Synthetic bacterial communities to dissect and direct plant microbiome function

植物生活在土壤中，土壤中蕴藏着极其多样化的微生物，在这些环境中，植物是这些微生物的肥沃养分来源。事实上，根创造了一个独特的物理和化学环境，由特定的微生物定植，尽管植物免疫系统的主要功能是保护植物免受病原体的侵害，但微生物对根和地上植物器官的定植还是发生了。因此，植物已经进化出了区分有益相互作用和致病相互作用的机制。在植物根部周围的土壤中，存在着一层薄薄的微生物群落，它们对植物有益。这包括促进植物生长、提高生产力、固碳以及抵御病原体。这项工作旨在将特定的细菌菌株或菌株集合部署到野生微生物群落中，以提高植物的性能。迄今为止，大多数实验确定的植物益生菌菌株的细菌或真菌在田间失败。这表明，为了成功地将有益微生物部署到野生微生物群落中，我们需要更好地了解控制它们入侵和持续存在于现有群落的规则。为了实现这一长期目标，我们需要了解特定的宿主和微生物遗传和化学信号机制，这些机制控制着复杂的土壤微生物群落向特定的和不太复杂的植物相关群落的筛选，这些群落有助于植物的生长。该项目旨在定义组织网络规则和分子机制，这些规则和分子机制控制菌株和小细菌群体的组装，导致植物的定植和性能的改变。最终目标是了解使细菌菌株能够入侵并持续存在于异质微生物群落的原理，无论是作为单一菌株还是作为小的，定义良好的，有弹性的合成联合体。成功将需要在宿主植物和微生物的基因组学、遗传学和生理学方面的实验专业知识，在生物间信号的化学方面，以及可调节生态系统的迭代实验扰动方面。从植物与微生物相互作用的控制、生命过程化学和群落生态学等多个学科角度来看，本研究具有重要的意义和可行性。为了实现这一目标，该项目将采用提供特定植物生长优势的新型测序微生物集合；这个集合中的许多分类群都适合于与宿主的单关联和作为定义复杂合成群落成员的机制研究。该项目超越了植物相关微生物群落的描述性观点，以产生和测试机制假设。该研究最终将有助于合理设计和利用自然复杂性的合成微生物群落的分子工程。该研究最终将导致预测性干预措施，通过合理利用益生菌微生物和微生物混合物调节特定土壤和当地环境的功能，提高植物健康和生产力，促进碳固存，调节内源性植物免疫系统功能。该奖项反映了美国国家科学基金会的法定使命，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。

Plants live in soils that harbor extraordinarily diverse microorganisms, and in these environments, plants serve as fertile sources of nutrients for these microbes. Indeed, roots create a distinct physical and chemical environment that is colonized by specific microbes, and microbial colonization of the root and the above-ground plant organs occurs despite a plant immune system whose primary function is to defend the plant against pathogens. Thus, plants have evolved mechanisms to distinguish beneficial interactions from pathogenic interactions. In the soil, in the area immediately surrounding the plant root, there exists a thin layer - a community of microorganisms - that provide benefits to the plant. These include contributing to plant growth, productivity, carbon sequestration, as well as can protect against pathogens. This work aims to deploy specific bacterial strains, or collections of strains, into wild microbial communities with the goal of improving plant performance. To date, most experimentally defined plant probiotic strains of bacteria or fungi fail in the field. This suggests that to successfully deploy beneficial microbes into wild microbial communities, we need to better understand the rules that govern their invasion into, and persistence in, existing communities. To achieve this long term goal, one needs to understand the specific host and microbial genetic and chemical signaling mechanisms that govern the winnowing of complex soil microbial communities into specific and less complex plant-associated communities that contribute to plant performance.This project aims to define the organizational network rules and molecular mechanisms that govern the assembly of strains and small consortia of bacteria resulting in colonization and alterations of plant performance. The ultimate goal is to understand the principles that make bacterial strains able to invade and persist into standing heterogeneous microbiome communities as either single strains or as small, well defined, resilient synthetic consortia. Success will require experimental expertise in the genomics, genetics and physiology of both host plants and microbes, in the chemistry of inter-organismal signaling, and iterative experimental perturbation of a tunable ecosystem. This research is significant and feasible from various disciplinary perspectives, including the control of plant-microbe interactions, chemistry of life processes and community ecology. To accomplish this goal, the project will employ the use of novel collections of sequenced microbes that provide specific plant growth advantages; many taxa in this collection are amenable to mechanistic studies in both mono-association, and as members of defined complexity synthetic communities, with the host. The project moves beyond descriptive views of plant-associated microbial communities to generate and test mechanistic hypotheses. The research will ultimately contribute to rational design and molecular engineering of synthetic microbial consortia that take harness Nature's complexity. The research will ultimately lead to predictive interventions that will increase plant health and productivity, facilitate carbon sequestration, and modulate endogenous plant immune system function through the rational utilization of probiotic microbes and mixtures of microbes tuned to function in particular soils and local environments.This 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.