Molecular mechanisms underlying the microbiota-influenced host growth-defense coordination

植物与环境微生物密切相关，作为无根生物，需要应对不断变化的生物和非生物条件以确保其生存。与植物相关的微生物，统称为植物微生物群，能够以各种方式操纵宿主的生长和免疫。研究表明，从多种健康植物中分离的根瘤菌共生菌可促进拟南芥根系生长，并抑制flg22和pep1等激发子肽引发的免疫反应。在这个拟议的研究项目中，我的目标是利用分子遗传学结合系统生物学和细胞生物学的方法阐明微生物群影响宿主生长-防御协调的分子机制。我的目标是建立一个全面的时间和空间分辨的分子模型，描述植物如何在复杂微生物群落的存在下协调其生长和防御。我之前的工作表明，植物硫酸化肽是根相关共生细菌的靶标，在引发子肽处理过程中操纵宿主根的生长防御协调，这表明在生长调节硫酸化肽和免疫调节引发子肽的感知之间和/或在随后的信号传导过程中存在串扰。我将解开这种串扰的分子基础，分析受体和信号成分的生化状态，以及下游基因表达谱。我还将利用一组与植物相关的共生细菌菌株，其基因组已被测序，以确定负责干扰宿主生长-防御协调的细菌基因。为此，我将使用在模拟植物条件的系统中培养的体外细菌培养物进行多组学实验，这将反过来用作跨组学全关联研究的输入。最后，我将结合大量已发表和未发表的拟南芥根与参与不同生活方式的微生物相互作用的转录组学数据，在共表达基因网络中选择潜在的关键调控枢纽基因。植物和细菌的反向遗传方法将被用于实验验证鉴定基因在影响宿主生长-防御协调以及根微生物群组装方面的功能。总的来说，我将阐明根相关共生细菌干扰宿主生长-防御协调的遗传框架。该框架将为进一步探索植物及其相关微生物群之间的分子对话以及解决植物免疫在控制根微生物群结构和功能中的作用奠定基础。

Plants live in intimate association with environmental microbes and, as sessile organisms, need to cope with changing biotic and abiotic conditions to ensure their survival. Plant-associated microbes, collectively called the plant microbiota, are able to manipulate host growth and immunity in various ways. We have shown that Rhizobiales commensal bacteria isolated from a variety of healthy plants promote Arabidopsis thaliana root growth and suppress immune responses triggered by elicitor peptides, such as flg22 and pep1. In this proposed research program, I aim to elucidate the molecular mechanisms underlying microbiota-influenced host growth-defense coordination using molecular genetics combined with systems biology and cell biological approaches. My goal is to build a comprehensive time- and space-resolved molecular model that describes how plants coordinate their growth and defense in the presence of complex microbial communities.My previous work showed that plant sulfated peptides are targeted by root-associated commensal bacteria to manipulate host root growth-defense coordination upon elicitor peptide treatments, suggesting the crosstalk between perception of growth-regulating sulfated peptides and immunity-regulating elicitor peptides and/or within the subsequent signaling processes. I will disentangle the molecular basis underlying this crosstalk analyzing the biochemical status of the receptors and signaling components, as well as the downstream gene expression profiles. I will also exploit a collection of plant-associated commensal bacterial strains, whose genomes have been sequenced, to identify bacterial genes that are responsible for the interference with host growth-defense coordination. To this end, I will perform multi-omics experiments using in vitro bacterial cultures cultivated in a system mimicking in planta conditions, which will be in turn used as an input for trans-omics-wide association study. Lastly, I will incorporate a large set of published and unpublished transcriptomic data of A. thaliana roots interacting with microbes engaged in different lifestyles to select potential key regulatory hub genes in a co-expressed gene network. Plant and bacterial reverse genetic approaches will be employed to experimentally validate the function of identified genes in influencing host growth-defense coordination as well as in root microbiota assembly.Overall, I will elucidate the genetic framework by which root-associated commensal bacteria interfere with host growth-defense coordination. This framework will form the basis for further exploration of the molecular dialog between plants and their associated microbiota and addressing the role of plant immunity in controlling the structure and functions of the root microbiota.