Hope from the Deeps for Coral Reefs

Eight miles south of the island of St. Thomas, under a blazing Caribbean sun, Tyler Smith and Marilyn Brandt watch the ocean floor scroll by. Below the rolling fiberglass hull of their research vessel is a reef, and with a camera lowered on a cable, they can see what’s living down there and what shape it’s in. Platters of what looks like stone covered with muted yellow moss drift past—mountainous star coral and boulder star coral, mostly—with purple sponges waving gently. At 125 feet down, it’s deep for this kind of reef. Every now and then a white patch on the coral appears, looking shockingly bright in the twilight of the reef.

Each plate is coated with hundreds of organisms a few millimeters in size. These coral polyps, as the individuals are known, look like tiny flowers. Within their cells, they host algae that garner energy from the sunlight through photosynthesis and share it with the coral. The polyps create calcium carbonate armor for themselves over the course of their lifetimes, and when they die, their empty armor is what the next generation of polyps anchors themselves to, creating, over time, an enormous mass of calcium carbonate with a thin rime of vibrant life—a coral reef. “You get into it for the aesthetics,” reflects Smith, a professor of marine biology at the University of the Virgin Islands on St. Thomas.

Coral reefs are built by individual polyps secreting calcium carbonate, which builds up over time to create elaborate structures.

But when the water temperature rises past a certain point and stays that way for weeks, as it has a marked tendency to do these days, the relationship between the coral and the algae breaks down. The algae are ejected from the coral, rendering it a ghostly white, and as time passes, the polyps starve to death. Along with a panoply of other threats, most of them traceable to humans—including ocean acidification, which interferes with corals’ ability to build their armor, overfishing, and sediment that smothers coral—this coral bleaching is part of the decline of reefs worldwide.

Some researchers think that deeper reefs, like the one off of St. Thomas, might be insulated from the worst of the damage by their distance from the warm surface. Last year, Smith and colleagues released a study  supporting the idea that deeper waters could be safe havens—the so-called deep reef refugia hypothesis. If the hypothesis turns out to hold, it might help make the difference between life and death for the builders of some of the planet’s most awe-inspiring ecosystems.

Refugia’s Origins

In 1969, ornithologist Jurgen Haffer put forth the idea that, over eons, scraps of humid forest could have served as long-term hideouts, or refugia, for bird species when their woodland habitat turned to dry savannah. When the coast was clear—or rather, moist—the birds, now perhaps evolved to be more different from each other than before, radiated outward again. Though the refugia theory started out as a way to explain the birth of new species, it has grown in importance in conservation biology. Researchers are actively seeking places whose preservation stands a good chance of aiding the survival of a large number of species.

For corals in particular, the idea can be traced back to 1996. While considering the causes of coral bleaching, Peter Glynn of the University of Miami wondered whether there weren’t places where death might not come so fast. Perhaps if cold water from the deeps welled up regularly to wash over shallow coral, or if species from the shallows could persist in deeper places, more secluded from the heat that starves corals on the heights, they might survive over the long term. And then they might send their seed to the decimated areas when the heat passed. In the years since, that simple statement has sparked a great deal of research. Glynn’s paper  has been cited nearly 500 times.

Some of the enthusiasm may stem from the fact that to be a coral scientist is to buy front-row tickets to a tragedy. Brandt, also a professor of marine biology at UVI, traces her vocation to falling in love with the reefs around Little Cayman Island on a summer research trip. Logan Williams, a UVI graduate student in marine biology who grew up on St. Thomas, recalls snorkeling among vivid, living corals as a child.

But starting in 1999, Brandt’s reefs began to disintegrate, succumbing to disease and probably stress from the periodic El Niño heating events that are becoming more frequent. “It was horrifying to watch,” she says. In Williams’ case, by the time she was in high school, the underwater landscape she remembered had fallen apart. “That was what made me become interested in studying coral,” she says. “I’ve heard other people say this, too. It’s like this for a lot of us.” Since 1960, more than 50% of the coral cover in the Caribbean has been lost, due in large part to bleaching, disease, and related problems.

Since Glynn’s regufia musings in 1996, reports of how a deep reef or a particular population of coral handled the heat and its aftermath have streamed in from around the world. Each one is a pixel in the picture of how deeper reefs respond to warming waters. But the picture is rather confusing. “People want to know, are they refugia? Yes or no?,” says Pim Bongaerts, a post-doctoral fellow at University of Queensland who studies the concept. “It’s not a black-and-white thing.”

When Coral Turned White

One problem is that many reports discuss a single bleaching event, leaving it unclear whether deep reefs are a useful refuge over the long term. Smith, who did his doctorate with Glynn, recently turned to a data set the latter had been constructing since 1973 to try to address this question.

About once a year, Glynn’s group had surveyed the corals in the Gulf of Chiriqui in Panama. In that time, two bleaching events had devastated the area, in 1983 and 1998. Glynn suggested that the analysis focus on the fortunes of one coral: Millepora intricata, a delicate species that’s especially sensitive to heat but lives in both deeper areas and the shallows.

They found that M. intricata had been completely wiped from the shallows in both events. However, small colonies had survived below 40 feet. Three to four years later, M. intricata reappeared in the shallows. Related species that did not have deep colonies never returned.

Coral reefs are among the most diverse and fragile ecosystems on the planet.

So far, so interesting, but what about the very long term? To see whether M. intricata had survived the heating events of the past 5,000 years, one of the team members cored two shallow reefs. In the resulting columns of calcium carbonate, the majority of what they saw was M. intricata. The related species that did not have deeper populations could not establish strong footholds.

Taken together, these results suggested that the deeper water was serving as a refugia for the species—that its ability to survive at depth is what separated M. intricata from its unlucky cousins. The study doesn’t confirm, using genetic analyses or by tracking larvae, that the deeper colonies seeded the shallow ones. But the evidence is suggestive, and there are no other sources of M. intricata larvae around. “The Millepora was a clear case,” Smith summarizes. “It’s a species that’s really just hanging on, and this depth refuge was the key to keeping them around.”

And just last month, researchers reported in Nature that depth was a major predictor of whether reefs around the Seychelles had recovered from the 1998 bleaching. Having measured everything from the fish population to the nutrient levels in the water at 21 reefs, they found that depth, along with the complexity of the reef’s branching structure, predicted whether it would recover 98% of the time. It set the community of refugia researchers humming.


Lately, closer to home, Smith and his colleagues have been considering the existence of depth refugia in the Virgin Islands. In the Caribbean, reef mortality from bleaching has been tremendous. In 2005, many places in the region lost 90% of their coral to bleaching and to the diseases that followed. By 2100, NOAA predicts that severe bleaching will be an annual event in the Caribbean. If deep reefs can act as refugia there, they could be a godsend.

Yet in records from 2005 to 2013, three different bleaching episodes had counter-intuitive effects on deep reefs. One year, shallow coral bleached and deep coral didn’t, which seemed to chime with the Panama study. But other years, the reverse was true. One year, in a somewhat unnerving turn of events, the thermocline—a layer of water separating the warmer, higher waters from the cooler depths—shifted. The deep reefs were no longer in a cooler zone, and they suffered. In the other year, the issue seems to have been that deeper reefs, accustomed to relative temperature stability, were damaged by temperatures that would not have bothered shallower coral.

“Especially after the Eastern Pacific stuff, I was very much up on this idea of a depth refugium. I thought we were heading down this path,” Smith recalls. But looking at the data from the Caribbean once again makes it clear how very complex the picture is.

Reefs of Tomorrow

The future of reefs is unknown, and in a certain sense unknowable—there are so many factors in play. But there will certainly be a great deal of mortality among corals in the coming years. “The future will be interesting. Probably sad,” Smith says that day on the boat, tying up at the dock. He hopes that deep refuges, when and if they exist, can help preserve some of the species and their relationships that make up today’s coral reefs.

Already, scientists in Australia are calling for greater preservation of deep reefs. Though they may be protected from the worst of the heat—at least some of the time—they are vulnerable to fishing and pollution. On their own merits, they appear to be home to a variety of new species and unusual ecosystems. And if they are refugia, so much the better.

Fortunately, depth refugia may not be the only way corals can grapple with the coming change. For instance, Steve Palumbi, a professor at Stanford, studies corals’ ability to evolve better heat resistance. There is some evidence that corals that can move to cooler waters are doing so. And on the island of St. John, just east of St. Thomas, Caroline Rogers of the USGS has discovered corals living in mangroves that appear to have survived catastrophic bleaching, despite living in warm, shallow water. Much of what allows corals to ride out hard times is still mysterious.

But the fact remains, even with these coping possibilities, that the world will be a very different place. The reefs of tomorrow will not look like those we know today, as coral scientists have already experienced. Brandt remembers showing an older diver photographs of beautiful stands of staghorn and elkhorn coral off the coast of Antigua, survivors of dying events that nearly wiped those species from the Caribbean.

“He got all misty-eyed,” she recalls. “He said, ‘I didn’t know that anything like that still existed.’ ”