Recently, various studies have documented the global distribution of microbiota in different eukaryotes. Such integrations of different biological individuals into physiological, immunological or evolutionary units are labeled holobionts. Studies on human and animal holobionts indicate that the microbiome deeply affects host’s health. However, despite the fact that plants make up the majority of the earth’s living environment, biodiversity, and food, the effect of the host-microbiome interplay on plants health, survival, environmental adaptation, stress tolerance, and evolution is widely neglected in plant biology and plant health management practices. Recent global environmental changes have exposed plants to unprecedented stresses, which demand effective genetic, epigenetic and microbial toolboxes to cope with. In addition, considering the risks of chemicals and genetically modified organisms, alternative plant health management systems are strongly needed. So far, by drawing on traditional conceptualization of biological individuals as physiological units with genetic homogeneity, especially plant health management strategies have targeted the plant without its microbial partners. Here, I investigate the effects of plants’ endophytic microbiome on plant health under abiotic stresses by integrating conceptual and practical perspectives to provide an alternative to the current plant health management systems. I develop a conceptual framework of plant individuality that rests not on the plant as a separate unit but as a plant holobiont. This highlights plants’ symbiotic interactions, shifts the target of plant protection, and allows designing new plant health management strategies to reshape plant health management practices.
