STREPTOMYCES SPP. AS SEED TREATMENT: HOW THEY HELP THE PLANT COPE WITH BIOTIC AND ABIOTIC STRESSES

Fusarium spp. are ubiquitous soil-borne pathogens that can affect different food and horticultural crops, causing vascular wilts, rots and damping-off diseases. Fusarium head blight, caused by Fusarium graminearum (Fg), is a major threat to global wheat production and food safety due to mycotoxin production such as deoxynivalenol (DON), that contaminates the harvested product. Similarly, in horticultural crops like tomato, Fusarium oxysporum f. sp. lycopersici (Fol) causes vascular wilts leading to significant yield losses. Abiotic stresses such as iron (Fe) deficiency and water scarcity are two of the most important agronomical concerns that pose a risk to food security. Both biotic and abiotic stresses are intensified by climate change, which in turn leads to an extent use of agrochemicals (pesticides, fertilizers) in open fields. In this regard, plant beneficial microbes (PBM) are a valuable option to lower plant diseases while maintaining crop productivity. Streptomyces spp. are Gram-positive soil-dwelling bacteria that are known as both plant growth-promoting rhizobacteria (PGPR) and biocontrol agents (BCAs) because of the bioactive molecules they produce that can both stimulate plant growth and limit pathogen diseases. Seed treatment and soil drench are two scalable routes effective for delivering promising strains from lab to field application. This PhD project aimed to evaluate Streptomyces-based strategies in wheat and tomato under both biotic and abiotic stress, and to decipher the Streptomyces spp. mode of action (MoA) through multi-omics approaches to link lab research to field trials. To achieve this, proteomics analyses of wheat roots exposed to a factorial combination of Fg infection, mild water deficit, and Streptomyces sp. DEF39 was carried out (Chapter I) revealing DEF39 capability to restore and enhance a PR-3 chitinase during the DEF39-Wheat-Fg tripartite interaction, otherwise suppressed by the fungus when alone in the pathosystem. Genomics analyses of Streptomyces sp. DEF17, coupled with greenhouse assays in tomato plants grown under Fe-limiting regimes, highlighted both the capability of the strain to produce siderophores and mobilise Fe and to increase plant height and Fe content in tomato leaves under Fe(III) supply, supporting a genome-to-phenotype in tomato (Chapter II). Untargeted LC-MS/MS was done to characterise tomato roots and exudates after seed biopriming using either DEF17 or Streptomyces sp. DEF19, together with functional assays ii against Fol. Both streptomycetes remodelled the tomato metabolome. DEF17-treated plants produced metabolites such as gamma-glutamyl dipeptides and phenylacetic acid derivatives that might explain Fol germ tubes repulsion in chemotropism assay, and the reduction of Fol disease severity in planta (Chapter III). Overall, omics analyses suggested an indirect, plant-mediated defence route that cannot be predicted from in vitro assays alone. Finally, the lab-to-field delivery was evaluated in Chapter IV. After seed biopriming, DEF39 induced an earlier seedling emergence in vitro than the control. A field trial was carried out in a rain-limited season in Carpiano (MI). Here, FHB severity was lower in DEF39 seed-treated plants compared to controls in Fg-infected plots. Non-infected plots exposed to drought showed comparable results regarding the total grain productivity (seed number), whereas seed weight was higher in DEF39 treatment. Regarding the tomato field done in Cornaredo (MI) an autonomous 3D canopy phenotyping robotic platform was coupled with agronomic and physiological analysis (data analysis ongoing). Across chapters, the thesis supports seed treatment and soil drench as a practical route to move from strain selection to field trials. Moreover, it demonstrates how omics approaches can be exploited to guide the lab-to-field delivery while potentially supporting strategies leading to the reduction in chemical inputs.