Paul Rainey

January 04, 2024

Please refer to and recent publications. If you need further information on the projects after having read these, please contact Paul <>. David <> will be the co-supervisor in both projects and will also be happy to answer your questions.

If you wish to apply for a position, please contact Paul Rainey by email (cc-ing David Rogers) providing a short motivational statement, names of two referees and a short CV (biosketch). Please pay particular attention to the advice provided here

1. Experimental evolution of killing and immunity between closely related strains of Pseudomonas flourenscens

The genomes of plant growth promoting bacteria (PGPB), including the laboratory evolution model Pseudomonas fluorescens SBW25, contain a complex arsenal of toxins targeting plant-pathogenic bacteria, fungi, and eukaryotes. However, these bacteria are not simply benevolent protectors of plants – their survival also depends on their ability to outcompete rival PGPBs. Comparing the genome of SBW25 to those of nearly identical strains reveals that regions of high divergence are largely restricted to loci associated with competition between close relatives: pyocins, contact-dependent growth inhibition systems, type six secretion system effector/immunity pairs, and other secondary metabolites. Indeed, competition experiments between closely related strains show extremely high levels of growth inhibition.

In this project, we set out to characterize the mechanisms of both killing and immunity, to observe how these interactions change during laboratory evolution experiments, and ultimately to shed light on how these loci evolve so quickly. Candidates should be career-minded, have a passion for understanding microbial interactions, population biology, genomics and evolutionary biology and be able to work independently, and yet as part of a team. Thinking outside of the box is a prerequisite.

The successful candidate will be trained in a wide array of techniques including genetic manipulation, flow cytometry, microscopy, bioinformatics, and will participate in experiments that expand the traditional boundaries of experimental evolution. 

2. Eco-evolutionary dynamics of nematode-colonizing bacteria in complex communities

Microbial communities are diverse, complex, and while patterns of diversity are often well documented, the eco-evolutionary dynamics of individual members remains poorly understood. This is particularly true of those dynamics that shape communities, determine function – including interaction with eukaryotic hosts – and which are driven by phages and other mobile genetic elements (MGEs). Extending recent work, we have established a collection of hundreds of Ochrobactrum strains (plus genome sequence) that colonise – and persist – in the nematode gut (the two of which persist within complex microbial communities).

We now wish to exploit capacity to introduce single Ochrobactrum strains into nematodes to determine the impact of ecosystem complexity on the dynamics of molecular evolution in focal Ochrobactrum lineage. We also aim to study the interaction between Ochrobactrum and the nematode using a combination of Tn-seq and epi-fluorescence microscopy. Finally, we seek to demonstrate the power of community-level selection to modulate the interaction between the nematode host and its microbiome.

The project is part of a DFG-funded programme of research on metaorganisms and offers a wide range of opportunities to network with a broad range of scientists. Candidates should be career-minded and passionate about research in microbial population biology, evolutionary genetics and show evidence of interest in the life of MGEs. In return, the successful researcher will receive training in a wide range of experimental and computational approaches, encompassing population genomics, experimental evolution and evolutionary genetics. Thinking outside of the box is a prerequisite.

Go to Editor View