Glass bead-based microcosms enable simultaneous profiling of root exudate and microbiome dynamics

Abstract

Plant roots host defined microbial communities that differ from those in the surrounding soil, and these communities shift dynamically in response to plant development and environmental changes. Whilst it is widely accepted that root exudates play a key role in the assembly and dynamics of root-associated microbial communities, the underlying mechanisms are not well understood. This is partly due to a lack of controlled experimental systems that monitor both microbiome- and exudate-dynamics simultaneously. Focusing on bacteria, we compared two microcosm systems commonly used in either root microbiome (clay particle-based) or root exudate studies (glass bead-based) for their suitability to simultaneously monitor both aspects. After inoculation with a synthetic community (SynCom), we evaluated these systems for plant performance, bacterial growth, and time-resolved community and exudate profiling. Both systems were characterised by higher community evenness and Pseudomonas abundances in proximity to plant roots. While clay particles impeded exudate recovery, the glass bead set-up allowed to uncover dynamic exudate shifts during bacterial community establishment. With this system, a transient increase of glucosinolates upon root colonisation with initially dominant Pseudomonas species was detected. Overall, the comparison showed that only the glass bead-based semi-hydroponic system was suitable for the simultaneous study of root microbiome and exudate dynamics.