Identifying the genetic determinants of barley colonisation by the growth-promoting bacteria Pseudomonas fluorescens

The global population will increase dramatically during this century which, together with the climate crisis, will pose an enormous challenge for food security. We will need to balance boosting food production with reducing agrochemical use in order to preserve natural ecosystems. To do this, exploiting the benefits that the rhizosphere microbiome has on plant health, growth and resistance to biotic and abiotic stresses has been proposed as a feasible strategy. In my project, I examined the interaction between barley, the fourth most important cereal crop, and the widespread beneficial bacteria Pseudomonas fluorescens. Plants can actively shape their rhizosphere microbiomes mainly through the secretion of root exudates whose composition depends greatly on host genotype. The ability of different microbes to utilise these exudates determines their success in the rhizosphere, which results in a shift in the rhizobiome composition. In my PhD, I first investigated the effect that barley genotype exerts on the overall rhizosphere microbiome and on the soil Pseudomonas population. I next examined the genetic features of the Pseudomonas populations linked to two particular barley cultivars, Chevallier and Tipple, and identified a set of cultivar-specific genes among the rhizosphere Pseudomonas isolates. These genes fell mainly into two categories: substrate transport and central metabolism, supporting the role of root exudates as the primary drivers of rhizosphere microbiome assembly. Next, I analysed the exudates composition of Chevallier and Tipple, and observed that the secretion of sugars and organic acids were the major differences between them. Finally, I screened a Chevallier x Tipple population for the secretion of fructose as a potential determinant of Pseudomonas recruitment, highlighting two large QTL in the barley genome. Overall, the ultimate objective of this project is to provide a basis to select more efficient biocontrol strains, and breed plants with an improved ability to recruit beneficial Pseudomona