The Microbiota-Root-Shoot Axis in Plant Health and Disease

Since 450 million years, roots of healthy plant are colonised by diverse communities of bacteria, fungi, and oomycetes which are known to extend host functions by protecting roots from disease or by promoting water and nutrient acquisition. More remarkably, recent evidence suggests that bidirectional signalling between belowground microbial commensals and distant aboveground host organs is likely critical for maintaining host-microbe homeostasis and plant health. Reminiscent of the critical role of the microbiota-gut-brain axis for modulating brain functions in animals, we recently obtained evidence supporting the role of the microbiota-root-shoot axis for integrating response to microbes belowground and response to light aboveground. MICROBIOSIS aims at thoroughly dissecting the bi-directional connections between microbial root commensals and shoot developmental processes using Arabidopsis and tomato as model plant systems. By testing the hypothesis that co-evolutionary history between microbial root commensals and their hosts have shaped complex regulatory circuits modulating plant health, MICROBIOSIS aims at unravelling the physiological relevance of the microbiota-root-shoot axis for maintaining host-microbe homeostasis and for integrating multiple stress responses occurring in distant root and shoot organs. Using multi-kingdom synthetic microbial communities, cutting-edge metabolome, microbiome and grafting techniques, as well as several innovative and advanced gnotobiotic plant systems in which below-ground and aboveground organs are physically separated, MICROBIOSIS has the ambition to 1) bridge the gap between functional biology and ecology, 2) decrypt root microbiota-dependant regulatory circuits promoting plant health, and 3) design synthetic multi-kingdom microbial communities with modular functions favouring resistance to multiple aboveground stresses.