Land plants continuously contact beneficial, commensal, and pathogenic microbes in soil via their roots. There is limited knowledge as to how the totality of root-associated microbes (i.e., the microbiome) is shaped by various factors or its pattern of acquisition in the root. Using rice as a model, we show that there exist three different root niches hosting different microbial communities of eubacteria and methanogenic archaea. These microbial communities are affected by geographical location, soil source, host genotype, and cultivation practice. Dynamics of the colonization pattern for the root-associated microbiome across the three root niches provide evidence for rapid acquisition of root-associated microbiomes from soil, and support a multistep model wherein each root niche plays a selective role in microbiome assembly.