Functional Dynamics Reveal the Response of the Crabapple ( Malus sp.) Phyllosphere Microbiome to Gymnosporangium yamadae Infection

The plant microbiome is crucial for maintaining plant health under disease stress. While considerable research has focused on belowground systems, the phyllosphere microbiome remains underexplored, particularly regarding its functional responses to pathogen infection. In this study, we investigated the phyllosphere microbiome dynamics of crabapple ( Malus ‘Kelsey’) infected by Gymnosporangium yamadae using metatranscriptomic sequencing across six stages of rust disease progression. Our analysis revealed a general increase in the diversity of fungi, bacteria and viruses in infected leaves. Notably, fungal diversity negatively correlated with bacterial diversity, reflecting competitive interactions during disease development. Microbial taxa in diseased leaves exhibited heightened expression activity compared to healthy leaves, with fungi progressively dominating the microbial community. Functional co-occurrence networks of the phyllosphere microbiome in infected leaves were more complex than in healthy leaves, suggesting adaptive reorganization in response to pathogen invasion. Differentially expressed genes at each stage were significantly enriched in carbohydrate metabolism pathways and gene regulation-related functions, enabling functional adaptations to rust diseases. Random forest modeling identified key microbial transcripts associated with pathogen abundance, including beneficial microbes like Saitozyma podzolica , which secretes glucan-degrading enzymes, and Mortierella elongata , involved in sterol biosynthesis and plant resistance. Conversely, Alternaria alternata emerged as a major pathobiome contributor, secreting enzymes that degrade plant cell wall components (e.g., pectin, cellulose, lignin, and xylan), and engaging in MAPK signaling pathways critical for pathogenesis. Our findings underscore the vital role of the phyllosphere microbiome in mediating plant-pathogen interactions and shaping disease progression, providing a foundation for microbiome-based strategies to enhance plant resilience.