Biocontrol of mushroom crop mycoparasites by novel Bacillus velezensis strains.

The cultivation of button mushroom (Agaricus bisporus) requires the design of tailor-made substrates that nourish the crop and promote morphology changes from mycelium to basidiome. The agronomic stages of mushroom development are also influenced by the microbiota present in the mushroom crop microcosm. These microbes can have a beneficial impact on mushroom growth, development and quality, or a detrimental impact through reduction of yield or quality (parasites, competitors or disease vectors). In this report, we describe the isolation of multiple strains of Bacillus velezensis from mushroom casing material and basidiomes. We show that these strains exhibit antifungal activity towards major mushroom mycoparasites in vitro and further characterise their mode of action. Full genomes of B. velezensis CM5, CM19, CM35, EM5 and EM39 were sequenced and annotated, which together with metabolic profiling of specialised metabolites produced by CM5, CM19 and CM35 suggested that the antifungal activity of these strains is likely to be linked to the production of the lipopeptide fengycin. The addition of these B. velezensis strains to a growth chamber trial with crops infected by Zarea fungicola strain 150/1 did not result in a statistically significant reduction in disease incidence compared to the chemical fungicide prochloraz-Mn. Despite in vitro results, no negative effect on mushroom yield was observed. The analysis of the quantitative microbiome during this trial suggests that microbial dynamics is consistent with a regular crop cycle. Additionally, the application of B. velezensis strain CM5 resulted in increased Gram-negative and Gram-positive bacteria. Genomic and analytical tools were designed and used to evaluate B. velezensis persistence in casing soil when the selected strains were artificially applied. B. velezensis population levels decreased significantly after application, potentially contributing to the lack of biocontrol activity observed in growth chamber crop trials. KEY POINTS: • Bacillus velezensis strains isolated from peat-based microcosms show significant inhibitory effects against major fungal parasites of mushrooms in vitro. • Genome sequencing and metabolic profiling correlated antifungal activity with the production of lipopeptides, particularly fengycin. • Novel strains did not significantly limit dry bubble disease under growth chamber crop trials-potentially due to low bacterial persistence.