Functional dynamics reveal the response of the crabapple ( Malus sp.) phyllosphere microbiome to Gymnosporangium yamadae infection

The phyllosphere microbiome plays a vital role in plant defense against airborne pathogens. In this study, we investigated microbial dynamics of crabapple (Malus 'Kelsey') phyllosphere across six stages of Gymnosporangium yamadae infection using metatranscriptomic sequencing. Infected leaves exhibited increased transcriptional alpha diversity of fungi, bacteria, and viruses, with a notable negative correlation between fungal and bacterial diversity. Microbial taxa in diseased leaves exhibited heightened transcriptional activity compared with healthy counterparts, with fungi progressively dominating the microbial community. Functional co-occurrence networks revealed increased complexity in infected leaves, suggesting a potential reorganization of the microbial interactions in response to pathogen invasion. These structural shifts were accompanied by significant functional changes, as revealed by functional annotation and random forest modeling, which showed significantly enhanced microbial carbohydrate metabolism and upregulated plant cell wall-degrading enzymes (e.g., PL3, CE8, and CE5) in diseased leaves. Key transcripts associated with these functions, originating from Termitomyces sp. J132 and Alternaria alternata, were opportunistically expressed and significantly positively correlated with host flavonoid glycosides, which serve as markers of rust lesion development. Additionally, diseased leaves showed activation of microbial pathways related to aromatic compound degradation and ascorbate metabolism, potentially contributing to redox homeostasis under host defense stress. At later infection stages, we detected high expression of genes encoding cell wall-degrading enzymes in Saitozyma podzolica. Together, our findings underscore the dynamic, functional role of the phyllosphere microbiome in modulating plant-pathogen interactions and shaping disease progression, providing a foundation for microbiome-informed strategies to enhance plant disease resistance.IMPORTANCEOur study reveals stage-specific shifts in the transcriptional activity and functional capacity of the crabapple phyllosphere microbiome during Gymnosporangium yamadae infection. We identified key microbial taxa potentially involved in pathogen facilitation or antagonism and elucidated their roles in plant-pathogen interactions. These findings highlight the importance of the phyllosphere microbiome in regulating plant health and suggest new avenues for microbiome-based approaches to improving plant disease resilience.