Data from: Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life-cycle in field-grown rice

Bacterial communities associated with roots impact the health and
nutrition of the host plant. The dynamics of these microbial assemblies
over the plant life cycle is however, not well understood. Here, we use
dense temporal sampling of 1588 samples from root spatial compartments to
characterize the bacterial and archaeal components of the root-associated
microbiota of field grown rice (Oryza sativa) over the course of three
consecutive growing seasons, as well as two sites in diverse geographic
regions. The root microbiota was found to be highly dynamic during the
vegetative phase of plant growth, then stabilized compositionally for the
remainder of the life cycle. Bacterial and archaeal taxa conserved between
field sites were defined as predictive features of rice plant age by
modeling using a random forests approach. The age-prediction models
revealed that drought stressed plants have developmentally immature
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.