Plants are constantly challenged by a diverse range of environmental and biotic factors, however, many of these phenomena and interactions have often been studied in isolation, which may not always be reflective of the dynamic situation in nature and throughout the plant life-cycle. Therefore, to understand the range of mechanisms and molecular toolkits that plants have acquired to sense and manage such interactions, a new holistic approach is required. This special issue includes several reviews and original research papers (introduced by Saijo et al. on pp. 1321-1323) that highlight efforts that are currently underway to understand such seamless and exquisite interactions between plants and other organisms.