Rhythmic Control of The Plant-Microbiome Holobiont

Abstract Background: Many physiological and metabolic processes in plants are modulated by a circadian clock. Rhizospheric microorganisms fed by root exudates provide beneficial functions to their plant host. The intricate connection between the circadian clock and the rhizospheric microbial community remains poorly understood. Results: We investigated the role of the Arabidopsis circadian clock in shaping the rhizospheric microbial community using wild-type plants and clock mutants (cca1-1 and toc1-101). We performed transcriptomic and metabolomic analyses and sequenced amplicons of the 16S ribosomal RNA gene to characterize gene transcription, root exudation and the bacterial communities, respectively, throughout the day (24 h). Deficiencies of the central circadian clock led to abnormal diurnal rhythms for thousands of expressed genes and dozens of root exudates. Bacterial community failed to follow obvious patterns in the 24-h period, and lack of coordination with plant growth in the clock mutants. Conclusions: Our findings suggested that the biological clock was an important force that drove plants to adjust their rhizospheric microbiomes for adapting to different growth stages.