Our aims were to (1) reveal the mechanisms of Acorus calamus root-assoicated microbiome assembly which microbiomes are interactively influenced by compartment niche, plant development and environmental factors; (2) uncover the temporal dynamics of microbial co-occurence network of bacterial and fungal communities across plant developmental stages; and (3) clarify the ecological functions of keystone taxa of microbes in the root endosphere at different stages of plant development.