Marine microbiology

Marine microbiomes and ocean health

Microorganisms represent important components of both free-living and host-associated marine ecosystems, performing vital functional roles that maintain global ocean health and productivity. Australia’s marine estate is facing extensive and rapid change as a result of global climate change, yet we still have a limited understanding of the marine microbiome diversity, structure, and function of the primary biotic determinants of ocean health.

At CMR, we study marine microbial communities using an integrated genome-centric approach to exploring functional and phylogenetic diversity. By focusing our research on the reef-building corals from Australia’s most iconic ocean habitat, the Great Barrier Reef, we aim to provide detailed insights into the beneficial roles of the microbiome in coral health and resilience.

How viruses impact coral function

Viruses are expected to shape the coral and its microbiome by infecting and destroying eukaryotic or prokaryotic cells, transferring genes to members of the holobiont that alter its metabolism, and influencing health and disease in this threatened animal. The Characterising the virome of Great Barrier Reef corals project aims to understand which viruses infect coral and its symbionts, and how they potentially impact coral functioning.

Mining metagenomes

Coral samples are collected from the Great Barrier Reef and brought to the lab for processing and shotgun sequencing. The resulting coral metagenomes are then mined for viral signal and examined using a range of bioinformatic tools. Using a novel fluorescence in situ hybridisation (FISH) technique, we can visualise bacterial and eukaryotic viral hosts in the organism.

We will develop a reproducible viral mining and analysis workflow for application to many species of coral across the Great Barrier Reef, and anticipate the discovery of novel auxiliary metabolic genes and viral markers of temperature sensitivity and robustness. Additionally, we are developing a method to visualise coral symbionts using FISH whilst circumventing the habitual challenges that this calcium carbonate encased auto-fluorescent animal presents.


The project will establish baseline, host-matched, and annotated viromes for corals, which will allow for further understanding of the roles they play in the holobiont. We also hope to develop a whole genome, strain-level visualisation method for corals – one of the most difficult systems to apply FISH to.

Accurate characterisation of microbial communities

Metagenomic sequencing analyses the total DNA from a given sample, therefore overcoming the challenges of previous sequencing approaches that rely on target-specific primers. However, host-derived samples have high amounts of host DNA that overwhelm any microbial DNA during sequencing, making it difficult to accurately characterise these microbial communities. Existing host depletion methods to enrich microbial DNA are time-consuming and expensive.

Novel host genome depletion method

The Host genome depletion and the microbiome of coral mucus and tissues project aims to optimise a novel host genome depletion method, which will be applied to coral samples in an attempt to reduce the costs of next-generation sequencing and improve data quality. The resulting protocol will not only help us better elucidate the community structure and function of the coral microbiome but will provide a technique to better characterise microbial communities in other organisms.

Chief Investigator


  • Megan Clay
  • Thien-Kim Nguyen-Phuoc

marine aerial