The Apple Microbiome: Structure, Function, and Manipulation for Improved Plant Health

Apple trees host diverse communities of bacteria, fungi, viruses, and other microbes that occupy all plant surfaces and internal tissues. In the past two decades, our understanding of these communities has burgeoned due to new technologies that allow culture-independent characterisation of microbial communities. In this chapter, we provide a comprehensive review of our current understanding of the composition and assembly of the apple tree microbiome. We discuss factors that shape variation in the microbiome, including host genotype, domestication, plant chemistry, and agricultural practices. Next, we discuss the consequences of the microbiome for plant health and the opportunities and challenges associated with attempts to manipulate the microbiome for improved sustainability of orchard ecosystems. Finally, we suggest future research priorities that promise to facilitate a paradigm shift in orchard management from viewing trees as individual organisms to viewing trees as diverse ecosystems that must be managed holistically to maximise the environmental and economic sustainability of production systems.