Vanishing secrets of the Barrier Reef The survey could not be more timely. In an paper published in the Proceedings of the National Academy of Sciences last month, scientists wrote that more than 50 per cent of the reef's coral has been wiped out over the past 30 years, and warned another half of the remainder could have gone by 2022 - meaning the reef will have shrunk to less than a third of its size in half a century. While the Great Barrier Reef's shallows are familiar to scientists and the estimated 1.5 million divers and snorkellers who visit every year, the vast majority of the reef lies deeper than 30 metres, putting it out of range of all but professional deep-sea divers and submarines. As such, very little is known about life on the deep reef and it is this hidden world that researchers from the Catlin Seaview Survey, the new Australian-led coral reef research project hopes to unveil over the coming months. Down at 30 metres, Catlin researchers will visit 20 separate sub-reefs that make up a section of the Great Barrier, using aquatic scooters to propel them through the coral jungle and a high-resolution panoramic camera to take 50,000 images, providing the most detailed picture of the reef ever produced. Below that, remote-controlled robot submarines will plunge to 100 metres to provide the first clear views of life in the reef's "twilight zone," where trial dives have unveiled a host of new species and ecosystems quite different to those just a few metres above. Dozens of specimens have been handed over to taxonomists for investigation, including the branched coral Acropora tenella which has been identified for the first time in Australian waters. By returning to the same spots year after year, and expanding the project to other reefs around the world, the scientists hope to understand how climate change and other threats are affecting the millions of different corals and marine species that live on them. For Ove Hoegh-Guldberg, the project's chief scientist, who began snorkelling on the reef as a 10-year-old in 1969, the survey offers the first chance to observe life at such a depth. "Over 90 per cent [of the Great Barrier Reef] was pretty much unexplored, which is an amazing fact," he says. Now with these deep-diving robots and some of the technology we are developing, the potential is there for unlocking those secrets. In a pilot dive last year we discovered four new species of coral for the Australian region and a new pygmy seahorse (Hippocampus denise) and that was just in six days. It is like going to the Amazon rainforest; there is a lot that is going to be discovered. During the first stage of the project, which began in September, researchers visited some of the Great Barrier Reef's most remote spots which lie up to 250km from the mainland, far away from the tourist dive sites. Prof Hoegh-Guldberg's team found themselves surrounded by fishes such as groupers - giant, pouting animals measuring more than a metre in length - as well as bright-red coral trout and several shark species which have been driven away from the coastline by tourism. Such is the diversity of life on the reefs, and the unchartered nature of their deeper waters, virtually every dive in the initial two-week phase turned up a new species, or at least a species new to Australian waters. But for all the excitement of new finds, there is the growing fear among researchers that their photographic records may soon be all that remain of the species they discover. Dr Pim Bongaerts, head of the deep-reef research team, says: "That does go into your head when you are photographing and filming the reefs. Pretty much every time we go out we find either new species or new species records - species we did not know Australia had. But I always have in my mind what my professors told me: that when they were my age and dived these reefs 20 or 30 years ago, they looked completely different. That is a pretty scary thought - that when you go down there you might be the first person to see these things, but also one of the last. The influx of Crown of Thorns starfish is only the latest threat to life on the reef. Climate change has led to rising sea temperatures (up by 0.5C in 25 years in parts of the reef) which in turn has triggered "bleaching"," where the sea becomes too warm for coral to survive; this can wipe out entire colonies. Burning of fossil fuels is also having a dramatic impact, with carbon dioxide from the atmosphere dissolving into the ocean and making the water more acidic. This limits the ability of corals to grow limestone skeletons. Rising ocean acidity has even been linked to "mad fish syndrome," where fish appear to mistake predators for members of their shoal. Experts believe the drop in pH level is interfering with their sense of smell, making it hard to distinguish one fish from another. The combined threats pose a bleak future for the Great Barrier Reef, and the predicted increase in extreme weather means the damage to ecosystems such as the reef is forecast to become more severe. Hoegh-Guldberg says: "When you look at a coral reef, there are over a million species estimated to live in there and we don't know half of them. We know they are out there because we keep discovering them - every year there are multiple species discovered for the first time. But as reefs disappear we get to what we call the 'Joni Mitchell moment," where you don't know what you've got until it's gone. At this rate we won't even have a Joni Mitchell moment for some of these species, because they will remain undiscovered and just disappear. Mapping the Great Barrier Reef: picture special