An underwater heatwave that bleached massive sections of the Great Barrier Reef in 2016 was so severe it immediately "cooked" some corals in the northern region, scientists say following the results of a major long-term study.

Key points: Study looked at impact of marine heatwave on the Great Barrier Reef two years ago

Study looked at impact of marine heatwave on the Great Barrier Reef two years ago Scientists already had good estimates of how much coral died in immediate aftermath

Scientists already had good estimates of how much coral died in immediate aftermath Research shows how rising temperatures have transformed ecology of reef

The study also revealed how the bleaching event transformed the makeup of the reef, and removed important habitats for fish and other marine animals.

"The mix of species in the future will be radically different from two years ago," said Professor Terry Hughes from James Cook University (JCU), who led the research published in the journal Nature.

"And that transition is already well underway."

The findings come as a scientific advisory body to the United Nations considers what parts of the natural world are on the verge of an environmental failure.

The JCU researchers said their work showed climate change was threatening the Great Barrier Reef with ecological collapse.

Reef changed 'forever'

Professor Hughes and his colleagues conducted aerial surveys of the entire reef, as well as detailed in-water surveys, at 63 locations along its 2,300-kilometre length, and combined it with data from satellite monitoring.

They did that early in 2016, just after the bleaching, and then repeated it nine months later.

Sorry, this video has expired Vision shows parts of the Great Barrier Reef after the heatwave

Scientists already had good estimates of how much coral died in the immediate aftermath of the heatwave event, but the new results show how rising temperatures have radically transformed the ecology of the reef.

Professor Hughes said the new results showed which coral species were "winners" and which species were "losers".

"There's a small number of species that are very robust to heat stress and they've survived quite well. On the other hand, the so-called losers [had] mortality rates of 90 per cent or more in the worst-affected portion of the reef," he said.

The species that were most affected by the bleaching were branching staghorn coral, which grow in complex spiky branches, as well as plate corals.

Corals respond differently to changing water temperatures; some are considered "winners" and others as "losers". ( ARC Centre of Excellence for Coral Reef Studies: Mia Hoogenboom )

"Branching corals provide the habitat — the nooks and crannies — that fish and other creatures rely on," Professor Hughes added.

In heavily bleached areas, reefs shifted from being dominated by these corals, to being dominated by slower-growing corals, with simpler shapes.

This transition happened on 29 per cent of the 3,863 individual reefs that make up the Great Barrier Reef, the researchers found.

They concluded the 2016 bleaching event was the beginning of a long-term transformation, which has altered the Great Barrier Reef "forever".

'They didn't die of starvation … They cooked'

The researchers were surprised not only by the magnitude of the mortality across different species, but also by the way the corals died.

Underwater heatwaves are thought to kill coral by stressing them, causing the coral polyps to expel the symbiotic algae that lives inside them.

That algae gives corals their brilliant colour, as well as providing most of their energy. So when the algae is expelled, the coral turns white, and must either regain its algae, or it slowly starves.

That happened, but in addition "many millions of coral" in the northern third of the reef were killed much more directly by the heat, Professor Hughes explained.

The colour morphs of Acropora millepora as the species responds to a bleaching event. ( ARC Centre of Excellence for Coral Reef Studies: Gergely Torda )

"We were very surprised to see a quarter of the corals die in just two to three weeks during the middle of the heatwave in March 2016," he said.

"They didn't die slowly of starvation, they died directly of heat stress. They cooked because the temperatures were so extreme."

Selina Ward, a coral reef biologist at the University of Queensland who wasn't involved in Professor Hughes's study, said that confirmed what she and others had seen anecdotally.

"I had colleagues up at Lizard Island as the bleaching was unfolding and they said to me at the time that it was awful being in the water, that it was very warm and very still, but also they got out of the water and they smelled bad," Dr Ward said.

"They were covered in goo and had to hose themselves off and that makes sense now because it was probably coral tissue that was sloughing off."

Underwater heatwaves on the rise, experts say

The Federal Government's Great Barrier Reef Marine Park Authority concluded the bleaching in 2016 was caused by a record-breaking marine heatwave, caused by a combination of climate change and the El Nino weather cycle.

Water on the reef was more than a 1 degree Celsius warmer than the average for that time of year, and for much of it there was little cloud cover that would offer corals respite from the heat stress.

"We're anticipating more of these events as global warming continues," Professor Hughes said. "We're into a new system.

"The Great Barrier Reef of today, or certainly in 10 or 20 years' time from now, will be a very different system from the reef that we've been studying for the last 30 or 40 years."

Sarah Perkins-Kirkpatrick from the Climate Change Research Centre at the University of New South Wales recently published work showing underwater heatwaves have increased in both their duration and frequency over the past century, with a sudden uptick since the 1980s.

As a result, on average around the globe, there are 54 per cent more days each year that are subject to a marine heatwave.

The main areas of coral bleaching in 2016 and 2017. ( Supplied: ARC Centre for Excellence for Coral Reef Studies )

"The sorts of events that cause coral bleaching will occur more often in the future," Dr Perkins-Kirkpatrick said.

She added she was shocked by the results of Professor Hughes's paper.

"I've got to say, it's catastrophic. Seeing all the news articles and seeing it evolve, it looked catastrophic," she said.

"But there might have been a glimmer of hope that it wasn't as bad or might recover faster than we thought. But this paper made the reality very present. The bleaching will forever change the Barrier Reef."

Reef threatened with collapse

The International Union for Conservation of Nature (IUCN) is in the process of developing a Red List of Ecosystems, which mirrors their influential Red List of Threatened Species.

Professor Hughes said his new paper should allow the Great Barrier Reef to be assessed in that framework.

The IUCN will categorise ecosystems that are threatened with collapse as either critically endangered, endangered, or vulnerable.

Professor Hughes said the Great Barrier Reef as a whole is likely in the endangered category.

"We showed that 29 per cent of it exceeded the threshold for collapse in the north. So the data we have for the Great Barrier Reef meets those criteria," he said. "It's certainly threatened."

Dr Ward agreed.

"We're not going to lose it tomorrow, but we're at the point where if we don't make some really dramatic changes to our emissions, then we are at risk. We're at risk of having a barely recognisable reef."