Broadacre crops are commonly infected with a variety of fungal pathogens, leading to sever yield and economic losses each year. In wheat for example, fungal pathogens cause an estimated average yield loss of 20% annually, which can reach nearly 100% in individua years. 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.
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 powerful antibiotic agents. 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), key genetic elements were identified which are correlated with antifungal activity against severe plant pathogens, including Fusarium oxysporum and Zymoseptoria tritici. This research improves our understanding of plant-microbe interactions, including translating in vitro results into in planta activity, and identifies BGCs with promising antifungal activity.