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The ecological dynamics of the atmosphere, plants, and soil play a crucial role in shaping how ecosystems respond to environmental changes. These three components are often viewed as a unified system due to their intricate connections. Within this system, the expression of high-level phenotypic traits is influenced by chemical interactions occurring at different locations. These interactions take place at the subcellular level within plant or microbial cells, between cells of plants and microbes, and in the extracellular space between plants and the soil/atmosphere. To fully understand, predict, and manipulate the behaviours of plant-atmosphere-soil systems and their impacts on the environment, it is essential to disentangle the complex network interwoven by various chemical interactions. This Collection invites submissions on the topic of unravelling the complexities of chemical mechanisms by which plants, microbes in soil, and the surrounding air interact and impact one another, shedding light on biotic and abiotic factors that orchestrate the play of this interconnected system.