A Cure for Coral Reefs?

Scientists hope that dosing damaged corals with probiotics could fortify reefs against pollution, disease, and climate change.

The Solomon Islands’ Marovo Lagoon is one of the most striking sights on Earth—an island-ringed inlet where seabirds circle, coconuts bob, and flying fish skitter across the waves. Thatched-roofed homes dot the shores, nearly swallowed by the dense green rainforest that covers the islands. But for coral microbiologist Rebecca Vega Thurber, the real marvels lie beneath our boat’s hull.

Today, Vega Thurber and her scientific team are heading to a sheer reef wall the height of a small apartment building, studded with brightly colored coral formations. After a 10-minute ride from where the main research vessel is anchored, the dinghy reaches the edge of the lagoon. Vega Thurber, her graduate student Grace Klinges, and the rest of the sampling team don their diving gear, then, one by one, tip their bodies over the side.

For about an hour, they drift slowly along the reef wall past a smorgasbord of healthy corals, anemones, crustaceans, darting surgeonfish, and parrotfish so bright they practically glow. The divers snap coral samples off the reef with their hands and place the samples inside their coral Rolodex: a fistful of zip-lock bags with holes punched in them, held together with a zip tie.

The reef here is spectacularly unspoiled, with more types of coral than Vega Thurber can collect and bag in the Rolodex. “It was almost overwhelming,” she reports afterward. Many of the corals here, she says, were species she’d never seen before—and all of them were vibrant and healthy, a reprieve from the dying colonies she’s been seeing elsewhere.

But what Vega Thurber is after, at this reef and at dozens of others she’ll visit during this six-week expedition, is not just the corals themselves. She and her team from Oregon State University want to probe the genetics of the microbes that live on the surface of corals and inside them. These tiny symbionts—mostly algae and bacteria—help coral colonies in a host of ways, from aiding their metabolism to producing compounds that ward off disease-causing bacteria. It’s as if the symbionts are warning would-be invaders: “Stay away; this is mine,” says Vega Thurber.

Getting a handle on exactly what these live-aboard microbes do for their hosts, Vega Thurber believes, could help stave off a mass extinction that many coral experts and environmentalists argue is already underway. Though the Marovo reef we’re visiting is still pristine, it is, increasingly, a rarity. Ocean warming, acidification, pollution, and destructive fishing practices are laying waste to many reefs that have thrived for millennia. In 2016, more than two-thirds of corals along a 700-kilometer (435-mile) stretch of the Great Barrier Reef died after an extreme episode of bleaching—a process in which heat-stressed corals expel beneficial algae that provide them with nutrients. In this state, it doesn’t take long for the corals to succumb to disease or simply starve to death.

Many reef systems around the world have suffered severe bleaching events caused by increased ocean temperatures, and researchers estimate that nearly all of the planet’s remaining coral reefs will be similarly decimated by the year 2050. Should these predictions play out, it would not only be an environmental disaster, but an economic and social one, too, as reefs are among the most important natural resources many coastal nations possess. For instance, according to a study conducted for The Great Barrier Reef Marine Park Authority, the reef brings about $5.7 billion into Australia’s economy each year through recreation, tourism, and commercial fishing.

Studies have found that the mix of microbes that live in and on corals—their microbiome—helps determine whether corals succumb to the stress of shifting environmental conditions. That’s why, for the past several years, Vega Thurber has been working to compile what is already the largest genetic database of coral microbial communities in the world, a venture called the Global Coral Microbiome Project.

Solomons Sampling Route

On their Pacific voyage, Rebecca Vega Thurber and her research team sailed through the Solomon Islands, sampling at three main reef sites along the way. From there, they headed west to Papua New Guinea to continue their data collection.

Data provided by TARA Expeditions.

By pretty much any measure, Vega Thurber (Becky, to anyone who’s met her at least once) is a badass marine biologist. She weathers bouts of seasickness like an old salt: “Take Bonine twice a day,” she advises, before noting dispassionately that “sometimes you end up barfing no matter what.” She pulls regular night-watch shifts alongside the crew of the research boat, TARA. And even after a grueling day of collection dives, followed by hours of coral sample processing, she leads yoga classes on TARA‘s swaying deck.

Vega Thurber has always had an affinity for the sea. Visiting family in the Dominican Republic as a kid in the 1980s, she loved to snorkel in the turquoise waters fringing the island. But in her teens, she started noticing that once-vibrant hubs of ocean life were disappearing, giving way to empty seas and bleached coral skeletons. As the reefs became increasingly degraded, she’d wonder: Where did all the fish go? Where are all the corals?

To outsiders, stories of struggling coral ecosystems might have seemed abstract. To Vega Thurber, the loss felt intensely personal—a world that had once seemed magical and timeless was fading in front of her. Her grief over this disappearing world fueled her interest in marine biology. She wanted to understand why the die-off was happening—and whether the kind of devastation she’d seen could be reversed.

Almost from the beginning of her career, Vega Thurber’s research was built upon the growing understanding that corals, far from being just colonies of animals, called polyps, are complex biological systems known as “coral holobionts.” These systems thrive on a balance of bacteria, algae, protists, and other microorganisms that live in or on the coral polyps. The microbes perform life-sustaining tasks for the corals, and in return, they gain a source of nutrients—the thick mucus corals produce—and shelter within the stony coral exoskeleton.

Over the past decade or so, the marine biology community has increasingly embraced the coral holobiont concept, and studies of these intricate biological systems have produced some of the most important marine science discoveries in recent years. For example, University of Hawaii researchers reported in 2009 that some corals transfer algal cells from their tissues into their eggs, thus helping ensure that stores of beneficial microbes can persist through generations. A few years later, a team at Saudi Arabia’s Red Sea Research Center found that placing corals in very salty water triggered a rapid change in their onboard microbial composition, which kept the polyps from becoming dehydrated.

To crack open the question of why corals were dying under environmental stress, Vega Thurber decided to map the functions of coral systems from top to bottom, and to track how those functions influence coral health over time. In the mid-2000s, during a post-doctoral stint at San Diego State University, she conducted experiments to test how corals’ onboard microbes would react to stress in the laboratory setting. She took samples of a common Hawaiian species of coral, Porites compressa, placed them in aquariums, and sequenced the genes of their microbes. Then she exposed the corals to one of four environmental insults—high water temperature, high pollution levels, low pH, or high levels of dissolved carbon dioxide. (The ocean absorbs atmospheric CO2, which ultimately leads to increased acidity.) After administering those insults, she sequenced the coral microbes’ genes again.

Just as Vega Thurber suspected, the coral microbiomes changed in distinctive ways depending on which stressor they’d encountered. The sample from the nutrient-polluted tank, for example, contained many organisms involved in repairing DNA damage, whereas the high-temperature tank had lost significant numbers of beneficial algae.

Even more striking was the one constant: All of the environmental insults caused the ratio of disease-causing to healthy bacteria to creep up. Any kind of stress, it appeared, left the corals more susceptible to destructive invaders.

It was becoming clear that balanced microbial communities were crucial to the well-being of corals. But vital details about how specific microbes contributed to coral health were still missing. Vega Thurber concluded that someone ought to create a library of coral microbiomes in the wild. And that someone, she felt, should be her.

Video by BioQuest Studios

While Vega Thurber knew that sequencing the DNA of coral microbes was critical to understanding these organisms and their role in coral health, she knew it would be necessary to sequence the organisms’ RNA as well. RNA, after all, codes for the proteins that do the cells’ work—turning nitrogen gas into usable nutrients, say, or vanquishing disease-causing germs. If scientists could sequence the DNA and RNA of microbes teeming on a wide enough variety of reefs, in varying states of health, Vega Thurber felt that they could really begin to understand how a coral’s microbial community affects its vulnerability—or resistance—to stress and disease. Along the way, they might also identify some of the specific microbes that foster coral health.

In 2013, Vega Thurber and Medina founded the Global Coral Microbiome Project with the aim of sequencing the microbiomes of as many corals as they could get their hands on. Since then, the project’s scientists have taken sampling trips to places as varied as French Polynesia, Singapore, and the Great Barrier Reef. And in 2015, Vega Thurber accepted an invitation from the TARA Foundation—a French organization that leads expeditions to study reef resilience in the face of warming oceans—to serve as chief scientist on board its main research vessel.

The partnership was a natural one. For Vega Thurber, part of the appeal was that she could treat the TARA Foundation expedition as a natural extension of the global microbiome project, adding a broad array of samples to her library. And TARA’s mission added a new dimension to her project.

TARA researchers planned to sample a few of the same coral species (as well as ocean water samples) at each of the sites the ship visited. Doing so would allow the team to track how those species were faring and how their microbiomes differed from one location to the next. At the same time, it would help Vega Thurber zero in on what drives shifts in the composition of microbiomes within species. At a highly polluted site, for example, coral might harbor an unusual number of microbes associated with coral disease. Or at an especially warm location—say, in the Caribbean Sea—a coral species’ microbiome might be missing Symbiodinium, the algae that turn sunlight into sugars to feed coral.

Analyzing these types of differences allows Vega Thurber to deduce how a reef’s microbial balance shifts when subjected to various types of stress, and which microbes confer resilience against stressors such as climate change, pollution, and invading pathogens. “Over 300 million years, these groups of bacteria were selected,” Vega Thurber says. Her goal now is to figure out exactly what role the coral microbes play in the reef ecosystem—and whether some of the microbes can be used deliberately to bolster reef health.

The answers to those questions are only beginning to emerge. Vega Thurber and her colleagues recently published a study about the roles that specific groups of microbes play in coral ecosystems. They found that bacteria of the genus Endozoicomonas protected coral from bleaching, while members of the genus Vibrionales signaled outbreaks of coral disease.

Processing the 30,000-plus samples from TARA‘s Pacific leg could take years. But based on the coral sampling and analysis Vega Thurber has already done, she hypothesizes that when environmental stress ratchets up, it is the corals with less diverse microbiomes that are most vulnerable to disease and eventual death.

Vega Thurber’s findings about coral microbes have caught the attention of marine biologists involved in crafting reef restoration plans. Erinn Muller, a coral ecologist at the Mote Marine Laboratory in Sarasota, Florida, sequences the genomes of corals off the Florida coast and in the Caribbean to figure out why corals get sick and how to boost their resilience. She thinks some fortunate corals possess genetic traits that make them more resistant to disease. But after sharing data and insights with Vega Thurber, she has come to the conclusion that onboard microorganisms are also key to protecting a coral’s health.

“Becky is the godmother of coral microbiome right now,” says Muller. Vega Thurber’s research, she says, has given her exceptional insights into who the important microbial players are in coral communities.

A few years ago, Muller scraped diseased surface tissue from coral colonies in the Florida Keys. When she sequenced the samples, she found that bacteria in the genus Rickettsia were about 50 times more common in diseased tissue samples than in healthy ones. When she told Vega Thurber what she’d found, Vega Thurber understood what was likely driving the connection. Her own data showed that Rickettsia tended to flourish where nutrient levels were elevated. The Rickettsia boom Muller was seeing, she suggested, likely meant that nutrients washed in from the land were polluting the surrounding waters and sickening the coral colonies. In the future, Vega Thurber believes, treating coral colonies like these with “coral probiotics”—beneficial microbes—or seeding reefs with corals containing such microbes could help the corals develop more balanced microbiomes that would give them a better shot at survival, even if nutrient conditions are slow to change.

Vega Thurber’s insights may ultimately prove to be a crucial element of reef-restoration projects around the world. That application could include one of the Mote Marine Laboratory’s most ambitious projects: to transplant more than a million lab-grown coral fragments into the wild within the next 15 years. This is among the largest restoration efforts Mote—or anyone else—has ever attempted. As of 2014, a combined total of only about 100,000 corals had been transplanted around the world by a variety of organizations. (So far, Mote has planted more than 20,000 coral fragments onto threatened reefs in the Florida Keys.)

Mote established itself as a reef rebuilding pioneer when staff marine biologist David Vaughan pioneered a technique called microfragmenting, which involves slicing tiny coral pieces from a larger colony with a band saw. The first time Vaughan tried this, he watched in wonder as the fragments began to grow about 25 times faster than uncut corals. Vaughan’s fast-track method for growing coral transplants has since become the linchpin of Mote’s reef restoration efforts.

But for large-scale reef rebuilding to be successful, transplanted corals have to be robust enough to stick around long term—and that’s where Vega Thurber’s ever-expanding coral microbiome knowledge is important, Muller says. “You don’t want to spend hundreds of thousands of dollars putting corals out that won’t be there five years from now.”

The first time Vaughan tried this, he watched in wonder as the fragments began to grow about 25 times faster than uncut corals.

While TARA is rolling gently over the waves or anchored for the night, life on board has an open-ended, timeless quality. During these unscheduled hours, Vega Thurber plays her ukulele, writes emails to her husband and 4-year-old son, or befriends curious Solomon Islanders who paddle up in their dugout canoes. But once the boat reaches a coral sampling site, a new, hectic rhythm takes hold.

After each successful dive, Vega Thurber, her graduate student Grace Klinges, and their French colleague Emilie Boissin spread their dripping quarry of zip-lock bags across a large wooden table on the main deck. “Oooh, these are nice pieces!” Vega Thurber says, scanning the day’s haul with a prospector’s grin. Before changing out of their gear or showering, the scientists start fishing coral samples out of the bags and snipping them into bits using a pair of bone-cutting pliers.

Some of the coral samples are frozen, by dunking them briefly in a large container of liquid nitrogen, so that researchers can later determine their precise place in the coral family tree. The researchers tackle other samples with hammers and chisels to break them up into more manageable pieces.

Once all the pounding and chiseling is done, Klinges and Vega Thurber use orange tweezers to retrieve the tiniest coral fragments—no bigger than cookie crumbs—and deposit them into finger-width tubes. These samples will be sent off to the French National Sequencing Center (also known as Genoscope), which will conduct microbial DNA sequencing to identify the microbes’ genetic code, and RNA sequencing to reveal what functions each microbe species performs.

Vega Thurber is interested in understanding the roles that various microbes play in sustaining coral colonies. Some bacteria, for example, are capable of turning nitrogen gas into a more usable form that photosynthetic algae can in turn use to feed their coral hosts. Others produce molecules that enable the bacteria to detect other microbes of the same type so they can coordinate in the formation of mucus layers that protect coral from disease. And certain strains of beneficial single-celled Symbiodinium algae are less likely to be expelled by corals when ocean temperatures increase.

Teasing apart the inner workings of microbes like these, sequencing the unique mixes of microbes on particular corals, and mapping coral microbiomes onto various ocean conditions, Vega Thurber says, could ultimately help turn struggling reefs into hotbeds of “super coral.”

After TARA leaves the Solomons and heads to nearby Papua New Guinea, Klinges will track how coral microbiomes change across a natural ocean pH gradient from 8.1 (more basic) to 7.9 (more acidic). As it happens, this is also about the same pH drop that’s predicted to occur in the world’s oceans over the next century as a result of CO2 emissions. Assessing the state of coral microbiomes in more acidic waters should give conservationists a preview of the microbial changes reefs will soon see, which could allow them to plan for these changes in advance.

To pass the time while processing coral samples, the scientists chat, or in Vega Thurber’s case, sing. One sweltering day, Vega Thurber swigs from her water bottle and starts belting a tune from the musical Les Miserables. Her bemused team members join in as they snip knuckle-sized coral pieces and stuff them into zip-lock bags.

But as Vega Thurber makes her way through the libretto and one character after another expires, a somber note creeps into the proceedings. “Everybody dies,” says Klinges, summarizing the musical matter-of-factly. For her, and perhaps for anyone who has visited declining reefs, the fate of the world’s corals feels much like that of those doomed French revolutionaries. “Within a year, you go back, and there’s nothing left,” Vega Thurber says.

That prospect of imminent destruction has prompted Vega Thurber to join forces with researchers who, like Muller at the Mote Marine Laboratory, are working to transform the state of real-world reefs. Among her newer collaborators is Brazilian microbiologist Raquel Peixoto, whose work is beginning to show that fortifying threatened corals with the right microbes could be a viable conservation strategy.

Recently, Peixoto—currently a visiting professor at the University of California-Davis—identified seven bacterial species that in one way or another benefit coral. She inoculated some samples of coral from the genus Pocillopora with these “good” bacteria, leaving other samples untouched. Then she purposely subjected all the corals to stress. In one trial, she brought the water temperature in the corals’ tank up to 30 degrees Celsius (86 degrees Fahrenheit). In another, she introduced a known disease-causing organism into the scene.

After 26 days, the corals that had been pre-treated with beneficial bacteria remained healthy, while the control corals showed obvious signs of bleaching. “We got really excited, because this was our first try,” Peixoto says. She hopes this strategy will help both naturally occurring and transplanted corals handle adverse environmental conditions. “If you just go to the reefs and give probiotics to the coral and they could resist this bleaching event, that would be amazing.”

There are major challenges ahead, of course—Peixoto will need to replicate her experiment in the wild and ultimately find a way to deploy coral probiotics on a large scale. Knowing the properties and functions of a wide variety of coral microbes will be crucial, and that’s why Peixoto sees the Global Coral Microbiome Project as essential to her work’s continuing success. She knows that microbes that benefit Pocillopora corals in waters near, say, South America, will not necessarily help other corals in the same waters or elsewhere. Instead, each coral species may have beneficial microbes that are unique to it—and these kinds of microbes are exactly what Vega Thurber is identifying as she sails the world’s oceans taking samples. “Making corals stronger, we can have hope,” Peixoto says.

Likewise, Nature Conservancy senior scientist Stephanie Wear sees Vega Thurber’s microbe-focused approach as part of a multi-pronged global strategy to bring reefs back from the brink. “The more we understand,” she says, “the more we can intervene.”

Some critics argue that introducing lab-grown corals or new microbes to natural reefs is risky, and believe reefs should instead be left to their own devices. If artificial reefs aren’t carefully planned, note scientists at the Florida Keys National Marine Sanctuary, they could threaten natural reefs or even provide shelter for invasive species.

Vega Thurber acknowledges that risk. But she argues that given the scope of the challenges reefs face, it’s necessary to take some risks to restore them in hard-hit areas. “It’s better to try than to do nothing at all,” she says.

Here in the Solomon Islands, there’s no need for measures like coral probiotics or reef rebuilding—at least, not yet. Mangrove trees surround many of the islands, and they help to protect the reefs by filtering out pollutants and trapping sediment that would otherwise flow into the open ocean. Vega Thurber says the reefs around the Solomons are among the healthiest she’s ever seen. “I didn’t see any disease, no bleached corals, no broken or trashed corals.”

One day, Vega Thurber, Klinges, Boissin, and I jump off of TARA with our masks and snorkels and swim out to an island about 200 meters (650 feet) from where we’re anchored. Even in this more or less randomly chosen spot, the reef’s diversity and abundance are astonishing. Butterflyfish dart past vibrant orange clusters of fire coral, so distinct from anemic-looking corals found elsewhere. Many threatened reefs can barely sustain animal life. But here, cone snails lurk in the shallows and clownfish frolic near green-tentacled anemones. It’s a reminder of what’s still possible, even as ocean temperatures and pollution levels rise around the globe—and also what’s at stake.

Few reefs Vega Thurber has visited approach this standard. She’s still haunted by a dive in 2016 at Ducie Island in the South Pacific, where most of the Pocillopora coral she saw were bleached. And even here in the paradise of the Solomons, some ominous signs are appearing. On one dive, the team found more than a dozen crown-of-thorns starfish (Acanthaster planci)—a species infamous for its capacity to decimate vast swaths of reef in a few short months.

It isn’t until my last day on the boat that I ask Vega Thurber the question I most fear will pain her. With changes to the world’s reefs coming so fast and furious, I ask, do you ever worry that there’s just not enough time for science to save them?

It’s a reminder of what’s still possible, even as ocean temperatures and pollution levels rise around the globeand also whats at stake.

I can tell right away that I’ve cut to the quick. Vega Thurber admits she had some dark thoughts when the news broke in 2016 about the Great Barrier Reef’s recent mass bleaching—especially since so many other reefs around the world were distressed and dying, too. “I was pretty depressed,” she says, explaining that she was afraid the reefs she studied would be destroyed. She blinks faster, and the rims of her eyes turn red. It’s the resignation of the firefighter who quells one blaze only to watch others arise in its wake.

Still, everything about the way Vega Thurber operates points to her essential conviction that things are not hopeless. If she’s going to bunk in a boat’s hold for weeks at a time, missing her family, staving off jags of nausea, and battling insomnia from anti-malarial drugs, it damn well isn’t going to be for nothing.

After a few moments, her optimism begins to resurface, and she relates what she and her colleagues call “bright spots.” In the late 1990s and early 2000s, reefs around the Seychelles Islands, off the coast of East Africa, endured a massive bleaching event in which up to 90 percent of corals died off. “Now if you go there, it’s beautiful,” says Vega Thurber. “There are these examples of recovery that are very hopeful.”

With enough focused intervention, she still believes, even cataclysmic reef setbacks can sometimes be overcome—perhaps with the help of robust coral transplants or carefully curated microbial blends. “We want to select for the hardiest members of the community,” she says. In the face of our collective failure to control carbon dioxide emissions, fortifying corals against ongoing environmental insults may indeed be the best way to save the reefs.

Map by James Davidson

Elizabeth Svoboda

Elizabeth Svoboda is a freelance science writer based in San Jose, CA. Her writing has appeared in Aeon, Quanta, the Washington Post, and Psychology Today, and she is the author of  What Makes a Hero?: The Surprising Science of Selflessness. Visit her at

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