A decade of understanding secondary metabolism in Pseudomonas spp. for sustainable agriculture and pharmaceutical applications

Abstract

Pseudomonas spp. have been widely studied for their plant growth promoting and antimicrobial metabolites. The genus got attention due to the production of array of secondary metabolites involved in the suppression of phytopathogens and ability to stimulate plant growth by means of nitrogen-fixation, production of hydrolytic enzymes, regulatory hormones, and solubilization of inorganic minerals. In recent years, research was focused towards identification of biosynthesis pathways and genes involved in the production of secondary metabolites that led to the discovery of novel metabolites including many new phenazine derivatives, quorum-sensing signals, rhizoxin analogues, cyclic lipopeptides, and a new class of alkyl-substituted aromatic acids. Identification of these biosynthetic pathways provided insights for their successful application in agriculture and for environmental sustainability. In addition, many genomic and metabolomic databases such as; METLIN, KEGG, GNPS, CFM-ID, MassBank, and MetaboLights, allowed exploring intricate metabolic pathways and significant genes involved in the biosynthesis of compounds. Several softwares, genome-mining tools and new techniques, such as MALDI-IMS and MALDI-FTICR MS were developed to facilitate the characterization of new metabolites. Additionally, use of MALDI-imaging techniques facilitated real-time visualization of complex microbial communities and their relationship with pathogens. Secondary metabolites of Pseudomonas spp. were also demonstrated for their apoptotic, anti-mitotic, nematocidal, herbicidal, anthelmintic, insecticidal, and phytotoxic effects. Total biosynthesis of metabolic derivatives and genetic engineering enabled to develop strains with improved yield of targeted bio-products. Availability and access to published genomic sequences and comparative bioinformatics tools helped in identification of strain-specific traits and development of multifunctional inocula. This review highlights significant advances in identification of Pseudomonas secondary metabolites for their successful agricultural and pharmaceutical applications.