Microbiome-guided evaluation of Bacillus subtilis BIOUFLA2 application to reduce mycotoxins in maize kernels

Abstract Fungal diseases are aggravating globally in crop cultivation despite of growing inputs of chemical fungicides. Ear rot and fumonisin contamination of kernels caused by Fusarium verticillioides lead to qualitative and quantitative reductions in maize production. In tropical agriculture, high yielding maize currently can only be assured through foliar protection using fungicides due to the high pathogen pressure. However, the use of chemical fungicides alone does not guarantee the protection of kernels. Recently, a tandem application of fungicides with the Bacillus subtilis strain BIOUFLA2 was identified as a promising strategy to control F. verticillioides-caused diseases. We have employed an integrative approach to assess changes in the microbiome of maize subjected to a combination of chemical and biological fungicides and contrasted it to conventional treatments. This was complemented with molecular and analytical monitoring of the pathogen and mycotoxin levels. Two sampling times were included (10 days after application of treatments and upon harvesting) and two maize fields to account for regional differences. A comparative analysis indicated a treatment-specific enrichment of bacterial and fungal OTUs that were not detectable in the maize microbiome of untreated plants. Both, the chemical and the tandem application of a chemical and biological pesticide resulted in the occurrence of unique OTUs. Samples subjected to these treatments harbored up to 22 additional OTUs. The lowest fumonisin concentration was observed in the treatment that encompassed BIOUFLA2 (field 1 = 0.29 ppm and field 2 = 0.77 ppm), while the conventional fungicide application resulted in the highest mycotoxin concentrations (field 1 = 3.84 ppm and field 2 = 10.02 ppm). Our study provided strong evidence that conventional treatments of maize with fungicides can promote mycotoxin levels in grains and that partial replacement with biologicals can increase the treatment efficiency.