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

在自然界中，健康植物的根和叶中含有大量的微生物，如细菌，这些微生物统称为植物微生物区系，有助于植物的生长和健康。越来越多的证据表明，植物免疫有助于塑造植物微生物区系的结构。然而，我们从植物-病原菌相互作用研究中获得的植物免疫机制在多大程度上可以应用于植物与植物微生物区系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，目前的微生物区系研究侧重于揭示植物微生物区系的静态结构，并保持描述性。因此，需要对植物微生物区系的活性功能进行分析，例如在植物偏转录组中。在宿主中分析细菌(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，而在植物中这一直是一个巨大的挑战。在这个项目中，我们旨在通过利用我们最近开发的方法来揭示植物免疫对细菌群落功能过程的影响，这些方法是我们最近开发的在拟南芥细菌病原体的植物转录组中的方法。我们观察到，在胁迫条件下，完整的植物免疫信号是为植物生长招募有益的细菌群落所必需的。下一步，我们将通过对野生型和免疫受损突变体植物中的细菌总转录组进行分析，确定与植物生长促进相关的细菌群落的功能特征(基因表达)。我们还致力于解决基本问题：植物免疫如何区分不同的共生细菌，从而促进微生物区系的结构和功能？我们假设，植物免疫通过1)通过特定的识别而独特地激活免疫反应和2)选择性地影响特定的细菌种类来区分不同的共生细菌。为了测试我们的双层识别模型，我们将使用植物免疫受体和信号突变体来研究植物对不同个体共生细菌转录产物的免疫反应。研究结果还将揭示共生细菌对植物免疫敏感或耐受的特定生物学过程。总之，这些研究将促进我们对植物微生物区系的功能理解，并阐明植物免疫对调节植物微生物区系结构和功能的影响。

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.