Going back in time to predict the evolution of future plant pathogen

Potato brown rot, caused by Ralstonia solanacearum plant pathogenic bacterium, is a globally important crop disease, belonging to the highest economic risk category in the UK. Thus far, all UK outbreaks have been associated with flooding or irrigation of potato crops from contaminated river water sources where the pathogen can persist by overwintering in the roots of its secondary host plant, Woody Nightshade.

Pathogen presence is currently monitored through annual, UK-wide river sampling by Fera Science to identify contaminated rivers that will be banned and cannot be used for irrigation. This sampling program has produced a valuable strain collection spanning 35 years of pathogen evolution in its natural environment. This project will use genomics, bioinformatics, and direct experimentation to establish how the virulence of R. solanacearum has evolved in the UK river network during the past three decades.

This project will use a combination of bioinformatics, microbiology, and plant biology to identify mechanisms and genetic changes in R. solanacearum virulence when evolving in environmental reservoirs. Work will be based on an existing 200-strain Fera collection, which has already been shared with and sequenced. This collection will now be characterised phenotypically and linked back to metadata (sample location and year) specifically focusing on:

Objective 1. Comparing variation in key virulence genes, focusing on effects of SNPs, deletions, and insertion sequence and prophage movement using bioinformatics. Friman lab has further developed a genome-scale model that can be used to model the effect of different variants on virulence gene networks, allowing in silico prediction of pathogen phenotypes.

Objective 2. Comparing variation in key virulence traits, including motility, attachment, metabolism, chemotaxis, stress tolerance, type three effector proteins, exopolysaccharide production, siderophores and several others. A subset of isolates will be characterised at the expression level using transcriptomics. This data will be used to validate in silico phenotype predictions obtained in objective 1.

Objective 3. Quantifying variation in pathogen virulence in planta. Friman lab has developed in planta assays to quantify changes in pathogen virulence using tomato assays, which will be used to characterise the whole strains collection. This will allow the identification of new potential marker genes for virulent pathogen genotypes in the UK that could be used to rapid epidemiological diagnostics.