Scientists map Great Barrier Reef's vast microbiome, identifying 360,000 viruses and 500 new bacterial species

More than a decade after the human microbiome was comprehensively mapped, scientists have now identified the vast communities of microbes that make up the Great Barrier Reef.

Analysing DNA from seawater samples of 48 reefs, researchers have mapped the microbiome of the Great Barrier Reef, documenting more than 360,000 distinct viruses as well as more than 500 new bacterial species not previously known to science.

The research, published in the journal Nature, was led by scientists at the University of Queensland and the Australian Institute of Marine Science (AIMS).

Dr Yun Kit Yeoh, a senior research scientist at AIMS and a senior author of the paper, described microorganisms as a “very important part of the reef ecosystem” that underpinned marine food chains.

“Many of the microbes on the reef can photosynthesise … like plants, they can take light energy [and] can convert carbon dioxide into oxygen.

“They are eaten by krill and other zooplankton which are then consumed by other animals.

“We haven’t been able to really study a lot of them except for a select few that we can grow properly in the lab on petri dishes.”

But recent technological advances have allowed scientists to sequence DNA taken from the environment, giving a fuller picture of these microscopic communities.

The field – known as metagenomics – is akin to solving thousands of jigsaw puzzles simultaneously; a single drop of seawater can contain the DNA of thousands of different microbes.

“We wouldn’t have been able to do this, say, 10 years ago, but fortunately computing power keeps increasing at an exponential rate,” said Prof Philip Hugenholtz, a microbiologist at the University of Queensland and a senior author on the paper.

The research, which first began more than five years ago, identified 808,585 viral genomes belonging to what the researchers estimate to be 362,802 different viruses.

The analysis also identified 5,283 bacterial and archaeal genomes representing 876 distinct species – 584 of which have never been documented before.

Hugenholtz said those large figures were expected. “This is just how huge the microbial world is,” he said. “We know that everywhere we sequence … there’s always new viruses turning up.

“I was a little bit surprised that we found over 500 new bacterial species.

“The human gut and the marine ecosystem I would say are the two most sequenced ecosystems on the planet.”

The discovery raises the question as to whether the species were unique to the Great Barrier Reef, or were yet to be discovered in other reef ecosystems, Hugenholtz added.

The researchers believe the mapped microbiome could be used as a reef monitoring tool. “We can now use it to start exploring what makes a healthy reef system,” Yeoh said. “Then we can examine how these microbes respond to, say, changes … associated with climate change, with heat stress, bleaching, human activity, or other environmental perturbations.

“Microbial communities can tell you an awful lot. Often you’ll see changes in the microbial populations before you see more visible changes [on the reef].”

The microbes in a particular marine area can indicate whether fishing has occurred in a no-take zone, for example. They can also indicate whether heavy metal contamination has occurred.

“It’s quite expensive to get a readout of heavy metals – it’s cheaper to get a readout of the changes that they have on microbial communities,” Hugenholtz said.

The researchers used long-read sequencing technology, which enables large strands of DNA to be read at one time, without the need to break them into smaller fragments.

Hugenholtz likens it to doing jigsaw puzzles with bigger pieces, “which means you’ll be able to put those jigsaw puzzles back together more easily”.