Molecular basis of plant microbiota function and its regulation by plant immunity

在自然界中，健康植物的根和叶上有大量的微生物，如细菌，统称为植物微生物群，有助于植物的生长和健康。新出现的证据表明，植物免疫有助于塑造植物微生物群的结构。然而，我们从植物-病原体相互作用的研究中获得的植物免疫机制的知识在多大程度上可以应用于植物和植物微生物群的共生成员之间的相互作用仍然是一个悬而未决的问题。此外，目前的微生物群研究侧重于揭示植物微生物群的静态结构，仍然是描述性的。因此，需要测量植物微生物群的活性功能的分析，例如在植物元转录组中。分析宿主中的细菌（Meta）转录组已被证明是了解宿主对动物系统中细菌功能的影响的有效方法，而在植物中它一直是一个重大挑战。在这个项目中，我们的目标是通过利用我们最近开发的拟南芥中细菌病原体的植物转录组的方法来解开植物免疫对细菌群落功能过程的影响。我们观察到，完整的植物免疫信号是在胁迫条件下为植物生长募集有益细菌群落所必需的。作为下一步，我们将通过在野生型和免疫受损的A.拟南芥突变体植物我们还旨在解决一个基本问题：植物免疫如何区分不同的细菌，从而有助于微生物群的结构和功能？我们假设植物免疫通过1）通过特异性识别特异性激活免疫应答和2）选择性地影响特定的细菌种类来区分不同的植物细菌。为了测试我们的双层判别模型，我们将使用植物免疫受体和信号转导突变体来研究植物对不同个体细菌的免疫应答和植物内转录组。研究结果还将揭示植物免疫敏感或耐受的病原菌的特定生物学过程。总的来说，这些研究应该促进我们对植物微生物群的功能性理解，并阐明植物免疫对调节植物微生物群结构和功能的影响。

In nature, roots and leaves of healthy plants host multitudes of microbes such as bacteria that are collectively called the plant microbiota, which contributes to plant growth and health. Emerging evidence shows that plant immunity contributes to shaping the structure of plant microbiota. Nevertheless, to which extent our knowledge of plant immune mechanisms that has been gained from studies in plant-pathogen interactions can be applied to interactions between plants and commensal members of plant microbiota remains an open question. In addition, current microbiota researches focus on revealing static structures of plant microbiota and remain descriptive. Thus, analysis measuring active functions of plant microbiota such as in planta metatranscriptome is needed. Profiling bacterial (meta)transcriptome in hosts has been proven to be an effective approach to understand the impact of hosts on bacterial functions in animal systems, whereas it has been a substantial challenge in plants. In this project, we aim at unraveling the impact of plant immunity on functional processes of bacterial communities by capitalizing on the methods that we have recently developed for in planta transcriptome of a bacterial pathogen in Arabidopsis thaliana. We observed that the intact plant immune signaling is required to recruit a beneficial bacterial community for plant growth under a stress condition. As the next step, we will identify functional signatures (gene expression) of bacterial communities that are associated with the plant growth promotion by profiling in planta bacterial metatranscriptome in wild-type and immune-compromised A. thaliana mutant plants. We also aim at addressing the fundamental question: how does plant immunity discriminate different commensal bacteria thereby contributing to microbiota structure and function? We hypothesize that plant immunity discriminates different commensal bacteria by 1) distinctively activating immune responses via specific recognition and 2) selectively influencing on specific bacterial species. To test our two-layered discrimination model, we will use plant immune receptor and signaling mutants to investigate plant immune responses to and in planta transcriptomes of diverse individual commensal bacteria. The results will also reveal specific biological processes of commensal bacteria sensitive or tolerant to plant immunity. Collectively, these studies should advance our functional understanding of plant microbiota and illuminate the impact of plant immunity on regulating plant microbiota structure and function.