Rhizosphere Rhythms: Unravelling Diurnal Microbiome Dynamics and Their Role in Plant–Soil Interactions

Objectif

The rhizosphere soil zone which surrounds plant roots is a crucial interface which acts as a conduit for biogeochemical cycling between the atmosphere, plant and soil, and hosts a distinct microbiome which has profound impacts on plant health and productivity, particularly by enhancing plant nutrient availability. As a result, management of the rhizosphere is central to the design of future agricultural systems which are both sustainable and resilient to global challenges. I have shown that the rhizosphere microbiome exhibits marked diurnal rhythmicity, so that rhizosphere plant-microbe interactions are far more dynamic than previously recognised. Crucially I have also demonstrated that abundance of rhizosphere microbes which control nitrogen (N) availability show strong rhythmicity. Since N-assimilation by the plant host is controlled by a circadian clock, this raises the intriguing possibility that microbiome rhythmicity may be coordinated by the plant clock so that the timing of microbial N-cycling processes coincides with plant nutritional requirements. RHYTHMS will test this hypothesis within model systems and at the field scale. In doing so it will unravel the mechanisms which drive microbiome rhythmicity for the first time, testing the hypothesis that rhythmicity is the result of an interplay between cyclic root exudation of labile carbon substrates and changes in plant immunity, modulated by the plant’s circadian clock and by turnover of microbiota by bacteriophages and protists, representing a novel microbial loop. New trait-based approaches for characterising rhythmic microbes based on genomic and transcriptional signatures will be devised which will have broad transformative potential across basic and applied research fields. The outcomes of the project will fill a major knowledge gap in our mechanistic understanding of how the rhizosphere operates as an extended plant phenotype and open new avenues to manage the rhizosphere for beneficial functions.