CORAL samples from Heron Island have found the Great Barrier Reef may be being eaten away from within by microscopic organisms.
Biologists from the ARC Centre of Excellence for Coral Reef Studies and the University of Queensland have found evidence that algae and other organisms that reside within dead coral will erode the skeleton at an increasing rate, as oceans continue to warm with climate change.
Spokeswoman Catalina Reyes said the phenomenon, combined with a slower growth of coral reefs because of ocean acidification, may make reefs more vulnerable to storms and cyclones.
"So fish, turtles, sharks, lobsters and other reef organisms may lose their homes, threatening reef biodiversity and the livelihoods of tens of millions of people," Ms Reyes said.
She said corals used calcium carbonate, or limestone, to build the reef structure.
As they accumulated carbonate and extended their skeleton, the old, dead parts were eroded by waves, currents, fishes, sponges and by tiny plants that lived inside the reef.
"There is a fine balance between accumulating and losing carbonate, and healthy reefs are the ones that gain more than they lose," Ms Reyes says.
"Anything that disrupts this balance puts coral reefs in danger."
Associate Professor Sophie Dove said coral reefs were already threatened by ocean acidification, caused by human carbon emissions dissolving into the oceans, because this process reduced the amount of carbonate in the seawater, causing the corals to build the reef at a slower pace.
But in the latest study, researchers found the lack of carbonate to build coral reefs wasn't the only challenge these ecosystems faced.
"Our research shows that when seawater is both acidic and warm - which is predicted to happen under future climate scenarios - coral reefs could be made more fragile by microborers, such as algae, blue-green algae and fungi that inhabit reefs and bore tiny holes in it that undermine the strength of the coral skeleton."
Ms Reyes said the most abundant type of algae identified in the study was also the world's most common photosynthetic microborer, capturing sunlight to fuel its activities.
It inhabits 85% of the world's corals and has an extraordinary ability to cope with low light conditions, allowing it to penetrate deep into coral skeletons.