Biocontrol properties from phyllospheric bacteria isolated from Solanum lycopersicum and Lactuca sativa and genome mining of antimicrobial gene clusters

Abstract

Background Biocontrol 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 tomato and lettuce phyllosphere that can promote plant growth and potentially antagonize human pathogens as well as plant pathogens. Subsequently, we mined into their genomes for discovery of antimicrobial biosynthetic gene clusters (BGCs), that will be further characterized. Results The antimicrobial activity of 69 newly isolated strains from a healthy tomato and lettuce phyllosphere against several plant and human pathogens was screened. Three strains with the highest antimicrobial activity were selected and characterized (Bacillus subtilis STRP31, Bacillus velezensis SPL51, and Paenibacillus sp. PL91). All three strains showed a plant growth promotion effect on tomato and lettuce. In addition, genome mining of the selected isolates showed the presence of a large variety of biosynthetic gene clusters. A total of 35 BGCs were identified, of which several are already known, but also some putative novel ones were identified. Further analysis revealed that among the novel BGCs, one previously unidentified NRPS and two bacteriocins are encoded, the gene clusters of which were analyzed in more depth. Conclusions Three recently isolated strains of the Bacillus genus were identified that have high antagonistic activity against lettuce and tomato plant pathogens. Known and unknown antimicrobial BGCs were identified in these antagonistic bacterial isolates, indicating their potential to be used as biocontrol agents. Our study serves as a strong incentive for subsequent purification and characterization of novel antimicrobial compounds that are important for biocontrol.

Comparative genomic analysis of Cohnella hashimotonis sp. nov. isolated from the International Space Station

“…All are uncharacterized except the two lassopeptides; these are moderate matches to the lasso peptide paeninodin which was characterized from the species Paenibacillus dendritiformis (Zhu et al, 2016 ). Paeninodin and BGCs showing similarity to it have been predicted in multiple Bacillus and Paenibacillus endophyte species and are suspected to have biocontrol properties that combat plant pathogens (Muñoz et al, 2022 ; Semenzato et al, 2022 ). The genomes of C. ginsengisoli, C. rhizosphaerae , and strain F6_2S_P_1 T all contained 2–3 predicted BGCs for paeninodin, with C. ginsengisoli containing one that is a 100% match, while C. nanjingensis (the most closely related species outside the C. ginsengisoli clade) contained a single paeninodin match.…”

One-Step Soft Agar Enrichment and Isolation of Human Lung Bacteria Inhibiting the Germination of Aspergillus fumigatus conidia

“…Traditionally, the enrichment and isolation steps are completely independent from the confrontation. Indeed, antagonistic bacterial strains are first isolated, and then tested against the fungal pathogen of interest in a second step [26,27]. Here, this whole approach is performed in one single step, thus directly enriching for bacterial strains that are antagonistic to the fungal pathogen of interest.…”

Inter‐ and intraspecific phytochemical variation correlate with epiphytic flower and leaf bacterial communities

“…The ability to actively control and shift the associated microbiota may be of particular importance to coping with pathogen pressure (Li et al, 2022). For example, the composition of specific core microbiota guarantees antifungal protection at certain stages of host plant development (Xu et al, 2022), defending the host plant against severe phytopathogens, passively as biological barriers (Legein et al, 2020) or actively by producing antimicrobial compounds (Muñoz et al, 2022). Furthermore, it has to be considered that bacterial colonizers can contribute to the phytometabolic profile, indirectly through consumption or alteration of plant metabolism or directly by metabolite synthesis of phytohormones, phytotoxins, and bioactive compounds (Compant et al, 2019).…”