I was the neoprene queen – Jacques Cousteau had nothing on me. Suckered into a tight black wetsuit, weight-belt on, the air-tank octopus grazing the back of my head, and my knees buckling under the burden of it all, I waited. Perspiration streamed down my face and prickled the back of my neck as I swayed heavily in the sweltering sun, eager to make my ungainly splash into the cool Coral Sea, off the north-east coast of Australia.

Having been there two years previously, I knew what glories lay ahead in the hidden water world, where fish shimmered like jewels among gardens of coral in fantastic colours.

“The coral’s not as good this year, because of El Nino,” the dive master had warned me while we loaded up the boat.

But nothing could prepare me for what I encountered on that dive.

The coral bed had been entirely drained of colour. I’d expected to see an underwater carpet of vivid pinks, yellows and purples, but the seabed looked as though it had been replaced by a polystyrene model, the colour of concrete. What remnants of life remained were fast being gobbled by a mass of crown-of-thorns starfish. It was profoundly shocking, and I swam anxiously back and forth trying to locate some evidence of the rich biodiversity from my visit two years previously. I ran out of air before I could find any.

Coral reefs are on track to be the first of the world's ecosystems to be entirely wiped out by humans. Some scientists estimate that reefs will have disappeared as soon as 2050 – many calculate atmospheric carbon dioxide concentration is already above the levels that will condemn corals to extinction.

If so, the Anthropocene – the Age of Man – will not only be far less colourful place, it will also be far poorer in terms of fish diversity, islands and coastlines will be more prone to erosion, and millions of livelihoods will be threatened. Coral reefs support a quarter of marine life on Earth – they contribute to half of the GDP in many Caribbean countries, from creating sandy beaches to harbouring the fish people eat. And as the sea levels rise, they provide vital protection against storm surges and inundation.

Double whammy

I had experienced the aftermath of the 1998 mass bleaching event caused by high sea temperatures from El Nino – globally, all coral reefs were effected, with 90% of the Indian Ocean’s colourful reefs killed, and 16% of reefs worldwide effectively destroyed. The effects caused by El Nino weren't related to human activity, but they give a chilling indication of our potential impact on marine life.

Before 1998, coral bleaching had been rare, localised and reefs recovered. Since then, there have been at least six major bleaching events, with the most recent and severe in 2010, when a vast area of Southeast Asia and the Indian Ocean was hit by warm waters, with Indonesian corals being particularly hard hit. When I dive now, I am shocked if I see healthy coral on a reef rather than the other way around.

Scientists estimate that over the past two decades at least 20% of Australia's Great Barrier Reef – the world's largest – has been destroyed, and up to 90% of coral has been lost in the Indian Ocean from East Africa to island states of Maldives and Seychelles.

Human-induced global warming has a double whammy effect on corals: higher ocean temperatures force the marine organisms to expel the colourful zooxanthallae algae that live inside its skeleton and that provide most of its nutrients; and oceans become more acidic as a result of absorbing higher levels of atmospheric carbon dioxide, slowing down the rate at which corals can build their calcium carbonate skeletons. During a coral bleaching event, reefs lose so much zooxanthallae that they become white and experience massive die-offs.

As if that weren't enough, pollution, over-fishing and boat-anchor damage also destroys reefs. Reefs are far more likely to recover from a global warming event if they are located in a protected area than if they are exposed to further human-related damage.

Reef survival in coming years will depend largely on the next-generation corals – on how well coral larvae settle on rock, metamorphosise into feeding polyps, and establish new reefs after extensive damage.

Scientists at the Smithsonian Tropical Research Institute in Panama have been growing coral polyps in different water temperatures and acid levels to see how it affects polyp growth.

"The biggest surprise was that neither temperature alone, nor acidification alone had a big effect on the growth or survival rate of the coral, even though the warming prompted zooxanthallae expulsion as expected," says researcher Aaron O'Dea. "Once we combined this moderate warming and acidification, though, we saw significant impacts: growth rate plummeted to almost half of the rate seen under the other conditions, and they were twice as likely to die."

The findings provide hope for one proposed conservation strategy: reducing ocean acidity by adding bicarbonates or lime to the water. Trials show that this could succeed, but we'd need to add around 10 cubic kilometres of lime (around 9,000 million tonnes) to the oceans every year to offset the effects of our carbon emissions. At the moment, we produce around 300 million tonnes of lime annually, mainly for the concrete industry, so the problem quickly becomes apparent.

Other scientists have suggested ways of reducing temperatures in the shallow waters that reefs grow, including erecting giant canopies to shade them.

Replanting efforts

A more practical method might be to garden the reefs in a similar way to how we tend our agricultural plots on land. To that end, scientists are breeding corals in special facilities that simulate different growing conditions, looking for varieties that are tolerant to higher temperatures, ultraviolet light (a problem since we created a hole in the ozone layer), and acidity, for example. One way of doing this is by exchanging the coral's algae species for more robust types.

The next stage is to plant the corals in the sea. Scientists around the world have created all manner of artificial reef for transplantation, from concrete balls to steel cages. One interesting design incorporates an electric current, which helps stimulate coral growth. I saw one of these on Vabbinfaru island in the Maldives, where researchers had submerged a huge steel cage called the Lotus on the sea floor. The 12-metre structure, weighing around 2 tonnes, is connected to long cable which supplies a low-level electric current. The electricity triggers a chemical reaction, which draws calcium carbonate out of solution in the water and it gets deposited on the cage structure .

Corals seem to find this irresistible because they use the same material to grow their protective skeletons, and the Lotus has been so thoroughly colonised by coral that it is difficult now to make out the steel shape beneath all the elaborate shapes and colour.

The El Nino Pacific-warming phenomenon of 1998 killed 98% of the reef around Vabbinfaru, so the scientists there have been able to compare the growth rates for corals grafted on to concrete structures on "desert" patches of seafloor, and those stuck on to the Lotus. Abdul Azeez, who led the Vabbinfaru project, said coral growth on the structure is up to five times as fast as that elsewhere.

The electric reef may also make the corals fitter and better able to withstand warming events, perhaps because the creatures waste less energy on making their skeletons. A smaller prototype device was in place during the 1998 warming event and more than 80% of its corals survived, compared to just 2% elsewhere on the reef.

The original designer of the Lotus, Wolf Hilbertz, who died in 2007, believed that his structures could be submerged across the world to repopulate reefs and protect shorelines. In reality, the cost and effort involved make it impossible to do except on a small scale. However, it is a useful technique for tourist resorts and to help small areas of reefs recover that have been hit by temporary damage, such as an oil spill or boat impact.

On a global scale, though, the prognosis for reefs and those that depend on these vital, protective fish nurseries, is grim. The only serious way to protect this hugely productive marine ecosystem is to slash our carbon dioxide emissions – and I'm not the only one who thinks we won't achieve this in time.

"By 2050, we may still have corals, and things we'll call 'reefs', but they will be massive limestone structures that were built in the past, with tiny patches of living coral struggling to survive on them,” says coral ecologist Peter Sale. By 2100, he thinks there will be no calcium carbonate reefs visible.

"We're talking here about killing off a whole integrated community of organisms that as been with us throughout our existence and long before there were people of any type on Earth,” says Sale.

The world will go on without reefs, he adds, but it is going to be very much inferior to the planet we have now.

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