Exploring the antifungal activity of the wheat microbiome

Abstract Wheat (Triticum aestivum) is a cornerstone of global food security, yet its productivity is threatened by fungal pathogens such as Fusarium graminearum, Zymoseptoria tritici, and Rhizoctonia solani. These pathogens not only reduce yield but can also compromise grain quality and food safety through the production of mycotoxins. Traditional control strategies, primarily reliant on chemical fungicides and resistant cultivars, face limitations due to evolving pathogen resistance, environmental concerns, and regulatory restrictions. In recent years, the plant microbiome has emerged as a promising frontier in sustainable crop protection. The wheat microbiome, encompassing microbial communities in the rhizosphere, endosphere (root and leaf), and phyllosphere, plays a pivotal role in plant health and resilience. These microbes can suppress fungal pathogens through diverse mechanisms, both directly and indirectly. This mini-review explores the antifungal potential of the wheat microbiome, highlighting key microbial taxa, mechanisms of action with a focus on the underlying biochemistry and molecular processes, and recent advances in omics and microbiome-based biocontrol strategies. This extends to a case study on our own endophyte biocontrol and biochemistry discovery pipeline. We detail the impacts of fungal pathogen exposure and farming practices on wheat microbiome composition and phytopathogen-suppressive traits and highlight pathways for harnessing microbial communities to enhance wheat resistance.