AT ESCAMBRÓN BEACH, just outside Puerto Rico’s capital city of San Juan, the ocean froths and rocks in the wind. Dark green algal blooms roil through the waves like great, tangled clouds. The sky above is clouded too, heavy and close. It’s hurricane season, and the chilly Atlantic gushes up to meet us on the beach as we gear up to dive, backs laden with weighted scuba equipment. We’re a motley crew of trainee divers, awkward and clumsy in our new gear. The divemaster signals to descend as it starts to rain, and we plunge through the choppy waves into the depths of the bay.

Below the surface, all is quiet. We use our long fins to propel ourselves downward into a tangle of seaweed. Plastic debris litters the ocean floor, refuse from the tourist-driven economy that drives the city above.

Minutes into the dive, I see a large brain coral through the murky water. One half of the spherical coral is a rich, healthy brown — grooved and elaborate like a human brain resting on the ocean floor. The other half, however, is a ghostly white. Lesions of sick tissue encroach across an ancient colony.

This is my first view of a now-common sight along Puerto Rico’s coastline: reef partially eaten away by the most lethal illness affecting corals in the Caribbean today.

Over the last few years, the disease, known as Stony Coral Tissue Loss Disease (SCTLD), has been rapidly devouring reef-building coral. It was first officially identified in Puerto Rico’s reefs in November of 2019, not long before early reports of a novel coronavirus began to emerge from Wuhan, China. And like Covid-19, SCTLD is leaving its mark. The disease affects the longest-lived and slowest-growing corals, and is moving across the Caribbean at an alarming rate.

“You can have a 500 year-old coral ... die in a matter of months, in a matter of weeks.”

In Puerto Rico, marine scientists have witnessed the deaths of thousands of corals and have done everything they can to stem SCTLD’s spread. In the last two years, they have monitored reefs, tried to determine how the disease spreads, treated diseased coral, and worked to restore failing reefs. In the summer of 2021, Puerto Rico Governor Pedro Pierluisi declared a state of ecological emergency over the island’s dying reefs, a first for the US territory. The declaration prompted a one million dollar allocation to tackle the crisis.

For coral ecologists like Fabiola Rivera Irizarry, who have been researching the spread of SCTLD since late 2019, these resources couldn’t be more welcome. In May 2021, she wrote an op-ed for the local publication El Nuevo Día, likening the epizootic disease to “a pandemic on the reef.” (Though, technically, the spread of SCTLD is still at the epidemic stage.)

“This is a deadly disease,” she told me in October. “You can have a 500 year-old coral, a coral my size, die in a matter of months, in a matter of weeks. For me as a marine ecologist to see these huge corals dying at such a fast rate, it’s very sad. It’s shocking, because I’m seeing the coral dying in my hands.”

ON A SUNNY MORNING last October, I met Rivera Irizarry in Vega Baja on the north coast of Puerto Rico. She agreed to show me a monitoring site where she had been tracking corals affected by SCTLD. Irizarry works for the Sociedad Ambiente Marino de Puerto Rico (SAMPR), which has been studying the spatial and demographic distribution of the disease across hard corals in three municipalities of Puerto Rico. She’s been responsible for visiting and tending to hundreds of corals every month for over a year and has witnessed firsthand the destruction wrought by SCTLD. Irizarry and her colleagues at SAMPR are largely responsible for pushing the government to declare a state of emergency and allocate funding to protect the island’s remaining corals.

When we arrived at the beach-access point, hidden behind a breezy grove of palms in a tucked-away neighborhood, the autumn wind blew strongly across the sea. Irizarry gazed out to the ocean and explained that it might not make sense to get in the water due to low visibility and choppy conditions.

We sat on the beach instead and talked about what she fondly describes as “her” corals. “I say my corals because I work in the area,” she said, smiling proudly. This sense of personal responsibility and stewardship is characteristic of Irizarry. Her Instagram handle is “@faveolata” — a play on her first name, Fabiola, and a nod to her favorite coral species, the mountainous star coral, Orbicella faveolata. She posts mostly pictures of herself in the field, surrounded by sparkling turquoise water and glorious seascapes. For Irizarry, her work as a marine scientist is an ode to the ocean surrounding her tropical island home.

“My earliest childhood memory of the ocean is being at the water, watching the waves come and go, and seeing the little shells and wondering where they came from,” she said. As she got older, that sense of wonder and curiosity compelled her to study marine ecology, to explore “this whole new world under the water that’s invisible for most people.”

Now working toward her PhD at the University of Puerto Rico, Río Piedras, Irizarry strives to protect the coral species of this invisible world that are affected by SCTLD.

Corals impacted by the disease include smooth flower corals and maze corals. They include endangered species like pillar corals, elliptical star corals, and mountainous star corals, which are indigenous to the Caribbean, as well as symmetrical brain corals, which are among the slowest-growing corals on Earth today. “They can grow maybe 5 millimeters in a year,” Irizarry said, “so we’re talking about a brain coral growing [the length of] the tip of your nail in one year.”

For scientists like Irizarry who study these intricate and ancient coral reefs, awe sits close to concern. Around the world, coral reefs have been dying due to climate change. Warmer temperatures cause corals to bleach and die, while ocean acidification inhibits corals’ ability to grow. A recent report from the Intergovernmental Panel on Climate Change warns that more than three-quarters of the world’s warm-water coral reefs could disappear with just another half-degree Celsius of global warming. Already, Australia’s Great Barrier Reef, Earth’s largest living structure, has lost half of its coral in the last 25 years.

SCTLD isn’t the only threat these endangered corals face. But in Puerto Rico, it has quickly become the most immediate — one that has occupied Irizarry’s time and energy since it first showed up on the island’s shores.

THE FIRST OFFICIAL SIGHTING of SCTLD in Puerto Rico occurred in November 2019, when coral ecologists diving in the Luis Peña Reserve off Culebra, an idyllic island northeast of Puerto Rico, discovered colonies riddled with the disease. The dive team included Edwin Hernández-Delgado, the senior scientist for SAMPR and a marine biology professor at the University of Puerto Rico. But this wasn’t the first time Hernández-Delgado had seen SCTLD.

A passionate marine conservationist and educator, Hernández-Delgado says that he first noticed signs of the disease in Puerto Rico’s reefs in 2018, near the city of Humacao on the island’s eastern coast. When he came across coral with sickly white spots, he knew he was witnessing something potentially devastating. Just a few years prior, in 2014, SCTLD had emerged for the first time in southeast Florida. Scientists there watched in horror as a 330-year-old mountainous star coral began to lose its color. Then, chunks of tissue started to break away. This coral had survived the Industrial Revolution, several hurricanes, and the impacts of widespread coastal development. Once it contracted this new disease, it died in a matter of months. The disease has since spread across 90 percent of the Florida Reef.

When he noticed similar symptoms on coral in Puerto Rico, Hernández-Delgado tried to warn his colleagues about a possible outbreak. He showed them pictures of afflicted corals, but they told him that without consistent monitoring it would be impossible to confirm that what they were seeing was SCTLD. Puerto Rico’s Department of Natural and Environmental Resources (DNER) dismissed his worries as well.

So far, marine scientists still aren’t clear on what causes SCTLD, though many agree that it must have bacterial origins.

“No one believed for more than a year,” Hernández-Delgado told me. In that time, the disease spread rapidly across the island’s reefs from east to west, decimating nearly 40 to 60 percent of Puerto Rico’s coral reef populations in its wake. Many of the impacted corals are 100 to 500 years old. “There’s an outrageous mortality of corals; [we’re] talking about losing from 40 to 60 percent of living corals within less than a year,” said Hernández-Delgado.

In November 2019, the wide-scale carnage at the Luis Peña Reserve was the undeniable proof Hernández-Delgado needed to convince his colleagues that SCTLD had arrived. At SAMPR, Hernández-Delgado formed a team, which included Irizarry, to conduct a study of infected corals in order to help ecologists understand the disease behavior and determine effective solutions. Irizarry compares their study to the recent global pandemic. “If you think about Covid-19, when this new strand of the coronavirus emerged, before developing these vaccines, there were a lot of scientists studying the disease to understand how SARS-CoV-2 works,” she said.

So far, marine scientists still aren’t clear on what causes SCTLD, though many agree that it must have bacterial origins. Nor are they sure how it spreads. Some researchers have suggested that it is carried over larger distances through ballast water in ships. Hernández-Delgado, who thinks researchers are too focused on figuring out the vector instead of the cause, has a different theory. He argues that as more coral cover is lost due to ocean acidification, the sudden vacancy in the reefs allows more room for algae to bloom, creating more food for the naturally-occurring microbial community in the ocean. As more corals die, more algae develop, which then continue to smother coral colonies and introduce more bacteria.

The outbreak of SCTLD in Puerto Rico, according to Hernández-Delgado, is therefore the result of a vicious cycle, a reinforcing loop that is changing the fundamental nature of an entire ecosystem.

ORIGINS OF THE DISEASE notwithstanding, scientists have discovered that amoxicillin has so far proven to be the most effective way to treat SCTLD. The antibiotic is mixed with a biodegradable, organic paste and spread directly on infected corals. According to researchers in Florida, amoxicillin has a 70 to 90 percent effectiveness rate of saving coral from the disease.

Nilda Jimenez, a marine biologist and coordinator of the Endangered Species Program at DNER, has been leading much of the treatment process. “One of the things we are dedicating a lot of time to right now is just going out to some of the reefs to provide treatment,” she said, “trying to save as many as we can.” Jimenez is also in charge of administering the emergency declaration funds from the government — a role she oversees from the frontlines as much as possible. When I talked to Jimenez in December, she was using vacation days to train volunteer divers to treat the disease with amoxicillin.

But using an antibiotic to combat a coral disease has its limits. One of them is logistics: More vessels, equipment, and trained drivers would be needed to reach all of Puerto Rico’s wild corals, especially those out in the deep ocean. Another is that follow-up treatments are often required after the initial application. There simply isn’t enough amoxicillin to go around. Jimenez has had to identify and treat only high-priority areas of Puerto Rico’s reefs, selected on the basis of various factors including coral cover and species present, weather conditions, and accessibility.

Another limiting factor is the use of amoxicillin itself. While antibiotics are currently the most effective option to treat SCTLD, the practice has been met with some resistance from government agencies concerned about the impacts of using antibiotics underwater. Potential negative impacts include the promotion of bacteria that’s resistant to antibiotic treatment and the slowing of coral growth.

SCTLD is proliferating in a world we’ve altered or altogether mishandled — a world increasingly unfit for coral.

These concerns have impacted how the team at SAMPR is able to use government funds. In 2021, SAMPR received a much-needed $216,000 grant from the National Oceanic and Atmospheric Administration dedicated to slowing the progress of SCTLD across Puerto Rico’s reefs, but the grant prevents Hernández-Delgado and his team from using these funds to purchase or administer amoxicillin, the only treatment proven to work. Other treatments that scientists are exploring include the application of beneficial probiotics to try to eliminate bacterial pathogens, and chlorinated epoxy, a treatment that was used to stop black band disease in Hawai’i. Both alternatives have had less successful results than amoxicillin.

Some scientists have grown frustrated with these sorts of hang-ups. “Although it has been declared an emergency, in my personal view, I don’t see it being treated like that,” said Jimenez.

Recently, Jimenez and her colleagues at DNER have started a coral-species rescue mission of sorts, saving samples of individual species that are dying out and storing them in a seed bank for future regrowth. “I think what we are doing is trying to save or have a storage of the minimum ‘seeds’ that will — eventually, once this catastrophe passes — help future generations,” she said. For its part, the SAMPR team is also managing restoration sites, where researchers and volunteers are transplanting corals grown in nurseries on land to try to encourage the growth of new reef systems where old ones have died. In the meantime, however, SCTLD continues to make its way across the reefs, with recent sightings as far west as La Parguera, a municipality on Puerto Rico’s southwest coast.

IN THE SAME WAY that Covid-19 has placed indelible pressure on hospitals and healthcare workers around the world, Stony Coral Tissue Loss Disease has pushed Puerto Rico’s coral ecologists and marine conservation community to their limit, even with the emergency funds from the government. With the antibiotic treatment, diving equipment, and trained staff needed to address this aggressive disease in short supply, it’s unclear how much of Puerto Rico’s reefs can be salvaged.

Back on the beach at Vega Baja, Irizarry also reminded me, somewhat ruefully, that even if SCTLD is treated successfully, coral reefs face a multitude of stressors. Part of her dissertation research, she explained, is determining how water pollution and runoff might inhibit the immunity of corals dealing with SCTLD. In other words, the disease proliferates in a world we’ve altered or altogether mishandled — a world increasingly unfit for coral.

“If we want to save the corals, it’s up to everyone, not just the scientists.”

In this sense, saving coral from a disease as aggressive as SCTLD will take multiple actions, big and small: treating and restoring reefs, curbing pollutants, cleaning up coastal communities, phasing out carbon emissions. It will require sustaining a world where corals flourish, along with the wealth of biodiversity that depends on them.

“If we want to save the corals, it’s up to everyone,” Rivera Irizarry said, “not just the scientists.”

ON THE BOTTOM of the ocean floor in Escambrón, a school of yellowtail snapper, endemic to these western Atlantic waters, has started to follow me. They seem almost curious, tracking my every move inquisitively as if to understand why a human would visit this far down in the deep. Their small, silvery bodies are divided in the middle by a slender yellow line that extends laterally toward their fins and forked tails. Yellowtails are mostly found around coral reefs, and in the two days we’ve been diving this part of the bay, I’ve seen them everywhere.

I spot another brain coral, this one a healthy brown. Swimming over with my yellowtail friends in tow, I remember that corals, too, are living creatures. They grow to form the foundation of a marine community. The brain coral is huge; an intricate, calcareous puzzle. I swim above it for so long, the markings on its surface begin to resemble an ancient map. I imagine that if you followed it, you would find the source of all thought or, at least, the memory of a time long forgotten.

Reporting for this story was supported by Nueve Millones.