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
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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.