Field Suppression of Fusarium oxysporum by Bacillus cereus Secondary Metabolite Biosynthetic Potential Revealed by Whole Genome Sequencing

Abstract

Fusarium basal rot caused by Fusarium oxysporum is a major soil-borne disease limiting onion production worldwide. Although Bacillus spp. have been widely investigated as biological control agents against Fusarium diseases, field-level validation and genomic characterization of biocontrol-associated traits remain limited. In this study, two onion-associated B. cereus strains, 23-046 and 23-052, were subjected to whole-genome sequencing to characterize their genomic features, and strain 23-046 was additionally evaluated for suppression of Fusarium occurrence under field conditions. The field experiments were conducted using soil drench application at the seedling-stage, soil incorporation, and combined application. Soil incorporation significantly reduced Fusarium recovery compared with seedling-stage soil drench application. In contrast, bulb height and bulb weight were not significantly affected by bacterial treatments, whereas sheath diameter significantly increased following soil incorporation, indicating improved vegetative growth without negative effects on bulb development. Complete genome sequencing using PacBio platforms revealed that strains 23-046 and 23-052 possessed circular chromosomes of 5.31 Mb and 5.45 Mb, respectively, while strain 23-052 additionally harbored a 456-kb plasmid enriched in genes associated with transcriptional regulation, defense mechanisms, and mobilome-related functions. Comparative genomic analyses identified multiple biosynthetic gene clusters associated with siderophore production and nonribosomal peptide synthetase pathways. These results presented the potential of B. cereus strain 23-046 for suppression of onion Fusarium basal rot under field conditions and show that strains 23-046 and 23-052 harbor biosynthetic gene clusters.