Much has changed on Belize’s coral reefs in the years since I got to know them. I feel a mix of emotions knowing that the first coral reefs I ever studied are not there anymore, not in a form that I would recognise from my first tropical dives. I’ve come to appreciate how lucky I was, belonging to one of the last generations of young marine biologists who studied coral reefs without a looming sense of the ocean unravelling. That note from my dive logbook about bleaching shows how differently I was thinking about reefs then compared to now.
Guilt has since caught up with me for my contributions to the downfall of reefs. I have flown across the ocean many times, playing my part as a rich visitor, leaving trails of carbon in the skies. And for a long while, I carelessly assumed the biggest changes in the ocean still lay way off in some unspecified point in the future. It’s obvious now that reef life was already shifting and altering around me; it just took me time to realise what was happening.
There are still coral reefs in Belize, but they’re very different than they used to be. For more than a million years, reefs in the Caribbean were dominated by a small set of stony coral species that grew fast and created the ecosystem’s complex limestone architecture. Staghorn and elkhorn corals, reaching their branches skywards in dense thickets, and massive boulders of Orbicella all played their key parts in building reefs. Over the past few decades, these foundational species have dramatically declined. In their place are smaller corals that grow much more slowly and don’t lay down as much reef-building limestone. There are also sponges and soft corals, which don’t make stiff limestone skeletons but grow in colourful fronds, fans, and feather dusters that sway and thrum in the current. Large seaweeds take up more space on reefs than they used to. These are novel ecosystems assembled by species that are coping with gradual environmental change as well as the sharp and increasingly common catastrophes that the ocean in the Anthropocene is delivering.
Across the region, many coral reefs are doing just as badly as those in Belize. In the past thirty years, corals on three-quarters of reefs across the Caribbean have declined. In 1998, mass bleaching killed off 8 per cent of the world’s stony corals. The survivors set about rebuilding the damaged ecosystems, releasing larvae, which settled and grew. It took ten years for reefs to regain their coral cover, but it didn’t last long. In the following decade (2009–18), at least 14 per cent of stony corals worldwide were killed—that’s more than all the corals currently living on Australia’s reefs. This century, coral cover on tropical reefs has been episodically ratcheting further and further down.
The lost corals were blasted, smothered, and poisoned, eaten by outbreaks of crown-of-thorns starfish, snapped off for aquarium displays, and killed by diseases. Most of all, though, coral reefs are getting sucker-punched by the climate crisis from all directions. Hurricanes are becoming more powerful and more likely to flatten reefs. Heat-stressed corals are more vulnerable to sickness and disease. Warming seas are losing oxygen, which in many places is stressing corals and will likely get a lot worse in the years ahead.
Mass coral bleaching kills corals across hundreds and thousands of square miles of reef within a matter of months. Most worrying are outbreaks that impact entire regions. In the summer of 2023, reefs yet again bleached throughout the Caribbean, from Cuba and Mexico to Costa Rica and Colombia. That year, an ocean heatwave in Florida drove sea surface temperatures above one hundred degrees Fahrenheit for the first time on record, and coral bleaching was devastating.
The heatwaves that trigger mass bleaching are striking worldwide more frequently, giving corals less time in between to recover. The Great Barrier Reef was hit by mass coral bleaching in 1998, 2002, 2016, 2017, 2020, and 2022. The 2022 event was the first to occur in a year when the Pacific Ocean was not expected to be so hot. In past years, mass bleaching was only likely in association with a strong El Niño, the periodic climatic phenomenon that pushes up sea temperatures over large tracts of the ocean, which climate change is making more frequent and intense. The cooler phase, La Niña, used to offer corals respite. But now mass bleaching can happen in any hot summer, regardless of which part of the El Niño–La Niña cycle the world is in.
Reefs also have to contend with another climate impact caused by humanity’s carbon dioxide emissions absorbing into the ocean, causing the pH of seawater to fall. This ocean acidification is reducing the availability of dissolved carbonate ions in seawater, the molecules that corals need to build their limestone skeletons. Other important organisms also need a good supply of carbonate ions to grow, including algae that incorporate limestone in their tissues and grow in pink and orange crusts over reefs, like layers of thick paint. Stony corals are the bricks that form a reef’s foundation, and encrusting coralline algae is the cement that binds the framework together.
To better understand what could happen to reefs in a warmer, more acidic ocean, scientists in Australia have built multiple miniature patch reefs in eighty-gallon aquarium tanks in a laboratory. They carefully assembled diverse mixes of corals and seaweeds, fishes, sponges, sea cucumbers, and other animals. Then they wound the clock forwards and exposed these mini-reefs to conditions predicted for the end of the century. The experiment ran for a year and a half, in which time some corals fared better than others. The winners were coral species that live as solitary polyps and don’t have chunky limestone skeletons. The losers were coral species responsible for building the limestone reef structures. They were impacted most when bathed in seawater that was not only warmer but also more acidic. Living in these conditions, they grew weaker skeletons—a coral equivalent of osteoporosis. This foretells of times ahead, possibly for thousands of years to come, when wild reefs may not be able to keep pace with rising seas and won’t grow upwards fast enough to stay living in the sunniest shallow waters. Reef-building species of stony corals can’t survive well in deeper waters because there’s not enough sunlight for their zooxanthellae to grow and supply their food. Even though they are ocean-dwelling animals, coral reefs can drown.
The endgame for coral reefs as we know them could come when there’s nowhere left in shallow seas with the right chemistry to allow stony corals and encrusting algae to grow. Instead of building and maintaining their limestone ramparts, reefs could start dissolving. Predictions of when this could happen remain highly uncertain. It could be as soon as 2030 or perhaps not until midway through the twenty-second century.
All these threats combine to depict the future of coral reefs in various shades of gloom. These are without doubt some of the world’s most vulnerable ecosystems. Coral reefs are also some of the best-studied parts of the ocean. Thousands of scientists are staring gimlet-eyed at reefs and attempting to understand how and why these ecosystems are transforming. And yet, there are still reasons to be hopeful.
Surveys in 2022 recorded the highest overall cover of coral on parts of the Great Barrier Reef in thirty-six years of monitoring, despite repeated bouts of bleaching and outbreaks of crown-of-thorns starfish. A few reefs were almost entirely covered in sprawling colonies of corals.
Generally, heatwaves don’t strike everywhere, all at once, with equal intensity, so while some reefs are getting stressed out and overheated, others remain cooler and healthier. Also, some reefs cope better than others with being baked at high temperatures, likely because of their past experiences. The thermal history of a reef matters. Those that have lived through previous temperature spikes seem less likely to bleach than others that haven’t undergone such extremes, partly because the most vulnerable corals are already dead. Among the survivors are signs that corals are toughening up and beginning to adapt to their warming ocean. In Palau, a cluster of remote islands in the western Pacific, reefs are apparently becoming more heat tolerant. A heatwave in 2010 caused widespread bleaching but seven years later, when similar hot conditions returned, there was little to no coral bleaching. For now, scientists haven’t determined why Palau’s corals are surviving heat better: if individual corals are acclimatizing or if there are genetic shifts taking place. On reefs in Panama, Pocillopora corals, which look like little cauliflowers, have been coping better with heatwaves as time has gone by. The key to their survival has been an alteration in the varieties of zooxanthellae living inside their bodies. They switch their algae for a more heat-tolerant variety that naturally occurs in the sea, and it makes them less inclined to bleach when the temperature rises. There are also broader hints that corals are adapting. Globally, since the 1990s, the average temperature that triggers the onset of mass bleaching has increased by a half degree Celsius.
Amid the dark shadows on today’s reefs, there are bright spots. Twenty years’ worth of underwater surveys on three thousand tropical reefs reveal a few dozen that shine out and are in a healthier condition than expected, based on a variety of factors that influence coral cover, such as water depth, hurricane damage, and the temperature regime. Bright spots are dotted across the globe, from reefs in Cauca on the Pacific coast of Colombia to Maui in Hawai’i, from Okinawa in southern Japan to Kien Giang off southwestern Vietnam; others are located in New Caledonia, the Philippines, Indonesia, and Malaysia, on the Andaman Sea coast of Myanmar, and in Ari Atoll in the Maldives. These reefs are doing better than the local conditions would seem to allow—and creating more room for hope.
Tropical reefs in shallow seas are critically important and frighteningly threatened, but they’re only a part of the story of the world’s coral reefs. A new vision for the future of coral reefs is emerging in parts of the ocean that are challenging to get to and that I’ve never visited. Often I’ve hovered beside steep walls of coral, gazed into the yawning blue below, and felt a strong urge to carry on down. I’ve seen giant fans and tall spirals of coral twisting up from the reef below. Shoals of fish have swooped overhead, then raced into the depths and out of sight. I’ve watched sea snakes wind their way to the surface to catch a breath before plunging back down beneath me, drawing curves through the water, and always I’ve resisted the temptation to follow them. Cumulatively, I’ve logged many days’ worth of scuba dives, but I’ve spent fewer than fifteen minutes of my life diving deeper than 130 feet. Much deeper, and I would get drunk on the nitrogen in the compressed air I’m breathing or fall unconscious from the toxic high pressure of oxygen. But coral reefs don’t stop at 130 feet, and an increasing number of diving scientists don’t either.
To unlock these depths, divers use equipment known as closed-circuit rebreathers, which instead of bubbling air into the water, as with a standard scuba kit, divers rebreathe their exhalations over and over. The technology was pioneered in the 1970s with a system called the Electrolung. A diver’s breaths are circulated through a scrubber to remove exhaled carbon dioxide and past an electronic sensor that monitors the gases and automatically keeps the oxygen at a safe level, topping up as necessary from a small cylinder. It’s critical to breathe not too much or too little oxygen; either can make a diver pass out, which quickly becomes lethal a long way underwater. Tragically, that does still sometimes happen. More scientists are undertaking the long training regime to use this technical equipment as safely as possible. Like pilots learning to fly an aeroplane, rebreather divers first learn how to do it, then log many hours of supervised diving time. Once fully qualified, divers can go on very long, very deep dives, lasting four or five hours, as far as five hundred feet down, allowing them to plunge into this indigo realm in bubble-free tranquillity and explore a region of coral reefs that used to be almost entirely out of bounds.
Between one hundred and five hundred feet down is the mesophotic zone. Here lie coral ecosystems that continue from shallower reefs and transition into a space that’s shared by species from nearer the surface and others that are found only deeper down. It lies in between the sunny surface seas and the dark “deep sea” proper, where sunlight is too weak to power photosynthesis. In the mesophotic, meaning “middle light,” there’s still just enough illumination for living organisms to use. Seaweeds grow in the upper reaches of mesophotic reefs, their pigments adapted to absorb the faint remnants of light seeping down. Stony corals with zooxanthellae inside their bodies grow to at least 210 feet down. Deeper in the mesophotic grow other types of corals that don’t have symbiotic algal partners to draw food from and instead entirely feed themselves. These include black corals with dark, shiny skeletons and octocorals that grab minute prey from the water with their eight-tentacled polyps. The mesophotic is the zone where coral ecosystems switch from being dependent on sunlight to surviving in semi-darkness.
Compared to the well-studied, scuba-accessible shallows, very little is known about the mesophotic zone. Nevertheless, the reefs here are clearly important, since they cover a far larger area of habitat than all shallow reefs combined. The Great Barrier Reef likely has an equivalent area of reef below one hundred feet as above. Globally, around 80 per cent of potential coral-reef habitat lies in the mesophotic. Of those reefs, only a small subset has been explored and studied so far, and enough is already known to show such reefs support unique biodiversity, of a composition unlike anywhere else in the ocean.
The mesophotic contains fish species that nobody has seen before. For every hour a rebreather diver spends searching the lower parts of this zone, they find an average of two species of fish that are new to science. Many of the deep-only species seem to occupy a small geographical range; they live only in one tiny part of the ocean, which for reef fish is unusual. Many mesophotic fish have stunning colours and patterns, like the rose-veiled fairy wrasse,c which lives on reefs more than two hundred feet underwater on the coral atolls of the Maldives, with its crimson-dipped head, golden body, and cobalt-fringed fins. The latigo fairy wrasse was found in the mesophotic zone beneath one of the busiest shipping lanes in the Philippines; this fish has pinstripes across its face and a metallic blue spot on its dorsal fin, and the male of the species has a scintillating, iridescent tail and long, whiplike pelvic fins, which he flicks in eye-catching displays put on for potential mates and rival males. On Kure Atoll in the Northwestern Hawai’ian Islands, 300 feet down, lives Obama’s basslet, a small fish with a yellowish-pink body and a thin, bright-yellow line running through its eyes. It was named in honour of President Barack Obama and his efforts to preserve the natural environment. A few weeks after the fish’s discovery, Obama announced the expansion of the Papahānaumokuākea Marine National Monument, which now encompasses the Obama’s basslets’ deep-water home.
Scientists are also finding some incredibly healthy and vibrant coral reefs in the mesophotic. In Tahiti, in 2021, divers visited a previously unknown reef, two miles long and between one hundred and two hundred feet deep, where colonies of coral cover every available piece of the seabed. Seen from above, they look like great piles of spiral shavings from carefully sharpened pencils. And these corals showed no signs of the mass coral bleaching that swept through the region three years earlier.
Reefs like these have spawned the hopeful idea that the mesophotic zone could be safe from the worst impacts of the Anthropocene, a deep oasis hidden away from troubles concentrated nearer the surface. Generally, the deeper underwater, the colder and darker it gets, so it stands to reason that deeper reefs are less likely to suffer from heatwaves and coral bleaching (light intensity and heat are both triggers for bleaching). Mesophotic reefs also lie deep enough to avoid getting smashed apart by hurricanes, and they lie below the reach of some methods of fishing.
Deeper reefs are indeed showing they can be less vulnerable to the climate crisis than their stressed, overheated neighbours above. Near to where divers found the deep reef in Tahiti, scientists studied two other French Polynesian reefs during a mass coral bleaching in 2019. Off both Mo’orea and Makatea islands, the proportion of bleached coral colonies declined dramatically with depth.d Below two hundred feet, there was almost no bleaching at all.
In some cases, though, thermal relief in the deep may be only temporary. In the 2016 heatwave on the Great Barrier Reef, fewer corals bleached in the upper parts of the mesophotic, at around 130 feet, compared to the shallows, because a cool current from below happened to sweep in while the heatwave was at its peak. At other times of year, the difference in temperature between the surface and deeper water is not as notable. Future heatwaves may not be so well timed.
As deep-diving scientists have gotten to know the mesophotic better, they’ve been exploring another promising possibility for the future of coral reefs. Perhaps these deeper, healthier reefs could come to the rescue of damaged reefs at the surface. Just as mangrove seeds floating from intact forests can help regenerate damaged areas, mesophotic corals and fishes could perform a similar service, although only if certain conditions prevail. First, there need to be species that span the boundary between mesophotic and shallow reefs. Depending on where in the world they look, scientists are finding depth generalist species among the corals. For instance, surveys in American Samoa have found almost two hundred coral species that live on shallow reefs, a dozen that live only in the mesophotic below one hundred feet, and sixty-three that occupy both zones. But the deeper corals will be of use to the shallower reefs only if the populations are mixing. It’s no use if mesophotic corals keep to themselves, and their eggs and larvae don’t venture nearer to the surface. Indeed, genetic studies are showing that some coral species do not mix, essentially subdividing populations by depth. This could be because physical barriers get in their way, such as currents sweeping down and not up, or there may be limits in how far the eggs and larvae move before settling, so they never make it to shallower reefs.
Fish have the possibility of roaming up and down throughout their lives between the mesophotic and the surface, and so they could use the greater depths to escape fisheries in shallower seas. In the Pacific, around the Mariana Islands, giant humphead wrasse, up to six feet long, are caught by divers spearfishing near the surface. More of them now live in mesophotic reefs than on shallower reefs, suggesting that the greater depths act as a de facto marine reserve and could become a last stand for this highly endangered species.
Exactly how important mesophotic reefs could be in helping shallower reefs recover remains uncertain. Scientists who dive frequently in the mesophotic are convinced these are distinct ecosystems, wholly separate from their shallow neighbours. What’s more, they’re seeing that the mesophotic is not in fact beyond the reach of human impacts. Invasive lionfish released in the Caribbean Sea have already spread into mesophotic reefs, potentially shifting the balance of these ecosystems. Hurricanes may not directly smash deeper corals, but storm-stirred debris and landslides can slump down steep slopes and smother ecosystems below. Plastic debris builds up at higher concentrations deeper underwater on coral reefs, peaking in the mesophotic, likely because stronger wave energy in the shallows sweeps plastics away, but when they rain down into the calmer depths, they tend to stay there. Many fisheries already exploit the mesophotic. Black corals in the mesophotic have been stripped out for the jewellery trade.
Regardless of how well connected they are to shallower seas, mesophotic reefs very much matter in their own right, for the ecosystems they harbour and the threats they face. And for now, they are poorly protected. Conservation plans for coral reefs are just beginning to include those at greater depths. Belize has long been a pioneer in protecting its seas and coasts. A century ago, in the 1920s, long before conservation went mainstream, the government set up a sanctuary on Half Moon Caye to safeguard the large colonies of nesting red-footed boobies. In 1982, it became the first marine protected area in Belize and in the whole of Central America. The country now has one of the most extensive networks of marine protected areas in the Caribbean. In 2019, the government tripled the highly protected no-take zones so they cover almost 12 per cent of the nation’s waters, including extensive areas of mesophotic reefs.
Marine reserves are important for the health of coral reefs for many reasons: they can prevent the smashing of corals by anchors, trawlers, and dredgers, and they can help reef fish populations recover from overfishing and boost catches in nearby fisheries. But they won’t be enough to guarantee that coral reefs survive unscathed throughout the Anthropocene ocean. They’re just not cut out to hold back the problems that threaten reefs the most.
A two-decade study in Belize surveyed fifteen sites across the reefs and found that stony corals declined by just the same amount inside and outside reserves. During the twenty-year time span, Belizean reefs were struck twice by mass coral bleaching, devastated by an outbreak of yellow-band disease, and hit by seven hurricanes. All these problems are linked to the climate crisis, and none of them paid any attention to the watery boundaries of marine reserves. Several other studies have similarly found no great difference in bleaching on protected versus unprotected reefs in other parts of the world.
It’s possible that, given enough time and enforcement of fishing regulations, coral reefs inside marine reserves will become healthier, and some will be more resilient and better able to recover from the grimmest global threats. Early theories predicted that protecting reefs from fishing pressure would help corals thrive. Parrotfish have been thought to play a key part in reef health. Like their rainforest namesakes, these fish have dazzling colours, and their teeth are arranged in a sharp, beaklike form. They graze reefs, scraping surfaces clear of large seaweeds that could outcompete corals, overshadow and abrade young corals, and even poison them with toxic chemicals. It was generally thought that allowing parrotfish and other grazing fish to rebound inside reserves would help corals survive. But that theory hasn’t been playing out neatly on reefs, and simplistic links between fishes, seaweeds, and corals may be weak, inconsistent, or nonexistent. That’s not to say that fish are inconsequential for reef health, just that they can’t be expected to bear the burden of saving reefs in the Anthropocene.
Even the most isolated and healthy reefs, such as those in the Chagos Archipelago in the central Indian Ocean, have been brutally hit by coral bleaching. In 1998, mass bleaching struck corals in the Chagos, and as happened elsewhere in the world, the reefs recovered, and corals regrew over the following decade. Then, in 2015 and 2016, while Pacific kelp forests were withering under the disastrous heatwave known as the Blob, sea temperatures were also rising across the tropics, and the reefs of Chagos suffered massive back-to-back bleaching events. For two years running, corals lost their colour, and the seascape faded to white. Close to 90 per cent of the dense thickets and wide tables of Acropora coral were killed.
Those scorching years were unprecedented. The destruction they caused was a huge wake-up call for scientists and conservationists, who watched as countless reefs bleached and corals died, including those in supposedly well-protected waters.
Still, there are glimmers of hope. In the Chagos Archipelago, when the reefs were struck by bleaching in 2016, a smaller portion of the corals died than in the previous year, suggesting the survivors had become more resistant to rising temperatures. And some reefs in Chagos are recovering faster than others, thanks in part to seabirds. On islands where tropicbirds, boobies, shearwaters, and frigate birds come to nest, nutrients from their droppings splatter on the ground and get washed out to sea. This runoff fertilises nearby reefs and encourages the growth of encrusting coralline algae, which cements reefs together and creates suitable surfaces for young corals to settle on. Long ago, visiting sailors released rats on some islands in the archipelago, and these rodent invaders have a keen appetite for seabird eggs. Rat-infested islands now have no seabird colonies and no nourishing guano. De-ratting islands is one approach to help restore seabird colonies and give recovering reefs an added boost.
Such efforts will likely contribute to reef health on a small scale, but ultimately the fate of coral reefs will be determined by how quickly heatwaves come along. As the interval between heatwaves shrinks, the less time reef ecosystems have to recover between the mass bleaching events they trigger. And the only way to limit the frequency and intensity of heatwaves is to limit greenhouse gases in the atmosphere.
Coral reef researchers and conservationists may differ in their opinions over what to do about the coral crisis—whether marine reserves are the key, for instance, and whether parrotfish really help—but on one matter, everybody agrees. The most hopeful version of reefs in the future will happen only if carbon emissions are drastically cut. Climate and ocean experts at the Intergovernmental Panel on Climate Change forecast that if humanity continues with business as usual, coral reefs as we know them today will mostly be gone by century’s end. If global temperature rise can be kept below 1.5 degrees Celsius, then maybe as much as one-third of corals stand a chance of surviving. And as the chances diminish that emissions will be driven down fast and far enough, more scientists and conservationists are deciding that the time has come to make alternative plans to try to keep corals and their reefs intact.
A few years ago, behind the scenes at a public aquarium in Florida, I learned that corals have a strong, distinctive smell. The aquarist who was showing me around pulled out a fist-size branching colony from a gurgling tank of seawater and waved it under my nose. It smelt like turpentine, and I tried to imagine the stink that wafts from a reef full of corals, all of them exuding chemicals as predator deterrents.
In that aquarium were two dozen species of Floridian corals, among them emerald-green cactus corals, brain corals, staghorn and elkhorn corals. I peered at fuzzy brown dots of new baby corals that were just a few weeks old, born when their parents had been placed together in a bucket at new moon and had spawned. Seen up close, with their peculiar coralline commingling of animal and stone, all these corals seemed robust. And yet, a pile of dead, white skeletons on the floor was proof of how sensitive they can be. Those corals had all bleached and died because an aquarist had moved them around their tank into spots where the illuminating lamps were a fraction brighter. The coral colonies weren’t accustomed to so much light, and it killed them.
The aquarium staff were growing corals not only to put on display to the public but to send to scientists who are working out how to keep them alive and encourage them to reproduce. Some of the corals I saw may have ended up being planted out in the wild. The number of coral restoration projects has been exponentially increasing as more efforts are made to breathe life back into damaged ecosystems. They aim to boost the cover of stony corals as the key metric for reef health and something that can be manually improved. A popular technique is to chip off small nubbins of branching corals from healthy colonies and transplant them onto degraded areas, cementing or tying them in place on the seabed. Propagating corals in aquariums is another way to do it.
As the ocean becomes hotter and more acidic, reef restorationists increasingly want corals that have been engineered to survive the Anthropocene. Designer, future-proof corals are not a pipe dream. In laboratories, scientists have already begun to enhance the ability of corals to withstand heat. One approach for toughening them up is a process known as experimental or assisted evolution. At its heart is an ancient practice that humans have been performing for millennia, in the way that our ancestors bred crops and domesticated animals. This involves selecting the animals or plants that have characteristics of greatest interest—the strongest horses, the biggest ears of wheat, the cutest puppies—then having those individuals breed and pass on their qualities to the next generation, and repeat. In the Anthropocene, generations of wild corals have the potential to adapt naturally to their changing environment, but it’s unlikely to happen fast enough for them to escape extinction. This is why scientists are working to speed up the process by breeding more heat-tolerant corals. Hybridisation is another old technique that’s being brought into play for corals. Pairing up different wild species can result in hybrid offspring that are fitter than either of their parents.
Breeding and evolving corals in captivity through multiple generations takes time, partly because spawning naturally occurs only once a year for many corals. Researchers are largely focusing instead on the rich mix of microbes living on and inside corals, which grow and reproduce much faster than the corals themselves. Important targets are the symbiotic algae that live inside corals and influence how sensitive they are to bleaching. Conveniently, zooxanthellae survive well outside corals and can be cultured in laboratories, where they divide and produce a new generation within a matter of days. Experimental evolution of zooxanthellae has already led to some impressive results. Over the course of one year, researchers incrementally raised the temperature in a culture of zooxanthellae; at each stage, they picked out strains that were surviving and growing best, then turned up the heat some more and repeated the process, again and again. By the end, they had zooxanthellae that were growing well at temperatures over ninety-three degrees Fahrenheit.
