Funded PhD opportunity in Evolutionary Microbiology at Trinity College Dublin: Investigating the interplay between pesticide use and antimicrobial resistance in soil bacterial populations, Dr S. O’Brien: Department of Microbiology, Trinity College Dublin, Start Date: September 2023

About the project: Antimicrobial resistance (AMR) is a pressing global issue that is expected to cause upwards of 10 million deaths a year by 2050.  While responsible antibiotic stewardship has been advocated as crucial for controlling AMR, emerging evidence suggests that reducing antibiotic use alone may not be sufficient for curbing or reversing AMR.

Anthropogenic activities, such as intensive agricultural practices, are now recognized as important and overlooked predictors of AMR evolution in natural bacterial populations, via mechanisms such as cross-resistance, co-regulation and co-resistance.

Agricultural chemicals in particular can be key drivers of AMR in non-target microbes, however we lack causative experiments that bridge the gap between simplified laboratory studies, and correlations based on natural soil communities. Your PhD project will investigate how agricultural pesticides drive AMR evolution in the soil-dwelling opportunistic pathogen,Pseudomonas fluorescens. 

This is primarily a wet-lab project using long-term experimental evolution of soil microbes, phenotypic assays, competition experiments and survival assays. There also may be opportunities for whole genome sequencing and some bioinformatics.

The candidate is expected to drive their own research, and will require excellent attention to detail, flexibility and the ability to work independently and part of a team. The candidate will also be expected to attend conferences and training courses throughout their PhD. 


A strong interest in evolution and ecology is essential.  Lab skills in microbiology are desirable. Candidates should have obtained at least a 2.1 in a relevant undergraduate degree or masters programme e.g. Biosciences, Zoology, Microbiology, Ecology, Environmental Sciences, Evolution.  Funding: Award includes an annual stipend of €25,000 plus tuition fees (either EU or Non-EU). 

Host laboratory: The O’Brien Lab is based at the Moyne Institute of Preventive Medicine, part of the School of Genetics and Microbiology at Trinity College Dublin. We are interested in the evolution, ecology and behaviour of microbes in a wide range of settings – from the clinic to the field, e.g.

  1. S. O’Brien, R. Kümmerli, S. Paterson, C. Winstanley & MA Brockhurst. Temperate Phage Drive Divergent Social Strategies in P. aeruginosa. 2019. Proceedings of the Royal Society B: Biological Sciences 20191794. 
  2. S. O’Brien, M. Baumgartner & A. Hall. Species interactions drive the spread of ampicillin resistance in human-associated gut microbiota. 2021. Evolution, Medicine & Public Health 9: 256-266
  3. S. O’Brien, D.J. Hodgson & A. Buckling. Social evolution of toxic metal bioremediation in Pseudomonas aeruginosa. 2014. Proceedings of the Royal Society B: Biological Sciences 20140858. 

How to apply:

Send a CV, cover letter, and contact details of 3 referees to siobhan.o-brien@tcd.ieApplication deadline: 17:00h (Irish Standard Time) July 14th 2023. Interviews will be held on July 27th 2023. 

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