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

Abstract

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 are, however, not well understood. Here, we use dense temporal sampling of 1,510 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 3 consecutive growing seasons, as well as 2 sites in diverse geographic regions. The root microbiota was found to be highly dynamic during the vegetative phase of plant growth and 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 forest 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.

Multilab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass

“…It could be that integrating these factors in future EcoFAB studies might increase the variability of the system. It will be important to investigate the reproducibility as well as the morphological and metabolic responses of plants to microbial communities and soil mineralogy, as natural soils were identified as main contributors shaping root morphology, plant C exudation, plant–microbe interactions, and rhizosphere extension (Bulgarelli et al ., ; Holz et al ., ; Koebernick et al ., ; Edwards et al ., ). Overall, we conclude that the reproducibility of plant traits in soil extract EcoFABs is a promising first step towards developing plant growth systems generating reproducible data that are relevant to field environments.…”

Transient interactions and influence among bacteria in field-grown Arabidopsis thaliana tissues

“…Microbial communities undergo shifts in diversity and composition as seasons change and their hosts mature (3,4). However, temporal variation of microbe-microbe interactions within these communities has not been characterized.…”

Belowground microbial communities respond to water deficit and are shaped by decades of maize hybrid breeding

“…There have been a limited number of reports in the literature on the temporal dynamics of microbial communities (Shi et al, 2015;Fierer, 2017;Edwards et al, 2018;Xu et al, 2018). Agroecosystems provide an excellent platform for analyzing temporal changes in microbial communities because the experimental design allows for replicated plots, which are large enough to be sampled multiple times.…”

“…This highlights the dynamic nature of the microbial communities that are associated with plant roots and suggests that single time point sampling only provides a limited snapshot of complex soil microbial communities. While some have suggested that the changes observed in microbiomes over time are related to plant development (Chaparro et al, 2014), more recent work show that in some cases residence time in the soil rather than plant development was more important (Dombrowski et al, 2017) or that both development and residence time play roles (Edwards et al, 2018) in temporal changes. This study clearly showed that changes in the root, rhizosphere and soil microbiome occur throughout the growing season in temperate soils where maize is grown.…”