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

这个INSPIRE奖汇集了传统上由生物局的综合有机体系统部、数学和物理科学局的化学部和计算机与信息科学与工程局的信息与智能系统部支持的研究领域。植物植根于富含微生物(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，使植物直接可利用矿物质，或通过抑制植物病原微生物的生长。植物根部表面，甚至是根部内部的微生物群落，发挥着特殊的功能，以保持它们与植物的联系。这个群落被称为根部微生物群落。关于植物相关微生物是如何从非常多样化的土壤微生物群落中组装而成的，人们几乎一无所知。该项目以来自纽约、北卡罗来纳州和加利福尼亚州的四个机构的不同研究人员为特色，他们的目标是使用从基因组学到计算机建模再到化学的跨学科方法，研究与植物根相关的细菌和真菌微生物。该项目的目标是学习如何创建定义的微生物群落，这些微生物可以作为“益生菌”应用于作物，从而改善植物健康和作物产量，并可能取代对疾病和化肥的化学控制。多元化的研究人员将通过北卡罗来纳大学的莫尔黑德科学中心，为本科生、研究生和博士后学者提供学习和指导机会。研究人员希望在纳米(化学信号)到厘米(小规模生态系统)的空间尺度上了解细菌、真菌和植物根之间(以及这些根中的微生物之间)之间的交流。根微生物组组织至少部分是确定性的，而不仅仅是生态位填充，至少在较高的分类水平上是这样。该项目将利用受控微观世界和统计建模来定义(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)管理从复杂土壤群落筛选到降低复杂性的内生植物群落的特定寄主和微生物遗传和化学信号机制。预期结果将导致：(1)定义影响植物生长的降低复杂性的测序微生物群落，并可部署在再定殖微观实验中，以定义并迭代测试驱动群落形成的原理的实验模型；(2)突变鉴定调节来自微生物和植物宿主的根微生物组组装的基因座；以及(3)提供特定植物生长优势的新型测序微生物集合，这些微生物能够在单一联合中进行详细的机制研究，并作为已定义的与宿主的复杂性群落的成员。

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.