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A two-year expedition across the Pacific Ocean has revealed that the microbes present on coral reefs there may be as varied as the microbiome of the rest of the planet’s ecosystems combined. This could mean we have vastly underestimated the total microbial diversity on Earth.

Coral reefs make up less than 1 per cent of the ocean, yet are home to nearly a third of marine species of animals and plants. An expedition launched in 2016 and led by at the University of Perpignan in France visited 99 reefs across the Pacific Ocean. At each reef, Planes and his colleagues collected seawater and took samples of three species of coral and two species of fish.

They sequenced a key section of DNA from bacteria and archaea present in the samples. Within the roughly 3 billion sequences that resulted, they found more than half a million unique ones, indicating vast microbial diversity. Samples from different parts of the ocean also had distinct microbiomes.

“The diversity of the corals is reflected in the diversity of the microbiome,” says at Sorbonne University in France.

Extrapolating those results to the microbiomes of hundreds of other coral species and thousands of fish species in Pacific reefs, the researchers say the total microbial diversity present on all those reefs would be nearly six times higher. They say this may be greater than some estimates of the microbial biodiversity of the entire planet.

Such microbial diversity plays an essential role in coral reef ecosystems. Some corals have symbiotic relationships with bacterial species, for instance. Other microbes accelerate nutrient cycling or protect against pathogens.

“The microbes really do run these ecosystems because they’re involved in so many different kinds of processes,” says at the University of California, Santa Barbara.

However, Planes says it is unclear how the microbiome is affected by factors driving the loss of macrodiversity in reefs, such as rising temperatures from climate change, ocean acidification and overfishing.

“There’s no direct link now between the decline of coral reef and changes in the microbiome,” he says. “That’s mainly because we know so little about the microbiome.”