Using population genomics to predict the epidemiology and evolution of R. solanacearum plant pathogen in the UK

Plant pathogenic bacteria cause considerable economic losses globally due to damage to crops. Bacterial wilt, caused by the Gram-negative quarantine bacterium Ralstonia solanacearum, is one of the most important bacterial crop diseases. In the UK, R. solanacearum causes potato brown rot. UK outbreaks have been associated with flooding or irrigation of potato crops from contaminated river water sources where it can persist by overwintering in the roots of its secondary host plant, Woody Nightshade. It is currently known that R. solanacearum densities peak in July-September when the water temperatures are high and that the strains isolated from disease outbreaks are highly related to the environmental strains isolated from water and alternative hosts upstream of the infested potato fields. While these findings suggest that environmental reservoirs play important roles in the disease outbreaks, it is still unclear how the R. solanacearum population has dispersed, expanded and evolved since the first disease finding in 1992.

This project will use population genomics and a collection of time sampled pathogen isolates to understand the epidemiology and genomic evolution of R. solanacearum in the UK river system. The studentship will address three research areas:

1) Global pathogen dispersal: comparison of UK isolates with an existing sequence database of R. solanacearum genomes to determine whether the UK population is genetically unique and locally adapted and to estimate the frequency of international dispersal.

2) Evolutionary dynamics: to what extent has R. solanacearum changed during the UK disease outbreaks since 1992? Can we identify quantitative traits that are important for pathogenic vs. environmental isolates by using genome-wide association approaches (GWAS)? Can we use genome difference to infer something about pathogen ecology and adaptation in environmental reservoirs and is R. solanacearum still evolving in the UK?

3) Spatial and temporal distribution of R. solanacearum genotypes: We will develop a genomic database that will help in identifying novel outbreak strains, to infer the likely geographic source of their origin and to match specific control management strategies against the given outbreak strain.

The project combines next-generation genome sequencing, bioinformatics and evolutionary biology to understand the dynamics of concurrent plant pathogen outbreaks. An ideal candidate will have a background in bioinformatics/computational/data sciences and a demonstrated interest in at least one of the main subject areas: microbiology, genetics or bacterial pathogenesis. Good understanding of evolutionary genetics would be an advantage.