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

该INSPIRE奖汇集了传统上支持生物学理事会综合生物系统司，数学和物理科学理事会化学司以及计算机信息科学工程理事会信息和智能系统司的研究领域。植物扎根于充满微生物（细菌、真菌和线虫）的土壤中。其中许多可以帮助植物更好地生长，例如，使矿物质直接被植物利用，或抑制植物病原微生物的生长。植物根表面的微生物群落，实际上是根内部的微生物群落，执行专门的功能以维持它们与植物的联系。这个群落被称为根微生物组。几乎没有人知道植物相关的微生物是如何从非常多样化的土壤微生物群落中组装的。该项目的特点是来自纽约、北卡罗来纳州和加州的四个机构的一组不同的研究人员，他们的目标是利用从基因组学到计算机建模再到化学的跨学科方法，研究与植物根部相关的细菌和真菌微生物。该项目的目标是学习如何创建可作为“益生菌”应用于作物的特定微生物群落，这将改善植物健康和作物产量，并可能取代疾病和肥料的化学控制。多样化的研究人员将为本科生、研究生和博士后学者提供学习和指导机会，并通过北卡罗来纳州大学的莫尔黑德科学中心进行推广。研究人员希望了解细菌，真菌和植物根部（以及这些根部中的微生物之间）在纳米（化学信号）到厘米（小尺度生态系统）的空间尺度上的通信。根微生物组的组织至少在一定程度上是决定性的，而不仅仅是生态位填充，至少在更高的分类水平。该项目将部署受控的微观世界和统计建模，以定义（1）在简化的合成群落中驱动根微生物组组装的原则，以及（2）特定的宿主和微生物遗传和化学信号机制，这些机制控制从复杂的土壤群落到复杂性降低的内生菌群落的筛选。预期的结果将导致：（1）定义影响植物生长的测序微生物的降低复杂性的群落，并且可以在再定殖微观世界实验中部署，以定义和迭代地测试驱动群落形成的原理的实验模型;（2）从微生物和植物宿主调节根微生物组组装的基因座的突变鉴定;和（3）新的测序微生物的集合，其提供特定的植物生长优势，并且在与宿主的单缔合和作为限定的复杂性群落的成员两者中，其适于详细的机理研究。

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.