摘要In nature, plants are colonized by various mi-crobes that play essential roles in their growth and health. Heterosis is a natural genetic phenomenon whereby first-generation hybrids exhibit superior phenotypic performance relative to their parents. It remains unclear whether this concept can be extended to the"hybridization"of microbiota from two parents in their descendants and what bene-fits the hybrid microbiota might convey. Here, we investigated the structure and function of the root microbiota from three hybrid rice varieties and their parents through amplicon sequencing anal-ysis of bacterial 16S ribosomal DNA (rDNA) and fungal internal transcribed spacer (ITS) regions. We show that the bacterial and fungal root microbiota of the varieties are distinct from those of their parental lines and exhibit potential heterosis features in diversity and composition. Moreover, the root bacterial microbiota of hybrid variety LYP9 protects rice against soil-borne fungal pathogens. Systematic analysis of the protective capabilities of individual strains from a 30-member bacterial synthetic community derived from LYP9 roots indicated that community mem-bers have additive protective roles. Global tran-scription profiling analyses suggested that LYP9 root bacterial microbiota activate rice reactive oxygen species production and cell wall bio-genesis, contributing to heterosis for protection. In addition, we demonstrate that the protection conferred by the LYP9 root microbiota is trans-ferable to neighboring plants, potentially ex-plaining the observed hybrid-mediated superior effects of mixed planting. Our findings suggest that some hybrids exhibit heterosis in their mi-crobiota composition that promotes plant health, highlighting the potential for microbiota heterosis in breeding hybrid crops.