PhD project: Predator-prey Dynamics in Model Microbial Ecosystems

Project description

Bacteriophages are viruses that prey on bacteria. They are already used to kill harmful bacteria in a range of contexts from medicine to agriculture, and this use is growing as the evolution of antimicrobial resistance (AMR) makes our current antimicrobial treatments more precarious. However, basic research is still needed to understand how bacteriophages function in the complex ecosystems where they are used as antimicrobial agents, e.g., in the human microbiome where thousands of bacterial species and their phages interact. Most studies have considered either single phage-bacterial pairs in vitro, or have been bulk, clinical studies of real treatments. The aim of this project is to bridge the gap by systematically studying how increasingly complex bacterial ecosystems interact with single or multiple phages.

The project will have both an experimental and a modeling component. Experimentally, you will measure the population dynamics of bacteriophages and bacteria in bioreactors, which are controlled environments where nutrients are inputted and waste removed over long periods. A likely trajectory is to first examine population oscillations in single bacterial and phage pairs, followed by studying multi-component ecosystems with competitor or cooperator species to mimic the complexities arising in real ecosystems. Theoretical modeling will be driven by the experimental development, and will be both analytical (e.g., dynamical systems and linear stability analyses) and numerical (solving differential equations and stochastic modeling). In the more complex ecosystems we would expect to see interesting features, such as chaos, opening up the possibility of rich mathematical analysis.

More broadly, we are also researching phage-bacterial interactions at the single-cell and small population levels, and integrating these levels with bulk measurements (as here) is an ongoing goal, so there will be the opportunity to extend the project in those directions

As part of the project you will be working in a very interdisciplinary environment and will have access to customized microscopes in the groups of Pilizota and Brown (located both in the School of Physics and Astronomy and in the School of Biological sciences), microfluidic production facilities and will regularly interact with other PIs working on soft matter, biological physics, microbiology as well as syntethic and systems biology and bioindustry and bioengineering:

http://pilizotalab.bio.ed.ac.uk/index.html

https://www.ph.ed.ac.uk/people/aidan-brown

https://www.ph.ed.ac.uk/icmcs/research-themes/physics-of-living-matter

http://www.synthsys.ed.ac.uk/

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