BPP Fall Seminar Series

Plants depend upon interactions with root-associated microbes for nutrient availability, disease suppression, and growth promotion. Through a large-scale study of root-associated microbiomes of cultivated rice by high-throughput sequencing, we identified a huge diversity of microbes, with over a quarter million taxa forming distinct communities that inhabit the soil near the roots, the root surface and the root interior¹. Analysis of the de novo assembly of root-associated microbiomes shows that microbiota acquisition occurs rapidly, following a multistep model. Major factors underlying variation in root microbial communities are geography, soil type, genotype, cultivation practices, such as organic vs. conventional. Exposure to drought results in a major re-structuring of the rice root microbiome, which might be indicative of a protective response to adverse environmental conditions^2,5. Root microbiomes are age-dependent, in that the composition of the root microbiota tracks plant development, with a consistent shift at the transition to flowering across genotypes. Thus, computational models can be used to predict plant age based on microbiome composition³. While it is well known that plants recruit their root microbiota from the soil, there is also a reverse effect of plant growth on soil microbiota over time, suggesting that continuous cultivation leads to “soil domestication”⁴.  For functional studies of root-associated microbiomes, a rice gnotobiotic system has been established, that reveals significant transcriptome changes in the plant in response to microbiome acquisition. In combination with synthetic communities, such controlled systems provide a promising route towards dissecting the complex interactions of root microbial communities with their host plants.