Primary research interest

Molecular microbial ecology, diversity and evolution

Additional role 

About me

I am a microbial ecologist whose research applies culture-independent molecular approaches to understand the structure and function of microbial communities in the environment. During my dissertation research (University of California, Berkeley) I was the lead author on one of the first studies to use metagenomics. In this work I investigated the metabolic potential and population diversity of microbial communities involved in acid mine drainage (AMD) generation, and demonstrated, for the first time, that metagenomic data could be used to reconstruct near-complete genomes directly from environmental samples.

My group at The University of Queensland is now using the metagenomic and metatranscriptomic approaches I helped pioneer, to investigate microbial communities in a wide range of different communities in both engineered systems and natural environments. My group is continuing to develop new ways to analyse genomic data by leading efforts in error correction for high-throughput sequencing platforms, single-cell sequencing and deep spatiotemporal metagenomics.

Research focus and collaborations

  • Molecular microbial ecology
  • Microbial diversity
  • Microbial evolution
  • The role of microorganisms in the biogeochemical cycles that underpin life on Earth
  • Phage – host interactions and co-evolution

International collaborators

  • Aalborg University, Denmark
  • Advanced Industrial Science & Technology (AIST), Japan
  • Cornell University
  • California Institute of Technology
  • University of Arizona
  • University of Colorado
  • Massachusetts Institute of Technology

Group members

Funded projects

  • ARC Linkage: From tailings to soil: in situ remediation in mine site rehabilitation
  • ARC Discovery:  Genome-level insight into the dynamics of a model coral microbiome
  • ARC Discovery: Intracellular manufacturing – high performance biomaterials from methane
  • ARC Linkage:  Iron cycling in wet tropical regimes: Bioleaching of chalcopyrite, goethite and hematite
  • U.S. Department of Energy – Biological and Environment Research: Pathways to carbon liberation: a systems approach to understanding carbon transformations and losses from thawing permafrost.
  • U.S. Department of Energy – Engineering Frontier Research Center Program:  Systems Level Dissection of Anaerobic Methane Cycling: Quantitative Measurements of Single Cell Ecophysiology, Genetic Mechanisms, and Microbial Interactions.
  • Gordon & Betty Moore Foundation:  Microscale experiments to understand a microscale world: combining microfluids and ecogenomics to investigate microbial processes in the ocean.
  • Great Barrier Reef Foundation: Sea-quence Bioinformatics Fellowships.
  • Queensland Government Department of Science, Information Technology, Innovation and the Arts (DSITIA) Accelerate Partnerships: Coral genomes along environmental gradients.
  • Queensland Government Smart Futures Research Partnerships Program:  Future gas through bioconversion of stranded and waste coal.

Teaching interests

  • MICR2000: Microbiology & Immunology
  • BIOL2202: Genetics

Achievements and awards 

Invited lectures

I have presented invited talks at more than 30 international meetings since 2007, including “keynote” presentations at the International Symposium on Microbial Ecology (2016), University of Calgary-Microbiome Symposium (2015), Metagenomics@Melbourne Symposium (2013 & 2015), the Microbial Genomic Research: A Frontier in Future Green Biotechnology, Chung Ang University, Seoul (2011) and the New Zealand Microbial Ecology Consortium, University of Auckland, New Zealand (2010).

My “invited” presentations include the Joint Academic Microbiology Seminars, Australian Museum, Sydney (2016), 15th International Symposium on Microbial Ecology (ISME15) Seoul, Korea (2014); CBA Biodiversity Genomics Conference, Canberra, Australia (2013), the 14th International Symposium on Microbial Ecology (ISME14) “The Power of the Small” in Copenhagen (2012), American Society for Microbiology (ASM), San Diego, USA (2010).

Synergistic activities

  • Editorial board member for the International Society for Microbial Ecology Journal, Environmental Microbiologyand Frontiers in Evolutionary and Genomic Microbiology.
  • Assessor for the following research funding authorities: Australian Research Council (ARC), National Science Foundation (NSF) – Systematic Biology & Biodiversity Program and National Science Foundation (NSF) – Biological Oceanography Program.
  • Reviewer for the following international journals: Nature, Science, Applied and Environmental Microbiology, PLoS Biology, PLoS ONE, ISME Journal, Nature Review Microbiology, Proceedings of the National Academy of Sciences.

Outreach and media exposure

  • Outreach - 2016: presentation about careers in Bioinformatics & ACE tour to 1st year UQ Bioinformatics students (18th & 19th May). Guest lecturer to undergraduate course "Genes, genomes and development" students at James Cook University (4th April).
  • Media exposure: my research has been published in more than 30 articles in the mainstream science media, including: ABC Science Feb 2014 (Methane microbe may speed up warming), Sydney Morning Herald Nov 2013 (Secrets from the Deep), F1000 Prime Aug 2013, Altmetric Jul 2013; Phys Org Jul 2013, Phys Org Sep 2008, Webwire Mar 2008, Phys Org Mar 2007, Scientist July 2006, Chicago Tribune 2006, Science Daily Feb 2004, Eureka Alert Feb 2004, Science Scoop Feb 2004, New York Times Feb 2004.