Disease-Suppressive Phyllosphere Microbiomes: A Perspective on Microbiome Transplantation for Sustainable Agriculture

The plant-associated microbiome is a key contributor to plant health, influencing nutrition, stress tolerance, and disease outcomes. Manipulating these microbiomes is a potentially powerful tool for plant disease management. However, the implementation of direct plant microbiome manipulation is rare, in contrast to medical fields, in which microbiome transplantation has been a growing focus of research for several decades, particularly for treatment of conditions such as Clostridioides difficile-induced diarrhea and bacterial vaginosis. This concept has more recently gained attention in agriculture, as rhizosphere microbiome transplants are being tested for their ability to promote crop health and productivity. A few research groups have also explored the potential of transplanting phyllosphere microbiomes to combat foliar phytopathogens. Microbiome transplantation could occur either as a direct transplant or following iterative passaging, in which beneficial traits are gradually enhanced through multiple transfers in set environments. In this Perspective, we discuss the concept and potential applications of phyllosphere microbiome transplantation to develop disease-suppressive microbiomes, including recent advances, and offer insights into its prospects for enhancing the sustainability of plant disease management. Before realizing the full potential of disease-suppressive phyllosphere microbiomes, however, several challenges need to be addressed, including establishment of standardized protocols, elimination of pathogens from the microbiome, and regulatory considerations.