The damage is a harbinger of what a warming future might hold for a wealth of tropical reef ecosystems, says lead study author Terry Hughes, director of the coral-reef centre at James Cook University in Townsville, Australia.
A second heatwave during 2017 also affected the health of the reefs, with nearly half the coral in shallow-water in the northern two-thirds of the Great Barrier Reef killed off, according to the study. In particular, elaborate branching corals that provide key fish habitat are being replaced by bulky, less intricate "dome-shaped" corals, Hughes said.
Australia's Great Barrier Reef suffered a "catastrophic die-off" of coral during an extended heatwave in 2016, threatening a broader range of reef life than previously feared, a new report has revealed.
The composition of coral assemblages on hundreds of individual reefs changed radically within just a few months of the heatwave.
Researchers call for more urgent action to prevent the Great Barrier Reef's decline as a result of climate change.
The sea is also home to tens of thousands of species, like turtles, snakes and whales. It's here and now. Fast-growing staghorn and tabular corals suffered the greatest in the demise, an adjustment in diversity that may reshape how the reef functions ecologically.
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The north-east coast experienced the heatwave, also known as a prolonged ocean warming event, in 2016 and according to a report by Nature Research triggered an "unprecedented loss of coral". "It will only be possible if carbon emissions are rapidly reduced", he said. Record high temperatures in 2016 were followed by another bleaching event previous year. "The bleaching will forever change the Barrier Reef".
The study warned that reef collapses could be a sign of things to come. But in the 2016 heat wave, 25 percent of the corals that died succumbed as a result of the heat itself.
Two findings surprised and unnerved the researchers. Generally, the higher the DHW, the higher the expected coral death.
The underwater heatwave eliminated a huge number of different species of coral during a process which expelled algae after the polyps were stressed.
Unfortunately, unusual low water temperatures, due to a change in Kuroshio current, have destroyed some of the corals in Japan, already affected by coral bleaching.
"One of the concerns around the coral reef world is that the gap between pairs of bleaching events is shrinking", Hughes said. Without their algal partners, the corals starve and die. "Before the study we didn't know where those tipping points were".
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Fish species are adjusting to the mass mortality of corals - some better than others.
"Biodiversity will likely be less, coral cover will likely be less", Hughes said.
Extreme temperatures, increased UV rays, disease, chemicals, silinity and exposure to air and rain at extreme low tides can cause bleached coral.
The study found that 29 percent of the 3,863 reefs comprising the world's largest reef system lost two-thirds or more of their corals, transforming the ability of these reefs to sustain full ecological functioning.
Still, 1 billion corals have survived.
The paper says extreme weather events, caused by man-made climate change, are "rapidly emerging as major contemporary threats to nearly all ecosystems", and suggests that while not all corals will be killed off, the shape and variety will be affected.
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"We're very concerned that the return period between events is now much shorter than the recovery time required", he told BBC News.