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

• Applicant: Professor Dr. Paul Schulze-Lefert, since 5/2021
• Subject Area: Organismic Interactions, Chemical Ecology and Microbiomes of Plant Systems ; Plant Genetics and Genomics
• Term: from 2018 to 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 401817050

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.

• DFG Programme: Priority Programmes
• Subproject of: SPP 2125: Deconstruction and Reconstruction of the Plant Microbiota "DECRyPT"
• Ehemaliger Antragsteller: Professor Kenichi Tsuda, Ph.D., until 5/2021