Synthetic bacterial communities to dissect and direct plant microbiome function

用于剖析和指导植物微生物组功能的合成细菌群落

• 批准号: 1917270
• 负责人: Jeffery Dangl
• 金额: $ 67万
• 依托单位: University of North Carolina at Chapel Hill
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-01 至 2024-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1917270&HistoricalAwards=false
• 关键词: Synthetic; bacterial; communities; dissect; direct

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.

植物生活在土壤中，土壤中含有非常多样化的微生物，在这些环境中，植物是这些微生物的肥沃营养来源。事实上，根创造了由特定微生物定殖的独特的物理和化学环境，并且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，但根和地上植物器官的微生物定殖仍然发生。因此，植物已经进化出区分有益相互作用和致病相互作用的机制。在土壤中，在植物根部周围的区域，存在着一个薄层-微生物群落-为植物提供益处。这些包括有助于植物生长，生产力，碳封存，以及可以防止病原体。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，以提高植物性能。迄今为止，大多数实验确定的细菌或真菌的植物益生菌菌株在田间失败。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管理它们入侵和持久存在于现有群落中的规则。为了实现这一长期目标，人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筛选成特定的和不太复杂的植物，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菌群的组装，从而导致定植，工厂性能的改变。最终目标是了解使细菌菌株能够侵入并持续进入常设异质微生物群落的原理，无论是单一菌株还是小的，定义明确的，有弹性的合成财团。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，生物体间信号传导的化学，以及可调生态系统的迭代实验扰动方面的实验专业知识。从植物-微生物互作控制、生命过程化学和群落生态学等多个学科角度来看，本研究具有重要意义和可行性。为了实现这一目标，该项目将采用新的集合测序的微生物，提供特定的植物生长优势，在这个集合中的许多类群是服从于单协会，并作为定义的复杂性合成社区的成员，与主机的机制研究。该项目超越了与植物相关的微生物群落的描述性观点，以生成和测试机制假设。这项研究最终将有助于合理设计和分子工程的合成微生物财团，利用自然的复杂性。这项研究最终将导致预测性干预措施，这将提高植物健康和生产力，促进碳封存，并通过合理利用益生菌和微生物混合物来调节内源性植物免疫系统功能，以适应特定的土壤和当地环境。该奖项反映了NSF的法定使命，并通过使用基金会的知识产权进行评估，被认为值得支持。优点和更广泛的影响审查标准。

项目成果

Specific modulation of the root immune system by a community of commensal bacteria

共生细菌群落对根部免疫系统的特异性调节

• DOI: 10.1073/pnas.2100678118
• 发表时间: 2021
• 期刊: Proceedings of the National Academy of Sciences
• 作者: Teixeira, Paulo J. P. L.;Colaianni, Nicholas R.;Law, Theresa F.;Conway, Jonathan M.;Gilbert, Sarah;Li, Haofan;Salas-González, Isai;Panda, Darshana;Del Risco, Nicole M.;Finkel, Omri M.
• 通讯作者: Finkel, Omri M.

A complex immune response to flagellin epitope variation in commensal communities

• DOI: 10.1016/j.chom.2021.02.006
• 发表时间: 2021-04-14
• 期刊: CELL HOST & MICROBE
• 影响因子: 30.3
• 作者: Colaianni, Nicholas R.;Parys, Katarzyna;Dangl, Jeffery L.
• 通讯作者: Dangl, Jeffery L.

Diverse MarR bacterial regulators of auxin catabolism in the plant microbiome.

植物微生物组中生长素分解代谢的多种细菌调节剂。

• DOI: 10.1038/s41564-022-01244-3
• 发表时间: 2022-11
• 期刊: Nature microbiology
• 影响因子: 28.3

The effects of soil phosphorus content on plant microbiota are driven by the plant phosphate starvation response

• DOI: 10.1371/journal.pbio.3000534
• 发表时间: 2019-11-01
• 期刊: PLOS BIOLOGY
• 影响因子: 9.8
• 作者: Finkel, Omri M.;Salas-Gonzalez, Isai;Dangl, Jeffery L.
• 通讯作者: Dangl, Jeffery L.

Root Microbiome Modulates Plant Growth Promotion Induced by Low Doses of Glyphosate

• DOI: 10.1128/msphere.00484-20
• 发表时间: 2020-08
• 期刊: mSphere
• 影响因子: 4.8
• 作者: D. Ramirez-Villacis;Omri M. Finkel;Isai Salas-González;Connor R. Fitzpatrick;J. Dangl;Corbin D. Jones;A. Leon-Reyes