Viewed from a satellite, Japan’s southern Yaeyama archipelago is a splatter of green blobs ringed in turquoise. Closer to Earth, those encircling lagoons take on more complex shades of blue, often streaked with white lines made by dive boats, cruise ships, rusting inter-island ferries and, more recently, the armed vessels of Japan’s Maritime Self-Defense Force.

Beneath liquid trails of tourism, transportation and regional tension are the kaleidoscopic colors of Japan’s largest and richest coral reefs. Down here, changes mirror the turbulence on the surface, as reefs grow and shrink, and aquatic species migrate in and out each season. These enduring oscillations are expected, but a newer change is pressing itself, sharply, into the lives of those connected to these islands: The colors are leaving. And “leaving” is the right word: Staring through the tempered glass of a scuba mask, what we see when we look at the color of coral is living tissue, the soft biomatter of a plant-animal slowly building a calcium carbonate skeleton. As sea-surface temperatures rise well beyond the average (and for longer periods) in summer, the plant half of the relationship — single-celled algae called zooxanthellae — leaves and, without a source of energy, the coral animal turns bone white. If the algae don’t return when waters cool, coral eventually dies, its skeleton decays and an entire reef can collapse.

In 1998, Ishigaki and other islands in the Yaeyama archipelago were hit by the first global coral bleaching event. Some parts of the reefs collapsed as a result. Bleaching events have returned in parts of the globe every three to five years since then, but in 2016 and 2017, particularly high sea-surface temperatures appeared back-to-back for the first time: Roughly 90 percent of Yaeyama’s coral was bleached in 2016 and, according to the Environment Ministry, more than 70 percent of the largest reef, the Sekisei Lagoon, died. In January, the ministry reported that roughly 49 percent of the remaining coral was bleached in 2017; we still don’t have accurate figures on how much has died. None of this is normal.

Here are the stories of people in the Yaeyama archipelago, particularly those on the main island of Ishigaki, whose lives are affected by single-celled zooxanthellae and climate change — two interrelated factors, microscopic and planet-sized, that determine the color of coral. The quantitative story of reef decay has been well told, even on these remote islands, but there are few stories that explore how changes to the Yaeyama reefs are affecting people, including reef scientists, hotel directors, guesthouse owners, government employees, tour guides and divers such as Harvey Tiew Lee Leong and his pregnant wife, Mikiko Ando Tiew.

Yonehara Reef lies in a coral-rich transparent lagoon on Ishigaki Island. | COURTESY OF DIVING SCHOOL UMICOZA

A dive school in the jungle

Leong and Tiew run Diving School Umicoza in a patch of jungle in northern Ishigaki, between a shrimp farm and cow paddocks, and looking out to an azure lagoon. Umicoza is one of roughly 200 dive schools/shops on Ishigaki, and specializes in excursions to the island’s northern reefs. During summer months, instructors will spend hours each day swimming over coral, alongside tropical fish, sea snakes and manta rays.

“When I first came here … lots of coral,” Leong says. He slides open the door to the garden at the center of school, leading the way to a view of the lagoon below, his tanned and tattooed arms barely showing beneath the black sleeves of a hooded sweatshirt. The coral now? “Dead,” he says. We both know the answer is an exaggeration, but not by much — over the past 20 years, significant amounts of the reef (some reports suggest more than half) have collapsed.

The waves break hard against the reef edge below, and clouds hang heavy, spitting into a cool northerly wind. The air smells like wet foliage. Droplets run down umbrella-sized taro leaves into soggy earth. Cane and cattle stretch around the headland to the south, leading to farmland where the SDF is building missile batteries to defend the island from invasion. Also worrying to locals is the invasion of tourists, whose numbers increase each year — in 2017, 1.3 million domestic and foreign visitors came to this island of almost 50,000 people and, since Ishigaki was named the world’s No. 1 trending travel destination by TripAdvisor in January, more are expected.

Geopolitical tensions and out-of-control tourism worry Leong and Tiew, but there are more immediate concerns troubling them today.

“We just hope the typhoons come (this year),” Leong says. “Each time the typhoon comes then the ocean temperature will go down a bit.”

Certain dive locations have been completely changed over the past two years due to mass-bleaching events. Anything that brings down the water temperature — even destructive typhoons — is desirable.

“Maybe in another 30 to 50 years we still can see something,” Leong says, thinking about how the reef might look to his children when they are older. “I hope coral is growing, I hope the next generation will also see them.”

Tiew will give birth to their second child later this year.

Umicoza does what it can to mitigate stress on the coral by limiting the number of dives it takes each day, and ensuring minimal damage occurs when they drop anchor. Tiew says that some unregistered dive shops, particularly those that have flourished as tourism booms, are not so careful. Umicoza also takes customers to see the changes to the reef: One photo from a group dive in 2017 shows a single blue branching coral amid the brown rubble of a collapsed reef. But there is only so much that can be done.

“The water temperature we cannot control, nor the typhoons,” Tiew says.

The scale of the problem exceeds them, their school, their island, the archipelago and nation. “It is a global thing,” Leong says. “If I’m just alone, I can’t do anything.”

Fish swim around healthy coral off the coast of Okinawa’s Ishigaki Island. | CAMERON ALLAN MCKEAN

The science of loss

In his sixth-floor Tokyo office, professor Hajime Kayanne rummages through papers. He answers many questions this way, by scouring the office for graphs, photographs, diagrams. The walls of his room in the Department of Earth and Planetary Science at the University of Tokyo are stacked with books on coral, and his view of the city outside is gradually being eaten away by the publications that no longer fit on the shelves.

Kayanne has been studying changes to reefs since around the 1990s. He is not equivocal about the causes of the changes. Here is the opening line to a research article published in January that is co-authored by Kayanne and 30 other scientists who work at 24 different institutions around the world: “The health of coral reefs is declining globally due to human-induced environmental changes.” The full implications of that simple sentence are hard to process.

“The rate of recovery cannot catch up with repeated bleaching — it’s not possible,” Kayanne says.

Before the first bleaching event in 1998, Kayanne says that Shiraho Reef — the specific location on the southeastern coast of Ishigaki that he has devoted himself to studying — “contained a high diversity of coral.”

“After the bleaching,” he says, “that diversity was lost.”

Witnessing the sudden deterioration of a rich coral garden is visually shocking, and has been used effectively by filmmakers and photographers in documentaries such as Netflix’s “Chasing Coral” or the BBC’s “Planet Earth II” series. In this footage, the complex reef cities of the northern Great Barrier Reef crumble to ruins following the widely publicized mass-bleaching event in the summer of 2016.

However, scientists such as Kayanne often attempt to take a less human view, by considering coral changes in the context of longer time scales. Although these considerations are rendered through the dry, emotionless language of science, they can be deeply disturbing, with “loss” occurring at hard-to-fathom scales.

“Coral reefs,” writes Charles Birkeland in his 1997 book “Life and Death of Coral Reefs,” “are especially sensitive and vanish about a million years before other groups of organisms each time there is a global mass extinction.” The full implications of that sentence are also hard to process.

Fish swim around healthy coral off the coast of Okinawa’s Ishigaki Island. | CAMERON ALLAN MCKEAN

Coral survives, rare species won’t

Associate professor James Davis Reimer, a Canadian marine biologist who runs a laboratory at the University of the Ryukyus on Okinawa’s main island, has spent his academic career wrestling with the microscopic and planetary at play in changing coral reefs.

Hours before flying back to his lab and family in Okinawa, Reimer agrees to meet in a crowded Tokyo restaurant to explain his experiences with the declining reefs of southern Japan.

He talks fast and passionately, his voice submerged under the clatter of cups, shuffling feet and morning conversations. Perhaps because he lives and works in Okinawa — and sometimes even takes his daughters to visit locations he is studying — the changes are felt more powerfully. His home is changing, and he sympathizes with those who live around Ishigaki. He says he doesn’t “usually cry,” but visiting sites where coral gardens have turned to “rubble” has affected him deeply.

“To go there and see it,” Reimer says, “it just hits you.”

Biodiversity and “ecological imbalance” are central concerns of Reimer’s.

“Biomass might not be down, but the number (of species) is,” he says in response to questions about the efficacy of cultivating heat-resistant corals. Cultivated coral may ensure that the size of reefs doesn’t change, but the biodiversity will drop significantly — only a handful of heat-resistant species have been cultivated so far in Japan. This is an important point: The future is less colorful than the present.

It’s not just about coral, but these bleached species are acting as early warning systems.

“In the next few hundred years,” says Reimer, “the number of animals is not going to decrease, the number of rare animals will decrease.”

He is quick to point out that this is not something that is going to happen, it’s a process that is already taking place. That said, “process” is arguably too benign for what Reimer is talking about: at best, a profound lack of biodiversity; at worst, widespread extinction.

“If it is already gone, it’s gone,” he says. “It’s not coming back.”

Coral lies on a beach near Shiraho Village. | CAMERON ALLAN MCKEAN

Tourism turns with the coral

It may be obvious that reef bleaching would directly affect those studying or working closely with coral, but the Yaeyama archipelago’s changing reefs are beginning to leave the water and enter boardrooms, the lobbies of luxury resorts hotels, tourist information counters and guesthouses. If the concerns of Kayanne and Reimer are correct, the changing reef will profoundly reshape what tourism looks like on Ishigaki.

Dai Takakura, acting director of the Ishigaki City Tourism Exchange Association, sits on a low sofa at the back of his office. The window outside looks out to other government buildings and the port, with the islands of the archipelago further south. He is aware of what is happening to the surrounding reefs, but also aware of the complexity of the situation: How does one change the temperature of the ocean?

If the reef really does collapse in certain areas, will that be a problem for the tourism department? “Problem,” he replies. One word is enough, but he goes on to explain that full magnitude of that problem has not manifested yet for the local industry.

He explains that existing environmental concerns — believed to be more local than global by many who work in tourism on the island — have led to meetings being held four times each year, which are attended by those whose livelihoods are connected to the island’s ecological wellbeing: Ishigaki City’s environmental office, tourism departments, fishermen, divers and volunteers. The main outcome of these meetings is knowledge-sharing. Attendees explain how they have mitigated environmental damage, from picking up garbage on beaches to cultivating corals.

Takakura acknowledges that the group talks about bleached coral, “but not about global warming,” he says.

Sharing knowledge is also a priority of Hoshinoya Taketomi Island, a luxury resort on a coral atoll 10 minutes by ferry from downtown Ishigaki.

Naoki Tagawa, director of Hoshinoya, says the resort is focused on protecting the cultural assets of the island and working closely with locals, but admits that the changing reef has affected his work.

He says the resort now holds lessons with “teachers on Ishigaki Island who know about the coral reef.” The teachers explain to staff “why corals are getting whiter.”

Alongside knowledge, the owners of Le Lotus Bleu, ryōkan-style accommodation in Ishigaki’s Shiraho Village, share experiences with guests. The married owners, Patrick Verniolle and Maiko Okutani, initially wanted to buy a house on the main island of Okinawa, but that changed once the airplane they were traveling to Ishigaki on broke through the clouds and they saw those green blobs ringed in turquoise.

“We are snorkeling in summer at least once a week,” Verniolle says. “Sometimes I take guests to the beach and we go swimming together.”

Sitting in his living room, with winter wind and rain teasing wooden door frames, he reflects on these excursions that have taken place during the past six years. The changes to the coral, he says, are “very visible — you can really see the degradation.”

One of the main reefs he visits with guests is Yonehara, a picturesque sliver of white sand leading into a coral-rich transparent lagoon. It’s enshrined in postcards and promotional brochures distributed to tourists at the airport, but more unstable than those images suggest.

“It is not as beautiful as before,” Verniolle says. “That is what all the people on the island are saying: It was much more beautiful, there were more colors.”

Life among the changing reefs

A snorkeller swims above a reef in the north of Ishigaki Island. | COURTESY OF DIVING SCHOOL UMICOZA

To see Yonehara for yourself, you will need to take the route from the city of Ishigaki that cuts directly across the island — past the construction sites of new hotels and resorts. Fleshy taro leaves spill onto the road, beside stalls selling fruit from local farms: papaya, mango, guava, dragonfruit. However, on winter days like today, these stalls are empty. In summer, the water at Yonehara will be thick with tourists snorkeling above the reef, but it is empty, too, except for a family of beach-combing Taiwanese tourists, and a lone snorkeler.

The water is crystal clear and warm. Even in winter, the surface temperature of the sea rarely drops below 23 degrees Celsius; in summer months over the past two years it has regularly risen above 30 degrees.

The current, pulling toward underwater passageways where the lagoon merges with the ocean, threatens to suck everything into waves breaking against the reef’s edge. Each collision sends spray into the air, hanging like the haze of a forest fire.

In the shallows, Porites corals (in the shape of small sunken moons) are dead, now coated in algae and seaweed. Patches of reef in the lagoon remain empty, and once-living fragments of coral line the sandy bottom. Further out, sea life is more lively and coral more resilient, but algae-ridden skeletons emerge here and there.

The reef is “less” than it was 50 years ago, 10 years ago, five years ago, two years ago, even one year ago — less rich, less rare, less colorful. This sense of loss over the Yaeyama islands’ ever-diminishing present reappeared in every interview for this article, as each person repeated the same phrase almost word for word: “It used to be more beautiful.”

A banded sea snake emerges from a coral table. | COURTESY OF DIVING SCHOOL UMICOZA

The downward spiral of thoughts is stopped by the sudden appearance of a poisonous (and shy) banded sea snake that emerges from a table coral. It twists around a school of fish on its way to take a breath at the surface.

For a brief moment, the sea snake turns to look at the human in the water, and both stare at one another, uncertain exactly of how to move forward, floating above a changing reef at the end of Japan and resisting the pull toward a less-colorful future.