The Florida Problem: A Special Report. Struggling crops. Salty aquifers. Invading wildlife. Piles of dead fish. The Sunshine State feels the squeeze of environmental change on its beaches, farms, wetlands, and cities. But what afflicts the peninsula predicts the perils that will strike north and west of Apalachicola, and so it demands our attention. If Florida is in trouble, then so are we all.

Just off the coast of the Keys, wind-driven swells toss our little boat like a bath toy. Nearly 30 feet below, in the blue murk, divers tend their plot: a sparse patch of sea-floor 10 meters square.

One swimmer hovers over a brain coral the size of a fish­bowl, studying its corduroy surface as she readies a syringe in one hand. She dispenses a droplet of white putty and dabs it onto the edge of the colony.

Back at the surface, Karen Neely, a Nova Southeastern University marine biologist with the easy manner (and tan) of someone who spends her professional life on the water, scans survey sheets marked with terse scribbles of observation. Coral reefs are bleaching around the globe, but Neely and her ­collaborators are grappling with a new, more mysterious epidemic. And to fight it, they’re using a weapon scientists never thought they’d unleash.

Stony corals, though easily mistaken for rocks, are animals. Each colony is made up of tiny tentacled polyps crowded together to form a living skin that grows, mosslike, over an elaborate ­calcium-carbonate skeleton laid down by generations of clones. Like all animals, they get sick. ­Bleaching—an increasingly common affliction where heat-stressed colonies expel their colorful photosynthetic algae and turn white—could be akin to an auto­immune disease. Bacteria and viruses threaten them too.

In 2014, a scientist diving just off Miami noticed some mangy-looking corals with white bull’s-eyes where dead tissue had recently peeled away from the skeleton. It was the first sighting of a new condition called stony coral tissue loss disease (SCTLD). The ailment would tear through reefs in waters along Broward and Miami-Dade counties over the next two years, targeting more than 20 different species, including massive mounding varieties like brain and boulder coral that make up the foundation of the reef.

The contagion can knock out an 800-year-old colony the size of a car in a matter of weeks. Important habitats vanished and the wave-breaking power of the reef diminished, leaving the shoreline increasingly vulnerable to storms. As scientists scrambled to assess the damage, the mysterious malady started chewing its way into the Florida Keys, sometimes moving 10 miles in a month. By January 2019, it had infected areas as far south as Key West, encompassing much of the national marine sanctuary that protects more than 50 kinds of coral and hundreds of species of fish. This wasn’t just another illness, but a plague. And it had infiltrated one of the best-preserved stretches of coral reef left in the U.S.

With no diagnosis to guide them—most marine microbes don’t thrive in lab cultures, making the usual approach to identifying diseases basically useless—scientists still sought solutions. One hint of hope: Infected colonies kept in captivity recovered with the help of antibiotics.

But putting anti­biotics into the ocean is problematic. The ­fish-​­farming industry uses them plenty but faces criticism for causing bacterial resistance in surrounding waters. The drugs also end up in marine food chains because waste­water plants have no way to remove the compounds from sewage and runoff. Now, with the blessing of the FDA, Neely and her colleagues are adding more chemicals to the load.

Neely and I take a boat from Ramrod Key, a lacy island in the Lower Keys where the ­tissue-​loss disease showed up a few months earlier. It’s a short ride to the site, where we gear up and, palming our masks to our faces, roll backward into the water.

From 20 feet up, it’s hard to see anything amiss. Fish dart around swaying purple sea fans. Mounds of living coral rise from the sand, swirled with velvety brown ridges or freckled with green-blue buds. As we swim closer, Neely ­zeroes in on a maze coral as wide as a tire, its tawny skin marred by white splotches. She points out a puttylike line scrawled midway through one of the bare spots. This marks where she applied antibiotics two weeks earlier. At the time, it was the edge of the infection. Now, she writes: “Ineffective, disease passed” on her waterproof clipboard. She pantomimes wiping away a tear below her mask.

Three of the four colonies Neely treated are still sick. In some cases, SCTLD sneaked through the pharmaceutical barrier. In others, new white spots popped up elsewhere. Only on the last, a boulder coral roughly the size and shape of an overstuffed ­ottoman, has the treatment mostly succeeded.

pink coral illustration
Death of the reef. illustration by Zohar Lazar

This is what it’s supposed to do,” Neely writes, indicating the line that has held off bacterial siege. On one side, the deeply ridged surface is plush and healthy; the other is a bare, razor-edged skeleton. Antibiotics won’t undo the damage, but they can keep it from spreading through the entire colony. When we surface, Neely admits she’s surprised the meds haven’t worked better. She seems thoughtful but not despairing. “We’ve been studying coral diseases for 30 or 40 years,” she points out. “We’re still in the Dark Ages. Our treatments are like sticking leeches on and hoping for the best.”

The history of humans intervening in wildlife disease is brief and strange. Over the past three decades, we’ve tried to treat prairie dogs for plague and help chimps fight ­Ebola. We’re battling on­going outbreaks of chlamydia in koalas and transmissible cancer in Tasmanian devils. Given the choice between losing species and medicating them, it seems, humans prefer playing doctor to undertaker.

In the ocean, however, we’re still out of our depth. “Where we are with coral disease is about where we were with human health in the 1800s,” says Andy Bruckner, the National Oceanic and Atmospheric Administration researcher in charge of coordinating much of the work on SCTLD, echoing Neely’s assessment. “On land you can cull animals, you can put up some barrier to prevent an outbreak from spreading. We can’t do that in the water.”

We do know that we’ve made the emergence and spread of infections more likely. Corals already stressed by heat or pollution get sick more easily, and damage from human activity can give pathogens a foothold. And while most blights go into remission when temperatures drop, Bruckner says, SCTLD does not seem to take winter vacations. That’s left reefs without their usual span of recovery time. ­SCTLD’s unrelenting progress has felled as much as a third of Florida’s corals, making it perhaps the most destructive illness ever to hit the reef.

Global warming makes these sorts of fast-growing, far-reaching, and seemingly unstoppable plagues more likely. “In a lot of cases, warming is at least a double whammy for disease,” explains Drew Harvell, Cornell University marine ecologist and author of the book Ocean Outbreak. “It can stress the host and make it more susceptible, and warmer conditions allow a lot of microbes to grow faster.” Hotter water likely contributed to the sea star wasting disease that was first identified in Washington in 2013 and quickly spread from Alaska to Mexico, as well as other recent die-offs in lobsters, oysters, abalone, and sea grasses.

This isn’t just a marine problem. Some studies suggest that heat made amphibians more susceptible to a fungus that’s driving many of them to extinction. Just an extra degree or two may enable infectious bacteria and fungi in every sort of ecosystem to grow faster, with fewer periods of dormancy. “A planet that’s good for microbes is not going to be that safe for us,” Harvell says.

Even with stakes as high as these, the decision to apply antibiotics is still risky. Widespread use in agriculture and medicine has already led to a rise in drug-​­resistant bacteria. To minimize the danger, Neely and her colleagues mix amoxicillin, a common, broad-​­spectrum antiseptic that killed the ­disease in lab trials, into a paste that slowly releases the drug into the coral’s tissues. The concoction hardens when exposed to seawater, making its contents less likely to seep into the ocean. As Neely and I saw firsthand, however, these targeted doses might fall short. Despite the millions of dollars marshalled in ongoing efforts to fight this outbreak, there aren’t enough bodies in the water to treat every diseased coral on every ailing reef before SCTLD obliterates them. Instead, researchers and managers are focusing on a handful of key spots where endangered species could vanish. There is no guarantee they can defeat such an aggressive pathogen, but they’ll fend it off as long as possible.

In the meantime, scientists have begun to explore other, more-​­audacious schemes, including a massive operation to rescue the rarest corals from the reef before they disappear altogether.

“I don’t know if we can do anything with him,” says Cynthia Lewis, squinting into a basin of seawater, where a piece of pillar coral about the size and shape of a leg of lamb is looking very unhappy. Lewis is deputy director of the Keys Marine Laboratory and a specialist in this particular animal. Extremely rare and susceptible to disease, the species boasts fewer than 50 genetically unique individuals in Florida. In 2018, with SCTLD advancing on some of these last holdouts, Lewis and Neely led a campaign to collect fragments from all the remaining colonies, preserving as much of their genetic diversity as possible.

dying coral reef
Antibiotics can save the colony from total destruction, but can’t revive ravaged coral. Steve Gittings / NOAA

This one is pale and pinkish, flesh fraying off its skeleton. The infection is so advanced that Lewis suspects she might not be able to save it, but she will pass much of the day trying. As Neely says, surfacing from a dive where she spent half an hour chiseling this chunk off an ailing colony, “It’s a lot of work for so little tissue, but when you have 70 pandas, you do a lot for each panda.”

Lewis pauses her examination to glance at her phone. Her contractor is calling. When Irma hit Florida in 2017, the Category 4 hurricane destroyed Lewis’ house on Long Key. She is still rebuilding more than a year later.

The reef shapes any storm’s impact on the Keys. Irma churned up 30-foot swells on the open ocean, but inside the protective buffer of coral, the surge was only 10 feet high—still enough to do a lot of damage but stripped of much of its destructive force.

As the ecosystem degrades, it loses its ability to absorb that energy. Previous diseases have already nearly eliminated species like elkhorn coral, which once grew in dense shallow thickets throughout the Caribbean. Now SCTLD threatens to demolish several others, and not just in Florida: Something that looks a lot like it popped up in Jamaica in 2017 and Mexico in mid-2018, and divers spotted telltale lesions off the U.S. Virgin Islands and the Dominican Republic early in 2019. If the infection continues to spread, pillar coral could disappear from the Carib­bean completely, along with a handful of other major wave-breaking species. Reefs will grow weaker with every storm, and it might be up to us to replenish their ranks.

A plump coral polyp clings to a ceramic tile; it’s barely bigger than a period, with light brown specks suspended through glassy flesh like dust in a sunbeam. “This is actually more high-tech than it looks,” Keri O’Neil jokes with me in the shade of a greenhouse outside Tampa. She’s tending to 60 of the tiny animals in a plastic dish pan.

O’Neil, senior coral scientist of the coral nursery at the Florida Aquarium, is a kind of no-boat Noah; she ushers animals onto land to give them safe harbor until the cataclysm passes. Her tanks are filled with rare specimens rescued as SCTLD took hold.

The dots she’s nurturing are the first pillar corals spawned and raised in captivity. At two months old, they are barely visible. Pillar coral grow only a couple of centimeters in a year, meaning each might take decades to get as big as Lewis’ leg-of-lamb patient. In the meantime, O’Neil and her staff clean the tiles they grow on with makeup brushes, and feed them concoctions of oyster eggs and supplements. And for the next gene­ration, they’re building a spawning facility containing tanks fitted with blackout shades and full-​­spectrum lights to mimic the natural cycles of moon and sun.

“It’s really just about giving them everything they would get in the wild,” O’Neil says. She believes this is the necessary next step in saving Florida’s reefs. Researchers will observe previously undocumented spawning behaviors and learn how to reestablish species when the current outbreak finally passes, whether that takes two years or 10.

To hear O’Neil describe the time and effort required to breed, raise, care for, and eventually replant these captive corals in an unspecified and uncertain future is to understand the ambitious scope of ongoing efforts in the Keys. Antibiotics may have been a shocking step, but they’re just the beginning; the end goal is a wholesale renewal of an ecosystem that has been slowly degraded over decades, worn down by pollution, overfishing, and climate change.

“It’s a big mission,” O’Neil admits, and it depends on some of the smallest creatures on the reef. In the tanks beside us, pieces of pillar coral extend their tentacles in the sunlight. The ­golden-​brown tendrils part and ripple in the current of the water-­filtration system, growing and waiting for an ocean in which they can survive.

This article was originally published in the Summer 2019 Make It Last issue of Popular Science.