Tissue-specific changes in endophytic bacterial and fungal communities of two pine species associated with pine wilt disease

Pine wilt disease severely threatens pine forests worldwide, yet coordinated shifts in endophytic bacterial and fungal communities across host tissues remain incompletely resolved. We analyzed 16S rRNA gene and ITS amplicons from needles, stems, and roots of healthy trees and naturally infected trees at the mid-to-late stages of disease in Pinus densiflora Siebold & Zucc. (Japanese red pine) and Pinus thunbergii Parl. (Japanese black pine). Tissue-stratified analyses revealed significant disease-associated differentiation of both bacterial and fungal communities in all three tissues. Bacterial communities showed stronger disease-associated restructuring, with significant shifts in both composition and dispersion, indicating centroid changes accompanied by increased within-group heterogeneity. Fungal communities also differed significantly with disease status, but dispersion changes were not detected. Needles harbored the greatest numbers of differential taxa in both bacterial and fungal communities, whereas fungal community-level differentiation was strongest in stems. Host species background significantly modulated needle bacterial communities as well as needle- and stem-associated fungal communities. Overall, pine wilt disease was associated with tissue-specific reorganization of the endophytic microbiome, with bacterial communities exhibiting greater heterogeneity and fungal communities showing compositional differentiation without detectable dispersion shifts.