Structures of the endophytic microbiota during heart rot development in Abies georgei var. smithii

Heart rot, caused by the basidiomycete fungus Fomitopsis subpinicola, poses a severe threat to the health of Abies georgei var. smithii, a keystone conifer dominating subalpine forests on Sejila Mountain in southeastern Xizang (Tibet), China. To understand the microbial dynamics associated with disease progression, we used 16S rRNA and internal transcribed spacer high-throughput sequencing combined with multivariate and co-occurrence network analyses to characterize structural changes in the trunk endophytic microbiota across healthy, asymptomatic (heartwood decay without external symptoms), and symptomatic (fruiting bodies present) trees. Heart rot progression is the dominant factor associated with microbial succession, explaining more variation than tissue compartment. The bark-associated microbiome exhibited the earliest and strongest shifts and may provide a useful target for future early assessment of heartwood decay. Microbial interaction networks, particularly cross-kingdom (bacteria-fungi) associations, exhibited a significant increase in negative correlations as disease progressed, suggesting a shift from predominantly positive or neutral associations toward more antagonistic interactions, which may reflect increasing ecological competition and progressive destabilization of the trunk microbiome during decay. A pivotal finding was the dynamic microbial response observed during the asymptomatic stage. At this stage, fungal communities had already diverged markedly, and disease-associated shifts involving taxa such as Vibrisseaceae and Microbacteriaceae suggested that microbial restructuring had begun before obvious external symptoms appeared.IMPORTANCEOur findings show that shifts in endophytic microbiome structure and network stability are detectable during heart rot progression. In particular, bark-associated communities responded earlier and more strongly than near-pith communities, suggesting their potential value in future microbiome-informed, less destructive approaches for early assessment of cryptic stem diseases.