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)
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 1,000 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), Pierre-Alain Chaumeil, Aaron Mussig, Donovan Parks
- Collaborators: Maria Chuvochina (DSMZ), Chris Rinke (University Innsbruck)
A genome taxonomy database for the Kingdom Fungi
Fungi are important constituents of the global biosphere recognised for their biotechnological applications and infectious potential. They currently lack a systematic genome-based classification compromising scientific communication and comparative analyses. This project aims to apply the successful Genome Taxonomy Database (GTDB) model developed for prokaryotes to the fungal kingdom to address this knowledge gap. Outcomes will include a website for interactive exploration of the resulting genome-based taxonomy and software that allows users to classify their own fungal genomes.
- Project team: Phil Hugenholtz, Pierre-Alain Chaumeil, Aaron Mussig, Donovan Parks
- Collaborators: Maria Chuvochina (DSMZ), Chris Rinke (University Innsbruck), Andrey Yurkov (DSMZ), Conrad Schoch (NCBI), Barbara Robbertse (RefSeq), Urmas Kõljalg (University of Tartu), Vincent Robert (BioAware), Konstanze Bensch (KNAW), Toni Gabaldón (IRB Barcelona), Igor Grigoriev (JGI), Dmitry Schigel (GBIF), Tobias Frøslev (GBIF)
Publications
Parks, D.J., Chuvochina, M., Rinke, C., Mussig, A.J., Chaumeil, P., Hugenholtz, P. (2022) GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy, Nucleic Acids Research, 50(D1), D785–D79. doi.org/10.1093/nar/gkab776
Tracing the emergence of cellular complexity in the phylum Planctomycetota
Cellular complexity distinguishes eukaryotic from prokaryotic cells. This project aims to establish the evolutionary origin of eukaryotic-like features within the bacterial phylum Planctomycetota, a broadly distributed bacterial lineage important to global carbon and nitrogen cycles. The project is designed to generate new understanding of the evolution of cellular complexity using the phylum as a model. In addition, the program aims to provide a comprehensive characterisation of the Planctomycetota, which has recently expanded from 3 of 33 classes due to recovery of genomes from the environment.
- Project team: Phil Hugenholtz, Kate Bowerman, Margaret Butler, Steven Li
- Collaborators: Rick Webb, Rob Parton
Understanding genome evolution through plylogenetic reconciliation
Phylogenetic reconciliation has emerged as a promising approach for studying microbial ecology and evolution. The core idea is to model how gene trees evolve along a species tree and to explain differences between them via evolutionary events including gene duplications, transfers, and losses. Phylogenetic reconciliation provides a natural framework for studying genome evolution including ancestral gene content inference, the rooting of species trees, and insights into metabolic evolution and ecological transitions.
- Project team: Phil Hugenholtz, Kate Bowerman, Siying Mao
- Collaborators: Tom Williams (University of Bristol), Gergely J Szöllősi (OIST), Adrián Davín (ETH Zurich), Anja Spang (NIOZ), Ben Woodcroft (QUT)
Publications
Williams, T.A., Davin, A.A., Szánthó, L.L., Stamatakis, A., Wahl, N.A., Woodcroft, B.J., Soo, R.M., Eme, L., Sheridan, P.O., Gubry-Rangin, C., Spang, A., Hugenholtz, P., Szöllősi, G.J. (2024) Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution, The ISME Journal, 18(1), wrae129, doi.org/10.1093/ismejo/wrae129
Coleman, G.A., Davín, A.A., Mahendrarajah, T.A., Szánthó, L.L., Spang, A., Hugenholtz, P., Szöllősi, G.J., Williams, T.A. (2021) A rooted phylogeny resolves early bacterial evolution, Science, 372(6542), doi.org/10.1126/science.abe0511
Davín, A. A., Woodcroft, B. J., Soo, R. M., Morel, B., Murali, R., Schrempf, D., Clark, J. W., Alvarez-Carretero, S., Boussau, B., Moody, E.R., Szantho, L., Richy, E.M., Pisani, D., Hemp, J., Fischer, W., Donoghue, P.C., Spang, A., Hugenholtz, P., Williams, T., Szollosi, G.J. (Accepted/In press) A geological timescale for bacterial evolution and oxygen adaptation, Science. manuscript