Genomic insights into a multispecies bacterial pathogen complex driving bacterial blotch in white button mushrooms

Bacterial blotch remains a major constraint to global white button mushroom (Agaricus bisporus) industry, yet its etiological complexity has been underestimated. Through a genome resolved, polyphasic approach applied to symptomatic mushrooms collected from United States, we uncovered an unexpectedly diverse complex of Pseudomonas species driving blotch disease. Beyond classical pathogens (P. tolaasii, P. gingeri, P. agarici, and P. "reactans", P. yamanorum, Pseudomonas sp. NC02), our analyses revealed a striking prevalence of P. azotoformans, a species not previously associated with mushroom pathology, alongside P. pergaminensis, P. monsensis, P. tensinigenes, P. simiae, Pseudomonas sp. Irchel 3A7, Pseudomonas sp. REP124 and two putatively novel lineages. Comparative genomics demonstrated pronounced heterogeneity in accessory genome content, with P. azotoformans exhibiting exceptional genomic plasticity indicative of broad ecological adaptability. Secondary metabolite profiling and white line assays further delineated species-specific chemotaxonomic signatures, underscoring the multifactorial nature of virulence. Collectively, this study provides the most comprehensive genomic and phenotypic characterization of blotch-associated Pseudomonas in Northern America, overturning the long-held paradigm of a single dominant pathogen. By establishing that bacterial blotch is multispecies disease complex, our findings redefine its epidemiology and lay the foundation for improved diagnostics strategies in mushroom production systems. The emergence and high prevalence of P. azotoformans underscore the limitations of diagnostic protocols focused exclusively on classical blotch pathogens and highlight the need for broader, genomics informed detection strategies. Collectively, this work offers actionable insights to strengthen production resilience and support the sustainability of white button mushroom cultivation as the world's most economically important specialty food crop.