Title: Functional manipulation of root endophyte populations for feedstock improvement.
DOE SC0010423
08/15/13-08/14/16
In this proposal, we aim to use bacterial isolates from Arabidopsis roots and roots of the emerging biofuels model, Setaria viridis to understand how the core microbiome functions to promote plant growth and protection against fungal infection. This is a collaboration with DOE-ORNL.
Project Summary: A major goal of the US bioenergy research program is to create plant feedstocks with reduced cell wall recalcitrance for sugar release that can be managed in a sustainable fashion on marginal lands of diverse edaphic conditions (e.g. soil nutrients, moisture and other qualities). It is increasingly clear that a variety of plant functions and traits are co-dependent on the microbial community that exists within and around them, especially the communities associated with the plant root system (rhizosphere). These complex communities of plants and microbes can benefit plant health and productivity in the face of changing environmental conditions by modifying host physiological traits including nutrient uptake, growth allocation patterns within and between above- and below-ground organs and related plant hormone signaling, microbial catabolism of toxic compounds in the root zone, and enhanced resistance to pathogens through competitive exclusion and ‘priming’ of the innate plant immune system. Hence, the plant microbiome contributes dramatically the extended phenotype of the combined plant and microbial genotypes to determine plant health and productivity. One specific avenue for improvements in plant feedstock productivity is to ‘let the plant tell us’ what microbial species from the complex soil metagenome are functionally relevant for plant productivity. This will require a careful definition of the rhizosphere-associated communities across diverse plant species in order to have the broadest applicability across the range of feedstocks that might be deployed. Our overarching experimental goal is to utilize two large, and expanding, sets of endophytic bacterial strains and three diverse hosts, chosen with explicit reference to both excellent (or emerging) genetic and genomic resources and bioenergy feedstock relevance: the reference flowering plant (Arabidopsis), a well developed perennial tree model (Populus), and an emerging model for C4 bioenergy crops, Setaria viridis. Deployment of these systems where each is most appropriate within a comparative framework will put us in a unique position to address questions regarding the robustness and reproducibility of microbe-mediated phenotypes across multiple plant hosts and laboratories, and will drive dissection of the dependence of host genetic properties on extended phenotypes for nutrient utilization and environmental influences on plant productivity.
We anticipate that we will deliver broad rules and fundamental science that will guide the subsequent generation of specific EC microbes or small consortia of EC microbes for future incorporation into feedstock development. We propose that feedstocks will ultimately be more effectively deployed and managed within the framework of understanding the interactions of host genotype, microbial community genotypes that ultimately determine edaphic profile of a potential feedstock. This will require understanding of the mechanisms guiding specific assembly of plant root microbiomes suited to local edaphic and climatic conditions.
The proposed research will ultimately lead to predictive interventions that will increase plant health and productivity, facilitate carbon sequestration, and modulate endogenous plant immune system function through the rational utilization of probiotic microbes and mixtures of microbes tuned to function in particular soils and local environments.