Unraveling plant–microbe symbioses using single-cell and spatial transcriptomics.

Beneficial plant–microbe interactions are critical to plant productivity in both natural and agricultural ecosystems due to benefits such as improved plant nutrition and abiotic stress tolerance. The legume–rhizobia symbiosis and plant–arbuscular mycorrhizal fungi symbiosis both involve continuous signaling and coordination between two organisms. Within symbioses, the development of novel microbial and plant structures is driven by symbiosis-specific gene expression in a few specific cell populations. Genetic engineering to take better advantage of these interactions relies on the identification of symbiosis-responsive plant and microbial genes that can serve as targets for modification. Applying single-cell and spatial RNA-seq to study plant–microbe endosymbiosis can facilitate the identification of such genes and improve our general understanding of the complex biology of symbiotic interactions. Plant–microbe symbioses require intense interaction and genetic coordination to successfully establish in specific cell types of the host and symbiont. Traditional RNA-seq methodologies lack the cellular resolution to fully capture these complexities, but single-cell and spatial transcriptomics (ST) are now allowing scientists to probe symbiotic interactions at an unprecedented level of detail. Here, we discuss the advantages that novel spatial and single-cell transcriptomic technologies provide in studying plant–microbe endosymbioses and highlight key recent studies. Finally, we consider the remaining limitations of applying these approaches to symbiosis research, which are mainly related to the simultaneous capture of both plant and microbial transcripts within the same cells. [ABSTRACT FROM AUTHOR]