Integrated genome mining and phytohormone profiling of six plant growth-promoting elite bacterial strains

Plant growth-promoting bacteria may act by enhancing soil fertility, nutrient cycling, and pathogen suppression. We analyzed the genomes and metabolomes of six strains, Chromobacterium violaceum CNPSo 1954, Pantoea agglomerans CNPSo 2602, Bacillus velezensis CNPSo 2657, Bacillus altitudinis CNPSo 2658, Bacillus safensis CNPSo 2725, and the novel species Pseudomonas sp. CNPSo 2799. Genomic bioprospection revealed diverse biosynthetic gene clusters (BGCs) involved in secondary metabolites production, accounting for 4.26% of the total genome in strain CNPSo 2602 and 18.03% in strain CNPSo 2657. An average of 79 carbohydrate-active enzymes (CAZymes) were identified per genome, with glycoside hydrolases and glycosyltransferases accounting for more than 50% of all identified enzymes. The strains exhibited distinct antibiotic resistance profiles, ranging from three (CNPSo 2658 and CNPSo 2725) to 12 (CNPSo 2602). All strains carried the genes for tryptophan-biosynthesis, and targeted metabolomic analysis confirmed the production of the phytohormones indole-3-acetic (IAA), indole-3-butyric (IBA), indole-3-pyruvic acids (IPA), and L-tryptophan (TRP), with strain-specific variation in metabolic profiles. These strains exhibited multiple growth-promoting and biocontrol traits, highlighting a potential as multifunctional next-generation bio-inputs for sustainable agricultural applications.