Microdialysis as an approach to unravel mechanisms involved in plant-microbe interactions shaping the rhizobiome

The rhizosphere is a critical microenvironment that plays key roles in plant nutrient availability, largely due to root interactions with rhizospheric microbes. However, we lack suitable methods that can investigate changes in rhizospheric community structure and function within the context of a dynamic, undisturbed soil. This study investigated the potential of using microdialysis to examine how root exudates affect rhizosphere microbiomes. Microdialysis has been used for low intrusive soil nutrient sampling at the scale of a fine root, with small membranes that also enable release of defined compounds. We evaluated whether microdialysis could simulate exudation, stimulate changes in a soil microbial community, allowing us to target microbes which responded most to exudation. Microdialysis successfully stimulated growth of fungi on probe surfaces, which were extracted and sequenced for identification. Microbial growth was also visualized with scanning electron microscopy. Microdialysis is a tool enabling dissection of interactions between root exudation and soil microbes, initially for individual compounds and later for more complex compositions.