The microbiome of forest trees is a major determinant of health and productivity, with roles in nutrient acquisition, stress tolerance, immune regulation, and disease suppression. Tree-associated microbiota therefore confer significant genetic and phenotypic diversity on their hosts, acting as an extended phenotype and facilitating host adaptation to environmental and pathogen threats. Here we synthesize current knowledge on the composition and function of the bacterial biota in the above- and below-ground compartments of forest tree species of boreal, temperate, and Mediterranean biomes. We make recommendations for future research priorities toward characterizing the bacterial biota of forest tree species and biomes, using integrated analytical approaches that include other biotic and abiotic components of the microbiome. Such integrated research approaches are critical to address the complex ecological factors that drive tree holobiont function at both individual and landscape scales, to safeguard global forest biomes and the ecological services they support.