Bacterial community dynamics associated with Pinus massoniana across progression stages of pine wilt disease

Aims Plant microbiomes display distinct spatial compartmentalization, yet their responses to disease disturbance across host compartments and disease stages remains largely unexplored. Methods This study characterized bacterial communities in five compartments of Pinus massoniana (needles, stems, roots, rhizosphere soil and bulk soil) across four stages of pine wilt disease (PWD; healthy, early, intermediate and late) using 16S rRNA gene amplicon sequencing and functional prediction. Results The results showed that bacterial community dynamics were significantly influenced by compartment and disease stage. Notably, the stem compartment exhibited substantial changes: Chao1 index significantly increased at the intermediate stage, whereas Chao1, Shannon and Shannoneven indices declined at late stage. Also in stem compartment, the late stage was characterized by marked enrichment of the phylum Proteobacteria, accompanied by elevated relative abundances of the genera Pseudomonas and Methylobacterium . In contrast, the phylum Actinobacteriota and its affiliated genus Acidothermus decreased markedly. Additionally, functional prediction revealed enhanced chemoheterotrophy and aromatic compound degradation pathways as disease progressed ( P < 0.05). By comparison, bacterial communities in needles remained stable across all stages. In roots, Mycobacterium was significantly enriched at early stage, yet little impact on community structure. Although obvious community restructuring was detected in rhizosphere soil at early and late stages, both rhizosphere and bulk soil harbored a high proportion of shared OTUs, without any significant shifts at the phylum taxonomic level. Conclusions This study identifies stems as the core compartment of PWD-induced microbial dysbiosis and provides a microbiome-based theoretical basis for monitoring and managing P. massoniana forest disease.