Through the looking glass: A single-cell view of plant-microbe interactions

Abstract

Plants interact with a vast variety of microbes that inhabit both above- and belowground tissues. Through their effect on host physiology and growth, plant-microbe interactions define the success of a plant’s life cycle. A key aspect of these interactions is the requirement for highly cell-type-specific responses from the plant, be it to form symbiotic structures in certain cells or to mount a highly localised immune response. There has been long-standing interest in uncovering the cell-specific transcriptomic changes that underpin these processes to better understand the establishment, functioning, and regulation of plant-microbe interactions. The recent optimisation of single-cell and spatial transcriptomics for plants now allows us to investigate these interactions in unprecedented detail. Here, we discuss how single-cell technologies can help unravel the many mysteries of plant-microbe interactions. We focus on the key lessons we have learned from recent single-cell studies in the field and highlight the current limitations of single-cell technologies. We also offer promising avenues for future exploration and conclude by suggesting experimental and bioinformatic considerations to maximise insights from past and future studies and help make the most of this new single-cell era in the field of plant-microbe interactions.