Manta rays and whitetip reef sharks glide past socially distanced visitors at Rio de Janeiro’s hangar-sized AquaRio aquarium. In a laboratory upstairs, above the main gallery, a new experiment is underway, one that marine scientists hope will enhance the survival prospects of the world’s coral reefs.

Twenty rectangular aquarium tanks, each about 20 centimeters wide, are arranged in a grid on the fourth floor. Each one houses a colorful assortment of coral fragments. The researchers will treat some tanks with cocktails of probiotics, a mix of bacteria designed to promote resilience under tough conditions.

Researcher João Rosado draws murky liquid into a pipette, then stands over the first tank and carefully depresses the plunger, squirting the mixture into the seawater. “Can you see that, like smoke?” says Rosado’s colleague Pedro Cardoso of the Federal University of Rio de Janeiro, through his face mask. “Those are the bacteria.” Cardoso is talking to me over a live video feed the team set up so I could witness the proceedings remotely. The gray bacterial cloud surrounds the coral like a shroud, settling on it. Later, Rosado will treat other tanks with probiotic-filled rotifers—microscopic marine animals that corals eat with their tiny mouths. Corals in a third set of tanks will get both treatments, and those in a fourth set will get none. The investigators will probe the various corals over the coming weeks to see if any of the regimens improve coral health.

The use of rotifers is a new attempt to get “good bacteria” to corals in distress. The results from the December 2020 experiment will help inform biologists’ intention to apply probiotics to reefs in the wild in hopes of improving their chances of surviving the high temperatures and disease outbreaks that are overwhelming them. Rosado and Cardoso’s trial—led by marine biologist Gustavo Duarte—builds on work by their mentor, Raquel Peixoto, who published the first probiotics experiments in 2015. She is a leader of the audacious and controversial rescue plan to administer probiotics in the ocean, which could change the ecosystem. Peixoto will apply probiotics in the Red Sea later this year, and conservation groups are eagerly exploring the concept. Although Peixoto and her contemporaries have conducted many lab experiments and will carefully restrict the first open-ocean tests, she says corals are so threatened it is “time for us to take some risks.”

Coral reefs cover nearly 285,000 square kilometers of ocean floor worldwide. They are largely concentrated into a dozen major chains, but they exert a global influence on marine and human life. Almost a quarter of marine species spend at least some part of their lives there. The reefs dampen storm surges and waves that can tear apart shorelines. They feed millions of people and account for almost $20 billion annually in global tourism.

BLEACHED CORALS on the Great Barrier Reef.
BLEACHED CORALS, such as these on the Great Barrier Reef outside Cairns, Australia, are vulnerable to starvation and disease that can lead to death. Credit: Brett Monroe Garner Getty Images

Yet the world’s corals are in a state of possibly terminal decline. Scientists first observed mass coral bleaching—a sign of starvation—in 1983, and by the 1990s they had started to link bleaching to changing sea temperatures. Between 1987 and 2019, oceans warmed 450 percent more than they did between 1955 and 1986. Since 1980, 94 percent of coral reefs have experienced at least one episode of severe bleaching. The Great Barrier Reef has suffered three such events in the past five years. A report from the United Nations Environment Program estimates that largely because of ocean warming, most of the planet’s reefs will suffer annual severe bleaching by 2034 and, without intervention, will be gone entirely by 2100. Global reef death most likely will continue even if countries begin to get their carbon emissions under control. To reverse the trend, “we have a very narrow window of time—basically a decade,” says Carlos M. Duarte, a marine ecologist at King Abdullah University of Science and Technology (KAUST) in Saudi Arabia. “The window is rapidly closing.”

Scientists developing probiotics see the treatments as more than a stopgap to postpone reef death. They think probiotics have a real chance to reverse some damage that has already been done, enabling once threatened corals to flourish and strengthening new human-bred corals that are transplanted onto ailing reefs. “It sounds so radical,” says Rebecca Vega Thurber, a marine microbial ecologist at Oregon State University. But, she adds, “with proper experimental design and application, it could be helpful.”

Big questions still need answers. When applied at sea, will probiotics wash away? Would the labor-intensive techniques cost huge sums of money when tried across reefs hundreds of kilometers long? And even the most avid backers acknowledge the risk they are running. In some ways, reef treatments sound a bit like geoengineering—sprinkling iron into the sea to encourage growth of algae that soak up carbon dioxide or spraying aerosols into the air to reflect the sun’s rays back to space, lessening global warming. Seeding reefs with bacteria might alter the ocean ecosystem at a fundamental level.

Some experts worry that certain bacteria could accidentally spawn new coral disease outbreaks, a possibility that arose in a recent lab test. And no one knows exactly how the treatments will affect ocean life further up the food chain, such as fish and crabs that feed on coral polyps.

As with climate change, however, the global prospects for reefs have become so dire that many conservationists think extreme fixes are needed. “It’s not a good position for scientists to be [in],” says Peixoto, now a marine microbiologist at KAUST. But she says the decision is clear. “We have to act. Otherwise, it’s going to be too late.”

Reef Repair

Researchers have been trying to restore damaged reefs since the 1970s. In 2000 Baruch Rinkevich of Israel’s National Institute of Oceanography started one of the first nurseries to raise young corals and transplant them onto reefs that had suffered damage from fishing, diving or storms.

Scientists started looking into specific fixes for bleaching a few years after that. In 2010 researchers at Florida’s Mote Marine Laboratory showed that by chipping fragments off of healthy corals in lab tanks they could trigger a Herculean growth response that promptly turns those fragments into full-fledged baby corals. (Corals can reproduce sexually by releasing eggs and sperm into the ocean or asexually by budding—essentially, cloning.) In 2018 and 2019 researchers in Mexico and Israel used the Mote team’s strategy to generate coral fragments and transplant them onto reefs just off Mexico’s Pacific coast. The new corals that grew from them showed an impressive survival rate of about 60 percent, despite the damaging effects of Hurricane Willa. On Florida’s reefs, corals the Mote team has grown from fragments merged into larger colonies that in 2020 began successfully spawning in the wild.

Breeding is another strategy. Since at least 2015 researchers at the Australian Institute of Marine Science (AIMS) and elsewhere have been trying in labs to selectively breed so-called super corals, which carry genes that help the animals withstand stress. Teams at the institute and the University of Hawaii’s Gates Coral Lab are creating these ultraresilient corals using “assisted evolution,” which involves selecting wild corals with desirable genetic traits, such as the ability to survive high ocean temperatures, then cross-breeding them to yield offspring with an abundance of the traits. In a 2020 lab study at AIMS, temperature-tolerant corals created this way proved up to 26 times more likely to survive extreme heat than other corals.

Yet another approach to helping corals is to enhance reproduction. In 2017 a team at the California Academy of Sciences, the Nature Conservancy and SECORE International, a conservation organization, began catching the eggs and sperm that healthy spawning corals release in the wild on rare but predictable nights. The researchers complete the fertilization in the lab, then transplant larvae onto needy reefs.

Researcher Kelly Pitts applies a paste laden with a single probiotic onto corals off the Florida coast
Researcher Kelly Pitts pumps a liquid form of probiotic onto corals off the Florida coast
RESEARCHER Kelly Pitts applies a paste laden with a single probiotic onto corals off the Florida coast in hopes of helping the animals fight stony coral tissue-loss disease (1). On a different dive she pumps a liquid form onto corals nearby (2). Credit: Hunter Noren, NSU, GIS and Spatial Ecology Laboratory (1, 2)

These techniques share a daunting drawback: restoration workers have to manipulate corals in a lab and refine ways to transplant them onto struggling reefs, a slow and costly process. It could be quicker and more affordable if a therapeutic could be administered directly to ailing corals in the wild. That prospect helped to lead researchers such as Peixoto to probiotics. And, theoretically at least, selectively bred lab corals, or chipped fragments, could also be treated with probiotics to make them more resistant to heat and disease before they are transplanted in the sea.

Coral formations are constellations of thousands of animals called polyps, each often smaller than a pinky fingernail. Every polyp hosts a variety of bacteria, algae, fungi and other microorganisms, collectively known as its microbiome. Like microbes in the human gut, these tiny residents carry out tasks that keep the whole system functioning. In recent years metagenomic analysis—sequencing the genes of the microbes on a polyp—has supplied a clearer picture of which tasks the microbes are performing. Scientists at the Massachusetts Institute of Technology, the Woods Hole Oceanographic Institute, and elsewhere have isolated bacteria that consume excess nitrogen, preventing nearby algal blooms that starve coral of nutrients. Other microorganisms degrade reactive oxygen species—molecules that damage coral cells—or help corals capture carbon for energy. Much as microbes in the human gut help to break down food, contributing to our nutrition and health, researchers theorize that beneficial coral microbes make the hosts more resilient to environmental stresses by supporting their overall health and warding off polyp disease and tissue loss.

As ocean temperatures rise, however, the microbial relationships within corals start to break down. Scientists at Oregon State University have found that bacterial communities on stressed corals often become unstable, potentially giving disease-causing microbes a chance to spread. Warming oceans, together with ocean acidification caused by higher carbon dioxide levels, also disrupt the microbe-aided calcification process that gives corals their structure, making it harder for them to repair damage. At the same time, stressed polyps expel their Symbiodinium algae, which turn sunlight into food for polyps, leaving them without a food source. This gives corals a characteristic bleached appearance that biologists recognize as a sign of doom because bleached polyps are also more vulnerable to disease. Peixoto has witnessed this alarming transformation firsthand.

A Disintegrating Universe

As a kid on vacation, Peixoto snorkeled the Brazilian reefs near Bahia, entranced by the vivid universe beneath her. On dives as an adult, she saw that universe disintegrating. Corals were turning into lifeless skeletons; the ones that were hanging on looked wan and sickly. “Every year is getting worse,” she says. “You dive and see 90 percent of the species dead.” Peixoto resolved to do something transformative, something that could revive wild corals. “We want to protect the diversity already there in the reef,” she says, “to make sure colonies can survive.“

She had a novel starting point in mind. In a 2010 experiment aimed at developing an alternative to the hazardous chemicals used to clean up oil spills in Brazilian mangroves, her team demonstrated that oil-sucking bacteria could break down the oil and promote plant health and growth. What if she could summon concentrated bacterial reinforcements to protect coral reefs? No one had tried probiotics, but she had a hunch they might work.

As a first move, Peixoto harvested tissue and seawater from the surfaces of local corals. Then she sequenced the bacterial genes in that mix to find species that carry out functions promoting survival. She grew the native microbes in culture and mixed bespoke cocktails for each reef environment. Her work paid off in late 2018, when she and her colleagues published a study showing that their tailored probiotic blend helped corals survive hot aquarium temperatures and resist disease.

One of Peixoto’s newest experiments, being reviewed by journals, goes deeper, appearing to show distinct mechanisms that probiotics may use to enhance corals’ health. Her team in Brazil placed four finger-length coral segments in each of 20 small tanks and assembled a cocktail of six bacterial strains from healthy Mussismilia hispida, a common South Atlantic coral. Every few days they removed a few segments, dripped a dot of probiotics onto their surfaces, and returned them to the tanks. Next they raised the water temperature on half the tanks.

The results weeks later were dramatic: more than a third of the control corals had died, but almost all the treated corals were alive. Detailed analysis revealed multiple ways the probiotics appeared to promote health. The treated corals less strongly expressed genes linked to inflammation. They also showed less gene activity related to cell death. That means corals “can even bleach, but it’s not to the extent that they lose tissue,” Peixoto says. “The probiotics provide them with this kind of buffer.” That buffer could give other restoration measures—such as super-coral breeding or spawning baby corals from fragments—a better chance to work. The right probiotics applied in the lab before transplantation could potentially increase the corals’ odds of survival.

The First Field Trial

On a crisp day in January 2020, scientists at Florida’s Smithsonian Marine Station applied a probiotic to coral in the ocean, the first time that had been tried. The probiotic, which they had been developing for three years, wasn’t a broad-spectrum blend like Peixoto’s. It was designed to counter a specific threat, one of the gravest to Florida’s reefs: stony coral tissue-loss disease. Researcher Kelly Pitts, who had joined the team in 2019 after working on antibiotic treatments at Nova Southeastern University, wanted to test probiotics as a more natural aid for coral health. She donned her oxygen tank and fins and descended from a small boat onto a reef ringing Florida’s eastern coastline off of Fort Lauderdale. At roughly nine meters deep, as Pitts tells the story, a clear plastic bag about half a meter across and pinned to the seafloor came into view, enclosing a coral formation like a dome.

The target inside was a great star coral that was more than a decade old (colonies can thrive for decades or even centuries). Some of the polyps were still a vibrant orange, but others had faded to khaki, a sign they might have been ravaged by stony coral tissue-loss disease. Pitts snaked a flexible tube under the dome’s edge, then attached a bacteria-filled syringe to her end of the tube. As she lowered the plunger, murky white liquid bloomed in the dome, thick enough to obscure the coral.

Pitts was excited but anxious. Her team had been testing its probiotics in tanks for months, but being out on the reef was completely different. What if the mixture escaped the bag? She felt the same apprehension during another test months later when she squeezed a probiotic gel, like toothpaste from a tube, onto a coral on the seafloor that was fully exposed to the water, no bag to encapsulate it. When the paste stuck fast to the coral despite surrounding water currents, her nervousness gave way to elation, and she laughed with joy, clapping her hands underwater.

Stony coral tissue-loss disease, which eats through polyps like acid, had laid waste to more than 96,000 acres of reef in Florida and the Caribbean since 2014. The disease—suspected to be bacterial—was spreading unchecked, killing large formations within weeks or months. By 2017 quelling the outbreak had zoomed to the top of the priority list for Florida conservationists. Using rapid gene sequencing, the Smithsonian Marine Station researchers identified a Pseudoalteromonas bacterium, present in small quantities on local corals, that produced the marine antibiotic korormicin.* In aquarium tests, concentrated doses of the probiotic bacteria kept the disease at bay.

During lab tests the researchers applied the bacteria to a range of corals from the broader reef to be sure it would not harm any healthy species. In a rush to get the disease under control, Florida researchers had been dosing corals with antibiotics such as amoxicillin since 2018—a drastic measure that was also killing scads of beneficial bacteria. Pitts hoped probiotics could get around that indiscriminate injury.

In late 2019 the Smithsonian team secured the state permits needed to plunge into ocean trials. Researchers were cautious and were mindful of the need to start small, but the disease was spreading so fast local conservationists were in favor of the proposed test run.

During the January 2020 field trial and another in September 2020, Pitts and her colleagues treated 14 coral formations using the dome method and seven others with the paste. When the team did an initial survey of the reef two weeks after the January trial, the disease’s progress had stopped in about 80 percent of the treated corals. Some of their patchy lesions were also beginning to heal. The growing COVID-19 pandemic, however, caused scientists to pause trials for a time.

MARINE SCIENTIST Raquel Peixoto tests probiotics in the lab.
MARINE SCIENTIST Raquel Peixoto tests probiotics in the lab. She plans to apply a multistrain bacterial cocktail in the Red Sea this year to help corals fend off bleaching. Credit: Raquel Peixoto Kaust

Unintended Consequences

All microbiology is contextual. Changing the concentrations of one “beneficial” type of coral bacteria can affect other key bacteria in the microbiome in ways that are hard to predict. For skeptics of coral probiotics, this complexity and unpredictability is a source of unease. “Maybe the function is temporarily good,” Vega Thurber says. “But it could easily switch to be something that has a negative effect.”

Hawaii Institute of Marine Biology molecular ecologist Ty Roach, who has done his own probiotic lab tests, worries about irreversibly changing a coral microbiome or an entire marine ecosystem. “The more I’ve tinkered with it, the more I’m concerned,” he says. In one unpublished study of his involving about 130 finger-length Porites corals in a dozen three-gallon tanks, some of the corals died of disease after his team inoculated them with a dose of their own native bacteria (not a tailored cocktail like those Peixoto makes). The first trouble Roach noticed was that certain corals formed thick sheets of mucus on their surfaces, as if they were irritated. Then small patches of polyp tissue started to die, like spreading canker sores. Roach was alarmed but not surprised. The coral’s natural bacterial mix includes microbes from the Staphylococcus genus, which is known to cause disease in humans.

Roach adds that there is scant peer-reviewed research that describes the exact biological mechanisms by which probiotics might protect coral hosts. “We’ve been able to make some corals withstand a little more heat,” Roach says. “How that works is very unclear.” And he wonders whether the treatments will affect other marine life. “A lot of other organisms are in direct interaction with these corals on the reef,” he says, including fish, algae and crustaceans. University of Derby aquatic biologist Michael Sweet, a longtime colleague and friend of Peixoto’s, supports probiotic methods if they can be proven safe. But he also echoes Roach’s concerns: “I don’t want to be the one responsible for releasing a superbug into the environment that becomes the next coral disease.”

How often probiotic treatments should be applied is also unknown. Human probiotics for digestive disorders often need to be taken every day or even twice a day. Researchers can only guess if applications, say, once a week or once a month would be enough to create a resilient microbial equilibrium.

Risk is just one practical consideration. At this stage, the cost of applying cocktails across an entire reef is hard to calculate. Peixoto says a little of the mixes she has created goes a long way, but it might cost up to $600 to $700 to treat one square kilometer of reef, assuming trained divers apply the probiotics (and assuming they have a dive boat of their own). An application might protect corals from heat damage for up to a month. On a wide scale, robots built for applying the compounds would be less expensive than human divers, she says.

Sweet recently reported that creating lab-grown corals through assisted evolution—transplanting them on a reef and monitoring them—would cost between $49 and $227 for each coral colony. Reefs often have tens of thousands of colonies per square kilometer. If probiotic bacteria were added to the lab-grown corals before transplant, the added cost “would be low,” Sweet says. But “if we need to redeploy the probiotics regularly, it could become an expensive method.”

Yet Roach and Sweet also know that reefs are in such peril that conservation funders will likely forge ahead with probiotics in the wild. “If there’s one thing we’ve learned,” says marine biologist Crawford Drury, Roach’s Hawaii colleague, it is that “if we start losing reefs, the willingness to do something extreme skyrockets.”

Indeed, big organizations are embracing the idea. The World Wildlife Fund in Brazil, which is financing some of Peixoto’s research, is optimistic about the technique’s prospects. In Brazil, the massive reef bleaching event of 2019 “turned the key” to exploring newer conservation options such as probiotics, says Vinicius Nora, a WWF Brazil conservation analyst. Australia’s Great Barrier Reef Foundation, which has committed hundreds of thousands of dollars to probiotics research, also sees Peixoto’s treatments as a promising way to fortify lab-grown coral intended for transplant. Foundation officials are working with Peixoto and Australian scientists to include probiotics in future restoration projects if further small-scale tests go well. “It’s a catch-up that we’re having to do,” foundation biologist Ove Hoegh-Guldberg says. “You’ve got to jump in with boots on and test a few ideas.”

Radical Determination

Peixoto understands her critics’ concerns. To help ease some minds, including her own, she is planning contained experiments this year at the 700-square-meter artificial ocean in the University of Arizona’s Biosphere 2. The tests will give a clearer look at how probiotic treatments might affect other ocean life. Still, she doesn’t spend a lot of time second-guessing her course. She admits she gets impatient with people who call for too much caution. She feels a moral obligation to use all means to save reefs. For Peixoto, that means deploying coral probiotics in oceans very soon. “If we don’t do anything,” she says, “they will die.”

Her next act will be staged at KAUST, which sits on a spit of Saudi Arabian coast that curls into the Red Sea like a lobster claw. From the docks, Peixoto can step into her dive boat and motor out to a shallow reef 10 minutes away, where schools of golden butterflyfish cruise over decades-old coral monoliths on the seafloor.

Because Red Sea reefs have thrived for years in high-temperature water, bacteria that limit heat damage here could help scientists learn how to confer heat resistance onto ailing corals elsewhere. The reef, Peixoto says, “is like my vault. I go there and get the gold.” Yet even stalwart Red Sea corals are starting to show signs of stress. A bleaching event devastated sections of reef in 2020, and experts fear worse is to come. Peixoto is fine-tuning a blend of bacteria she hopes to apply on the reef this year, while still ramping up experiments in Biosphere 2. The trial will be the first time she and her team test probiotics in the ocean.

Some Red Sea reef formations are separated by long stretches of empty seafloor. This will make it easier for Peixoto to apply probiotics to one formation while leaving the next-closest ones untouched. “These will be very small and well-controlled experiments,” she says.

Even so, the test will be a different approach than what the Smithsonian team used in Florida. The Smithsonian’s treatment was a single microbe deployed to treat a specific coral disease. Peixoto will dose corals with a multistrain cocktail that has a much broader aim—to fortify corals against bleaching and the ill health that follows. As in the past, Peixoto will isolate beneficial microbes from local corals and mix them into a custom slurry. She will exclude any groups of bacteria known to cause disease and will first conduct detailed risk assessments in tanks at the university to make sure the cocktail does not cause any adverse coral health effects in a small setting.

If that test goes smoothly, she will eventually apply her mix to several reef formations, about two square meters each. The microbes will be delivered via strips of time-release, water-resistant adhesive that sticks to the corals or to nearby sediment. After a few weeks Peixoto will assess how the health of treated corals compares with that of controls. Periodic checks will continue for a year, and throughout the process she will monitor nearby fish and other large organisms such as sponges for unintended bacterial effects.

Peixoto recognizes the magnitude of this next act, but the widening coral ghost towns she sees on her dives have strengthened her commitment to err on the side of radical intervention. She is an optimist, with an innovator’s faith in the power of bioremediation. She knows some people might call her hasty. Yet Peixoto and others think bold intervention is simply required now. “If we develop all the technologies, we can still have beautiful reefs,” she says, “rehabilitated reefs that can thrive.” Without that targeted assistance, she sees a long undersea dark ages ahead.

*Editor’s Note (4/27/21): This sentence was revised after posting to correct the name of the bacterium that was identified.