Bacteriome shifts in Agaricus bisporus associated with wet bubble (Mycogone perniciosa) and dry bubble (Lecanicillium fungicola) diseases revealed by 16S metataxonomics

Agaricus bisporus (AB) cultivation is significantly affected by wet bubble (wet bubble disease caused by Mycogone perniciosa (MP)) and dry bubble (dry bubble disease caused by Lecanicillium fungicola (LF)) diseases. The role of bacterial communities in bubble disease development remains poorly understood. This study characterized the bacteriome of healthy AB and compared it to those mushrooms infected with MP or LF by sequencing the V3-V4 region of the 16 S rRNA gene amplicon on the Illumina MiSeq ultrasequencer and analyzing the data generated with Qiime2. Significant differences in bacterial community composition were observed between healthy and infected samples, with Enterobacteriaceae_A_729055 reaching 70.72% ± 1.14% SD relative abundance in MP-infected samples compared to 27.12% ± 19.05% SD in healthy samples, and Pseudomonas_E_647464 dominating LF-infected samples (58.62% ± 4.39% SD). Reduced alpha diversity indices were observed in MP-infected samples (Shannon's index: p = 0.027; Faith's phylogenetic diversity: p = 0.038; Pielou's evenness: p = 0.038). However, this study employed a limited sample size (n = 3 per group) with no technical replicates, limiting statistical power. Species-level identifications are provisional and require validation through full-length 16 S sequencing. Several bacterial taxa displayed differential abundance patterns suggesting ecological importance during infection; however, correlation does not establish causality, and the roles of these bacteria remain correlative rather than mechanistic. Further functional studies are needed to determine whether these bacterial shifts are drivers of pathogenesis, consequences of infection, or ecological responses to altered tissue chemistry.