Compositional shifts in the root microbiota track the life-cycle of field-grown rice plants

Bacterial communities associated with roots impact the health and nutrition of the host plant. While a multitude of static factors are known to influence the composition of the root-associated microbiota, the dynamics of these microbial assemblies over the plant life cycle are poorly understood. Here, we use dense temporal sampling of spatial compartments to characterize the root-associated microbiota of field grown rice (Oryza sativa) over the course of three consecutive growing seasons and two sites in diverse geographic regions. The root microbiota was found to be highly dynamic during the vegetative phase of plant growth, then stabilizes compositionally for the remainder of the life cycle. Bacterial taxa conserved between field sites can be used as predictive features of rice plant age by modeling using a random forests approach. The age-prediction models were used to reveal that drought stressed plants have developmentally delayed microbiota compared to unstressed plants. Further, by using genotypes with varying developmental rates, we show that shifts in the microbiome are correlated with rates of developmental transitions rather than age alone, such that different microbiota compositions reflect juvenile and adult life stages. These results suggest a model for successional dynamics of the root-associated microbiota over the plant life cycle.