Nature paper logs 800,000 genomes from 48 reefs

Scientists have catalogued more than 800,000 microbial genomes in Great Barrier Reef waters, uncovering over 500 previously unknown bacterial species and more than 300,000 distinct viruses.

The work appears in Nature and draws on DNA extracted from seawater collected at 48 reefs. The project was led by the University of Queensland and the Australian Institute of Marine Science.

Authors describe it as the first broad survey of microbes living in the open waters of reef systems across the Great Barrier Reef. They also built the Great Barrier Reef Microbial Genomes Database for other reef researchers to use.

Professor Philip Hugenholtz of the University of Queensland said the database will let scientists test what a healthy reef microbiome looks like and track how it changes after bleaching, storms, sediment, fishing and other pressures.

48 reefs and 362,802 viruses

Across the dataset, the team identified 5,283 bacterial and archaeal genomes that grouped into 876 species. About two-thirds were absent from public databases.

Researchers also recorded 362,802 viral types. Among them was Crassvirales, a group of viruses that infect bacteria and was first identified in human gut samples in 2014.

In addition, the study recovered complete chromosomes from Bathycoccus and Ostreococcus directly from seawater. The paper describes both as among the Reef’s most abundant microalgae.

Dr Yun Kit Yeoh, a senior research scientist at AIMS and senior author, linked the result to rapid advances in DNA sequencing. He said new tools now allow microbiome studies at the scale of the Great Barrier Reef.

Yeoh said those microbes matter well beyond coral habitats because microalgae produce much of the oxygen humans breathe and support ocean food chains, from krill and zooplankton to coral polyps and whales.

Twenty years ago, researchers could barely identify many of the hidden microbial communities linked to humans, plants and animals. Since then, sequencing methods have opened similar work in plant health, human health and now reef waters.

Dr Steven Robbins, first author and team lead at the University of Queensland, said collecting and sequencing microbial DNA from the ocean was challenging because seawater mixes many closely related organisms together in a tiny sample.

James Cook University, the University of Melbourne and the University of Tasmania also contributed to the research.