Skip to main content

Scientists Are Learning How to Help Coral Reefs Save Themselves

By understanding corals’ strengths, scientists can guide conservation efforts

Emily Howells scuba over Great Barrier Reef coral
Emily Howells surveys coral bleaching on the Great Barrier Reef. | Grant Cameron

Cody Clements never saw the eel coming. The marine ecologist was collecting corals for an experiment in shallow waters off the island of Mo'orea, French Polynesia, when a six- to seven-foot moray eel shot out from a crevice in the reef. Before Clements could react, the creature sank its teeth into his hand and began yanking it around like a rag doll.

The eel released Clements' hand from its powerful jaws, but he quickly realized his ordeal was just beginning.

"My thumb was, like, dangling off," he said. "It was pretty bad. To be honest, in the moment I thought I might bleed to death."

Thinking quickly, Clements used his rash guard as a tourniquet while he rushed to shore. But preventing blood loss was no easy task. Moray eels, which rarely attack humans, have backwards-jutting teeth and toxic mucus that cause notoriously painful, bloody wounds. Fortunately, Clements made it back to shore and was taken to the hospital on Mo'orea, where he received 67 stitches. He underwent surgery in Tahiti the next day. Ten weeks later, the scientist had a scar extending the length of his palm, but he could finally move his thumb again.

Moray eel
Moray eel. | David Clode/Unsplash

Before he suddenly found himself grappling with the question of his own survival on the reef, Clements, a postdoctoral fellow at the Georgia Institute of Technology, was puzzling over a matter of life-or-death for reefs themselves — how does the diversity of coral species impact a reef's survival and productivity?

"Other people have tested how coral diversity impacts the number and diversity of local fish communities and things of that nature," said Clements. "But, 'How does biodiversity of corals impact corals?' That was a fairly novel question."

As climate change warms the world's oceans to ever-higher extremes, coral reefs face a bleak future. A 2021 report found that 14% of the world's reefs died due to rising ocean temperatures between 2008 and 2019.

As the situation grows more dire, researchers like Clements are going the extra mile to understand what makes corals tick. By learning how corals survive under different conditions and why some seem to be hardier than others, scientists may be able to assist corals in their battle against extinction.

These research efforts are as varied as the corals themselves. Some scientists are investigating how corals function as communities while others are hunting for specially adapted "super reefs." Still others are selectively breeding corals in the lab or applying biomedical techniques to understand the genetic basis of heat tolerance.

But while playing to corals' strengths may make some difference in helping these vital ecosystems withstand climate change, scientists urge that these efforts be paired with curbing emissions.

Chess Board Corals

To investigate the impact of coral diversity on coral communities, Clements leveraged a method of planting corals that he had recently developed, which involved planting corals in Coke bottles.

"I can just screw them in and then unscrew them and weigh them," he said. "It's an easy way to manipulate them."

Building on this technique, Clements assembled what he calls "chess boards" — Coke bottles with sawed-off necks embedded in cement blocks (the chess board squares), with corals planted in each bottle. To sufficiently replicate different levels of community diversity for an October 2021Science Advances paper published with Mark Hay, a professor in the school of biological sciences at Georgia Tech and an associate editor at Science Advances, Clements assembled 48 chess boards, each with 18 corals. The chess boards were assembled at random from a pool of nine coral species, with plots containing either one, three, six, or nine different species.

chessboard coral experiment
Clements' "chess board" coral experiments. | Cody Clements

The researchers found that corals performed better in more diverse communities — at least, to an extent. Their performance peaked with three to six species, then declined again as the number of species per chess board rose to nine.

"We're still trying to chase down the mechanisms, but my pet hypothesis is that when you have multiple species present, it potentially helps dilute disease," said Clements. "I was seeing in some of my single species plots that a coral would start to get sick and then [the disease] would start spreading in the community. That also goes on in agriculture. There's evidence that if you have mixed-species crops and a disease comes through, [the crop diversity] is going to create barriers for transmission."

Clements noted that while these findings are encouraging, it is still difficult to know how findings about the benefits of diverse coral communities may benefit corals beyond his chess boards.

"We're testing the basic scientific notion, but extrapolating that up to how we're going to use it to rehabilitate reefs is much harder. I picked those nine species because they are some of the most common ones I see. But you don't ever really see that many species in an area as small as the 40 by 40-centimeter experimental coral plots that we created for our experiment."

"We're working from a shifted baseline, going out and looking at a reef that's really degraded now," he added. "But it might not have been like that in the past."

Searching for Super Reefs

When Hannah Barkley was a graduate student, she and her colleagues discovered that some reefs have superpowers.

At the time, Barkley, now a Hawai'i-based research marine biologist with the National Oceanic and Atmospheric Administration, was working with coral researcher Anne Cohen, who runs a lab at the Woods Hole Oceanographic Institution in Falmouth, Massachusetts. Researchers at Cohen's lab were interested in understanding how reefs respond to ocean acidification — especially ways in which some reefs show resilience to this major threat to coral ecosystems. As an ocean absorbs carbon dioxide released into the atmosphere from fossil fuel-emitting activities, its pH falls, resulting in fewer calcium minerals that coral reefs need to build and repair their skeletons, slowing their growth.

"The problem is that identifying resilience to ocean acidification is really challenging," said Barkley. "Most of what we know about ocean acidification has come from controlled laboratory studies. But laboratory conditions and laboratory responses don't always play out as we might predict in a real-life field setting."

To overcome the limitations of lab studies, Barkley said coral researchers have turned their attention to ocean locations where natural processes produce low pH conditions in the wild.

"None of these sites are perfect analogues for ocean acidification," Barkley said. "But when we look at them together, they can tell us something about how reefs might respond to pH changes in the future and what the most sensitive responses are to ocean acidification."

Among these sites are the Rock Islands of Palau, an archipelago of over 500 islands in the western Pacific. Coral reef environments in the area have an average pH of only 7.8, while most other reefs currently have pHs of about 8 to 8.1 — a result of the long time the water lingers in the bays as it winds around labyrinthine rock, gradually growing more acidic.

"The Rock Islands are special because they currently experience predicted end-of-century conditions, both in terms of temperature and pH," said Barkley, referring to ocean heat and acidity projections for the end of the 21st century. "They have very low pH and very high temperature."

For a study published in Science Advances in 2015, Barkley and colleagues traveled to Palau to observe reefs on the archipelago. They found that the low-pH Rock Island reefs had the highest coral cover and coral diversity of any of the reefs they studied on Palau, even those living at high pH levels, where the researchers would have expected corals to do better.

In contrast to most laboratory results preceding the study, the team also found that low pH didn't inhibit the corals' growth — they grew as fast in low-pH conditions as they did at high-pH conditions. The only downside to decreasing pH that Barkley and colleagues observed for corals in Palau was increasing rates of bioerosion, when organisms like mollusks or bivalves eat away at the coral skeleton.

"This result was really exciting because it was the first time that anyone in the coral reef community observed coral reefs that were not only surviving end-of-century pH conditions, but actually appeared to be thriving. Since then, we've seen other examples and other places with corals that share similar adaptive capacities," she said.

The Cohen Lab has uncovered such " super reefs" in the Dongsha Atoll of the South China Sea, Racha Noi, Thailand, and Kanton Island of the Phoenix Islands in the Republic of Kiribati.

Low pH coral reef in Palau. | Hannah Barkley
Low pH coral reef in Palau. | Hannah Barkley

Barkley is quick to note that the study's findings don't imply that corals are off the hook when it comes to surviving increasingly acidic waters.

"Ocean acidification is still a threat to coral reefs," she said. "But we do see these unique places like Palau, where there are special coral reef communities that over the hundreds of thousands of years they've been exposed to low pH, have figured out how to deal with low-pH conditions. However, most reefs won't have the luxury of that long timeframe due to the rate of progressive ocean acidification over the century."

In a follow-up to the Palau study, Barkley and colleagues conducted a laboratory experiment in which they took corals from the low-pH sites on their trip and corals from the high-pH sites and put them in different pH conditions. These included ambient pH conditions on the high-pH reef, ambient conditions on the low-pH reef (the conditions they expect most reefs will see by the end of the century), as well as pHs that were lower than most reefs were expected to experience. They found that the low-pH corals remained healthy and continued to grow at the same rate regardless of what pH they were made to endure.

"This is important because it suggests that they're not only surviving now, but have the potential to withstand further decreases in pH in the future," said Barkley.

The researchers also conducted a habitat-swapping experiment in which they moved corals from a low-pH Palau reef to a high-pH reef and vice-versa, then observed them over 17 months.

"The transplants all died, which was not the result we expected," said Barkley.

"But I don't think this means that these corals can't ultimately seed populations or be the source of coral transplants to other areas," she added. "I think it means the answer is not that simple and that pH is one of many environmental variables that differ between various sites. Corals are so supremely adapted to the specific environment in which they live that it is not just a question of pH in terms of their ability to survive elsewhere."

A La Niña Bleaching Event

In May 2022, Emily Howells found herself with a front row seat to watch a massive bleaching event unfold at the Great Barrier Reef — a process in which corals expel their algae under stressful conditions, turning them white and causing many to starve. It was the kind of event that would have been almost unheard of during La Niña years in the past, when temperatures are generally cooler and wetter. But Howells knows firsthand how fast the reef is changing.

"From my own observations, I can report that I've observed bleaching each year I've been out working on the Great Barrier Reef for the past few years," she said. "And that's not something I have seen, say, when I was a Ph.D. student."

Rapid heat stress experiments test coral thermal tolerance. | AIMS/ Jo Hurford
Rapid heat stress experiments test coral thermal tolerance. | AIMS/ Jo Hurford

Howells is a coral biologist at Southern Cross University in Australia, where she studies the genetic basis of coral heat tolerance. Howells also works with the Reef Restoration and Adaptation Program, measuring variation in heat tolerance among individual corals across the Great Barrier Reef.

"We have a couple of focal coral species and we are sampling up to a thousand corals of those species," said Howells. "We measure and rank their heat tolerance in a rapid heat stress experiment, and then see how much of the variation in heat tolerance among individuals can be explained by their genes."

While Howells admitted it is still too soon to identify the roles different genes play in corals' abilities to tolerate higher temperatures, her team's early research results show that there is a lot of variation in heat tolerance among individuals. The reasons behind this variation are bound to be complicated.

"There are many genes and variants that contribute to the heat tolerance of corals," she said. When Howells began receiving reports from other colleagues about signs of bleaching on the Great Barrier Reef, she and her team went back to one of their research sites in an affected area to see how the corals they had tagged (each with their own GPS identifier) were holding up. While Howells found that most corals had probably experienced some bleaching, she noticed plenty of variation.

"We saw some that were severely bleached, kind of a glowing white color, and others that were living side by side that seemed to be doing okay," she said. "We look forward to kind of incorporating those observations in our understanding of the genetic basis of heat tolerance in corals and seeing if they share the same genetic variants as corals that we've identified as being heat tolerant in previous experiments."

Persian Gulf Fathers, Indian Ocean Mothers

When Howells was a postdoc, she spent time doing research at New York University Abu Dhabi, a campus located in the capital of the United Arab Emirates, which rests on an island off the mainland in the Persian Gulf. Compared to most bodies of water that support tropical coral reefs, the gulf is sweltering — 36°C (96.8°F) or 37°C (98.6°F) in the summer.

To discover whether it was possible to transfer the genetic variants that gave the Persian Gulf corals their heat tolerance into the offspring of less-heat tolerant populations, Howells collected fragments of coral colonies from the reef and brought them to the university's lab. Next, she ventured to a reef on the Indian Ocean side of the United Arab Emirates, where temperatures are cooler, and collected fragments of the same coral species. Once she had gathered all of the specimens together, Howells waited patiently night after night for the corals to spawn.

Persian Gulf Platygyra coral spawning. | Anna Scott
Persian Gulf Platygyra coral spawning. | Anna Scott

At last, Howells and her colleagues succeeded in breeding 50 families of coral larvae — some with both parents from the same region and others with fathers from Abu Dhabi and mothers from the Indian Ocean.

The findings, which were published in Science Advances in August 2021, revealed that selective breeding of corals from an Indian Ocean population with heat-adapted fathers from the Persian Gulf increased the thermal tolerance of offspring to the same level as those with both parents from the Persian Gulf.

"I thought that we would see some gain in heat tolerance, but I didn't think that it would be as high as what we saw," said Howells. "That was really a strong demonstration that heat tolerance is genetically determined and can be passed on to other populations [by selective breeding]."

CRISPR for Corals

Before Phillip Cleves turned his attention to corals, his focus was biomedicine.

"It was always kind of the plan," he said. "When I was an undergrad, my 'aha' moment was when I learned that corals have algae that live inside their cells, undergo photosynthesis, and feed the corals. To me, as a young scientist, I was completely blown away by that."

Today, Cleves runs a lab at the department of embryology at the Carnegie Institution for Science in Baltimore, Maryland, where, like Howells, he works to understand the basis of resilience to heat stress in corals.

"What we're doing in my lab now is trying to apply biomedical techniques to corals, to better understand their genetics and molecular biology in order to better prevent and ameliorate the effects of climate on these ecosystems," said Cleves. "Just like it's important to understand the molecular basis of human diseases, we think that if we understand the molecular basis of coral biology we can better predict and make therapeutics to help preserve corals, just like we do for human diseases."

Cleves pointed out that even though coral reefs are being wiped out an unnerving rate — 30% of the Great Barrier Reef was destroyed during a 2016 heat wave — scientists actually don't know much about how corals work at the genetic level.

"The reason we know so little is because corals are really hard to study in the lab and we didn't have genetic tools like we have in other systems to really understand the genes involved," he said.

In recent years, Cleves has helped to overcome this barrier by developing and applying CRISPR/Cas9 genome-editing technology to coral specimens from the Great Barrier Reef. "In the short term, what we're really excited about using CRISPR for is to be able to ask, really for the first time ever, 'what do genes do in coral?'" said Cleves. "We've been able to characterize some genes as master regulators of the coral heat stress response. So we have some clues as to the types of genes that protect corals from heat stress, and we're interested in developing these tools to better understand how corals work at the genetic level."

"I think it's mostly us in collaboration with great people around the world using genetic engineering to study corals right now," he added. "I hope there's going to be more attention to it and that the [coral gene editing] method will expand so that we'll really understand what's happening."

Cleves hopes that scientists might eventually be able to find genetic determinants for corals that can withstand future climate scenarios, helping to focus limited conservation efforts on those most likely to withstand the coming changes.

"My dream would be that with a deeper understanding of what genes make corals resilient to climate change, we could go out into the field and use that genetic information," said Cleves. "Wouldn't it be cool to have like a 23andMe for corals? Or you go out and you say, okay, this animal, this animal, this animal — these ones have genotypes that make them the corals of the future."

But Cleves' dream does not involve manipulating the genomes of corals in the wild. He limits his genetic engineering efforts to the lab, where he and his team try to make mutations that confer extra resilience on corals. The end game is to find resilient corals that already exist in nature and to propagate these evolutionary winners.

Montipora capitata coral, one of the species in Cleves' study of diagnostic markers of heat stress
Montipora capitata, one of the coral species in Cleves' study of diagnostic markers of heat stress. | Ryan McMinds

"The idea of making genetically modified coral and releasing it is not really something that we are thinking about because our understanding of genetic information and the genetic basis of coral biology is really in its infancy," said Cleves. "We don't know the genes that could enhance tolerance even if we wanted to do that. Also, there would be a lot of regulatory and ethical considerations about releasing genetically modified corals."

Not all of Cleves' coral research involves gene editing. In a Science Advances paper published in January 2021, Cleves, first author Amanda Williams, and colleagues extracted and analyzed metabolites involved in growth and development from bits of Hawaiian corals that they bleached in a lab to investigate their physiological responses to bleaching. The researchers identified several metabolites that may offer diagnostic markers for heat stress in wild corals.

Strong Emissions Targets Matter

When it comes to saving coral reefs, Cleves admires scientists' myriad ideas. "There's talk about…kind of everything," he said. "Assisted gene flow, probiotics, and moving corals from one part of the world to another."

"For all of these conservation efforts, we want to make sure that we're doing the appropriate scientific research to understand that the things that we're trying to do will actually benefit the ecosystems in the long run," he said. "There's nothing that I've seen that I have been particularly nervous about. I think there are a lot of really smart people doing smart things. I'm curious to see what the benefits, if any, of these conservation efforts are."

But ultimately, Cleves is convinced the strategy with the greatest chance of success would be to let corals do what they do best.

"I think the most promising scaling-up for conservation would be the type of scaling-up that led to the existence of the Great Barrier Reef in the first place — the fact that animals like reproducing and like growing where it's appropriate for them to grow," he said. "I think the really important thing to do is to meet climate emission targets. The collapse of coral reefs is one of the early, traumatic things that's happening with climate change, and if we don't change our behavior, then that's how it's going to continue. The other things that are predicted will continue to happen."

Howells agreed that promising coral reef conservation strategies have their limitations. Noting that her own research does not focus on implementing interventions, she concluded that selective breeding could potentially make a difference — but only for particular species in particular locations.

"You cannot counter the effects of global warming with solutions like this," Howells said. "Restoration efforts can only ever be deployed at a subset of reefs because of cost and logistical constraints. However, what you can do is give certain species a helping hand and target high-value populations."

"We'll try every technique we can to save reefs, but one of the best things to do would just be to stop putting so much carbon in the atmosphere," added Clements. "Otherwise, you're trying to put a Band-Aid on a wound that needs emergency surgery."

[Credit for associated image: Ruby Holmes]