Half of the two billion corals lived across Australia’s Great Barrier Reef in 2015 are believed to have died in the three years since then, according to a new study.

A major heatwave caused mass coral bleaching in 2016, wiping out 30 per cent of its shallow-water corals in the nine months between March and November that year.

Since then, smaller bleaching events have continued and the corals have continued to die out. In the summer of 2017, unusually warm waters hit the reef again, triggering further bleaching in areas which had survived the previous year’s heatwave.

The Great Barrier Reef harbours extensive areas of deep coral reefs which are much more difficult to study and were previously considered a refuge from higher water temperatures near the surface.

But the new research demonstrates the 2016 mass bleaching of the Great Barrier Reef was not restricted to shallow depths, but also affected deep reefs more substantially than scientists had estimated.

Published today in the journal Nature Communications, the study provides evidence both shallow and deep reefs are under threat from mass bleaching caused by warming waters.

Lead author of the research, Dr Pedro Frade, from the Centre of Marine Sciences at the University of Algarve, said the team was astounded to find bleached coral colonies down to depths of 131 feet (40m) beneath the ocean’s surface.

“It was a shock to see that the impacts extended to these dimly lit reefs, as we were hoping their depth may have provided protection from this devastating event,” he said.

The team also used remotely operated vehicles to study corals 328 feet (100m) beneath the waves.

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Then they conducted surveys during the height of 2016’s bleaching across a number of sites on the northern Great Barrier Reef. Overall, they recorded the major bleaching or death of almost a quarter of corals at the deep sampling points, while confirming previous reports of impacts on close to half the shallower corals.

Impacts on the deep reefs were severe. They found 40 per cent of coral was bleached and six per cent dead at 40 metres. This was a lesser impact than at shallower depths where 60–69 per cent of coral was bleached and 8–12 per cent dead at 5–25 metres.

The authors reported they had observed the upwelling of cold water had given deeper reefs some protection in the early summer, but this cooling effect was lost by late summer when upwelling stopped.

“Unfortunately, this research further stresses the vulnerability of the Great Barrier Reef,” said Dr Ove Hoegh-Guldberg from The University of Queensland, where the study was conducted. “We already established that the refuge role of deep reefs is generally restricted by the limited overlap in species with the shallow reef. However, this adds an extra limitation by demonstrating that the deep reefs themselves are also impacted by higher water temperatures.”

Coral bleaching is linked to global warming and occurs when stresses from higher water temperatures cause the corals to expel symbiotic photosynthetic algae, draining them of all colour and eventually causing them to die.

Bleaching is becoming an increasingly common phenomenon, spelling disaster for coral reefs across the world.

Earlier this year a study also published in Nature found the Great Barrier Reef is unlikely to recover from the devastation caused by the 2016 heatwave.