Great Barrier Reef Microbiome Survey Identifies Hundreds of New Species

Discovery of New Microbial Species

The study, led by the University of Queensland (UQ) and the Australian Institute of Marine Science (AIMS), identified 5,283 different bacterial and archaeal genomes. These genomes represent 876 distinct species, with 584 of them never having been documented before—approximately two-thirds of the total. Prof. Philip Hugenholtz, a UQ microbiologist and senior author of the study, noted that he was a little bit surprised to find over 500 new bacterial species, though he emphasized that the microbial world is vast and new viruses frequently appear during sequencing.

In addition to bacteria, the team identified 808,585 viral genomes, which they estimate represent 362,802 different viruses. Among these discoveries were Crassvirales, a virus that infects bacteria and was first discovered in human guts in 2014. The researchers also recovered complete chromosomes directly from seawater for the two most abundant microalgae on the reef: Ostreococcus and Bathycoccus.

Technological Advances in Metagenomics

The research relied on “long-read” sequencing technology and metagenomics, a field Prof. Hugenholtz compares to solving thousands of jigsaw puzzles simultaneously. This technology allows for the reading of large strands of DNA without breaking them into smaller fragments, making it easier to assemble microbial genomes. This was particularly important because many ocean microbes have low levels of G and C (two of the four DNA bases), which, combined with the complexity of the communities, had previously hindered such research.

Prof. Hugenholtz stated that the ability to perform this survey was not possible 10 years ago, but has become feasible as computing power has increased at an exponential rate. The study also included contributions from the University of Melbourne, the University of Tasmania, and James Cook University.

Ecological Importance and Reef Monitoring

According to Dr. Yun Kit Yeoh, a senior research scientist at AIMS and senior author of the paper, these microorganisms are a very important part of the reef ecosystem that underpin marine food chains. Dr. Yeoh explained that microalgae produce most of the oxygen humans breathe and are consumed by zooplankton and krill, which in turn feed animals ranging from small coral polyps to large whales.

The researchers believe the mapped microbiome can serve as a monitoring tool for the reef. Dr. Yeoh noted that microbial populations often show changes before visible changes appear on the reef, allowing scientists to examine responses to environmental perturbations such as:

• Climate change and heat stress
• Bleaching and storms
• Sediment and human activity
• Fishing in no-take zones

Prof. Hugenholtz added that monitoring microbial communities can also indicate heavy metal contamination, which is a cheaper alternative to directly measuring heavy metals.

Data Accessibility

The findings have been compiled into the Great Barrier Reef Microbial Genomes Database, which is hosted by the IMOS Australian Ocean Data Network. This database is available to all reef scientists to help them explore what constitutes a healthy reef microbiome. According to News, this effort complements long-term monitoring of the Great Barrier Reef that AIMS has conducted for more than 40 years.