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As mysterious disease kills Florida’s reefs, a massive ‘Noah’s Ark’ effort tries to save them

By Krishna Sharma, Miami Herald
Published: September 12, 2021, 10:45am
4 Photos
The Florida Coral Reef Rescue Center in Orlando preserves hundreds of specimens that researchers hope will serve as sort of a seed bank for future restoration. Special lighting gives the room a bluish hue and is designed to mimic the marine environment.
The Florida Coral Reef Rescue Center in Orlando preserves hundreds of specimens that researchers hope will serve as sort of a seed bank for future restoration. Special lighting gives the room a bluish hue and is designed to mimic the marine environment. (SeaWorld Parks & Entertainment/TNS) Photo Gallery

MIAMI — In 2014, a mysterious coral disease known as Stony Coral Tissue Loss Disease was first identified off Miami. In the years since, it has raged like an underwater wildfire, becoming what some scientists call the worst marine epidemic they have ever witnessed.

Stony coral disease has scorched the already struggling reefs of South Florida and caused some species like Florida’s picturesque pillar coral to go locally extinct.

And now its spreading fast through the Caribbean.

The threat is so serious that it has produced an unprecedented national research and “Noah’s Ark” rescue effort, where almost 2,000 corals have been pulled out of Florida’s waters and quarantined in aquariums around the country.

These “reef-ugees” can be found at facilities in 14 different states, ranging from a massive coral laboratory in Orlando to a zoo in Nashville to a butterfly pavilion in Denver. Scientists plan to eventually use the offspring of these specimens to replant Florida’s waters once the aquatic plague passes. At least that’s the hope in an otherwise dire projection.

“The days of truly wild coral reefs are probably over,” said Andrew Walker, president and CEO of the nonprofit Fish & Wildlife Foundation of Florida. “Especially in the light of climate change.”

However, researchers remain optimistic that emerging science might someday restore or at least revive Florida’s declining reefs. “We need corals to be resistant to other problems too: rising water temperatures, increasing salinity and the like,” said Walker.

For a decade or more, scientists have been replanting thousands of corals off the Florida coast each year in an effort to combat what had already been a serious decline — but a dramatically scaled-up production rate would be necessary for large-scale restoration. Corals are slow growers, needing decades or even centuries to create what are now considered mature reef systems. Plus, scientists don’t know when or if stony coral disease will completely pass, so this unprecedented effort is shooting for the moon.

Researchers are trying everything they can think of to make corals stronger in an increasingly inhospitable ocean. Some are breeding them like crops for tougher offspring. Others are studying disease-fighting bacteria as a probiotic line of defense. Some are even testing enhanced natural options, like deploying lobsters as bodyguards against coral-eating snails and crabs as janitors to keep corals clean from algae.

A coral plague

Corals around the world have been in decline for decades and this stony coral disease has pushed the Florida Reef Tract to its limits, spurring the flurry of new coral research.

The tract is a scythe-shaped swath of reefs starting near Port St. Lucie that curves along the heavily developed southeast coast past the Keys and westward into Dry Tortugas National Park. In the 1970s, corals covered 50-70% of the tract according to Les Kaufman, a professor of biology at Boston University who specializes in coral reef ecology.

By 2013, that number had dropped to around 10% from assorted coral diseases, climate change and human impacts in South Florida such as agricultural runoff, sewage outflows, dredging and coastal development. Today, after seven years of the destruction from stony coral disease, live coral coverage in the tract hovers as low as two%.

“I’ve been working with wildlife diseases since the early ‘90s and I’ve never seen a disease be this devastating,” said Andrew Stamper, conservation science manager for Disney’s Animals, Science, and Environment. Disney is providing funding and expert research teams to combat the marine epidemic.

Expertise is needed because stony coral disease is as enigmatic as it is lethal. Some scientists wonder if it came from foreign lands by ship ballast water, while others question if it might have always been hanging around until corals became immuno-compromised by climate change and pollution.

Scientists aren’t even sure if it’s a bacteria or a virus. Stamper prefers to call it a syndrome rather than a disease until they better understand what is causing the corals to get sick.

“Corals are pretty much animal, rock and plant all wrapped up in one,” said Stamper. “A whole ecosystem in one little organism. And that makes it tricky to figure out what’s affecting them.”

An underwater Rome

Coral is an animal whose head looks like a tiny, slimy feather duster. After finding a nice neighborhood to settle down in, its soft body, known as a polyp, slowly grows a hard calcium inner-skeleton.

The polyp can clone itself, sometimes hundreds to thousands of times, to create a giant interconnected colony of polyps covering a skeleton of rock-hard armor. Polyps also host colorful plantlike microbes that set up a nutrient exchange market within the animal.

Corals congregate to form reefs, which cover less than 1% of the ocean’s floor yet harbor one-quarter of all marine life — a bustle of colorful fish, sharks, sea turtles and others amid calcium architecture.

But underwater Rome wasn’t built in a day. “It’s taken thousands of years for these reefs to build up,” said Stamper. “It’s taken less than a decade for them to really come tumbling down.”

There are many coral diseases out there but they usually affect a small part of the coral from which the animal can recover. Stony coral disease however infects the entire head, said Stamper, annihilating the creature.

After a reef gets blighted, it can extinguish the entire food chain and leave only marble-like ruins of coral skeletons behind, a marine metropolis turned ghost town.

“But it’s not all a death and destruction story,” Stamper said. “The amount of people involved with this and all that they’ve given has been breathtaking.”

The rescue effort

In 2018, state and federal scientists realized the marine disease was spreading faster than it could be controlled. With almost half of Florida’s 45 coral species vulnerable, the Association of Zoos and Aquariums (AZA), a non-profit representing zoos and aquariums throughout the country, rallied a network of over 20 sites across the country to harbor coral evacuees in whatever facilities they could muster.

Much of the research work is overseen by the Florida Keys National Marine Sanctuary, which was first established in 1990 to address the declining reef system.

Beth Firchau is the project coordinator for the AZA Florida Reef Tract Rescue Project. Historically, she said, only two or three% of corals in the reef tract had a disease at any given time. Now, with the presence of stony coral disease, it’s estimated that over 60% of corals are diseased.

“We’ve got [evacuated] corals in the mile high city of Denver, we’ve got them in the inner city of Camden, New Jersey, we’ve got them in Texas, we’ve got them in Iowa,” she said. “We’ve got them all over the country, safekeeping those corals for a point when the state of Florida decides that it’s time to propagate them and send their offspring back out.”

While SeaWorld, an AZA constituent, was searching for a property to house its share of the stony diaspora, a coral sales company was serendipitously selling a large coral storage facility and state-of-the-art equipment in Orlando. That facility turned into the Florida Coral Rescue Center (FCRC).

“It was perfect,” said Jim Kinsler, aquarium manager at SeaWorld and facility manager of the FCRC. “All we had to do was purchase the equipment, take over the lease, and move forward.” Today, over one-third of all the 2,000 rescued corals are sheltered there.

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“This is the most unique partnership we’ve ever been involved with,” said Kinsler, referring to the fact that large companies like Disney and SeaWorld were partnering with federal agencies, state agencies, universities, museums, aquariums, and plenty of other affiliates to try and save Florida’s devastated reefs.

“We’ve done step one, which was to get all of these corals into a safe, controlled environment,” said Kinsler. “And now we’re ready to move into the next steps.”

Breeding a new generation

State universities such as the University of Miami, University of South Florida and Nova Southeastern have been working on crossbreeding corals to produce heat- and disease-resilient offspring.

“The good thing is corals lend themselves for people to help out,” said Disney’s Stamper. “Corals spawn thousands and thousands of offspring that can be put out with armies of volunteers. So it’s a good community-related effort.”

Sometimes, it’s volunteers replanting corals. And all those eggs leave ample room for laboratory experiments as well.

Erinn Muller is a senior scientist with the Mote Marine Laboratory & Aquarium and manager of their Coral Restoration Program and Coral Health and Disease Program. “Basically, we pick and choose the mom and dad corals to test for heat and disease resistance,” said Muller. By selecting specific parents, they try to produce offspring with desirable traits.

Inspiration for good coral genes can be found at Florida’s Newfound Harbor, which has been planted with corals screened for climate change resilient traits since 2015. Since then the stock has survived a bleaching event, a Category 4 hurricane and by happenstance is resilient to the disease. Muller and Mote postdoctoral fellow Hanna Koch want to mirror that success and figure out how to get those resilient genes in future corals.

“Sometimes this is mistakenly thought of as re-engineering a reef,” said BU’s Kaufman, “but that’s rarely the case.” The heat- and disease-resistant corals are not genetically engineered like GMO crops are. Rather, scientists are breeding them for traits already present in the wild, something humans have done for millennia to make more desirable crops.

Groups such as the United Kingdom’s Horniman Museum, the Mote Aquarium, the University of Miami, Nova Southeastern and the California Academy of Sciences have made marked progress in breeding corals in laboratories more predictably — a challenge because corals require specific and sultry environmental cues, like a full summer moon, to get them in the mood.

These breeding experiments will be complemented with novel new ideas to try and give replanted corals the best possible chance for survival.

Coral ‘yogurt’

The word “probiotic” has become a grocery store buzzword for any fermented foods like yogurt that boost the human microbiome, which is the trillions of bacteria, yeast, and other microbes that thrive in our guts. Those microbiomes are critical to human health and nutrition and only recently are scientists unraveling a similar system in corals.

Corals are chock-full of marine microbes — one teaspoon of coral mucus can contain hundreds of thousands, if not millions, of bacterial cells. And it seems that a healthy coral microbiome can make it disease-resilient.

Scientists want to make a probiotic that boosts coral microbiomes so they can naturally fend off the disease.

So far, the results look good.

Blake Ushijima, assistant professor at the University of North Carolina Wilmington, is collaborating with researchers at the Smithsonian Marine Station at Fort Pierce and Nova Southeastern to produce the first ever underwater bacterial probiotic in a groundbreaking attempt to prevent and treat stony coral disease.

Unlike popping open a cup of Chobani, coral probiotics are putting a bag around the corals and squirting the mixture into the water around them. The results are still in early testing but the probiotic-boosted corals seem to remain healthy while their un-boosted counterparts wither away.

“We don’t know how some of the probiotics are working,” said Ushijima. “Possibly the microflora create an antimicrobial compound,” killing stony coral disease with medicine made by microbes for microbes. Or perhaps the friendly microbes take up all the space and nutrients available on coral so none is left for whatever causes the devastating infection to grow.

Curiously, the same antibiotics humans take when sick also seem to treat stony coral disease. However, that is not a good solution to move forward with, said Ushijima. Pumping antibiotics into an ocean where they can freely spread with the currents would likely bring a host of other problems such as antibiotic resistance, which is when too many antibiotics are used and an incurable version of the disease pops up. Antibiotic resistance in humans is declared one of the world’s top ten threats to global health by the World Health Organization, so the idea of flirting with an underwater version of it is not appealing to scientists.

Probiotics, however, might prevent and treat the infection without threatening other marine life. “Microbes will always outsmart us,” said Ushijima, “so why not use microbes against microbes.”

While making coral probiotics is relatively new, labor intensive and costly, Ushijima’s lab is working to make the process more efficient. Still, scientists admit it will be a long time before they comprehensively understand how the microbiomes and immune systems of corals work.

“I would compare this to the war on cancer,” said BU’s Kaufman. “Cancer has turned out to be an astoundingly complex process and can only be approached through a deep, deep basic understanding of the immune system. Well, we don’t have that basic understanding of coral immune systems yet. So what we’re embarking upon is not a technological quick fix, but rather an exploration of inner space. And that is thrilling.”

Lobster bodyguards

The disease can make corals vulnerable to predators, too. So other researchers are looking for things that might naturally prey on coral predators — what scientists call “bio-controls.”

For instance, some marine snails eat coral. Normally that’s not a big deal, but when corals are weakened from stony coral disease those snails could go from gentle grazers to genocidal gastropods. This is where the spotted spiny lobster, a native of South Florida, comes into play. It might eat those snails and, if so, could be deployed as bodyguards for replanted corals.

Casey Butler, a doctoral student at Florida International University and lobster biologist with the Florida Fish and Wildlife Research Institute, plans to catch wild spotted spiny lobsters this summer and explore their stomach contents to reveal if they might help control the snails. “We’re trying to see if we can rehabilitate our coral reefs and this is just a weird new way that might work,” she said.

Infected corals can also get suffocated by blankets of algae, but certain crabs might “mow the algae lawn” and keep them healthy. If so, crabs might be deployed as janitors — as long as the lobster bodyguards don’t maul them. The marine food chain isn’t as simple as big fish eat little fish.

Researchers hope to have more conclusive results within the next year.

An underwater pandemic

In a way, Florida is grappling with two pandemics — but much of the public is unaware of the one going on under water.

“We’re living in a full-scale environmental collapse in real time,” said Colin Foord, marine biologist and co-founder of the science-art initiative Coral Morphologic. “And that is terrifying. Everywhere you look, there’s these cascading domino effects and feedback loops not working in our favor.”

But with catastrophe comes change, some of it positive. “Nothing like this has happened before,” said Mote Lab’s Muller. “Hundreds of people all working together in near real time to find a solution is unprecedented in the science community. Usually, researchers keep things close. But this crisis can’t wait for people to publish their work in peer-reviewed publications.”

Her statements mirror those about science norms changing with the global rush for a COVID-19 vaccine, another pandemic that coral scientists are quick to reference.

“This disease has swept through the reef tract, a national treasure, like a raging fire,” said Michelle Ashton, director of communications for Fish & Wildlife Foundation of Florida. “And if COVID-19 has taught us anything, it’s that life is fragile and disease is real.”

Mote Lab’s Muller highlights how this rescue effort might globally inspire similar rescue projects. “Efforts in Florida are leading, or being a liaison, for efforts around the world,” she said. “From the Great Barrier Reef to Indonesia to the Caribbean, people are looking to Florida to guide efforts because this is new and revolutionary.”

But another challenge is right in the backyard. Some scientists fear the poor quality of many of Florida’s coastal waters, increasingly tainted by pollution and algae blooms, could undermine even the most cutting-edge science efforts.

“Up and down the coast of South Florida is noxious water from Lake Okeechobee,” said BU’s Kaufman. “South Florida canal systems are full of untreated industrial and agricultural waste. And on top of these layers is anthropogenic climate change. … Cleaning up our act and doing something about climate change is paramount. People need to realize that they will lose this whole fragile place and the Florida way of life.”