Genomic Insights and Comparative Genomics of Bacillus Species Having Diverse Mechanisms of Biocontrol Against Fungal Phytopathogens

Abstract

Pathogenic fungi affect a large number of crop species that are the main threat to food production and storage. Generally, chemical-based pesticides are supposed to be effective in controlling pests in agriculture; however, intensive use of chemicals has led to the development of resistance of the pathogen. It is also a potential threat to all kinds of life on earth. Bacillus species, which are well-known to promote the growth of plants with antagonistic activity against phytopathogenic fungi, are considered as safer and sustainable control agents for crop management. Genome-based studies enable us to understand the genetic elements of Bacillus strains for the survival in the rhizosphere, plant growth promotion, root colonization, chemotaxis, and motility. To extend the understanding of the potential antifungal capacities, 286 Bacillus genome sequences having the ability of biocontrol have been described. The genomic analyses identified biosynthetic gene clusters encoding secondary metabolites associated with biocontrol activity. Different Bacillus strains were found to dedicate approximately 8.5–18% of the whole genome in the biosynthesis of non-ribosomal peptide synthetase (NRPS) clusters encoding lipopeptides surfactin (srf), iturin (itu), fengycin (fen), and siderophore bacillibactin (besA, dhbACEBF) which have antifungal activity. Emerging bioinformatics tools based on multiple protein-coding loci comparison and core genome phylogenomic analyses have been employed to distinguish novel species in Bacillus taxa. Comparative genome analysis of the publicly available Bacillus strains allows for identifying the closest relatives. It can identify unique genes associated with secondary metabolites biosynthesis encoded in a strain. The production of antimicrobial compounds indicates Bacillus sp. as an ideal candidate for use as a biocontrol agent.