19-BBSRC-NSF/BIO: A holistic approach to understand drought adaptation in plants, their symbionts, and free-living microbiomes

Drought is devastating to agricultural productivity, and drought intensity and frequency are expected to increase in the coming years. Despite ongoing studies to address the crisis, we are far to find a single solution that will solve it; only combinations of different strategies applied across the AgriFood sector has the potential to achieve transformative effects. For example, recent evidences suggest that soil microbes that live in close association with plants may play a role in plant drought tolerance. Hence, controlling the beneficial interaction of these microbes with the plant is an excellent strategy to help manage water content in the plant. This project proposes to use molecular tools, experiments under controlled conditions, and cutting-edge plant physiological characterization to disentangle the plant-microbe relationships in the context of adaptation to drought stress. This project would advance our progress toward both, understanding the evolution of this interaction, and the development of microbial tools or techniques to improve drought resilience in agroecosystems.

Root-associated microbes can profoundly affect the physiology and health of their host plants, and these interactions are shaped by genetic variation both in the host species and in microbiome members. Because plant microbiomes are largely derived from the broader soil community, the constituent microbial lineages encounter environmental stressors both with and without a host. It is unknown whether the same microbial genes and traits contribute to stress tolerance and survival in both situations, or whether there is a fitness trade-off between host-associated versus free-living stages. Similarly, it is unknown whether microbiome adaptation to a given environmental challenge impacts the ability of a plant host to withstand the same challenge. The rationale for the proposed work is that we lack clear examples of how adaptation to a shared environmental stressor affects symbiotic interactions between plants and microbial communities. Using drought as a model stressor, we will combine natural environmental gradient sampling, experimental evolution, and physiological assays with shotgun metagenome sequencing to disentangle the genetic, physiological, and ecological interdependencies that shape the evolution of plant microbiomes. Because community-level adaptive responses involve both evolutionary processes and ecological processes, we focus on how they combine to affect emergent microbiome properties: metagenome content and direct assays of microbial influences on plant physiology.