Reefs along the Florida Keys were mostly spared, thanks to Hurricanes Katrina and Rita, which circulated cooler waters into the area, Eakins says.
But reefs in the eastern Caribbean, including the U.S. and British Virgin Islands and Puerto Rico, were the most severely affected.
Last fall marine biologists in Puerto Rico reported that 42 coral species on some reefs had bleached.
More recently, Miller says, colleagues there have seen coral colonies more than 800 years old die in a matter of weeks.
Miller says a colleague diving on a reef 10 miles (16 kilometers) from St. John was surprised to see die-offs caused by the disease occurring as far down as 90 feet (27 meters).
"This mortality is occurring on many different species there, the very slow-growing, major reef-building species," he said. "And that's what makes it so dramatic and so alarming."
Caroline Rogers is a U.S. Geological Survey (USGS) marine ecologist who has spent 22 years on St. John.
She said she recently dove near a 5-foot (1.5-meter) coral colony in Mayo Bay only to discover that "it is entirely dead now."
The sight was shocking, she says. "That coral has undoubtedly been there for hundreds of years, and it died over the course of several weeks."
"Corals live really close to their upper thermal limit, so small increases in temperature can have very devastating consequences," she said.
Rogers says the rapid die-off is particularly distressing, because some reef-building corals grow only the width of a dime in a year.
Biologists fear the die-offs will further degrade coral reefs in the Caribbean, a region that by one estimate has already lost 80 percent of its coral cover over the last three decades.
"You're down to the point where you really can't afford to lose that much [more]," NOAA's Eakin said.
Miller, the Park Service fisheries biologist, said that "the trickle-down effect of this [bleaching and die-off] is pretty devastating."
The loss of living coral reefs, which act as nurseries for countless fish and marine species, will adversely impact fisheries and biodiversity, Miller says.
"If the reefs go away, these fish populations are irrevocably changed."
"[The reefs'] state of health is not good," said Nancy Knowlton, a marine biology professor at the Scripps Institute of Oceanography at the University of California, San Diego.
"Reefs have collapsed catastrophically just in the three decades that I've been studying them in many places," she said.
Knowlton, who also directs the Center for Marine Biodiversity and Conservation at Scripps, says different factors negatively impact reefs in different places.
In addition to large-scale threats such as coral disease, reefs suffer localized threats such as pollution runoff and damage caused by dynamite, boat anchors, and recreational divers.
Miller and other resource managers say local impacts are highly destructive and that regulating them may offer the best hope for protecting the world's remaining coral reefs in the near future.
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