Unveiling the phyllosphere Microbiome: Guardians of tree health and environmental resilience

Abstract

The phyllosphere—the aerial habitat of plants, which includes the endosphere and episphere of plant tissues—harbors diverse microbial communities that significantly influence tree health, productivity, and resilience. Despite increasing attention to plant-associated microbiomes, a critical knowledge gap remains regarding how phyllosphere communities in trees shift from protective networks to disease-promoting assemblages under environmental and pathogenic pressures. This review addresses this gap by synthesizing emerging insights into the transition from a healthy phyllosphere microbiome to a pathobiome—defined here as a pathogen-dominated, dysbiotic microbial state that destabilizes host–microbe interactions and amplifies disease susceptibility. We highlight the ecological and molecular mechanisms by which beneficial taxa mediate antibiosis, niche competition, and induced systemic resistance, while also examining how pathogen invasion and climate-driven stressors disrupt these networks. Integrating evidence from multi-omics and synthetic community experiments, we demonstrate how advances in microbiome science are uncovering causal links between microbial dynamics, host immunity, and disease outcomes in trees. Furthermore, we assess how biotechnological innovations—ranging from microbial inoculants and phage therapy to microbiome engineering—offer transformative opportunities for sustainable forest management. Yet, substantial challenges remain in translating laboratory discoveries to field-scale applications, particularly in establishing causality and ensuring ecological stability across diverse forest ecosystems. By consolidating current evidence and framing future research priorities, this review underscores the central role of phyllosphere microbiomes in shaping disease resilience and offers a roadmap for leveraging microbial functions to promote sustainable forestry and climate-adapted ecosystems.