Continental scale deciphering of microbiome networks untangles the phyllosphere homeostasis in tea plant

•The critical mechanisms underlying the microbiome assembly in the tea plants are revealed.•There is a trade-off between stochastic and deterministic processes in microbiome assembly in the tea plants.•Assembly processes were dominated by deterministic processes in bulk and rhizosphere soils.•The stochastic processes in roots and leaves was critically driven by amino acids for environmental selection.•The core taxa assembled in phyllosphere could attenuate the virulence of a prevalent foliar pathogen.