Decoding Plant-Microbiome Interactions at Single-Cell and Spatial Resolutions

Plant-microbiome interactions are crucial for plant health, promoting growth and enhancing resilience under stress conditions. These interactions are highly heterogeneous, shaped by diverse plant cell types and the complex spatial distribution of microbes. However, our current understanding remains predominantly at the tissue level, lacking the resolution to fully capture this heterogeneity. As a result, the genetic networks that govern how plants foster beneficial microbiomes remain largely unexplored. This Fellowship aims to address these gaps by employing cutting-edge single-cell multiomics and spatial mapping technologies. Using Arabidopsis thaliana and the well-characterized 35-member synthetic microbial community (SynCom35) as model systems, I will integrate single-cell transcriptome and chromatin accessibility assays to map transcriptional and epigenetic changes in root cells in response to microbial colonization. This approach will provide novel insights into the cellular mechanisms and genetic networks underlying plant-microbiome interactions. Additionally, by utilizing and further developing PHYTOMap, a multiplexed 3D spatial gene expression analysis platform, I will simultaneously spatially map plant gene expression and microbiome distribution. By integrating single-cell and spatial omics data, I will reconstitute spatially-resolved plant gene regulatory networks that interact with specific microbiome members. Furthermore, I will functionally characterize these predicted regulatory networks, aiming to lay the foundation for genetic engineering to enhance plant interactions with beneficial microbes, offering new strategies for optimizing plant growth and resilience. Altogether, this research will significantly advance our understanding of plant-microbiome interactions at single-cell and spatial resolutions, providing a foundation for innovative approaches to enhance crop resilience and agricultural sustainability in response to global challenges.