Ancient and complex, the rare blue coral reef of Shiraho, Ishigaki Island -- part of the Ryukyu island chain, Japan's southernmost -- is one of the world's biggest and perhaps oldest blue coral reefs. Though only 3 km long, it contains at least two-thirds the number of species of Australia's 2,000-km Great Barrier Reef.

Coral is found in Japan all along the Ryukyu chain, which extends south of Kyushu down to the Yaeyama Islands, 100 km northwest of neighboring Taiwan. Among the most diverse ecosystems on Earth, coral reefs support an amazing variety of marine life, and are as valuable underwater as the tropical rain forest is on land.

A rich source of seafood and natural medicines, they also act as a natural barrier to shorelines, protecting them from tropical storms and typhoons.

A coral reef is actually a colony of animals called polyps. Using tiny nerves and muscles, the soft-bodied polyps capture food at night, and avoid predators by hiding in the hard coral during the day. Nourishment, such as plankton, is is taken equally by each individual. In species with separate sexes (some are hermaphrodite) males release sperm which is carried by the current to the waiting eggs of their female counterparts. Offspring, called planula, then float through the currents looking for a new place to build their own communities.

Coral grows slowly -- about 1 cm per year -- and the Shiraho reef is estimated to be at least 1,000 years old.

A snorkeling trip into the reef, where the blue coral has grown to 2 or 3 meters high in places, is a dreamlike experience. The ecosystem has tremendous scientific importance; for example, there are classes of marine life there that have not yet been studied at all, and growth rings on the blue coral can be examined to measure environmental changes in the last millennium.

But in many places, the coral has lost its color. White "bleached" coral is either dying, or is already dead. "It's not normal," says Rie Oi, a marine ecologist and instructor at Ishigaki Resort Polytechnical College.

"This year was especially bad; the summer was hot, and there was a lot of heavy rain." She is referring to the akatsugi runoff, red tropical soil that washes off farms and construction sites and ends up in the sea, cutting off the coral's necessary oxygen and light.

Since Okinawa was returned to Japan in 1972, there has been an onslaught of public works projects typical of Tokyo's development model for cash-strapped regions: uniform, standardized, and blind both to the unique local environment and the needs of the community.

Some conservationists estimate that in the three decades since then, as much as 90 percent of Japan's coral has disappeared.

World Wide Fund for Nature staff in Japan, and volunteers at Shiraho village, have been monitoring the red soil runoff problem all around the island, by testing water samples for soil content.

On a scale of 1-8, where 1 is clearest, all readings are between 6 and 8.

"We are working as much as possible with local people, farmers, fishermen and City Hall," says Yasumura Shigeki of WWF. For farmers, greenbelt farming "is one option, where they put a border of grass around the crops to prevent loose soil from escaping. But doing that takes time and money, so the farmers need support."

But local factors are not alone to blame; there have also been recent widescale coral-bleaching events. Bleaching is a complex process linked to climate change, where increasingly warmer seas kill the algae that grow on and nourish the coral, which turns white and eventually dies.

The five warmest years in history have all been recorded in the last two decades, and unprecedented increases in coral-bleaching events worldwide have happened during the same time.

But the biggest shadow looming over the reef's future is Okinawa's three-decade-old plan to build a new airport at Shiraho village.

The initial 1979 nationally financed proposal to build directly onto the reef was opposed by local residents; the debate later attracted wider attention, and the International Union for Conservation of Nature and Natural Resources attempted to have the reef designated a World Heritage Site.

The airport project stalled, only to be recently revived in the changed political climate and with the proposal of an alternate site on land. However, Karadake, just north of Shiraho village, is the site of three bat caves as well as home to the crested serpent eagle, a protected species.

Though Okinawa Prefecture insists the red soil won't threaten the reef thanks to newer construction methods, one conservationist dismisses this as "mere armchair theory spinning."

Environmentalist Maggie Suzuki criticizes the plan as "nominally improved," saying, "The authorities appear to be once again willfully ignoring conservation groups and researchers, who are even better informed about the situation than they were 30 years ago. Authorities should be planning how to restore and maintain the biological integrity of the reef rather than planning a project that will obviously impact on it further."

The other issue, inseparable from science or politics, is the eroding cultural heritage of local people and their centuries-old way of life beside the reef, enjoying its bounty and protection. WWF staffer Takashi Kobayashi worries that in the push toward modern consumer culture, such precious ecosystems won't be appreciated until they are gone.

"A lot of young people just think about money. The sea is something they see every day and take for granted. We have to renew an appreciation among them about what a wonderful natural asset we all have."