The Great Barrier Reef has a microbiome too

Scientists have documented thousands of different microbes contributing to healthy reef communities as a step to using them to measure and monitor changes. 

More than 800,000 microbial genomes, identifying over 500 new bacterial species and over 300,000 distinct viruses have been found in the waters of the Great Barrier Reef. 

The invisible population was documented using DNA found in samples of seawater from 48 reefs by a team led by The University of Queensland and the Australian Institute of Marine Science (AIMS).

UQ microbiologist Professor Philip Hugenholtz said the group has created the Great Barrier Reef Microbial Genomes Database which is available to all reef researchers.

“Now we can start to explore what makes a healthy reef microbiome and how these invisible communities respond to changes on the Great Barrier Reef such as bleaching, storms, sediment, fishing and other stresses." 

-Professor Hugenholtz

AIMS senior researcher Dr Yun Kit Yeoh said advances in DNA sequencing over the past 20 years had allowed scientists to document, understand and start to modify the communities of microbes that contribute to plant and human health. 

“The latest advances have now enabled us to study microbiomes across a massive ecosystem, the Great Barrier Reef,” Dr Yeoh said.  

“These microbes are important. Microalgae produce most of the oxygen we breathe and underpin food chains in the open oceans.

“They are eaten by krill and other zooplankton which are then consumed by other animals from the smallest coral polyps to the largest whales. But, until now, we couldn’t see these communities.

“This study will complement long-term monitoring of the Great Barrier Reef, which has been conducted by AIMS for over 40 years.”

Dr Steven Robbins, team lead at UQ, said collecting and sequencing microbial DNA in the oceans was challenging. 

“The ocean likes to mix everything up. A single drop of water can contain thousands of different but often very closely related microbes – they’re really complex communities,” Dr Robbins said. 

“And many ocean microbes are adapted to low-nutrient conditions typical of ocean ecosystems, which leads to them having low levels of G and C, 2 of the 4 bases that form the double helix of DNA. 

“It’s the combination of that low-GC and the complexity of the communities that has hindered this kind of research. 

“In this study, we used new ‘long-read’ sequencing technologies that bypass issues of complexity and low-GC to make it much easier to assemble the jigsaw puzzle of each microbial genome. 

“What was a puzzle with tens of thousands of pieces becomes a simple puzzle, with far fewer pieces for the average microbial genome.”

Highlights of the team’s discoveries include:

• Identifying 5,283 different bacterial and archaeal genomes, representing 876 distinct species of which two-thirds are new to public databases and available to study for the first time.
• Identifying 362,802 different kinds of viruses including Crassvirales, a virus first found in human guts in 2014. It was originally thought to be a potential indicator of the presence of human or animal waste, but as this study shows, it is also found in the open ocean waters of the Reef. 
• Recovery of complete chromosomes from Bathycoccus and Ostreococcus directly from seawater, 2 of the most abundant microalgae on the Reef.

Read the research in Nature. 

Collaboration and acknowledgements