Broadacre crops are commonly infected with a variety of fungal pathogens, leading to severe yield and economic losses. Typically, these pathogens are controlled via the breeding of resistant wheat genotypes or the use of synthetic fungicides. However, the lifespans of these treatment options are limited, as fungal pathogens are steadily evolving to overcome both fungicide treatments and genetic resistance. This challenge is exacerbated by pathogens that reside in soils and infect underground plant tissues, as antifungal treatments rarely penetrate beneath the surface soils. Therefore, novel methods of crop protection are needed in preparation for a chemically limited future.
The wheat microbiome is a largely untapped source of novel antifungal agents. Endophytes from the bacterial phylum Actinomycetota (Actinobacteria) are commonly isolated from wheat tissues and surrounding soil, while also commonly expressing biosynthetic gene clusters (BGCs) that produce diverse secondary metabolites. Therefore, this research endeavoured to identify strains of plant associated Actinobacteria with promising antifungal properties for use in agricultural systems. Using a combination of long read whole genome sequencing, genome mining and antifungal bioassays (both in vitro and in planta), BGCs were identified which are correlated with antifungal activity against severe plant pathogens, including Fusarium oxysporum and Rhizoctonia solani. Further metabolomics work identified the antifungal metabolites are synthesised by Actinobacteria in root systems, highlighting the prospect of antifungal agents being produced in situ in rhizospheres, where they are most effective at controlling plant disease.