This action funds an NSF National Plant Genome Initiative Postdoctoral Research Fellowship in Biology for FY 2020. The fellowship supports a research and training plan in a host laboratory for the Fellow who also presents a plan to broaden participation in biology. The title of the research and training plan for this fellowship to David Thoms is "The Role of the Damaged-Induced Immune Response in Shaping the Plant Root Microbiome". The host institution for the fellowship is the University of British Columbia and the sponsoring scientist is Dr. Cara Haney.

Improving agricultural productivity and efficiency is of extreme importance due to the pressures of a growing population, increasingly sporadic weather patterns, and human-induced land degradation. Therefore, improving plant health and productivity in a manner that preserves the health of our limited arable land is of utmost importance. While some bacteria and microbes are known to be harmful to plants and animals, many that make up an organism's microbiome have been shown to provide significant health benefits. Bacteria present in the plant microbiome can promote plant growth, productivity, tolerance to harsh environmental conditions, and resistance to pests and pathogens. Taking advantage of the beneficial interactions between plants and bacteria is an ideal alternative to chemical-based fertilizers and pesticides. However, how plants promote positive associations with bacteria while avoiding harmful interactions is poorly understood. This project seeks to understand how plants select for beneficial bacteria while simultaneously evading bacterial pathogens. This project will focus on how plants can sense damage caused by bacterial pathogens and use that to identify, target, and eliminate harmful bacteria while leaving the beneficial bacteria intact. Training objectives include acquiring new skills and knowledge in bacteriology, next-generation sequencing, and microfluidics. Broader impacts will include the creation of educational electronic learning modules for children and adults along with the scientific mentorship of students to help increase the diversity in STEM related fields.

Understanding how plants exclude pathogens while allowing establishment of a microbiome is of major importance for diverse host-microbiome-pathogen interaction systems. This project uses a genetically tractable and high-throughput model system consisting of Arabidopsis and its associated pathogens and commensals, for which a multitude of genetic, molecular, and cell biology tools exist. It has previously been shown that plant sensing of cellular damage can trigger an immune response. This research will test the hypothesis that a localized damage signal triggered by a root pathogen could provide a cue that allows plants to distinguish pathogenic from commensal microbes. Preliminary data indicates that a plant opportunistic pathogen, that is a close relative of a known commensal, can induce a damage response on roots. The first aim of this research blends single-cell quantitative microfluidics with microbiome community ecology to understand how damage-induced immune signaling shapes plant microbiome interactions. The second aim combines forward genetics with plant physiology and cell biology to determine how beneficial microbes modulate plant immune signaling. Collectively these aims will identify how a plant immune system distinguishes between beneficial and pathogenic microbes to ultimately shape a healthy microbiome. In the face of a rising population and changing climate, this knowledge is essential for improving agricultural outputs via plant breeding programs that simultaneously bolster plant disease resistance and improve interactions with beneficial microbes. The data generated by this project will be available in public repositories such as NCBI and will be uploaded online onto a preprint server ( prior to acceptance into a peer-reviewed journal.

Keywords: rhizosphere, microbiome, plant immunity, plant defense, Arabidopsis, microscopy, microfluidics, DAMP, PAMP, cell damage


National Science Foundation (NSF)
Division of Integrative Organismal Systems (IOS)
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Diane Okamuro
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Thoms, David
United States
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