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

PLoS Biology
Joseph EdwardsVenkatesan Sundaresan

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 sugg...Continue Reading

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Citations

Jan 25, 2019·Proceedings of the National Academy of Sciences of the United States of America·Matthias L BerensKenichi Tsuda
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Datasets Mentioned

BETA
PRJNA386367
PRJNA392701

Methods Mentioned

BETA
genotyping
PCR

Software Mentioned

Python
ggplot2
PandaSeq
Ninja
edgeR
PERMANOVA
BetaReg
randomForest R package
Stats package
R

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