By Jim Melvin
Photography by Jesse Godfrey ’11 and Madison Williams

Coral reefs in the Florida Keys, Caribbean and throughout the world are in dramatic decline. A graduate student from Clemson has made it her mission to help restore one of the ocean’s most-endangered and invaluable species.

When Hurricane Irma slammed southern Florida this past September, the monstrous storm’s one-two punch of wicked winds and widespread flooding tore apart homes, businesses, roads and bridges.

The hurricane didn’t stop there. Beneath the surface of the warm waters of the Florida Keys, Irma’s rage also took no pity. Swirling currents powerful enough to roll boulders shredded portions of the Keys’ imperiled coral reefs.

About a month after Irma’s untimely appearance, a young scientist from Clemson donned scuba gear and plunged into the waters of the Middle Keys to examine the damage firsthand. Lingering silt and debris made for poor visibility, but the scientist was still able to see well enough to confirm her fears. The coral reef — the first of six she would visit during her latest research venture — had been scoured. Soft corals, algae and sponges were obliterated. Stony corals fared better, but half of even those were damaged or destroyed.

It was a grim discovery. But the worst disaster can have a silver lining. It became her quest to find one.

Kylie Smith holding a coral sample.


Kylie Smith has been making the long journey from the foothills of the Appalachians to the seas of southern Florida for the past six years, diving deep into the salt water of the Florida Keys as she completed her master’s degree and is now finishing the research for her Ph.D. She has spent hundreds of hours studying the creatures that inhabit coral reefs, measuring fish abundance, testing water quality and acidification levels, and also transplanting fragments of coral and recording their rates of survival and growth.

Coral reefs represent some of our oldest and most diverse ecosystems. They serve as spawning and nursery grounds for ocean species that feed millions of people. They create a staggering array of jobs in the fishing, recreation and tourism industries. They even protect shorelines from erosion by lessening wave height and force. But this invaluable natural resource has been in alarming decline for the past three decades. About 80 percent of what existed as recently as the late 1970s is now dying or dead. Marine biologists consider these reefs to be the most critically imperiled ecosystem on the planet.

The rapid decline of corals started in the Caribbean. Disease, physical disturbance and bleaching were the most obvious culprits. But this trio of enemies has been around — just like coral itself -— for millions of years. So why has such a precipitous downturn occurred in just 30 years?

Corals thrive in a narrow temperature range — about 75-86 degrees Fahrenheit. When water temperatures rise above 86 degrees for extended periods, corals become more susceptible to disease, competition, predation and mortality.

Climate change appears to be the accelerator that could potentially cause the extinction of coral. Rising levels of carbon dioxide in our atmosphere are trapping heat, and about 90 percent of it is being absorbed by our oceans. Given current temperature trajectories, some estimate that there could be no corals left anywhere on Earth as soon as 2050.

None of this has gone unnoticed. In the Florida Keys and elsewhere, several organizations are transplanting coral fragments by the tens of thousands in hopes of restoring existing reefs and creating new ones. But most of the transplants fare poorly, simply because what is causing them to deteriorate remains insidiously in place.


Marine biologists don’t always end up living near the ocean. Michael Childress came to Clemson from Idaho State University, about a four-day drive from the Florida Keys. He had begun doing underwater research in the Keys in 1991 when he was a graduate student at Florida State University.

Childress is an evolutionary behavioral ecologist whose research focuses on understanding how marine animals respond to habitat loss. He came to Clemson in 2001 and is now an associate professor of biological sciences. Over the past 15-plus years, Childress and his students have managed to make dozens of trips to the Keys to study spiny lobsters, blue crabs and anemone shrimp. They’ve helped finance these trips by doing everything from using National Oceanic and Atmospheric Administration Sea Grant awards to holding bake sales.

Smith began working with Childress in 2010. After earning her bachelor’s in ecology and evolutionary biology at the University of Colorado Boulder, she came to Clemson as a research assistant and then became a master’s student. When Childress and Smith began to discuss her research options, Smith mentioned that she was interested in studying corals.

“I didn’t work on corals,” Childress recalls. “So, when Kylie said that she wanted to do a project about corals, I told her that — at least at first — it would have to be related to some aspect of animal behavior, because that’s what my lab at Clemson does. Eventually, we decided that Kylie would begin by studying the effects of parrotfish populations on the health of coral reefs.”

Parrotfish are herbivores, and one of their favorite foods is macroalgae that compete with corals for nutrients and space. The decline of corals in the Florida Keys was accompanied by a dramatic increase in fleshy and turf algae. Smith’s initial research tested the hypothesis that a loss of reef herbivores was one of the main reasons for this. But she ended up finding little evidence that high parrotfish populations were rescuing coral communities. This became the subject of her master’s thesis, which she defended in 2015.

“For the first three years, we watched just over 2,500 parrotfish, documenting their feeding behavior,” Smith says. “In the end, we didn’t find any major effects on coral health. Now, we are focusing more on parrotfish habitat use and territoriality to see if we can get a better understanding of their impacts on the reef.”

Smith’s early research taught her many things about coral reefs. For instance, different species of corals seemed to have different sensitivities to warm-water conditions, which can cause coral to turn completely white. This is called coral bleaching, and it occurs when corals expel algae that reside in their tissues. Corals can survive bleaching events, but the resulting stress often causes widespread damage.

“Looking at the interactions that have been taking place between these organisms had been the foundation of my research,” Smith says. “But we’ve had other offshoots. We’ve looked at the effects of overharvesting of fish. We’ve looked at how differing water quality can influence some of these relationships. And we’ve monitored how changes in temperature can influence coral growth.”

This invaluable natural resource has been in precipitous decline for the past 30 years. Marine biologists consider these reefs to be the most critically imperiled ecosystem on the planet.

Childress’s undergraduate Creative Inquiry class has functioned as a research team for Smith in her master’s and doctoral work. The composition of the class changes a bit from semester to semester, but these students have traveled back and forth to the Keys, become dive-certified and participated in almost every facet of Smith’s research. Childress has mentored Smith, and Smith in turn has mentored these undergraduate students who have caught her passion for the world underwater.

In 2013, Smith conducted her first coral restoration study. She and her team transplanted 84 fragments on seven reefs in the Middle Keys. What happened next proved to be a stark lesson in coral sensitivity. She witnessed that prolonged periods of higher- than-normal water temperature can cause coral bleaching and mortality in both transplanted and native corals.

“In 2014 and 2015, we had some major warming events in the fall months. And that triggered mass bleaching events across the Caribbean, including here in the Keys,” Smith says. “Some of the corals we had transplanted showed signs of bleaching, while others didn’t. But by following our corals, we saw that they seemed to recover more quickly and be more resilient in 2015 than they had been in 2014. And so, we think that there might be some local acclimatization going on. This could mean that corals that have previously experienced high temperatures are better able to resist bleaching the next time they occur.”

What Smith learned between 2013 and 2015 prompted her to broaden her focus to include a wider range of interactions in the coral reef community. In 2016, she began to devise a structured-equation model that could be used to predict the best conditions for coral transplant success. Her hope was that environmentalists who might eventually follow this model would be able to increase survival rates. To test her model, Smith picked out eight near-shore and offshore reefs in the Middle Keys that differed in structure and composition.

In early 2017, the final phase of her doctoral research was set to begin.


Smith chose to transplant 192 fragments of four different varieties of corals at the eight reefs. Each variety would have 48 fragments. The corals varied in vulnerability. Acropora cervicornis (Acer), a branching coral also called staghorn, was the most vulnerable and is an endangered species. Siderastrea radians (Srad), a stony coral known as starlet, was the hardiest.Orbicella faveolata (Ofav), a stony coral called mountainous star, and Porites astreoides (Past), a stony coral known as mustard hill, fit somewhere in between.

Step one was to secure the coral fragments and transfer them to holding tanks. Step two was to transplant the fragments. Step three was to document the growth and survival rates every several months from October 2017 through June 2019. Step four was to compare reef and transplant data with her predictive model to see if it worked.

In March 2017, Smith, Childress and four other members of the Creative Inquiry team — Kara Noonan, a new graduate student; Randi Sims, a recent Clemson graduate with her bachelor’s in conservation biology; and undergraduates Sydney Whitaker and Sara Rolfe — traveled to the Florida Keys National Marine Sanctuary coral nursery in Key West to harvest fragments of Srad, Ofav and Past.

“When we got into the water, the visibility was barely the length of our arms,” Childress says. “The crates were suspended beneath docks in the marina, and we had to pick out the correct fragments in near darkness. This turned out to be one of the most challenging dives of the entire project. But in the end, we were able to get at least 48 fragments of each of the three species. We later obtained our staghorn fragments from an offshore nursery.”

Some of the fragments were too large and had to be cut to the appropriate size — approximating a silver dollar — using a table saw. Corals are extremely sensitive to changes in water temperature but are quite hardy when it comes to being cut to pieces. The fragments were transferred from Key West to holding tanks at the Keys Marine Laboratory in Long Key.

Smith and her team then constructed a couple of hundred PVC frames that would be used to mark the locations of each transplant. For identification purposes, each coral would also have an individually numbered tag. Fifty-meter-long transect tapes would serve as orientation on the reefs.


Cruising wide-open in an 18-foot skiff on the ruffled waters of the Florida Keys is not for the faint of heart. Leaps and bounds bruise your senses — and also your knees and lower back.

But once you arrive and drop anchor over a coral reef in the Florida Keys, you realize that the raucous ride is most definitely worth it. The bluebird sky and the surface of the sea are both magically beautiful, but what lies 15 feet or so beneath the surface dwarfs all else. This is why Smith does what she does.

It is now June 2017. Smith and her team, already adorned in wetsuits, don scuba gear and prepare to plunge into the warm water. Their assignment today is to transplant coral. Three of the varieties will be put in place using a cement mixture. The fourth, the fragile staghorn, will be attached using concrete nails and tie-wraps.

Noonan has been assigned the unenviable task of mixing cement with silica powder in plastic bowls and then placing fist-sized globs of it into plastic ziplock bags. By the end of the day, she is so covered with powder, she looks more like a Greek statue than a scuba diver.

“There’s a reason they use trucks to make cement,” she says sardonically.

With Noonan remaining onboard, the other four members of the team go about the arduous process of transplanting dozens of fragments of coral. Whitaker and Rolfe take turns bringing the cement and coral fragments down to the first PVC marker. Smith then smooshes the cement onto the relatively flat surface of dead coral skeleton and presses the living coral fragment into the cement. Amazingly, the cement starts to harden — even though it is underwater — and the fragment holds. One down, 191 to go.

Meanwhile, Sims records what species of coral is transplanted where, making sure that everything is well-organized and properly documented. “I’ve done a lot of data collection and analysis with this project, both in the field and in the lab at Clemson,” Sims says. “And it’s been really cool to see the way the project has grown.”

At the end of the day, they are exhausted. And this is just one day out of many before all the fragments are in place.


Even the most precise and best-laid plans can be derailed by unexpected circumstances. When Hurricane Irma struck the Florida Keys, it didn’t just damage existing coral; it also wiped out many of the corals Smith had worked so hard to transplant.

When Smith and her team visited six of their research reefs in October 2017, they discovered that more than 50 percent of her transplanted corals had been either killed, crushed, dislodged or buried in sand by the storm. As feared, the fragile staghorn corals had suffered the most damage — almost 80 percent lost — while about 50 percent of the hardier stony corals appeared to have survived.

What Smith found regarding the corals did not surprise her. But something else did. The macroalgae that had previously smothered the reef were gone.

This was the silver lining Smith had been searching for. Now, in addition to being able to study the survival rates of her coral transplants, she would be able to research how wild corals thrive when macroalgae are removed from the equation, and also, how long it will take for the macroalgae to rebound.

“The hurricane added another dimension to my research. We’ve never been able to study a reef that was devoid of algae, so this became an unexpected opportunity,” Smith says. “We’re going to have to alter the original model a bit, but it will remain an important part of what we do.”

Smith, who is scheduled to receive her Ph.D. in December 2019, has concluded that despite the severe effects of thermal bleaching and hurricane disturbance, the reef communities of the Florida Keys are hanging in there because of the tenacity of a few species of corals that show high resilience.

“It’s a bit ironic, but since the hurricane, a lot of things are going in the coral’s favor,” Smith says. “With the macroalgae gone, at least for now, there will be less competition for food. And with the corals scrubbed bare, there is more clear space for new coral larvae to settle and start to establish. So all of this gives us a set of conditions to test the model’s predictability under circumstances that we didn’t intend when we started.”

The good news is that reefs are well-adapted to recover from natural disasters. The bad news is that climate change doesn’t come and go as fast as a hurricane, and the most fragile corals are still disappearing at alarming rates.

The starkness of this reality has caused some researchers to give up. But not Smith. When the silt from Hurricane Irma finally settles, she’ll be back at work, displaying the kind of resilience she hopes to find in her coral transplants.

Siderastrea sidereal coral, before
and after Hurricane Irma.

Jim Melvin is director of public information and marketing for the College of Science.

© Copyright - Clemson World