Plant-derived and Streptomyces bio-compounds for the sustainable management of fungal pathogens and weeds: in vitro and in vivo studies

Modern agriculture is facing new challenges because of the increasing limitations on chemical pesticide application due to their negative effects for human health, environment, and biodiversity, like, the increase of chronic diseases, the accumulation in soil, water, and food, and the loss of beneficial microorganism and pollinators. These limitations promoted the shift from traditional to modern agriculture. Differently from traditional agriculture, modern agriculture is based on the application of natural means, like agricultural wastes and biocontrol agents (BCAs), for the management of fungal pathogens, weed, and insects. The aim of PhD thesis was to evaluate some natural products and microorganisms as putative botanical and biological fungicides through the following activities: 1. The effect of high and low dose application of agricultural wastes against the main fungal pathogens and weeds of wheat and tomato, the main crops of the Foggia province, as well as their phytotoxicity on the crops; 2. the protective and promoting effect provided by novel BCAs on wheat and tomato, followed by their metabolomic and genomic characterization to understand their mechanisms of action. Based on in vitro results, bergamot (Citrus bergamia) peel, pomegranate (Punica granatum) peel, and the organic commercial product EP5 were selected to assay their efficacy in vivo by performing greenhouse experiments. High dose application resulted to be effective in controlling Fusarium algeriense, F. culmorum, and F. oxysporum f.sp. dianthi and the development of Alopecurus myosuroides and Lolium multiflorum, but it also shows a phytotoxic effect on the roots of wheat plants. Interestingly, the powders keep their efficiency against the fungal pathogens and weeds over time without showing any phytotoxic effects on wheat roots. The potential phytotoxic effect could also be avoided by using low doses of the powders. Indeed, by halving the used dose, bergamot, EP5, and pomegranate are still efficient against the soilborne fungal pathogens of tomato (Agroathelia rolfsii, F. oxysporum, Sclerotinia sclerotiorum) and its weeds (Amaranthus retroflexus, Chenopodium album, Solanum nigrum) without showing any phytotoxic effects. Among three potential BCA Streptomyces strains, Strep_22 resulted to be the most efficient strain in in vitro and in vivo conditions against the soilborne fungal pathogens of wheat and tomato, promoting at the same time the growth of the crops. The genomic characterization revealed that the strain belongs to the species Streptomyces syringium. The potential application of S. syringium Strep_22 is confirmed by the high number of gene clusters that encode for antifungal secondary metabolites. Indeed, the main produced compounds were indole alkaloids, diketopiperazines, and phthalates, which are known for their applicability against fungal pathogens, weeds, insects, and nematodes.