Fig. 7

Schematic representation of the two-step interaction between PGPB and plants mediated by DNA methylation and root recruitment. Purple circles indicate the PGPB inoculum. Green circles represent methylated cytosines. In the early phase, inoculation with PGPB induced variation in the rhizosphere microbiome. Plants adapt to the dynamic rhizosphere microbiome through comprehensive changes in transcription profiles, including DNA methylation-related genes, which results in the modification of DNA methylation. The influences of inocula on the rhizosphere microbiome weaken along with the elimination of the inoculum from the rhizosphere microbiome. In the late phase, the altered DNA methylation regulates gene expression to facilitate plant growth, and a stable rhizosphere microbiome is assembled by recruitments of roots