Root exudate chemistry affects soil carbon mobilization via microbial community reassembly

Plant roots are one of the major mediators that allocate carbon captured from the atmosphere to soils as rhizodeposits, including root exudates. Although rhizodeposition regulates both microbial activity and the biogeochemical cycling of nutrients, the effects of particular exudate species on soil carbon fluxes and key rhizosphere microorganisms remain unclear. By combining high-throughput sequencing, q-PCR, and NanoSIMS analyses, we characterized the bacterial community structure, quantified total bacteria depending on root exudate chemistry, and analyzed the consequences on the mobility of mineral-protected carbon. Using well-controlled incubation experiments, we showed that the three most abundant groups of root exudates (amino acids, carboxylic acids, and sugars) have contrasting effects on the release of dissolved organic carbon (DOC) and bioavailable Fe in an Ultisol through the disruption of organo-mineral associations and the alteration of bacterial communities, thus priming organic matter decomposition in the rhizosphere. High resolution (down to 50 nm) NanoSIMS images of mineral particles indicated that iron and silicon co-localized significantly more organic carbon following amino acid inputs than treatments without exudates or with carboxylic acids. The application of sugar strongly reduced microbial diversity without impacting soil carbon mobilization. Carboxylic acids increased the prevalence of Actinobacteria and facilitated carbon mobilization, whereas amino acid addition increased the abundances of Proteobacteria that prevented DOC release. In summary, root exudate functions are defined by their chemical composition that regulates bacterial community composition and, consequently, the biogeochemical cycling of carbon in the rhizosphere.