Single-cell transcriptomics reveal heterogeneity in plant responses to the environment: a focus on biotic and abiotic interactions

Abstract

Environmental cues, from biotic or abiotic origin, are major factors influencing plant growth and productivity. Interactions with biotic (e.g. symbionts and pathogens) and abiotic (e.g. changes in temperature, water or nutrient availability) factors trigger signaling and downstream transcriptome changes in plants. While bulk RNA-sequencing technologies have traditionally been used to profile these transcriptional changes, the heterogeneity of the responses, caused by the cellular complexity of organs, might be masked by homogenizing tissues. Thus, whether different cell types respond equally to environmental fluctuations, or whether subsets of the responses are cell-type specific, are long-lasting questions in plant biology. The recent break-through of single-cell transcriptomics in plant research offers an unprecedented view on cellular responses under changing environmental conditions. In this review, we discuss the contributions of single-cell transcriptomics towards the understanding of cell-type specific plant responses to biotic and abiotic environmental interactions. Besides major biological findings, we present some technical challenges coupled to single-cell studies of plant-environment interactions, proposing possible solutions and exciting paths for future research.

Keywords: Abiotic stress; RNA-sequencing; biotic stress; cell heterogeneity; drought; environmental stress; heat; pathogens; rhizobia; single-cell transcriptomics.