The Plant Root-Associated Microbiome Viewed Across Diverse Plant Species and Developmental Stages

Soil microbes are important mediators of plant nutrition, growth, and resistance to biotic and abiotic stresses. Plants acquire root-associated microbiomes that are distinct from that of the surrounding soil. We have previously reported¹that for cultivated rice, the root-associated microbiome has a relatively small dependence on the host plant genotype. We have now investigated the effect of wide interspecies host variation on assimilated root-associated microbiomes within a single environment. We find that host microbiome variation does not reflect host plant phylogenetic relationships and that rice plants enrich for a unique rhizospheric and endospheric microbiome compared to other host plants growing in the same environment. A comparison of the root-associated microbiomes of rice with microbiota of soil from cultivated fields and non-cultivated soils, suggests that rice cultivation changes the overall soil microbiome in rice fields not only through agricultural inputs and water submergence, but also through specific enrichment of microbial taxa by rice plants. We have also studied variations in the microbiome through the lifecycle of rice plants under field conditions. We find that the composition of the microbiome shifts throughout vegetative growth until the initiation of reproductive growth, whereupon the microbiome stabilizes. These results suggest that plants select for different microbiota as they undergo developmental changes from germination to reproduction.

¹Edwards, Joseph, et al. "Structure, variation, and assembly of the root-associated microbiomes of rice." Proceedings of the National Academy of Sciences 112.8 (2015): E911-E920.DOI:10.1073/pnas.1414592112