Tree of life

Metagenomics and single-cell genomics have opened a path to characterising uncultured microbial diversity (so-called 'microbial dark matter'), estimated to represent more than 85 per cent of life on Earth.

This new knowledge could provide a greatly improved understanding of how life evolved.

See the projects that we're working on, below.

Exploring the ‘black box’ of archaeal metabolism

The development of high-throughput sequencing and bioinformatic techniques has allowed metabolic capabilities from novel and uncultivated archaeal lineages that have previously been undescribed to be inferred. Now, the challenge is to cultivate these recalcitrant Archaea from their native environments.

While many of these novel Archaea are found in hydrothermal vents, hot springs, coal seams, seeps or industrial waste streams that are rich in hydrocarbons, their growth requirements remain unknown. The implication is that there is a dependence of these species on non-traditional growth substrates in these environments.

This project aims to identify non-traditional mechanisms of growth using cultivation-based techniques.

Project team: Paul Evans, Gemma Laird, Ruochen Chao, Cheong Xin Chan
Collaborators: Jianhua Guo

Genome evolution, diversity, and innovation

We study the innovation of Eukaryote genomes relative to the organismal adaptation to diverse ecological niches, including extreme environments. Using comparative genomics, we identify genome features, gene content, functions and/or pathways that are specific to distinct ecological niches. Our research spans from microbes, drought-resistant plants, weeds and corals to jellyfish.

Project team: Cheong Xin Chan (CI), Hisatake Ishida
Collaborators: Debashish Bhattacharya (Rutgers University), Mikael Boden, Luke Guddat, Cebrina Nolan, Andrew Walker, Glenn King, Tim McDermott (University of Montana), Gary Schenk, Jamie Seymour (JCU), Hwan Su Yoon (Sungkyunkwan University), Shauna Murray (University of Technology Sydney), Uwe John (Alfred Wegener Institute for Polar and Marine Research)

Scalable phylogenomic approaches

Highly scalable phylogenomic approaches are needed to make evolutionary sense of the ongoing deluge of sequence data. We are developing and exploring the use of alignment-free methods in large-scale inference of genome evolution as networks, beyond the conventional tree-like assumption of evolutionary history. We argue that phylogenetic signal captured this way from whole-genome data can guide taxonomic classification, particularly among eukaryotic microbes.

Project team: Cheong Xin Chan (CI), Hisatake Ishida
Collaborators: Debashish Bhattacharya (Rutgers University), Ira Cooke (James Cook University)

Exploring the evolution and ecology of non-photosynthetic Cyanobacteria

Oxygenic photosynthesis is one of the most important processes on Earth, providing it with oxygen required for us to live. Until recently, it was thought that all Cyanobacteria are photosynthetic but this dogma was recently challenged by the discovery of two non-photosynthetic lineages. This project aims to identify members from these lineages and characterise their functional capabilities. We will study the metabolic pathways of these organisms using innovative bioinformatics, culturing and electron microscopy techniques.

Project team: Rochelle Soo (CI), Phil Hugenholtz, Paul Evans
Collaborators: Rick Webb

Changing the classification status quo with a global genome-based taxonomy

A grand challenge in biology is the reconstruction of the complete evolutionary history of life on Earth. A major hurdle to this goal has been the inability to culture most microbial species which comprise the bulk of evolutionary diversity. However, new molecular techniques have removed this hurdle and more than 1000 new microbial species are being revealed each month through sequencing of environmental samples.

We aim to organise both cultured and uncultured microbial diversity into a systematic evolutionary framework to replace the current highly flawed and incomplete classification of microorganisms. The systematic classification of the microbial world is timely and will enable fundamental insights into ecology and evolution. This work will build on the success of the Genome Taxonomy Database prototype.

Project team: Phil Hugenholtz (CI), Maria Chuvochina, Pierre-Alain Chaumeil, Aaron Mussig