Antagonistic activity of Indigenous Algerian Trichoderma spp. and their secondary metabolites against major wheat crown rot pathogens

Background Fusarium crown rot (FCR), caused mainly by a complex of Fusarium species, is a destructive wheat disease worldwide that reduces yield and contaminates grain with mycotoxins. In Algeria, previous studies have shown that Fusarium culmorum is the pathogen most commonly associated with FCR, alongside Fusarium pseudograminearum, Microdochium nivale, and M. majus. To support sustainable disease management, this study investigates the biocontrol potential of indigenous Trichoderma strains against FCR pathogens through in vitro and in vivo assays using in vitro confrontation tests and in vivo seed treatment bioassays. The antagonistic activity was evaluated with emphasis on antibiosis mediated by bioactive secondary metabolites, some of which were isolated and tested individually against F. culmorum (Fc111). Results The tests conducted in vitro (direct and indirect confrontation) and in vivo revealed the antagonistic potential of these strains. Direct confrontation led to 44.25–90.63% inhibition of mycelial growth across the tested pathogens, with Trichoderma frequently overgrowing the colonies. In contrast, indirect assays mediated by VOCs resulted in 0.97–33.59% inhibition, indicating a relatively weaker antagonistic effect. Seed treatments with four Trichoderma strains reduced FCR severity by 17.43–77.75% compared to controls. The three strains Trichoderma atroviride (Ta.09), Trichoderma orientale (To.15) and Trichoderma afroharzianum (Taf.17), were found to produce distinct secondary metabolites, which change depending on the culture conditions. Notably, the strain To.15 proved to be a rich source of secondary metabolites, including 4-phenyl-1,3-butanediol, which, to the best of our knowledge, is reported in this study for the first time as a metabolite of fungal origin. Several other compounds newly identified in Trichoderma, and additional metabolites, such as bisvertinolone, which was previously known in the genus, are reported here for the first time in strain To.15. The antifungal activity of the crude extracts and the main metabolites from each strain were evaluated against the Fc111 strain at different concentrations. Among these, the major compound from Ta.09, 6-pentyl-α-pyrone (6-PP), exhibited a significant inhibition rate, at the lowest concentration (100 µg plug-1), against Fc111 compared to the secondary metabolites identified from the other two strains. Conclusion These strains showed promising potential for controlling FCR disease, with diverse secondary metabolites, especially 6-PP in Ta.09, likely playing a key role in their biocontrol efficacy. These findings underscore the potential of these strains, as well as 6-PP, as candidates for integrated FCR management strategies and for the development of future biopesticide formulations.