Work package 1: We study the evolution of plant-recruited root microbiomes across the plant kingdom. With precision-based methods, we analyse the root microbiome dynamics and plant response and performance of 100 wild and cultivated plant species -related to the five most important food crop families – grown under four major types of stress: nutrient deficiency, drought, pathogen infection and herbivory. This quantitative phylogenetic approach allows us to obtain a deep evolutionary understanding of stress-induced recruitment by plants of their root-associated microbiota, and the functions that the microbiome provides to the plant under different environmental stress conditions. We are also looking to understand the extent by which cultivated crop species have lost these co-evolved microbial benefits, and how to harness identified plant traits and microbial functions in future crop systems.

Work package 2: In collaboration with our international partners, we investigate how microbiome recruitment and functionality change when plants are grown in soils at their centres of origin. Here, we take a selection of wild and domesticated plant species back to their origin, and determine how the taxonomy and functionality of the root microbiome changes under conditions where plants are exposed to different stresses. We hypothesize that plant domestication has led to a reduced microbial diversity and functionality. This is a topic of great debate in the field, and our comprehensive approach will provide key information to guide future breeding programmes towards crop varieties that maximize profitable functions from their root microbiome.

Work package 3: In work package 3 we investigate the mechanisms by which plants selectively recruit their microbiome under conditions of environmental stress. We identify and characterise common and unique recruitment mechanisms by plants, and – using the data from WPs 1 and 2 – explore how these recruitment processes have been affected by 100 years of intensive plant breeding to maximize crop performance in high-input agriculture. We look at plants have evolved different capacities for  using specific microbiome functions to cope with stress, and how microbes affect known and novel stress-adaptive signalling pathways in plants. This work will yield insight into plant genes and processes that can be targeted in breeding programmes for future elite crops that are better capable of utilising profitable functions from the root microbiome in agricultural systems.

Work package 4: Ultimately, our aim is to harness plant-beneficial functions of the root microbiome. Therefore, we explore the functional basis of microbial mechanisms encoded by the rhizpsphere microbiome that facilitate plant stress resilience. This will yield microbial functions and the underlying genes that confer stress resilience to the plant. This knowledge will allow us to select for plant genotypes that maximize profitable functions from the microbiome and design complimentary “personalised” microbiota formulations to optimise the plant-microbiome traits that promote stress resilience.

Work package 5: Fundamental knowledge generated in WP 1-4 is key in driving the development of strategies that harness functions from the root microbiome for future stress-resilient crops that require less
input of fertilisers and pesticides. This WP will function as an innovation incubator in which potential game-changing discoveries from WP 1-4 will be studied in detail to enable translation of these findings to future application in a microbiome-assisted agricultural context. In collaboration with our international and industrial partners, promising MiCRop outputs will be rigorously tested in the field, and tailored for optimal field performance. This will be accomplished via optimised crop genotypes and accelerated microbial evolution of premium rhizosphere competence traits.