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A major longterm study has shown that 30% of the Great Barrier Reef coral died in a catastrophic nine-month marine heatwave in 2016.

The report, published in the journal Nature, shows that the underwater heatwave that bleached massive sections of the Reef in 2016 was so severe it immediately ‘cooked’ some corals in the northern region.

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

Professor Terry Hughes from James Cook University (JCU), the Director of the ARC Centre of Excellence for Coral Reef Studies, who led the research team, explained “the mix of species in the future will be radically different from two years ago ... and that transition is already well underway."

Professor Hughes told Guardian Australia the 2016 marine heatwave had been far more harmful than historical bleaching events, where an estimated 5% to 10% of corals died.

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.

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.

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", adding “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% or more in the worst-affected portion of the reef."

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

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% 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".

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.

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.

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, advising “we showed that 29% of it exceeded the threshold for collapse in the north. So the data we have for the Great Barrier Reef meets those criteria.”

Report co-author Professor Andrew Baird said the coral die-off had caused “radical changes in the mix of coral species on hundreds of individual reefs”.

The researchers estimate half of the corals in shallow-water habitats in the northern Great Barrier Reef have been lost.

Professor Baird added “the Great Barrier Reef is certainly threatened by climate change, but it is not doomed if we deal very quickly with greenhouse gas emissions. Our study shows that coral reefs are already shifting radically in response to unprecedented heatwaves.” 

Images: Coral bleaching on the Great Barrier Reef.

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