Using phages as a precision tool to control pathogen abundance and virulence in the plant rhizosphere microbiome

In this proposal, we will develop a predictive framework and holistic understanding of how to control plant pathogenic Ralstonia solanacearum bacterium in the plant rhizosphere microbiomes by using bacteria-specific viruses, phages. The aims of this project are: (A) to better understand the ecology and evolution of pathogen-phage-plant interactions in the plant rhizosphere, and (B) to use this information to develop, manufacture and validate a novel phage biocontrol application in collaboration with industry partners (iMEAN, APS Biocontrol and Fera). First, we will determine if phages can be used to 'precision control' pathogens in complex rhizosphere microbiomes and if phages are safe to the plants and non-pathogenic bacteria in the rhizosphere using lab and plant infection experiments (microbiological co-culture assays; 16S rRNA sequencing, pathogen-specific qPCR and infections using Microtom tomato model in plant growth chambers). Second, we will test if phages can be used as 'evolutionary tools' to select for less competitive and non-virulent pathogen genotypes using experimental evolution, genome-scale metabolic modelling (project partner: iMEAN) and direct validation linking mutations to pathogen competitiveness and virulence (microbiological assays for virulence trait expression; direct virulence measurements using Microtom; catabolism with Biolog assays; direct competition assays against fluorescently labelled ancestral strain). Third, we will explore if phage-mediated changes in pathogen virulence and microbiome composition predictably alter plant immune responses having potential additional beneficial effects on the plant health using plant transcriptomics (and RT-qPCR) and bacterial metatranscriptomics in factorially designed infection experiment. Finally, we will design, manufacture (project partner: APS Biocontrol) and validate phage biocontrol combinations in greenhouse experiments using potato (Project partner: Fera).