INSPIRE Track 2: Defining the Organizational Principles of Microbial Communities Colonizing Plant Roots

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This INSPIRE award brings together research areas traditionally supported in the Division of Integrative Organism Systems in the Directorate for Biology, the the Division of Chemistry in the Directorate for Mathematical and Physical Sciences, and the Division Information and Intelligent Systems in the Directorate for Computer & Information Science & Engineering. Plants are rooted in soil teeming with micro-organisms (bacterial, fungi and nematodes). Many of these can help plants grow better by, for example, making minerals directly usable by the plant, or by inhibiting the growth of plant-pathogenic microbes. The community of microbes on the surface of plant roots, and indeed inside the root, perform specialized functions to maintain their association with the plant. This community is called the root microbiome. Almost nothing is known about how plant-associated microbiomes are assembled from the very diverse soil microbial community. This project features a diverse group of investigators located at four institutions from New York, North Carolina and California, who aim to use interdisciplinary approaches from genomics to computer modeling to chemistry, to study the bacterial, and fungal microbes associated with plant roots. The goal of this project is to learn how to create communities of defined microbes that can be applied to crops as "probiotics" that will improve plant health and crop yield, and may replace chemical controls of disease and fertilizers. The diverse investigators will provide learning and mentoring opportunities for undergraduate, post-graduate and post-doctoral scholars, and via outreach through the University of North Carolina's Morehead Science Center. The investigators wish to understand communication between bacteria, fungi and plant roots (and between microbes in those roots) at spatial scales of nanometers (chemical signals) to centimeters (small scale ecosystems). Root microbiome organization is at least partly deterministic, as opposed to merely niche filling, at least at higher taxonomic levels. The project will deploy controlled microcosms and statistical modeling to define (1) principles driving root microbiome assembly in simplified synthetic communities, and (2) specific host and microbial genetic and chemical signaling mechanisms governing the winnowing from complex soil communities into reduced complexity endophyte communities. Anticipated results will lead to: (1) definition of reduced complexity communities of sequenced microbes that influence plant growth and can be deployed in re-colonization microcosm experiments to define and iteratively test experimentally models of the principles that drive community formation; (2) mutational identification of loci that tune root microbiome assembly from both microbes and plant hosts; and (3) collections of novel sequenced microbes that provide specific plant growth advantages and that are amenable to detailed mechanistic studies in both mono-association, and as members of defined complexity communities, with the host.