were doing years and even decades ago.

We take cores using a drill, powered by compressed air from an oxygen tank. The corals that we core grow in a dome/sphere shape. The living coral tissue is only at the surface of the sphere, up to a few centimeters thick (about 1/3 of an inch at most). Deeper below is the old skeleton, which no longer has living tissue in it.

The cores we take are between 1 and 2.5 inches in diameter. So we are only affecting that surface area of live coral. The polyps that are around the core hole are unaffected. We then plug the core hole using a cap made from underwater epoxy or cement, so that the plug is level with the unaffected polyps that surround the core hole. Those polyps can then grow “sideways,” that is, they divide asexually to produce new polyps that spread over the clean epoxy-cemented area. These new polyps then continue growing upward with the rest of the colony.

We have monitored cored colonies in many places and have never observed mortality from coring. These new polyps in the cored area grow a little bit more slowly as they spread over the area, but then they catch up to the rest of the colony as they start to grow upward.

If we put our coral cores in a CAT scanner, you can see bands of growth, much like the rings in trees. With Cohen and her students Hannah Barkley and Tom DeCarlo, we discovered a particular kind of band produced by the coral when it is bleaching. By looking for these bleaching bands, you can determine how a coral colony responded to temperature spikes in past years.

Across the oceans, a climate cycle called the El Niño Southern Oscillation (ENSO) can cause strong heat waves during its El Niño phase. This can lead to widespread bleaching and coral mortality. Some reefs are more heavily affected by El Niño, bleaching heavily and sometimes losing nearly all their coral. Some of these reefs may take decades to recover, while others are resilient and bounce back fairly quickly. Looking at the cores from many regions we can better pinpoint which reefs are resilient and which are resistant to bleaching despite high temperatures.

An important part of the Super Reefs initiative is to uncover how Super Reef corals tolerate conditions that kill or stifle corals elsewhere. This can help us better understand corals’ ability to adapt and evolve, and give us insight into the future of coral reefs.  

Huskies and chihuahuas  

So, just how do these reefs defy the odds? Can these reefs help other reefs that aren’t as tough? Building on the research cited above, I’m adding an additional tool—genetics—to help further elucidate this mystery. 

As a graduate student in the MIT-WHOI Joint Program, I teamed up with Cohen Lab to study these resilient corals. My goal is to better understand how they tolerate relatively extreme conditions. To answer these questions, I had to go to the source. I joined the team’s expeditions aboard sailboats and research vessels, dove the reefs and took small tissue samples from which I could extract DNA. I focused on a coral that is commonly found across the Indo-Pacific: Porites lobata. This species, which grows like a sphere, can reach the size of small car and live for hundreds of years.

Using DNA allows me to determine how closely related, or “genetically connected,” corals from different reefs are to one another. This tells us whether offspring from one reef have dispersed to other reefs where they were able to reproduce and incorporate themselves. If the larval offspring from one reef can’t physically make it to a second reef, or can’t survive to adulthood even if they do, then these reefs don’t exchange genetic material. We would consider them genetically isolated. In nature, populations usually lie on a spectrum between fully connected and fully isolated. 

Connectivity and isolation can be beneficial in different circumstances.  When newcomers reproduce with individuals in an established population, their offspring may have novel genetic combinations that may be even better suited for that environment, so that more of them survive, reproduce, and prosper. In such a case, connectivity aids the well-known process of natural selection.

But that’s not always the case. Isolation can sometimes make natural selection more efficient by letting it pick winners without bringing in new players in every round. New “blood” may bring new tricks, but it can also wash out the tried-and-true ones.

Let’s take, for example, our beloved fluffy companions: dogs. Dog breeders created breeds by selecting for characteristics that were best suited to certain environments or tasks. A husky is well equipped to tolerate cold temperatures, frolic in the snow, and pull sleds. A chihuahua, not so much.

Now, if breeders wanted to develop a small dog that was well suited for places with both very cold winters and very hot summers, then mixing a chihuahua and a husky may just yield the combination of genetics they need. Connectivity in this case would be beneficial. However, it would have been much more difficult for the breeder to get the qualities they wanted in a husky if they kept adding a chihuahua parent into the line every few generations. Here, connectivity would have worked against becoming better adapted to cold conditions.

Seeding resilient reefs

Nature does its own breeding through natural selection. In Palau’s Rock Islands for example, corals that can’t withstand warmer temperatures or low pH probably won’t make it. In the central Pacific, corals that can’t tolerate periodic heat spikes can get filtered out. The degree to which these reefs are isolated or connected from other nearby reefs can make this process more or less efficient.

By studying DNA of corals from reefs that live under more extreme conditions, I can determine if their resilience is more likely enhanced by being genetically isolated, or if perhaps some other aspects of the environment help them offset stressful conditions.

At the same time, as our oceans warm up and conditions in reefs around the globe become more extreme, connectivity can play a vital role in spreading corals that are better at dealing with those conditions to new places. Figuring out where they might spread is where my field, population genetics, can help.

Measuring how related different reefs are to one another can also tell us how often offspring from one area make it to another. If two areas are genetically connected now, they will likely remain connected in the near future. If we combine genetic connectivity information with knowledge of where the more tolerant reefs are, then we can begin to build a map of which reefs can serve as sources for resilient corals and which other reefs dispersing larvae of tolerant corals can go to and thrive.

The Rock Islands are a current-day simulation of what scientists expect temperature and pH conditions at coral reefs worldwide will be like in a few decades. In other words, over time, conditions in the outer reefs will become more and more similar to how the Rock Islands are now. The corals that have adapted to and thrive under conditions in the Rock Islands could start providing more offspring into the outer reefs. This dynamic can provide a stream of new heat-tolerant baby corals that can replenish and maintain the outer reefs over time. The same dynamic can help sustain reefs across larger spatial scales, such as the central Pacific.

Scientists are searching for other reefs like those in Palau and the central Pacific that may fare well into the near future. It is important to remember, however, that these Super Reefs won’t be able to save all the world’s corals. They will be exceptions in a global trend of reef decline. Taking care of our oceans and our planet should be a top priority. As much as corals would like to keep up with our changing world, we need to do what we can to slow down climate change and give them a better chance to catch up.  

This research was funded by National Science Foundation, the Dalio Foundation, Inc., the WHOI Access to the Sea Fund, the WHOI Ocean Venture Fund, the WHOI Coastal Ocean Institute, the MIT Sea Grant Office, The Nature Conservancy, New England Aquarium, and the Robertson Foundation. The Charles M. Vest Presidential Fellowship, the National Defense Science and Engineering Graduate Fellowship Program, Gates Millennium Scholars Program, the Martin Family Fellowship for Sustainability, the American Association of University Women, and the J. Seward Johnson Fund provided funding for Hanny Rivera.

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