Tea varieties modulate rhizosphere microbiome assembly via root metabolite-mediated selection

Abstract

Plant variety-specific belowground environment shapes rhizosphere microbial communities, yet the mechanisms underlying tea plant (Camellia sinensis) variety-driven microbiome assembly remain unclear. We integrated multispectral phenotyping, soil physicochemical analysis, microbiome sequencing, and root metabolomics, to compare three clonal tea varieties, Zhongcha 108 (ZC), Jinxuan (JX), and Jinmudan (JMD). Results showed that significant differences in canopy phenotypes were observed among tea varieties, as manifested by distinct spectral reflectance and vegetation indices. Microbial community structure differed significantly among all varieties at both phylum and genus levels. ZC enriched photoautotrophic taxa (e.g., Cyanobacteriales, Acetobacteraceae) and saprotrophic fungi. JX favored chemoheterotrophic bacteria (e.g., Oceanobacillus, Brevibacillus) and undefined saprotrophs. JMD enriched bacterial genera like SBR1031 and arbuscular mycorrhizal fungi (e.g., Paraglomerales). Soil physicochemical properties were typically at higher levels in JX than that in ZC and JMD, and correlated negatively with bacterial phyla Verrucomicrobiota, Acidobacteriota, and Chloroflexi, and fungal phylum Glomeromycota. Root metabolites, especially amino acids, sugars, and diterpenoids, were key drivers of microbial assembly. Correlation analysis identified Acidobacteriota, Chloroflexi, and Firmicutes as key bacteria, and Zoopagomycota as key fungus linked to varietal variation of metabolite profiles. Predicted microbial functions revealed that ZC associated with photoautotrophy, JX/JMD with chemoheterotrophy and nutrient cycling. JMD specifically enriched arbuscular mycorrhizal functions. Variance partitioning analysis (VPA) revealed that the drivers of microbial assembly were kingdom-specific. Root metabolites emerged as the dominant factor explaining the variance in bacterial communities. In contrast, the variance in fungal communities was primarily explained by the shared effect of soil properties and root metabolites, indicating a synergistic interaction. Our findings reveal that root metabolites are the dominant factor underlying tea variety-driven assembly of the rhizosphere microbiome, offering microbiome-driven strategies for precision plant breeding and management.