Plant Genetics for Study of the Roles of Root Exudates and Microbes in the Soil

Abstract

The rhizosphere contains a great variety of microbial organisms, at least partly in response to the large quantities of organic compounds that are actively exuded by plant roots. The roles of these exudate compounds, and of the microbes in the root zone, are largely unknown. In order to dissect the relationships between soil microbes, plant exudates, and plant function, we planned to use host genetics to identify exudate–microbe correlates that segregate with specific plant genes. An exudate capture and characterization system was developed for Arabidopsis thaliana, but none of the six most-reproducible phenolic peaks analyzed by HPLC were found to vary in either ecoptypic analysis or the analysis of mutagenized populations. This surprising recalcitrance to genetic investigation led us to move immediately into the metagenomic studies that were originally planned to follow identification of plant genes that controlled microbial population and exudate presence/absence. Using approaches that distinguished between the microflora in the soil around the root, on the root surface, and inside the root, we found that each of these zones differed dramatically in microbial populations and that major differences were seen in the populations depending on the grass species employed (Zea vs. Sorghum vs. Panicum) as host. For instance, fungi were much more abundant in both quantity and diversity within and attached to the root than they were in the rhizosphere soil or in the soil prior to the presence of plant roots. These preliminary studies indicate the great potential for future investigations of the plant-determined chemical and organismal diversity in the soil.