NSF Postdoctoral Fellowship in Biology FY 2020: The Role of the Damaged-Induced Immune Response in Shaping the Plant Root Microbiome

本行动资助NSF国家植物基因组计划2020财年生物学博士后研究奖学金。该奖学金支持奖学金获得者在主办实验室的研究和培训计划，该奖学金获得者还提出了扩大生物学参与的计划。David Thoms的研究和培训计划的标题是“受损诱导的免疫反应在塑造植物根系微生物组中的作用”。该奖学金的主办机构是英属哥伦比亚大学，赞助科学家是卡拉·哈尼博士。由于不断增长的人口、日益零星的天气模式和人为造成的土地退化所带来的压力，提高农业生产力和效率是极其重要的。因此，以保持我们有限的可耕地健康的方式改善植物健康和生产力是至关重要的。虽然已知一些细菌和微生物对植物和动物有害，但组成生物体微生物群的许多细菌和微生物已被证明对健康有重大益处。存在于植物微生物组中的细菌可以促进植物生长、生产力、对恶劣环境条件的耐受性以及对害虫和病原体的抵抗力。利用植物和细菌之间有益的相互作用是化学肥料和农药的理想替代品。然而，植物如何促进与细菌的积极联系，同时避免有害的相互作用，人们知之甚少。该项目旨在了解植物如何选择有益细菌，同时避开细菌病原体。该项目将专注于植物如何感知细菌病原体造成的损害，并利用它来识别、瞄准和消除有害细菌，同时保持有益细菌的完整。培训目标包括获得细菌学、下一代测序和微流体学方面的新技能和知识。更广泛的影响将包括为儿童和成人创建教育电子学习模块，以及为学生提供科学指导，以帮助增加STEM相关领域的多样性。了解植物如何在排除病原体的同时允许微生物组的建立，对于多种宿主-微生物组-病原体相互作用系统具有重要意义。本项目使用由拟南芥及其相关病原体和共生体组成的遗传易处理和高通量模型系统，为此存在大量遗传，分子和细胞生物学工具。以前的研究表明，植物对细胞损伤的感知可以引发免疫反应。这项研究将验证一个假设，即由根病原体触发的局部损伤信号可以提供一个线索，使植物能够区分病原微生物和共生微生物。初步数据表明，植物条件病原菌是一种已知共生菌的近亲，可以引起根系的损伤反应。本研究的第一个目的是将单细胞定量微流体与微生物群落生态学相结合，以了解损伤诱导的免疫信号如何影响植物微生物组的相互作用。第二个目标是将正向遗传学与植物生理学和细胞生物学相结合，以确定有益微生物如何调节植物免疫信号。总的来说，这些目标将确定植物免疫系统如何区分有益微生物和致病微生物，最终形成健康的微生物群。面对不断增长的人口和不断变化的气候，这些知识对于通过植物育种计划提高农业产量至关重要，这些计划可以同时增强植物的抗病性并改善与有益微生物的相互作用。该项目生成的数据将在NCBI等公共存储库中提供，并在被同行评审期刊接受之前在线上传到预印本服务器（bioRxiv.org）。关键词：根际，微生物组，植物免疫，植物防御，拟南芥，显微镜，微流体，DAMP， PAMP，细胞损伤该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

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 (bioRxiv.org) prior to acceptance into a peer-reviewed journal.Keywords: rhizosphere, microbiome, plant immunity, plant defense, Arabidopsis, microscopy, microfluidics, DAMP, PAMP, cell damageThis award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.