Simon McIlroy

Dr McIlroy is a microbial ecologist specialising in the development and application of methods for the visualisation and characterisation of microorganisms within their natural environment. He spent the early part of his research career working on the microbiology of wastewater and anaerobic digesters for biogas production, earning his PhD from La Trobe University and working as a postdoctoral research fellow at the Centre for Microbial Communities at Aalborg University, Denmark.

He now primarily works on anaerobic methanotrophic archaea in freshwater sediments, initially as a senior postdoctoral researcher at the Australian Centre for Ecogenomics (ACE) at the University of Queensland, and now as an ARC Future Fellow and Group Leader at the Centre for Microbiome Research at QUT.

Research Focus

Microorganisms play critical roles in nutrient cycles in the environment and several biotechnological processes. An important example is the known role of microorganisms as key drivers of the cycling of the greenhouse gas methane in the environment, yet the metabolic strategies they employ are poorly understood and it is predicted that only a fraction of the diverse species responsible have been identified. Microorganisms are also employed for nutrient cycling and removal from wastewater, yet these systems often unexpectantly fail and our understanding of the species responsible is somewhat superficial. To address such knowledge gaps, Dr McIlroy’s team applies meta-omic and novel single-cell visualisation methods to the characterisation of a range of microbial ecosystems to identify the key microorganisms and the metabolic pathways they utilise. Understanding these systems increases our ability to predict their response to changes (i.e. climate) and our ability to intervene. Dr McIlroy is always open to discussing potential opportunities for young researchers to join his team.


+61 7 3443 7332

Project themes

Selected publications

A full list of publications can be found at Google scholar. or through ORCID.

  1. Leu, A.O.*, McIlroy, S.J.*, Ye, J., Parks, D.H., Orphan, V.J. and Tyson G.W. (2020) Lateral gene transfer drives metabolic flexibility in the anaerobic methane oxidising archaeal family Methanoperedenaceae. mBio. 11. e01325-20. *Equal first author.
  2. Fernando, E.Y., McIlroy, S.J., Nierychlo, M., Herbst, F.A., Schmid, M.C., Wagner, M., Nielsen, J.L., and Nielsen, P.H. (2019) Resolving the individual contribution of key microbial populations to enhanced biological phosphorus removal with Raman-FISH. ISME J. 13. 1933-1946.
  3. McIlroy, S.J., Onetto, C.A., McIlroy, B., Herbst, F.-A., Dueholm, M.S., Kirkegaard, R.H., Fernando, E., Karst, S.M., Nierychlo, M., Kristensen, J.M., Eales, K.L., Grbin, P.R., Wimmer., R., Nielsen, P.H. (2018) Genomic and in situ analyses reveal the Micropruina spp. as abundant fermentative glycogen accumulating organisms in enhanced biological phosphorus removal systems. Front. Microbiol. 9. 1004.
  4. Karst, S.M., Dueholm, M.S., McIlroy, S.J., Kirkegaard, R.H., Nielsen, P.H. and Albertsen, M. (2018) Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias. Nature Biotech. 36: 190–195.
  5. McIlroy, S.J., Karst, S.M., Nierychlo, M., Dueholm, M.S., Albertsen, M., Kirkegaard, R.H., Seviour, R.J., and Nielsen, P.H. (2016) Genomic and in situ investigations of the novel uncultured Chloroflexi associated with 0092 morphotype filamentous bulking in activated sludge. ISME J. 10: 2223-2234
  6. McIlroy, S.J., Szyszka, A., Starnawski P., Saunders, A.M., Nierychlo, M., Nielsen, P.H., and Nielsen J.L. (2016) Identification of active denitrifiers in full-scale nutrient removal wastewater treatment systems by application of stable-isotope probing, microautoradiography and fluorescence in situ hybridisation. Environ. Microbiol. 18: 50-64
  7. McIlroy, S.J., Saunders, A.M., Albertsen, M., Nierychlo, M., McIlroy, B., Hansen, A.A., Karst, S.M., Nielsen, J.L., and Nielsen, P.H. (2015) MiDAS: The field guide to microbes of activated sludge. Database. 2015: bav062
  8. McIlroy, S.J., Albertsen, M., Andresen, E.K., Saunders, A.M., Kristiansen, R., Stokholm-Bjerregaard, M., Nielsen, K.L. and Nielsen, P.H. (2014) “Candidatus Competibacter”-lineage genomes retrieved from metagenomes reveal functional metabolic diversity. ISME J. 8: 613-624
  9. McIlroy, S.J., Kristiansen, R., Albertsen, M., Karst, S.M., Rossetti, S., Nielsen, J.L., Tandoi, V., Seviour, R.J. and Nielsen, P.H. (2013) Metabolic model for filamentous “Candidatus Microthrix parvicella” based on genomic and metagenomic analyses. ISME J. 7: 1161-1172
  10. McIlroy, S.J., Tillett, D., Petrovski, S. and Seviour, R.J. (2011) Non-target sites with single nucleotide insertions or deletions are frequently found in 16S rRNA sequences and can lead to false positives in fluorescence in situ hybridization (FISH). Environ. Microbiol. 13: 33-47