Leading microbiome research excellence to understand the role that microorganisms play in health and diseases.

Marine symbiosis research projects

The genomic basis for the beneficial role of the coral microbiome

Dr. Lauren Messer

Tropical coral reefs are some of the most productive ecosystems on Earth, despite their locality within nutrient-limited marine waters. This paradigm has resulted in decades (or rather a century) of research into the ecological success of reef-building corals, revealing their intimate relationship with microorganisms. The most notable is the single-celled algae from the family Symbiodiniaceae which provides fixed carbon, bioavailable nitrogen, and contributes to sulfur cycling within the tissues of the coral animal. Corals associate with a diversity of bacteria, archaea, viruses, and other microbial eukaryotes, yet their functional contributions remain largely unexplored.

The application of novel molecular techniques to study the coral microbiome has largely been limited to taxonomic marker gene surveys due to inherent complexities in disentangling coral host and microbiome nucleic acids – a problem common to other host-associated microbial communities. Using a combination of cell size fractionation and ultra-deep metagenomic sequencing, our team have reconstructed some of the first microbial genomes directly from coral tissues (bypassing the need for cultivation). However, this methodology is expensive and resource intensive, and so we are actively developing new approaches, that could be applied to any sample type, to tackle this technical limitation.

We have recently published the first genome-centric view of a coral microbiome for the massive, thermally resilient coral Porites lutea. This work has revealed the potential for the bacterial and archaeal members of the coral microbiome to contribute to carbon fixation, sulfur, and nitrogen cycling, in addition to the Symbiodiniaceae (Robbins et al., 2019, Nature Microbiology doi:10.1038/s41564-019-0532-4). We are currently expanding upon this work to investigate the functional role of the core microbiome of a thermally sensitive coral species, Acropora tenuis, and performing comparative genomic analyses of microorganisms from five other coral species. The insights gained from this work will provide a comprehensive understanding of the role of microbiome in maintaining coral health, and may provide tangible targets to promote resilience to stress through manipulation of the microbiome.

Characterising the virome of Great Barrier Reef corals

Ms. Megan Clay

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 aim of this project is to understand which viruses infect coral and its symbionts, and how they potentially impact coral functioning.

In this project, 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. We also use a novel fluorescence in situ hybridisation (FISH) technique to visualise bacterial and eukaryotic viral hosts in the organism.

This project will develop a reproducible viral mining and analysis workflow, which is applied to many species of coral throughout the Great Barrier Reef. We 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.

Host Genome Depletion and the Microbiome of Coral Mucus and Tissues

Ms. Kim Nguyen-Phuoc

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.

The aim of this project is 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.