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Pathogenic co-infections in plants significantly impact microbial diversity and disease outcomes, yet their effects on microbial community structure and ecological processes remain unclear. Tobacco plants were co-infected with  Ralstonia solanacearum  and  Neocosmospora falciformis . 16S ribosomal RNA and internal transcribed spacer amplicon sequencing were used to assess bacterial and fungal communities, respectively, in infected tobacco stems. The results were compared between co-infected and healthy control tobacco plants to assess the effects of infection. Co-infection reduced microbial diversity and shifted community structure, promoting ecological specialization. Network analysis revealed synergistic interactions between the pathogens, enhancing virulence through positive correlations with certain microbial taxa. Conversely, some taxa exhibited antagonistic effects, potentially limiting pathogen proliferation. Deterministic processes were found to dominate microbial community assembly under infection conditions, significantly reshaping the microbial landscape compared to healthy control plants. This study highlights the profound effects of co-infection on microbial diversity, community composition, microbial interactions, and community assembly processes in tobacco plants. These findings provide valuable insights for developing more targeted plant disease management strategies by manipulating microbial communities.

Fungal and bacterial pathogenic co-infections mainly lead to the assembly of microbial community in tobacco stems