Harnessing Spatial Transcriptomics to Unveil Host-Microbe Interactions in Arabidopsis thaliana Leaves

Abstract

Microbial infections affect plant host’s gene expression by activating the innate immune system and signalling, such as phytohormone pathways. Recently, characterization and localization of host response to microbial infection and quantification of bacterial diversity have led to advances in plant infection biology. However, we lack an understanding of how the spatial microbial networks and hotspots are distributed on a leaf and how these factors affect the host tissues’ gene expression per location.To fill this gap, we applied an innovative, high-throughput technology originally developed for mammalian tissues, Spatial Transcriptomics (ST), to outdoor-grown Arabidopsis thaliana leaves. ST enables the simultaneous quantification and visualization of transcriptional profiles in tissue sections at 55-μm resolution. We applied several advancements to the original method to study the concerted, multimodal microbial infection processes and host’s response in A. thaliana leaves. First, we showed that the introduction of tissue treatments facilitate spatial capture of plant mRNAs while preserving the complete morphology of the plant tissue. Second, we demonstrated the capture of bacterial and fungal diversity from outdoor grown A. thaliana leaves. Third, we unveiled leaf-scale spatial microbial hotspots indicating microbial distributions on a leaf surface. Finally, we revealed the concerted spatial microbial networks and their impact on host’s gene expression. In conclusion, our results indicate the feasibility of studying joint gene expression profiles of different organisms. Our approach can be extended to different plant systems, such as crop species, to elucidate complex infection processes where the spatial component is key for understanding plant disease states