Earth Healthy Planet Marine Studies Initiative

Reefs Under Siege

Coral reefs are in decline around the world. A team of scientists is trying to understand why.

Photos by David Baker and Justin Smith

The nose of the Boston Whaler dips into the trough of the wave for a stomach-dropping second. The crew and divers now face a wall of water topped by the frothing curl of a break. They ride up so steeply that the boat seems about to topple backward. The pilot, Mohammad, guns the throttle, charges over the top and slips down the other side.

Before they can catch their breath, he circles back to make another run at dropping anchor on the windward side of the stack of coral jutting from the ocean floor just below the surface. This reef called Shib Nazar is located off the Red Sea coast of Saudi Arabia, and it’s the first structure these waves have met after rolling across hundreds of kilometers of open water. No wonder they’re angry.

Mohammad somehow manages to anchor just short of where the waves pound the reef’s outer wall. Four Oregon State University divers in back of the boat hurriedly strap on weight belts and hoist heavy tanks onto their shoulders. They eye each other nervously as the craft bucks over the swells.

“Very dangerous here,” Mohammad says, gesturing toward the break, the words of caution slicing through the language barrier. He wants the team to enter quickly and not dally on the surface, where waves threaten to toss them onto the shallow corals.

Ryan McMinds sits on the gunwale of the rocking boat. The OSU Ph.D. student is the youngest member of the team but also the most experienced diver. He calmly holds his facemask and regulator in place with one hand and tumbles backward into the water. He rights himself and signals to the boat that he’s OK. On the opposite gunwale, Jesse Zaneveld, a post-doctoral researcher, follows suit.

A few more frantic moments pass as the rest of the team enters the water and gathers on the surface. But when they submerge beneath the crashing chaos, the surge becomes a smooth rocking and pushes them toward a massive wall of coral before it draws them gently away again. It takes only moments to adjust to the rhythm.

A baroque vista of colorful corals in every imaginable shape greets them. There are twisted fingers, tangled thickets, boulders and smooth patterned mounds that look like cartoon brains. This first glimpse of a coral reef inspires awe. But the scientists are already descending, zeroed in on an interesting cluster. These massive marine structures are built by colonies of tiny marine invertebrates, and the researchers work with their noses inches from these animals that look more like miniature flowers than the architects of marine ecosystems.

coral reefs in the Red Sea

A Global Problem

McMinds and Zaneveld have traveled halfway around the world to gather coral samples. They chip small fragments from the colonies and use syringes to collect mucus. It’s not the slime that interests them; it’s the bacteria contained within the liquid. Back on the boat, they’ll store the samples in a “dry shipper,” a container filled with liquid nitrogen that instantly freezes the samples until they can be taken to the lab for gene sequencing.

It’s all part of the Global Coral Microbiome Project, an ambitious study funded by the National Science Foundation and led by Rebecca Vega-Thurber, assistant professor of microbiology at Oregon State. From labs in Corvallis to reef ecosystems in the Red Sea, the Caribbean and Great Barrier Reef off Australia, she and her team seek to understand how corals and other organisms — particularly the microbes they host — have co-evolved. The fish, the corals and algae that live inside of them all have a role to play, but ultimately the reefs reflect a balance between growth and decay.

When the balance tips, things go wrong. Disease may result as the proportion of good to bad bacteria slips, she says. Before the 1980s, diseases in corals were largely undescribed because they were so rare. Now diseases are rampant in regions like the Caribbean. When corals disappear, entire ecosystems collapse.

“Corals are the foundation species of tropical reefs; that is, they essentially build the infrastructure necessary for reefs to flourish and be so biodiverse,” adds Vega-Thurber. Reefs have been called the rainforests of the oceans, though they are vastly older than their terrestrial counterparts. It’s estimated that 25 percent of all marine species depend on these habitats for food, shelter and nurseries to rear their young.

Reefs also provide benefits, so–called “ecosystem services,” to humans. Half a billion people count on reef fish as their only source of daily protein. Reefs protect coastlines from waves and storms. Their molecular biodiversity has led to the discovery of life-changing pharmaceuticals. The list of what is lost as they disappear quickly becomes alarming.

Most of the causes of decline can be traced to human activity. Rising ocean temperatures related to climate change lead to events like coral bleaching, which weaken or kill corals en masse. More intense and extensive storms leave damaged reefs in their wake. And as oceans absorb increased levels of C02, acidity increases faster than species can adapt. Pollution and runoff add nutrients that upset the microbial balance of corals. Overfishing removes species that have specific roles to play in maintaining ecosystem balance. The litany of pressures is daunting.

Vega-Thurber hopes to find solutions that will help these habitats survive. “If we understand what microbes are doing and what their sensitivity is to those (stressors), then we can predict which corals might do well in the face of climate change.”

Her collaborator in Saudi Arabia agrees. “Research provides a very important underpinning, because it provides the foundation to put items into action,” says Christian Voolstra at his lab at KAUST, the King Abdulla University of Science and Technology near Jeddah.

Last winter, Voolstra’s lab hosted McMinds and Zaneveld, providing them access to a full range of tools, from the latest gene-sequencing equipment to boats that carried the researchers out to Shib Nazar, one of KAUST’s “house reefs.” The university, barely five years old, is a vast collection of grand academic buildings and luxurious student residences still under construction, built on bare desert directly on the shore of the Red Sea. It provides an ideal scenario for studying corals. Samples can be collected in the morning and processed in a full-service facility in the afternoon.

When it comes to the global decline of corals, the entire Red Sea can be seen as a natural laboratory. “It’s a very warm sea. It’s a very young sea. We can essentially follow the evolutionary trajectory of what organisms did to survive here,” Voolstra says of his home waters, which glint blue in the background through the monumental windows of his laboratory building. While climate change pushes ocean temperatures higher around the globe, healthy reefs still manage to thrive here. “In a way, you can relate to the Red Sea as a future ocean scenario.”


Until taking Voolstra’s class, Ph.D. student Ghaida Hadaidi didn’t grasp the scale of the threats facing the precious resource lying just off her country’s coastline. She began to dig into research publications on corals. “I started to get interested in coral bleaching. I was fascinated. I didn’t know anything about that,” says Hadaidi, who discovered a whole new world just below the surface of the water. And it’s worth saving, she says. “We just throw everything into the sea and we don’t care. This is actually wrong, and we should raise the awareness for everyone. There’s amazing life down there.”

McMinds, like Hadaidi and anyone who experiences tropical corals, is dazzled by their beauty and diversity. But their aesthetic value is not what he thinks of first when it comes to their decline. “If we lose these really diverse environments, we lose the microbes that go along with them. And the microbes themselves contain a lot more diversity than their hosts.”

Over the long term, reefs will survive, McMinds believes. They will adapt. They may be different, but nature will find a way. His research partner agrees.

“Over hundreds of millions of years, coral reefs — or something just as spectacular — will bounce back,” Zanafeld says, “but humans may not be around to see it.” So he holds out hope that their work can help lead to conservation of these ecosystems for current and future generations. “We want to preserve these reefs for us and for our children. We want to experience that diversity and wonder.”


A Cluster of Coral Knowledge

For Vega-Thurber, coral decline is a personal issue. Her father, an immigrant from the Dominican Republic, infected her with a fascination for marine habitats. A doctor by training and an intrepid conchologist by passion, he collected and hand-labeled shells, she displays in a case in her office. The Caribbean reefs that inspired her father, and where she snorkeled as a child, have been decimated by coral decline. “If we don’t, as a community and a society, try to fix what we’ve done to these areas, they certainly will be gone in the next generation,” she says with a matter-of-fact tone that belies her emotional connection to these places.

Mementos of her travels adorn her office. A license plate from Florida stands beside a tiki idol carved for her by a colleague in Hawaii as a good luck token. Next to the memorabilia from her field research, a photo of Flynn, her two-year-old son, is a reminder of what she leaves behind when she goes into the field and why the work matters.

While she heads into the field as often as possible, Vega-Thurber’s teaching schedule keeps her from covering the globe herself, so she relies on her team. Trusted field researchers like McMinds and Zaneveld are key to the project’s success. She sends her tiki idol along with them. Even a scientific project can use a little luck.

And Vega-Thurber also counts her fellow faculty members a part of her good fortune: Many of her Oregon State colleagues are hard at work trying to figure out the causes and consequences of coral decline.

A Home for Algae

Virginia Weis, chair of OSU’s Department of Integrative Biology, has been studying corals for a quarter century. She focuses on the relationship of corals to the photosynthetic algae that live inside of their tissue. These algae feed the coral polyps and provide them with their brilliant colors. It’s a partnership. The tiny marine invertebrates provide a home for the algae, which in turn provide nutrients and energy to their hosts. Over time, this symbiosis between coral and algae leads to the production of hard calcium carbonate skeletons that become the physical structure of the reefs.

“My interest is in how that partnership works,” says Weis. “How they make decisions about who goes with whom, and of course in the context of reef pressures, what happens when things start to go wrong.”

The breakdown in the balance between corals and algae can have serious impacts on reefs. Coral bleaching is just one example. It occurs when coral immune systems reject their algal symbionts. A vibrant reef turns into a ghostly boneyard of dead, starving and disease-ridden corals. Some reefs never recover.

Weis has visited reefs around the world, but she also studies bleaching and symbiosis in her lab. She uses a species of tropical sea anemone common on coral reefs. “Anemones engage in symbiosis like corals do, and with the same types of algae,” Weis explains. She affectionately refers to “my animals” in tanks lining the bench and refrigerator shelves of her lab.

While the key to understanding coral bleaching will likely lie in powerful new gene-sequencing tools, it’s the change she’s seen in her students throughout her long career that gives her the most hope. “In young people, I’m hearing, ‘I want to help. What can I do to make the world a better place?’ I find it’s a profound generational difference.”

Weis finds this drive to solve problems in other young faculty and coral scientists on campus as well.

Assistant Professor Eli Meyer has found another way to study corals far from the tropics. He breeds them in his lab. In a former storage closet two floors below Weis’s lab, he has rigged computer-controlled tanks with lights programmed to emulate the sun and moon.

The brooding corals in the tanks have successfully spawned. To demonstrate, he takes a small square tile out one of the tanks and points to a coral the size of a grain of rice. It’s a year old. It takes patience to grow coral.

“I came into the coral world and was a little disappointed that everyone is going off into nature, doing one-off experiments and going back into the lab. There was no way to ever reproduce any experiments,” Meyer says. His career path in marine biology was cemented in his mind from his first frigid snorkeling experience in Maine at the age of seven, but a short diversion into the world of plant genetics gave him a new perspective on how to study these animals. “In the plant world, they don’t take no for an answer when it comes to growing their organism. If you’re a plant biologist, you’re going to have a greenhouse and grow your plant in that greenhouse.”

The question Meyer hopes to answer with his coral “greenhouse” is whether there’s a genetic basis for variation in thermal tolerance of corals and their ability to survive events such as coral bleaching. If variation is genetic, then corals can potentially adapt to a warming ocean.

Kerry McPhail, associate professor in the Oregon State College of Pharmacy, studies coral microbes in the field. In a sense, she’s an agent of “ecosystem services.” A medicinal chemist, she looks to reefs as untapped sources of new drugs. “Microbes are the absolute best chemists out there. Their chemistry is unlike anything synthetic chemists can really think of without inspiration,” says McPhail, after returning from a recent trip to a different stretch of Saudi Arabian reefs.

Drug discovery and coral reef diversity go hand-in-hand, and they provide a way to communicate the value of these habitats. McPhail’s team found a promising molecule in Coiba National Park in Panama in an area threated by onshore development. “The discovery of that compound has helped to justify the preservation of that area,” she says.


Shifting Baseline

In the heart of the Willamette Valley, Oregon State may seem like an odd place to find a concentration of coral experts, but the Lizard Island Research Station is not. This collection of breezy labs with interconnected walkways and aquaria fed by water pumped from a sandy beach lies in the shadow of Cook’s Look, the tallest peak overlooking Australia’s Great Barrier Reef.

In 1770, Captain James Cook climbed this island’s summit and gazed out at the patchwork of pastel blues and greens that stretch to the horizon in all directions. His heart sank. The words he wrote in his journal hang in the research station’s main breezeway:

“Sunday, 12th…when I immediately went upon the highest hill on the Island, where, to my Mortification, I discover’d a Reef of Rocks laying about 2 or 3 Leagues without the Island.”

For Cook, the “Reef of Rocks” was a maze, a dangerous navigational nightmare that was frustrating his exploration of Terra Australis, still unknown to Europeans. But today we actually know what the native aboriginal peoples understood for tens of thousands of years: Those reefs are among the richest, most diverse ecosystems on the planet and a cornerstone of life in the ocean.

While visiting Lizard Island on a fellowship in 2014, Ryan McMinds helped establish the template for fieldwork on the Global Coral Microbiome Project. There he collected samples as a proof-of-concept for the project.

Situated on the world’s largest barrier reef, Lizard Island is surrounded by coral diversity. The magnificent reefs are visible from shore. The shadows of turtles and sharks drift over them. From such a vantage point, it’s hard to take a pessimistic view on the outlook of their survival. To Cook’s dismay and our delight, Lizard Island seems rich in coral.

This scene underscores a problem with understanding coral habitats, or any ecosystem in decline, what ecologists call the shifting baseline. Here’s the idea: What we accept today as normal overlooks the steady transformation that has taken place in the past. The reefs we see today are vastly different from what Cook saw in 1770, or what the native aboriginal people saw for thousands of years before that.

One scientist who has studied the reefs at Lizard Island long enough to witness the modern shift in the baseline is the station’s director, Anne Hodgett. Efficient, no-nonsense, friendly and capable, she has been co-directing the station for 25 years with her husband, Lyle Vale. In that time, she’s seen more than a thousand scientific papers published by visiting researchers.

Hodgett has also seen entire stretches of reefs damaged by storms, overtaken by algae and destroyed by ongoing infestations of crown-of-thorns sea stars. These animals prey upon corals, and the sea stars’ population has exploded in recent years, decimating large portions of the Great Barrier Reef.

“If we lose it, it would be a tragedy, an absolute tragedy,” Hodgett says. “And I’d like to think that it wouldn’t happen on our watch: my generation or our children’s generation. But I think it’s going to.”

Her comments echo concerns expressed in another community several hundred kilometers away, on another remote and stunning stretch of beach in Queensland. The Aboriginal Shire of Yarrabah is an impoverished community with few jobs and no businesses. Some of the young men have found employment in government-run crown-of-thorns sea star eradication programs, giving them a way to connect with the habitat that once provided their people with a livelihood.

Errol Neal, the mayor of Yarrabah, holds out hope for the economic prospects of his town. He plans to establish an eco-tourism industry, and his vision includes cruise ships and resorts. But for the moment the only vessels in the harbor are the rusted skeletons of wrecks.

Despite Neal’s optimism that people will want to pay good money to visit this pristine coastline along the Great Barrier Reef, he’s also witnessed a shift in the baseline. He recalls gathering the eggs of seabirds on nearby islands as a boy, when villagers would take only what they needed to subsist. The eggs are gone. There are also fewer turtles than he remembers.

“They say all good things don’t last forever, but we managed to maintain that for thousands and thousands of years,” says Neal. “And more recently, things have been really sad because the beauty of this land has been deteriorating — the reef, the natural wonders — simply because people don’t regard aboriginal history serious enough.”

When asked to share some traditional cultural stories about the reef, Neal initially demurs, saying it isn’t his place. But at the end of an interview he shares this: “In the old stories, they say when the Mother gets mad at us, then the seas will begin to boil.” Did a forty-thousand-year-old culture understand the shifting baseline? Did their Mother warn us about climate change?


A Fighting Chance

Half a world away, while McMinds and Zaneveld scour KAUST’s house reefs in search of new species and collections to bring back to Vega-Thurbers’ lab at Oregon State, Ghadia Hadaidi studies genomics and marine biology and awaits her chance to explore the world that lies just beyond her country’s coastline. The late King Abdulla created the institution as a “beacon of knowledge” and symbol of tolerance and learning in the heart of the Islamic world. Inside its walls, women have more freedoms than elsewhere in the country, and international scientific collaboration and progressive thought are encouraged.

While the Great Barrier Reef is among the most studied — it’s a world heritage site and a source of national pride with numerous research stations and universities devoted to its understanding — the Saudis are just learning about the rich diversity that lies off their longest coastline. Along with Oregon State, KAUST is at the forefront of a growing awareness that these precious marine resources need protection.

As a Saudi woman working her way toward a Ph.D., Hadaidi is fulfilling the promise of KAUST in a part of the world where women’s education isn’t always encouraged, where they’re not even allowed to drive. It’s not an easy path, but she impressed Voolstra with her persistence. He can choose from a global pool of qualified doctoral candidates. But as a master’s student, Hadaidi showed up at his office door weekly until he agreed to take her on in one of his handful of Ph.D. slots.

Hadaidi has yet to dive in the spectacular KAUST reefs. In her culture, it’s not an easy feat for women to explore the ocean. At the swimming beaches, you never find women in the water. At the most they’ll hike their abayas and wet their feet along the shore. Now, there are even rumors circulating through KAUST that women won’t be able to secure diving licenses under the new regime.

But Hadaidi is not deterred. She has signed up for a scientific dive course and eventually hopes to have a chance to experience a Red Sea environment that few of her countrywomen have ever seen.

The human spirit, like nature, will find a way.

Editor’s note: Read a 2015 paper by Stephanie L. Ware and Rebecca Vega Thurber, “Sewage pollution: mitigation is key for coral reef stewardship,” in the Annals of the New York Academy of Sciences.


David Baker
David Baker
Justin Smith
Justin Smith

Editor’s note: David Baker and Justin Smith of Oregon State Productions have been following the work of Rebecca Vega-Thurber and her team in Australia, the Red Sea, French Polynesia and the Caribbean. They are working on a film about her research, Saving Atlantis, due out in 2017. You can learn more here.

One reply on “Reefs Under Siege”

Hey Guys! Nice article. Im currently doing a science project on corals and have some questions that I need help with. The coral that Im using now was taken from some beach in Okinawa 5 years ago. But the thing is the coral totally didnt react when was put in acid? Is it because the coral is dead?

Comments are closed.