Genome Mining of Antimicrobial Gene Clusters from Phyllospheric Bacteria Isolated from Solanum Lycopersicum and Lactuca Sativa to Identify Biocontrol Properties

Abstract

BackgroundBiocontrol agents are sustainable eco-friendly alternatives for chemical pesticides that cause adverse effects in the environment and toxicity in animals including humans. An improved understanding of the phyllosphere microbiology is of vital importance for biocontrol development. Most studies have been directed towards beneficial plant-microbe interactions and ignore the pathogens that might affect humans when consuming vegetables. In this study we extended this perspective and investigated potential biocontrol strains isolated from the tomato and lettuce phyllosphere that can promote plant growth and antagonize mammalian pathogens as well as plant pathogens. Subsequently, we mined into their genomes for discovery of antimicrobial biosynthetic gene clusters (BGCs), several of which are good candidates to produce protectants against microbial plant and mammalian pathogens.Results The antimicrobial activity of 69 newly isolated strains from a healthy tomato and lettuce phyllosphere against several plant and mammalian pathogens was determined with plates assays. Three strains with the highest antimicrobial activity against the relevant pathogens were selected and characterized (Bacillus subtilis STRP31, Bacillus velezensis SPL51, and Paenibacillus sp. PL91). All three strains showed a plant growth promotion effect by the production of volatile compounds (VOCs) on tomato and lettuce. In addition, genome mining of these isolates showed the presence of a large variety of biosynthetic gene clusters. A total of 39 BGCs were identified, of which several are already known, such as bacilysin, bacillibactin, surfactin, subtilomycin, etc., but also several novel ones. Further analysis revealed that among the novel BGCs, one NRPS and two bacteriocins are encoded which were analyzed in more depth.Conclusions Several antimicrobial BGCs were found in the selected strains, including the rediscovery of known ones, but also the discovery of novel ones. Our study serves as support for subsequent examination and characterization of novel antimicrobial metabolites, and the possibility of developing biocontrol agents.