Root exudation and rhizosphere microbial assembly are influenced by novel plant trait diversity in carrot genotypes

Root exudate composition can influence rhizosphere microbial recruitment and is tightly controlled by plant genetics. However, little research has profiled root exudate in vegetable crops or determined their role in rhizosphere microbial community and metabolite composition. It is also not well understood how root exudates and resulting rhizosphere dynamics shift across plant trait diversity and with the development of novel crop genotypes. To address these knowledge gaps, this study paired metabolomics and microbiome analyses to evaluate associations between the composition of exudates, soil bacterial and fungal communities, and soil metabolites across four genotypes of organically produced carrot of differential breeding histories, including two experimental genotypes. Plant genotypes modified soil microbial diversity and composition, and differentially recruited bacterial taxa. Bacterial rhizosphere recruitment from bulk soil was genotype and root exudate-mediated, while fungal recruitment was not. Moreover, root exudate composition was distinct in an heirloom genotype and a novel nematode resistant genotype, compared to other genotypes tested. Root exudate and rhizosphere metabolite composition was decoupled, and soil metabolites more strongly associated with fungal than bacterial communities. Taken together, the results of this study suggest that novel crop trait diversity and breeding histories hold consequences for the functional potential of soils through the diversification of root exudate mediated plant-microbe interactions. •Four genotypes of phenotypically diverse carrots were grown in a field setting.•Root exudates were differentially abundant across genotypes.•Bacterial recruitment to the rhizosphere was genotype and root exudate-mediated.•Genotype diversity influences soil bacteria by modifying plant-microbe interactions.