Identification of Conserved Pathways in Bacillus Strains Known for Plant Growth-Promoting Behavior Using a Multifaceted Computational Approach

Abstract

Bacillus strains have long been recognized for their beneficial interactions with plants, enhancing growth, nutrient uptake, and stress resistance. Understanding their molecular mechanisms and plant-microbe interactions is crucial for harnessing their potential in sustainable agriculture. Here we used ten strains from the 5 Bacillus species namely Bacillus velezensis, Bacillus subtilis, Bacillus atrophaeus, Bacillus altitudinis and Bacillus amylofaciens, which are previously reported for PGPR activity. A comparative analysis of these strains was performed to determine their evolutionary relationships, which revealed that Bacillus velezensis and Bacillus amyloliquefaciens are closely related based on underlying genetic and proteomic similarities. Bacillus altitudinis strain LZP02 was the most distantly related to all the other selected strains. On the other hand, Bacillus atrophaeus strains GQJK17 and CNY01 are shown to be closely related to each other. Mauve alignment was performed to determine the genetic relationships between these strains. The LZP02 strain exhibited several unique inversions harboring important genes, such as betB, ftsW, and rodA, which are important for bacterial survival. Proteomic analysis highlighted important pathways that were conserved across these strains, including xenobiotic biodegradation and metabolism, biosynthesis of polyketides and nonribosomal pathways, and biosynthesis of secondary metabolites, all of which have been shown to be involved in plant growth promotion.