Despite Many Threats, Some Coral Reefs Are Thriving

Despite Many Threats, Some Coral Reefs Are Thriving
A school of twinspot snapper (Lutjanus bohar) use the complex structure of coral reefs for shelter. Credit: Brian Zgliczynski; 100 Island Challenge

RAROTONGA, COOK ISLANDS—Twenty-one degrees, 12 minutes south of the equator, 2,771 miles south-southeast of the southern tip of the island of Hawaii, 30 feet below 4-foot swells, Nicole Pedersen swims slowly, wearing a wetsuit, headband, and full scuba gear and carrying a custom-built plexiglass-and-PVC case the size of a tackle box. Within it, twin DSLR cameras automatically photograph a reef a quarter-mile off the coast of Rarotonga. It’s the last of 12 dives she and colleagues from the Scripps Institution of Oceanography have made over three days of their research expedition here.

Pedersen, 25, is a staff researcher at Scripps, part of the University of California, San Diego, and the image digitization coordinator for a natural experiment called the 100 Island Challenge, launched in the summer of 2016. The images she’s gathering—4 billion pixels comprising 70 to 80 gigabytes of data, just from today—will ultimately help the team build a three-dimensional model of the 100-square-meter (1,076-square-foot) plot of reef Pedersen is swimming over in a lawn mower pattern.

As she gently flaps her black-and-yellow fins, maintaining as constant a speed as is possible underwater where waves and currents can toss her off course, marine ecologists Stuart Sandin and Brian Zgliczynski swim alongside her, counting every fish in the plot and marking on a waterproof data sheet each one’s species and approximate size. The more than 4,000 dives the team will make over five years are the data-collection component of an unprecedented attempt to characterize five examples of every type of reef on the planet—twice—to see how each is responding to climate change, ocean acidification, pollution, overfishing, and the other insults humans have been throwing at many of them with increasing frequency and intensity over the last few decades.


The 100 Island Challenge is so wildly ambitious that even one of its co-leaders, Scripps coral reef ecologist Jennifer Smith, thought it would be absurd to try when Sandin, the project’s lead investigator, and Zgliczynski, a postdoctoral researcher, pitched it to her several years ago. “You guys are idiots,” Zgliczynski says she told them.

Over a dinner of wahoo fillets and Cooks Lager, the local brew, following the first day of diving in Rarotonga, the scientists say they could already see that the island’s reefs, alive with new growth of diverse coral species and crowded with fish scraping away excess algae, are not like those that have dominated the news lately. “Coral reefs are bleaching four times as frequently as they did in the 1980s, scientists say,” read a Washington Postheadline in January. “Coral Reefs at ‘Make or Break Point’, UN Environment Head Says,” blared another January story in The Guardian. “Coral reefs at risk of dissolving as oceans get more acidic,” announced Reuters in February.

Nicole Pederson pilots the mosaic camera system taking images of the coral reef ecosystem off the coast of Rarotonga. Credit: Brian Zgliczynski; 100 Island Challenge

Unchecked coastal development pollutes reefs; illegal, unreported, and unmonitored fishing depletes them; carbon dioxide emissions inhibit their ability to grow; and historic ocean warming has in recent years caused back-to-back bleaching events that threatened reefs worldwide, including potentially as much as half of the Great Barrier Reef’s northern corals. Still, although the bad news is undeniable, it’s not the only story. “And it’s not the story when communities take control of their marine ecosystem,” Sandin says. “When a community is engaged and listens to what’s underwater, they can keep it going.”

The group of scientists Sandin and Smith have assembled thinks at least some reefs have the potential to survive another—inevitable—mass bleaching event like those that struck the South Pacific in the El Niño year 2014-15 and again in 2015-16. Confirming this is vital to protecting them, other scientists agree, because if people view a problem as having no solution, they tend to tune out.

“There are a lot of bad things happening to coral reefs, and to ignore that would be crazy,” says Nancy Knowlton, Sant Chair for Marine Science at the Smithsonian National Museum of Natural History. Nevertheless, reefs can recover when they are free from other stressors, such as pollution and overfishing, she says, so “simply to have a ‘coral reefs are doomed’ attitude is not particularly helpful, and not particularly accurate.”


Locally, such an attitude could lead to harmful new development, or to dumping sewage on reefs, because what’s the point of denying the permits if the reef is just going to die anyway? The aim of the 100 Island Challenge is to figure out which reefs recover well, why they’re more resilient, and how to transfer whatever properties are saving them—be they biological, managerial, or environmental—to other coral reefs and coral species.

“You’ve got a huge number of islands across the planet that are beautiful, unique storehouses of biodiversity and provide resources for humans, so if we can develop the technologies that are working at each of these sites, they become good test cases for other islands and other reefs,” says Ove Hoegh-Guldberg, professor of marine science at The University of Queensland in Brisbane, Australia.

Sandin and Smith, both 45, who are married, are acting on preliminary evidence that local reefs with good water quality and healthy fisheries are more likely to recover quickly from bleaching. “Some places we work in the Central Pacific did experience quite extensive warming and the reefs did bleach,” Smith says. “We documented that, and we were able to go back and found a lot of corals were actually able to recover.” She also points to corals that have adapted to warm seas, such as those in lagoons that experience temperature spikes daily and seasonally.

Palmyra Atoll, a U.S. Minor Outlying Island between Hawaii and Rarotonga, showed signs of recovery just eight months after a major bleaching event. Smith, who has photographed corals off Palmyra every year since 2009, hypothesizes that the lack of pollution and fishing played a role in enabling its corals to recover so dramatically. “They’re more likely to recover than a reef experiencing runoff, sewage, overfishing, and so on,” she says.

The group has identified 100 reef sites, from the East China Sea to the Lesser Antilles, to serve as a sample of all reef types: those with high to low levels of food (three levels), those with high to low population density (three levels), and high vs. low elevation islands (two levels). That makes 18 combinations, and there are five islands of each. (The leap from 90 to 100 was about “project branding,” Smith explains.)


Trained volunteers in the lab in San Diego tag each species visible in the 3D models, which can show coral babies as small as one square centimeter across, so the experiment provides a nearly complete taxonomy of corals at each site. The scientists also take a fish census at each site, employing more or less the same method used to count elephants in Tanzania.

Recording the location with GPS, they plan to revisit each reef after two or three years and repeat these painstaking processes to see how it’s changed. Temperature, water quality, fish population, coral species, and other variables are measured across the sites. (Expeditions are planned for the same time of year to account for seasonal variability; in any case, with so much data, any such variability will essentially wash out, Sandin says.) By referencing those variables against island factors such as the particular oceanography, the benthic dimension—how much of the ocean bottom is comprised of reef, sand, etc.—and human influences like how much fishing occurs there (and whether it’s for eating or for selling off-island), they hope to find out why the changes have occurred.

The research isn’t merely academic. The hope is that local managers where reefs are suffering will implement policies similar to those in place where they’re doing well. “People are always excited to hear what’s going on on other islands,” Sandin says. At each island, the team seeks partnerships with local fisheries managers and other governmental agencies, scientists, and environmental NGOs representing the people who live on the reefs and depend on them for their livelihoods. The team also provides partners with trip reports and 3D photomosaics of the area at the conclusion of each expedition.

In Rarotonga, before they had even dunked their heads in the ocean, Sandin, Pedersen, and Zgliczynski visited members of the House of Ariki, a parliamentary body composed of traditional leaders from most of the Cooks’ 12 inhabited islands and atolls. The House is constitutionally tasked with making recommendations to the elected Parliament on certain issues—including, currently, a government plan to allow seabed mining of manganese nodules (which the House has embraced), and a proposal to build sewage pipes that will send nutrients into the ocean. The latter could deplete fish populations by encouraging algae growth that will harm the corals; the project is still in the design phase and hasn’t yet been presented to the House.

They met in what had been the living room of a private home where the House now maintains its offices; ceremonial carvings and fabrics, and photos of past traditional leaders decorated the place. A few current members, most of whom are women, wore flowered headdresses. Facilitating the meeting was Teina Rongo, a marine biologist who is well respected locally for his Ph.D. from an American university as much as for hailing from a prominent family on the island.


After introductions and a Christian prayer, the president of the House, Travel Tou, addressed the visiting scientists. “It is important that you came to us because we are not sure if the government is moving forward,” he said. “If we don’t protect the land, the results will be seen in the ocean, so we have a hard job.” Sandin then told the assembled leaders his intentions in Rarotonga and explained the experiment, expressing his hope of finding “good collaborators” among the leaders and elsewhere in Cook Islands. “We are available to engage in conversations to find a way we can learn from one another,” he said.

President Tou replied that in 2017, 15 scientific researchers came through the House, presenting their projects just like Sandin had done. The House endorsed all of them. “We requested, ‘When you finish, please—we want to know what you have found so maybe you can advise things that need to be looked at to protect our livelihood.’” But only one of the 15 had responded.

After the meeting, over lunch at a new restaurant on the north shore that Rongo is convinced will be doomed when the next cyclone hits, he explained how people on the outer islands manage their fishery. Island residents fish using traditional methods such as spears and nets hand-woven from plant fibers—no “European-style” rods or nets—and distribute their catch communally. “They close an area [to fishing] sometimes, and rotate set-aside areas every one or two years,” he said. “They’ve been doing this for hundreds of years.” Little enforcement is needed, but when it is, one punishment is to require violators to sit with the children at community gatherings.

Rarotonga is a different story. The Cooks are divided between a southern group of islands and a northern group, 91 square miles of land scattered across nearly 800,000 square miles of ocean. Rarotonga is in the southern group. The more connected people are to the main island—where the majority of Cook Islands’ 17,000 people are spread out, mostly near the coast, across an area a little larger than Manhattan—the worse they are at protecting their reef, Rongo said. It’s part of Western values’ corrupting influence on local culture: “The mentality is, if you speak English, you’re smart. But we’re losing the culture by losing the language. The ethic of conservation is transmitted through the legends and songs.” Teaching natives how to fish and farm also leads to their caring about the resources, he said. “Even if they go on to be engineers or business people, they’ll have that foundation.”

Western influence here is more than just cultural: A warming ocean confers direct threats to the health of Cook Islanders. Illness caused by eating fish contaminated with the toxin ciguatera is expected to rise with sea temperatures. Warmer oceans increase the frequency of cyclones and coral bleaching events, both of which can increase the abundance of microorganisms that carry the toxin. Rongo, who wrote his Ph.D. thesis on the disease, draws a direct correlation between a series of six cyclones during the El Niño year of 2004-05 and the highest incidence of human ciguatera poisoning on record.


Sandin sits on the stern of the boat the team has hired for about $1,000 a day, festooned with an elaborate array of gear hanging off his buoyancy compensator: Two dive reels, each with a 25-meter (82-foot) cable; a camera; a PVC monopod that attaches to the camera to photograph a set area in order to establish the scale of the 3D model; and a clipboard with the data sheet for the fish count. (Somewhere on his person, he hopes, is a pencil.) He spits into his mask and affixes it over his eyes and nose, then dumps over the side a red float with a GPS attached. It serves the dual purpose of alerting the boat’s skipper, and any others who might happen by, of the presence of divers below, and marking the precise location of the dive so the researchers can find it when they return in two years to survey the site again. He joins the regulator with his mouth, checks its flow on a gauge, and spills backward into the water.

The team has three jobs each dive: gathering images for the 3D photomosaic; counting fish; and deploying devices for in-situ measurements. Satellites can estimate sea surface temperature, and a network of buoys deployed across the tropical Pacific to predict El Niño provides exact measurements, but upwelling, currents, freshwater inflows, and other factors can cause nearshore temperatures to vary from that of the water above, even at depths as meager as 10 meters (33 feet), where they’re diving today. At a subset of sites, one diver—in Rarotonga it’s Zgliczynski—is tasked with mounting thermometers about the size of a bottle of hot sauce, which will log the temperature every 45 minutes until the researchers come back to pick it up in two years. He attaches them to a threaded rod that he hammers into the reef, which also marks the location of the plot Pedersen is photographing.

One diver calibrates the camera, a Nikon D7000 digital SLR, by photographing a 21.5-centimeter by 28-centimeter (8.5-inch by 11-inch) chessboard pattern, printed on underwater paper and affixed to a PVC board. “The angles are never perfect [when photographing underwater], so if you take multiple pictures of a known distance apart, we can adjust for that,” Pedersen explains. Once that’s done, Pedersen starts swimming a meter or two off the ocean floor, making sure to advance slowly enough that each photograph contains about 80 percent overlap with those preceding and following it.

Meanwhile, Zgliczynski and Sandin count fish—not so easy, given that fish move. (Smith teaches a class at UCSD on tallying marine fish and plants, with field trips offshore of Catalina Island, so often this is her job when she’s on an expedition.) They unwind the cables from the dive reels so they know they’re sampling a consistent distance every time, and swim back and forth three times marking every species they see and its approximate size, from which they will later estimate biomass in the area. The fish-counters must take care not to get in the way of the photographer; although the software that creates the models from the images automatically excludes any objects in motion, if they slow Pedersen down the camera’s timer will cause too much of one piece of the plot to be captured, throwing it off.

This work is not without its hazards. In the southern Line Islands last summer, Pedersen was diving a steep slope in 2.5-meter (8-foot) surf when a set of waves that salty types call a “widowmaker” rolled through as she photographed the shallowest section of the reef. One propelled her through a crevice in the reef leading to where the waves were breaking. The camera rig was lost, and Pedersen’s regulator was pulled from her mouth. “I definitely thought I was going to die,” she says, but after about 20 seconds under whitewater she was able to locate her backup regulator and the set passed, allowing her to swim out of the break and to the surface.

After a day of diving, the team’s work isn’t done. First all the gear must be rinsed of corrosive saltwater and left outside to dry, which takes a while in the 85 percent humidity that’s common here during cyclone season. Sandin thumbs through a book, Reef and Shore Fishes of the South Pacific by John E. Randall, to figure out what kind of fish they’ve seen; it turns out species that are supposedly endemic to other islands—such as a type of wrasse, a small cigar-shaped fish—are present in Rarotonga as well. “People won’t believe we saw it except that we have photographs,” Zgliczynski says. “We don’t know if it’s moving farther from the equator [because of climate change], or what. It could be random dispersal through the water column, which is how they maintain genetic diversity.” He’s taking apart a 360-degree camera, images from which will create a virtual-reality experience that can be installed at Scripps’ Birch Aquarium for public viewing. “We can come back and show figures, but that’s boring,” he says. “This gives people an opportunity to be like, ‘Oh, shit, that’s what Millennium Island looks like? There’s sharks everywhere!’”

When he’s done with the VR camera, Zgliczynski needs to record the metadata—logging the latitude and longitude of the dive sites so they can produce maps at the lab in San Diego, and linking data with instruments and locations. It’s coming up on 12 hours since the group left for the docks this morning.

Meanwhile, Pedersen uploads images to a Windows laptop as another computer whirrs away creating a 3D model from the 2,000 or so images gathered during one of yesterday’s dives; a video of the model will be copied onto a thumb drive and delivered to the Cook Islands Ministry of Marine Resources in the morning. The software runs a process called a structure-from-motion algorithm, and can take anywhere from one day to nearly three weeks, depending on the complexity of the site. With seven computers making models simultaneously back at the lab, around 800 have been built so far, with another 600 or 700 in the queue.

Sandin and Smith are exploring the limits of how technology can advance their project. They’d like to develop augmented-reality versions of the models that show how things will progress on a reef under various management practices, based on what they’ve observed at similar reefs with different practices. If people can see an alternate reality and watch how fish grow under various management scenarios, the idea goes, they might be inspired to change what they’re doing.

The scientists hope to be able to deploy underwater autonomous vehicles in place of a human photographer someday, and back in San Diego, engineers at UCSD have experience inventing such machinery. Robots in various stages of development, each roughly the size of a rice cooker and looking very much hand-made, cover a table in the office of Scripps’ Jules Jaffe, who helped design the imaging system used to find the Titanic. He would like to create a swarm of robots that can do Pedersen’s job, freeing her for analytical work. “I thought it’d be cool instead of them swimming around, getting six hours of bottom time per day,” he says.

Up the hill at the Jacobs School of Engineering, computer science and engineering professor Ryan Kastner builds computer systems for oceangoing AUVs. “The amazing thing about Stuart and Jen is they’re really pushing the technology edge,” he says. “I’ve worked a lot with marine scientists and there are some people that say, ‘We’re going to do what works.’ Then there’s a smaller camp that says, ‘Let’s see how we can take advantage of these technological innovations that are coming along,’ and that is the really cool aspect of the 100 Island Challenge.” Within a few years, cheap imaging sensors could be placed into the underwater environment to collect huge amounts of data, perhaps mapping an entire reef instead of just samples to answer bigger scientific questions.

The concerns of Paul Allsworth are more immediate. He’s president and director of internal affairs of Cook Islands’ Koutu Nui, a traditional governmental body like the House of Ariki. The last day of the Rarotonga expedition, the team met with him in a conference room as the roar of the ocean and the crowing of feral roosters could be heard through its slatted windows, open to the breeze. Sandin expressed hope for a future expedition to the outer islands. Allsworth told him that on the outer islands, where he grew up, “The fish are getting smaller, and the catches are getting much, much reduced, and they have to go out further. We don’t know why. So we welcome the technical expertise that your team has.” Pedersen then opened her laptop and showed Allsworth one of the models from the week’s dives.


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