On SS april 2006 David Kline then at STRI blamed it on Sewage see quote 
Less than 10% of the sewage in Central America and the Caribbean receives any sewage treatment at all, so all these chemicals and compounds are going directly onto the reefs, and when I tested a large suite of stressors to look at what was affecting the corals directly, what we found out is that the normal players - nitrogen and phosphate - weren't causing damage directly to the corals, and an unexpected result was that simple sugars or organic carbon was causing high levels of coral mortality; up to 90% mortality in my experiments. 
We wanted to figure out why these simple sugars are such a problem, and when we did further research what we found is that corals have bacterial communities that are part of their normal, healthy, symbiotic communities, but when simple sugars are added at too high a levels, these same bacteria can grow out of control and cause mortality and disease. This problem is even worse because pollutants such as nitrogen and phosphorus stimulate algal growth, and many reefs in the Caribbean and throughout the world actually are going through a transition from being dominated by corals to being dominated by algae, and the first product of photosynthesis is glucose or a simple sugar. So when these algae start to grow out of control they release simple sugars which affect the corals which can lead to further coral death. So in the Caribbean we're in this kind of scary positive feedback loop where, with over-fishing and pollutants increasing the amount of algae, as well as inputs of organic carbon from land runoff and sewage, corals are being overgrown by the bacteria that are normally beneficial, leaving the high level of disease and mortality.
- Science News: Sugars and Bacterial Growth Kill off Coral Reefs
Coral reef death has been attributed to a number of factors including declining water quality ... said David Kline, PhD, a post-doctoral researcher at STRI. ..

- Eric's article sewage, causes acidification not CO2 Kline is only 33 now working in Oz on GBReef was stri
science, health & technology
Also in this section :
Future reefs: what climate change and pollution are doing to coral
WHO calls for more mental health investment
What climate change and pollution are doing to the coral reefs
by Eric Jackson 
David I. Kline has been associated with the Smithsonian Tropical Research Institute (STRI) for the past decade or so, both when he was getting his PhD at Scripps and in various post-doctoral research projects. Now he's with the the University of Queensland, that place in Brisbane, Australia that has the Great Barrier Reef for its marine biology lab and he back at STRI, working with a grant from Rio Tinto aluminum and various others to find out what it and what is not damaging the world's coral reefs. Reef damage is particularly severe in the Caribbean Sea, and STRI's lab in Bocas del Toro is particularly suited to study the phenomenon.

Kline spoke at the Tuesday afternoon science lecture series on September 5, to a crowd composed primarily of scientists, down in number a bit from a few weeks ago when so many students from universities around the northern industrialized countries were studying at STRI between school years.

The message was ominous: 80 percent of the coral coverage in the Caribbean Sea has been lost over the past 30 years. There are some likely suspicions about why that is. In the past decade, there has been a 20 percent increase in population along the coastlines in the Caribbean, and less than 10 percent of the sewage that all these people generate is treated. Although certain political and religious denominations make it an article of faith to deny it, the planet is warming and that's causing complex changes in the enviroment in which corals live as well as everywhere else.

Corals are holobionts, complex ecological structures in which colonies of single cell organisms of different species cohabit. The rock that one considers "coral" is the hard carbonate shell laid down by previous generations of coral animals, which in their living state are infested with algae both in the tissues of the polyps and the cystalline skeletons. These formations are also inhabited by fungi, and infected by bacteria.

"In a healthy coral, bacteria are maintained in a homeostasis," Kline explained, but in experiments in which bacteria cultured from those taken from the mucus tissues healthy corals are introduced, the corals have died. It's not the bacteria per se, but an environmental stress that allows the normal balance to get out of whack that becomes deadly, so Kline and his research partners invented lab equipment that allowed them to dose 400 different coral samples with 40 different chemicals, ranging from the usual suspect phosphates and nitrates through asphalt, sewage and its various components, sediments typically created by erosion and various of the compounds found in storm runoff.

Phosphates and nitrates, it turned out, caused none of the mortality. Sugars, however --- glucose, lactose, dextrose and so on --- were deadly, because of the carbon. "Carbon loading was disupting the stasis between bacteria and coral," Kline concluded. "Organic carbon causes mortality by increasing bacteria growth."

Further experiments have suggested that "something released by the algae is what promotes the bacteria growth" in a process that appears to have "positive feedback loop" and "spells really bad news for Caribbean corals." It seems, he added, that the branching corals are worse affected than the massive ones.

One of those branching corals, Acropora, has been particularly hard-hit, and so has been the subject of special studies. The immediate culprit is a malady known as white band disease, where an infection by an unknown pathogen marches up the coral in a white band, inexorably killing it. Acropora "used to be the dominant shallow water corals, and now they're all gone." Actually, some do survive, enough to allow scientists to study white band disease.

And where do some of these corals survive? In distinct areas off of Isla Colon and Isla Bastamentos in the Bocas Archipelago. Kline and his colleagues are looking at ecological and genetic factors, trying to figure out why white band disease is more contagious among the Isla Colon corals than the ones off of Isla Bastamentos.

There seems to be an association of white band disease with the Rikettsia bacteria, but Kline thinks that this is not the only microbe at work. He thinks that water quality may be a major factor, and the specific quality that he suspects is temperature. "There may be a link to global warming" in the massive Acropora die-off, he opines. But he doesn't really know --- that's why he's here doing more experiments, that might confirm certain hunches or send him off looking in other directions.

So why is an aluminum company funding this research? Well, it takes a lot of energy to extract alumnium from bauxite and a lot of carbon dioxide is emitted while generating that energy. Rio Tinto is Australia's biggest creator of C02 emissions, and the possibility that this might change seawater chemistry and affect the corals of the Great Barrier Reef is something that the company would like to know about sooner rather than later for both practical and public relations reasons. That's why it's funding the Future Reefs Project at the University of Queensland.

The world's coral reefs are all in danger, Kline said, "Public enemy number one is global warming. Public enemy number two is ocean acidification." It's the changes in water acidity, not the addition of carbon, that are most threatening to corals from C02 emissions. When PH goes up, the corals' ability to make calcium carbonate skeletons goes down, and that trend gets even worse as the temperature rises.

However, different corals and algae react differently to these stimuli, so Kline is predicting not so much that corals will disappear, but that there will be great ecological shifts in coral structures with certain species favored over others.

Some corals may survive acidification caused by rising CO2 levels
(3/29/2007) Several studies have shown that increased atmospheric carbon dioxide levels are acidifying the world's oceans. This is significant for coral reefs because acidification strips carbonate ions from seawater, making it more difficult for corals to build the calcium carbonate skeletons that serve as their structural basis. Research has shown that many species of coral, as well as other marine microorganisms, fare quite poorly under the increasingly acidic conditions forecast by some models. However, the news may not be bad for all types of corals. A study published in the March 30 issue of the journal Science, suggests that some corals may weather acidification better than others. 

coral is a net producer of CO2
Some coral may be resistant to acidification, reefs still doomed
A Fine Discovery Some coral may be resistant to acidification, reefs still doomed The world's oceans are on track to be more acidic by 2100 than they've been for 20 million years, thanks to our fiendish friend carbon dioxide. But research by Israeli scientists shows that the coral polyps living in underwater 
30 Mar 2007 Daily Grist