The health of plants depends on numerous environmental factors. All plants, including trees, live in close relationship with microorganisms. Plants harbor microbial communities in above-and below-ground tissues, where plant-associated microbial communities are influenced by environmental conditions and host genotype. The microbiome of trees is composed of mutualistic, commensal, and pathogenic microorganisms. Mutualistic microorganisms can help trees obtain nutrients (e.g., phosphorus and nitrogen) and defend against plant pathogens. Ecological interactions between different microbial groups directly influence host health, and endophytic microorganisms can inhibit pathogen growth or induce the expression of genes related to tree defense against these adverse organisms. Hence, understanding host-microbiome-environment interactions are crucial for modulating tree health.