Reef Refugia

In Belize, scientists are studying a thriving coral reef and helping to spread its resilience into other reefs around the Caribbean.

(Editors’ note: This story was updated in December 2023 to reflect recent observations by researchers that even some of the most resilient coral colonies in the Caribbean can be pushed beyond their limits.)

A multitude of tiny, colorful fish speckle the water above a thicket of coral like a tossed handful of confetti. The tangle of living branches is their front stoop. As I swim near, the fish sense danger and dive all at once into the negative space between coral branches. But the research divers I’ve joined at this reef in northern Belize are here for more than just fish. Their main focus is staghorn coral (Acropora cervicornis), a once-common species that has become rare across the Caribbean.

All reef corals provide habitat for animals like fish, urchins, crabs, and shrimp, but staghorn coral is particularly welcoming because of its numerous branches. Some grow in meandering paths. Others are pencil straight. The bulkiest are as wide as a flute; the smallest as narrow as a pinky finger. Over time, the golden-hued branches form a jumbled scaffolding. Coral polyps—hundreds of thousands of tiny, anemone-like animals that live in each colony—emerge from the goosebumped upper branches.

For more than 200,000 years, staghorn corals were among the most common coral species in the Caribbean and western Atlantic, their natural range. In recent decades, though, up to 98 percent of staghorn coral colonies have died in this region. Like other corals here and worldwide, they’ve succumbed to disease, changes caused by climate change, declining water quality, damage from certain fishing practices, and other pressures. These are ongoing problems and the effects of climate change are becoming worse as shallow seas overheat more frequently. Yet somehow, at times when staghorn corals were dying elsewhere, the corals survived at this unassuming reef known as Coral Gardens, an ecosystem awash in sundrenched water just a short boat ride from the bustling town of San Pedro, Belize.

It’s December 2022 and I’m joining researchers at Coral Gardens who have studied the reef for over a decade, uncovering its long history of resilience. However, even resilient corals have their limits. A year later, the team would find these corals decimated after months of extreme heat, which created particularly deadly conditions for corals in Florida and throughout the Caribbean this past year.

Coral Gardens is what’s called a patch reef—an isolated area of corals that grow in quiet water sheltered from waves—and is just one of the many reefs that make up the Mesoamerican Barrier Reef, the second largest barrier reef in the world. For Lisa Greer, a geologist at Washington and Lee University in Lexington, Virginia, Coral Gardens is also a beacon of hope.

“We’ve spent far too much time documenting things dying,” says Greer. She’d like to understand why this reef is living. To that end, Greer has come to Belize each year—typically in June and December—since 2011 to monitor Coral Gardens, often with Macalester College geologist Karl Wirth, Smith College professor emeritus Al Curran, and a rotating cast of other scientists and undergrads.

Now, a dozen years after their first visit, Greer, Wirth, and I swim through shallow, 82-degree F water, toting measuring tools, notebooks, and cameras. Over several days, we’ll photograph about 140 square meters of coral. Greer and boat captain Narciso Valdez will swap out monitoring instruments that are tucked into the reef. Curran and his spouse Jane Curran will snorkel above for a broad perspective on what’s changed. And Wirth, clipboard in hand, will identify which species of fish dart in and out of the staghorn branches at certain spots within Coral Gardens—a task that requires the same stillness and patience as birdwatching.

The scientists hope that monitoring the reef’s health and analyzing environmental data from the site will help them understand what factors allow corals to thrive in this particular spot—and whether their resilience could help save other reefs.

Greer spent the early part of her career studying two types of reefs: modern Caribbean reefs, floundering as corals died and slimy algae cover increased, and fossilized reefs, which, although now long dead, thrived for several thousand years. The first time she dropped into the shallow water at Coral Gardens, following a tip that Al Curran had passed on from San Pedro locals, she realized this was a type of reef she’d only heard about—one that’s healthy. “It just… it took my breath away,” recalls Greer, who now leads the research program at Coral Gardens. “This is what they used to look like. I thought, oh my gosh, this is what they’re talking about.”

When scuba equipment first became widely available in the mid-20th century, divers found vast thickets of staghorn coral in Caribbean reefs, branches golden-hued with life as far as the eye could see. But within a few decades, that changed. The species started to die in the 1960s, leaving drab skeletons behind. This was one in a series of coral casualties. Closely-related elkhorn coral (Acropora palmata), the other prominent Acropora species in the Caribbean, had started to decline a decade earlier. According to historical ecologist Katie Cramer, both may have been affected by a drop in water quality caused as booming human populations and newly-developed chemical fertilizers caused nutrient levels in water to spike with additions of sewage and agricultural runoff.

Then, in the mid-1970s, researchers discovered that the once colorful polyps of Caribbean Acropora corals were peeling away, exposing their pale skeletons—evidence of white band disease, which increased the rate of Acropora decline. In the 1980s, coral bleaching began to spread through the region as climate change increased ocean temperatures, causing corals of many species to expel the algae that live symbiotically within their bodies. Corals rely on the sugars these algae make through photosynthesis, so bleaching leaves them weak and often without enough food to survive. Some bleached corals recover once water temperatures return to normal enabling them to regain their algae. Some die before waters cool. There’s evidence that heat has made white band disease more deadly, as well.

Today, the International Union for Conservation of Nature lists staghorn coral as critically endangered, the gravest designation for a species that still exists in the wild. Caribbean reefs have suffered declines of many species, but staghorn coral has been among the hardest hit. Now only small and isolated populations remain, although in some Caribbean reefs, like Dairy Bull Reef in Jamaica, there are signs that staghorn coral is returning. There, tumbleweed-shaped thickets now grow atop the skeletons of corals that died decades ago. And a hybrid between the two Acropora species, known as Acropora prolifera, is flourishing on some Caribbean reefs, a sign that it may be better able to cope with the barrage of threats to coral health than its parents.

A couple of years after Greer’s first visit to Coral Gardens, she and her team began studying the reef’s underlying structure to understand whether the thriving staghorn corals were bouncing back after the struggles of the 20th century or whether they had lived through those difficult times. The skeletons of coral ancestors typically lie below the living surface of a reef, making it possible for scientists to assess its history based on its layers of growth. During the decades when staghorn colonies were dying throughout the Caribbean, Greer’s team found no major breaks of growth at Coral Gardens—no evidence that the staghorn corals had been decimated. In fact, staghorn corals there appeared to have grown more or less continuously for over a century, according to age dating by University of Wollongong (Australia) geochemist and paleoecologist Tara Clark. The Coral Gardens reef appeared to be serving as what scientists call a refugium.

Refugia are places that shelter species through times of climactic upheaval or other environmental change. Much like Covid lockdown in a small apartment, refugia typically offer conditions that are just livable, not ideal. For corals, ideal conditions include water that’s neither too hot nor too cold, low levels of pollution and disease, plentiful fish to graze away algae that can otherwise outcompete corals for space, and predators that keep grazing fish populations in check. But a refugium may be small and isolated and some conditions may not be ideal, making life more challenging for corals. Refugia may also be spots where corals have increased ability to survive challenging conditions.

During the last Ice Age, such places helped reef life make it through wild fluctuations in sea level. Now, scientists are searching the tropics for refugia that may serve a similar role as global warming marches onward.

Floating above the largest thicket of staghorn at Coral Gardens, it’s easy to conclude that nearly all of it is alive. In reality, though, very few reefs—here or elsewhere—are entirely covered with live coral. Estimating the percentage of living coral and tracking how it changes over time is the next step in Greer’s effort to estimate this particular patch’s chances of surviving into the future.

Breathing from the tank on her back, Greer unwinds a tape measure as she swims over the reef, laying a transect line along which the team can collect data. Then, she frames each square meter of reef along the tape with a square of PVC pipe. Wirth swims above to take a photo of each plot as she moves. Then I take the same photo as a backup. After they’ve collected data along five transect lines, the team will digitally trace the live coral in each image, calculating the percentage that is alive. They’ve repeated this process at least annually for 11 years.

So far, the data suggest that although this reef’s staghorn coral is persistent, it’s not invincible. Between 2016 and 2017, Coral Gardens lost nearly half of its living staghorn coral. The largest thicket suffered the largest loss. When Greer’s team started monitoring it in 2012, living coral cover there was over 50 percent—similar to the proportion of live corals on healthy Caribbean reefs decades ago. But by 2017, the number had dropped to just 18 percent, about average for a Belize reef today.

Two instruments nestled within the reef, each about the size of a Tic Tac box, have helped explain why. Lightly encrusted with limestone and algae, each small plastic container holds electronics that have been recording water temperature every hour of every day since 2012. The data show that 2016 was abnormally warm, and stayed warm for an abnormally long time, due to the one-two punch of El Niño and climate change. While El Niño is a natural cycle, when combined with climate change, tropical oceans heat up far more than usual—a phenomenon that has now reappeared in 2023, sending reefs into hot water and causing widespread coral bleaching in the Caribbean this summer.

The corals endured yet another blow when, after more than two months of heat stress in 2016, Hurricane Earl made landfall in Belize on August 4 of that year, felling trees and scattering debris from damaged buildings across San Pedro. The researchers found that staghorn corals continued to die off after the storm. Only a few colonies were broken or overturned by the storm’s waves, but waves can also cause a flurry of sediment which the researchers suspect may have been lifted up from the seafloor, causing harm to corals by abrading coral polyps or smothering them with sand grains. Given the reef’s location far from shore and river outlets, they think it’s unlikely that sediment was carried into the reef from coastal runoff. Greer and her team found no evidence that storms over the past century caused the corals to die. They believe that Hurricane Earl may have added insult to injury—many corals, already weakened by heat stress, could not survive the storm.

Yet the staghorn corals in this particular place have shown the ability to bounce back. After the 2016 decline, the amount of living cover stabilized and eventually started to increase in some areas. In 2019, the largest staghorn thicket had jumped up to 25 percent live coral cover. By 2022, when I follow the team collecting data on the reef, there is 35 to 40 percent live coral—a near-complete recovery. This occurred even as other coral species on the reef, like brain coral (mainly species of Pseudodiploria) and star coral (Orbicella species) have bleached. That suggests that the staghorn didn’t simply recover because environmental conditions improved. Something else appears to be going on—perhaps a genetic advantage or an ability to acclimate to warmer water. Recent research has found that there are a number of different ways that corals—at least some species—may be able to increase their resilience to heat. This can include adaptation over many generations, which passes on beneficial genes. Corals are also known to adjust their gene expression or swap their symbiotic algae for a heartier variety. At Coral Gardens, it’s unclear what gives the staghorn coral the ability to bounce back. “It is under threat,” Greer says in 2022. “But it still is remaining somewhat resilient.”

But even corals with extraordinary resilience can reach a breaking point. For Coral Gardens, the breaking point would occur in 2023, when water temperatures rose to more than 30 degrees C (86 degrees F) by late May and remained hot until late fall. What had been a refuge became intolerable. When Greer and Wirth dove into the water at Coral Gardens for their usual fieldwork in December 2023 they found no living staghorn coral across their transects. It was a thicket of stony skeletons, almost every branch covered in algae. Corals that had survived for more than a century, weathering numerous threats, had perished in the heat.

As sea temperatures warm and reefs become increasingly vulnerable, Belizeans are taking action to help their reefs survive.

As we wrap up our effort to photograph corals across the reef, I get the unnerving sensation of being watched. Looking up, I spot a group of tourist snorkelers staring down at us. Our exhaled bubbles race up to them. When captain Narciso Valdez helps us clamber back aboard our vessel, Al and Jane Curran point out the tour boats, which arrived while we were underwater. A catamaran motors in from the south, joining the flotilla. It anchors and yet more snorkelers pour from its broad deck into the water.

Coral Gardens reef currently sits unprotected between two marine reserves, which leaves it more vulnerable to damage from activities like tourism. But its proximity also means that it has received special attention from staff at the adjacent Hol Chan Marine Reserve. In 2020, Kirah Forman-Castillo, then the reserve’s science director, started a project to spread the resilient staghorns from Coral Gardens into areas of the reserve that had lost most of their living coral cover. The reserve collaborated with Fragments of Hope, a Belize-based non-profit organization focused on reef restoration. Together, the team harvested staghorn corals from Coral Gardens, snapping off finger-sized pieces totaling no more than a tenth of each colony.

To add genetic diversity, the team also harvested staghorn coral fragments from other healthy colonies in northern Belize, but Forman-Castillo noticed there was something different about the staghorns at Coral Gardens—it was much harder to snap their branches. While there could be other reasons, she suspects this strength has something to do with the Coral Garden staghorns’ genetic adaptations, which may also help it survive.

Forman-Castillo’s team transported all the fragments in buckets of seawater to protected, shallow waters just south of the reserve’s namesake channel through the barrier reef —“hol chan” is Mayan for “little channel.” There, they’ve created a coral “nursery”—a place where the fragments can grow safely. When waves break corals, the surviving pieces can naturally form new colonies; reef restoration projects like this one are now capitalizing on this innate ability at sites around the world. Experts say that reef restoration is an effective strategy to help the ecosystem survive this century, along with efforts to address the causes of climate change and reduce pollution.

Greer pulls up the anchor and Valdez takes us about two miles northeast of Coral Gardens to see what Forman-Castillo and her team have been up to. We find the coral nursery in a calm, turquoise sea. It looks like an underwater table, about 10 feet across, with its metal legs anchored into a seagrass bed. Most of the “tabletop” is made of rope strung across a metal frame at foot-wide intervals. Forman-Castillo and her team had previously tucked the small fragments of staghorn coral from Coral Gardens and elsewhere between each twisted strand, suspended above the seafloor like acrobats on a tightrope. Now, six months later, the little corals are growing branches in all directions. A nurse shark often loiters under the table; Forman-Castillo jokes that the shark works as nursery security.

In a year, she explains, the staghorn corals will fill the ropes like garlands of tinsel. Then, the team from Hol Chan will carefully remove each rope and tack it to dead coral skeletons in the reef beyond. In their new home, the corals will continue to grow, eventually cementing themselves to the reef’s limestone framework of dead corals, hopefully becoming a human-built refugium over time. The batch we’re looking at is the second to grow in the nursery; the first already lives on the reef alongside a few small surviving colonies. The transplanted nursery colonies are now up to two feet across and seem to be thriving in their new home.

Yet while they’re relatively small, these corals aren’t babies. In fact, they’re quite old. Because they are from fragments of mature corals, they carry the genes of colonies that have lived for decades or even centuries. Colonies with the same genes are called a genet. A survey of Acropora colonies in northern Belize estimated that the region’s oldest staghorn coral genet is more than 400 years old. The youngest was 62 years old. Given their age, these northern Belize genets all survived the stresses that killed other corals in recent decades—a good sign that they have the ability to persist through challenging conditions. They could even survive thousands of years into the future; the oldest known Acropora genets, found in Florida, have been around for over 5,000 years.

Staghorn coral is a favorite for reef restoration in the Caribbean both because it creates superb fish habitat and because it grows comparatively quickly, adding three to 11 centimeters to its branches each year. But including other coral species is important for boosting reef diversity. And adding corals that have more robust limestone skeletons may also help reefs keep up with sea level rise, building upward fast enough to remain within the shallow, sundrenched depths that corals require. Scientists have developed a new technique called microfragmentation that speeds up the growth of other species for restoration projects. Using a saw, researchers cut small slices from coral colonies, often no more than a centimeter wide, which stimulates tissue growth, and produces new clones at a faster rate. Unfortunately, many projects have put microfragmentation efforts on hold as Stony Coral Tissue Loss Disease (SCTLD), which attacks many slower growing species, spreads through the Caribbean. The disease was first identified in Florida in 2014 and spotted near San Pedro in 2020.

The restoration effort at Hol Chan Marine Reserve is one of many projects aiming to increase live coral coverage on Belize reefs. Fragments of Hope has trained about 90 Belizean coral restoration experts and employs many of them to care for corals in nurseries and monitor restoration sites. As of 2022, they’ve grown about 170,000 corals in 28 nurseries throughout coastal Belize. They’ve planted those corals into more than 17 restored reef sites in seven marine protected areas. Eighty-two percent of the first corals added to restored reefs survived and, over the years, these colonies have expanded to cover 60 to 70 percent of the restoration areas.

But you can’t just build a reef anywhere. It’s important to choose the right places to restore, says Lisa Carne, Fragments of Hope’s founder and director. It needs to be an environment where environmental conditions will support corals’ needs: surfaces for corals to attach to, little or no runoff of freshwater and sediment from land, and nearby grass beds and mangroves where reef wildlife can spend some portion of their lives. A good site also has water flowing in from elsewhere and mixed by currents and tides, making it less likely for the reef to overheat. The restoration site at Hol Chan Marine Reserve has these qualities plus one more: the protection of the reserve’s boundaries.

Soon, Coral Gardens may have that, as well. For several years, Hol Chan has been interested in adding the reef to the reserve and in late 2022, Forman-Castillo submitted a proposal, currently under review, to officially change Hol Chan’s boundaries to include the reef. She’s now in a new role as the Belize coordinator for the conservation nonprofit MarAlliance and remains an advocate for Coral Gardens.

In a world where corals continue to die at an alarming rate, these resilient reefs—both natural and human-built—are places where they might survive.

If the reef becomes part of the reserve, staff would install permanent moorings to protect the site from anchor damage. Tour boats would have to pay fees to use the area, and proceeds would go toward managing the reef. The designation would also ban fishing, which could help ensure the region’s fisheries continue to thrive while also keeping the reef ecosystem in balance.

Organizations like the World Wildlife Fund (WWF) are looking for more refugia within Belize reefs as well. “I think we need to identify these healthy resilient reefs for sure and put them under some form of protection,” says Nadia Bood, head of the WWF’s Belize Program Office. In a world where corals continue to die at an alarming rate, these resilient reefs—both natural and human-built—are places where they might survive.

After scoping out the coral nursery, Greer, Wirth, and I meet Lisa Carne and several of her colleagues from Fragments of Hope at the nonprofit’s first restored reef, about 100 miles south of Hol Chan Marine Reserve, at Laughing Bird Caye National Park.

Crowded with corals and bustling with fish, the reef offers a vision of what Hol Chan’s restored reef could become in a decade or so. In the years since Fragments of Hope added nursery-grown corals to the site, they have continued to grow wild. Snorkeling through shallow water above the thickets, they look much like the natural reef at Coral Gardens. In some spots, their living tangle of branches forms a mosaic of amber hues across the seafloor. In other spots, the pale lumpy skeletons of dead corals peek through the living—the only evidence that this reef hasn’t always thrived.

Before it was restored, the reef at Laughing Bird Caye had lost nearly all of its coral, likely because of the same cocktail of stressors that bludgeoned most Caribbean reefs in the latter half of the 20th century. Carne started restoring it in 2009. Over 10 years, her team grew tens of thousands of Acropora coral fragments in nurseries, including elkhorn coral, staghorn coral, and a hybrid of the two, and installed them atop dead coral skeletons on the seafloor. Fragments of Hope now monitors the reef from the air above with a drone. The 2020 drone photo shows that corals expanded to cover 7 percent more of the seafloor than the year before. In the 2021 photo, live corals cover 14 percent more area than in 2020.

To help the restored reef remain a refuge in a warmer future, Carne and her team focused on finding corals that had already proven themselves resilient. Much as she and Hol Chan staff would later harvest the resilient staghorns from Coral Gardens, her team harvested corals for Laughing Bird Caye from resilient pockets on southern Belize reefs, which may also be refugia, albeit undocumented ones. Corals there already survived in water prone to overheating. In theory, at least, they may be better adapted to survive as the climate warms. Fragments of Hope would find in 2023 that many of these stalwart corals didn’t bleach even after months in hot water. But some were unable to cope, their ghostly white skeletons standing in contrast to the golden tones of neighboring colonies. Carne and her team will use the corals that persisted in the heat for future reef restoration.

“How are you going to adapt if you don’t have sex?”

— Lisa Carne, Fragments of Hope

It was important, Carne explains, for the transplanted corals to come from several different places to keep genetic diversity high in the restored reef, which increases the chances of even greater diversity through sexual reproduction. Corals can reproduce asexually, adding new polyps—perfect clones of their neighbors—as a colony’s branches extend in length, which is a mainstay of reef restoration. But sexual reproduction requires different genets—genetically different corals of the same species, not clones—and is necessary for species to adapt and, hopefully, survive long term if waters warm slowly and corals have enough time to adapt. Most corals sexually reproduce through spawning, during which polyps send gametes into the water. Hopefully pairs of gametes—egg and sperm—unite through fertilization to produce coral larvae, combining genes from two parents. Carne and her team make sure that there is a great mix of genes in their reefs in hopes that corals will be able to adapt over many generations of combining genes, increasing resilience to heat and myriad potential disasters. “How are you going to adapt if you don’t have sex?” Carne asks. “You cannot have evolution and adaptation if you’re not crossing your chromosomes with something else.”

To ensure that exchange, Fragments of Hope has filled the shallow water around Laughing Bird Caye with 17 genets of staghorn coral, 30 genets of elkhorn coral, and three genets of hybrid Acropora. As a result of spawning, there may now be new genets at the reef. From the edge of Laughing Bird Caye, Carne looks out at the reef offshore and wonders, hopefully, whether new coral offspring are out there with the traits they’ll need to survive in a changing world.

WWF has helped support Fragments of Hope since 2009, and over that time Nadia Bood has watched the benefits of Belize’s restored reefs extend beyond corals to other creatures too. “Those restored sites have biodiversity coming in,” she says. “You can see different species of fish and crustaceans in those sites. Even at the nursery tables, you can see different organisms recruiting to the tables and using [space] underneath the table as habitat as well.” Even before their charges are moved to the reefs, the nurseries take on a life of their own.

As we snorkel the reef near Laughing Bird Caye, we see plenty of evidence of the biodiversity Bood referred to. There’s a tiny juvenile monochrome drum fish that flits back and forth below an overhang of coral, its long dorsal and tail fins waving like ribbons. Large schools of grunts, parrotfish, and other grazing fish flow over the corals in glimmering formation. The water crackles with the sounds of their eating, and of shrimp snapping their claws.

Carne introduces us to a small bright blue fish—the endangered Maya hamlet (Hypoplectrus maya), found only in shallow waters off coastal Belize. Once I know what a Maya hamlet is, I start to notice them throughout the restored reef. Most loiter solo, each next to a thicket of coral, their azure color perfectly complementing the corals’ honey-hued symbiotic algae. These corals—artificially planted and tended by people—now shelter multiple species.

Will refugia like this one be enough to save staghorn coral and other reef species from extinction? If seawater becomes too hot, most are likely to fail, as Coral Gardens failed in the heat in 2023. Models predict that Australia’s Great Barrier Reef will lose many of its pockets of safety if the climate warms beyond three degrees Celsius. But if humans finally manage to reduce their greenhouse gas emissions enough to limit climate change, and resilient corals manage to persist, it’s possible these sanctuaries will be able to shepherd reef life safely into the uncertain future. Perhaps, hopefully, corals can one day spread beyond their refuges again, and even thrive, as they have in the not-too-distant past.

Lisa S. Gardiner

Lisa Gardiner

Lisa S. Gardiner is a writer, geoscientist, and educator. She is the author of the award-winning book, Tales from an Uncertain World: What Other Assorted Disasters Can Teach Us About Climate Change (2018) and her writing has appeared in Scientific American, Inside Energy, Science Friday, and other publications. She is currently working on a narrative nonfiction book about coral reefs of the past, present, and possible future.

Karl Wirth

Karl Wirth

From the intricate patterns of coral to the majestic dance of sunbeams on the ocean floor, Karl Wirth is captivated by the wonders of the sea. His lifelong fascination with nature has shaped his journey both as a geology professor and a scuba instructor. He's not just content with exploring; he's passionate about sharing these discoveries with his students and others. With each photograph, Wirth aims to unveil the wondrous beauty found in the details and complexity of the natural world. Now living on Cozumel, surrounded by Caribbean reefs, he finds daily inspiration in the very waters that have always fueled his passions.

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