Biosynthetic diversity and antifungal potential of soil-derived Saccharomonospora strains

Abstract Soilborne fungal pathogens pose persistent challenges to sustainable agriculture, driving demand for biological alternatives to synthetic fungicides. While actinomycetes, particularly Streptomyces have yielded numerous antifungal compounds, less-explored genera, such as Saccharomonospora represent untapped sources of novel bioactive metabolites for plant protection. Our previous work identified Saccharomonospora as strongly associated with plant disease suppression in organically-amended soils and harbored numerous uncharacterized biosynthetic gene clusters (BGCs). Here, we investigated the biosynthetic capacity and antifungal potential of Saccharomonospora using comparative genomics, untargeted metabolomics, and in vitro bioassays. Cell-free supernatants from six strains (five soil-derived type strains and one novel isolate) were evaluated against three Fusarium phytopathogens. All strains inhibited at least one pathogen, with S. xinjiangensis and S. viridis R81 exhibiting the highest and broad-spectrum activity. Metabolomic profiling of the two most bioactive strains and one moderately active strain ( S. cyanea ) revealed that ∼40% of detected metabolites were shared across the three strains although their relative abundances varied. S. xinjiangensis and S. viridis R81 displayed higher abundances of shared metabolite classes than S. cyanea , including alkaloids, polyketides, and peptide derivatives. Comparative genomics across the genus revealed that most BGCs, particularly those encoding non-ribosomal peptides synthetases and polyketides synthases, were strain-specific and had low sequence similarity to characterized BGCs. In contrast, BGCs encoding, indole, ectoine, arylpolyene, and terpene were ubiquitous across the genus. Collectively, these findings demonstrate that Saccharomonospora produce antifungal metabolites and harbor diverse, uncharacterized BGCs, positioning this “less-explored” actinomycete genus as a promising source of bioactive compounds for managing soilborne fungal pathogens. Importance Actinomycetes have historically been rich sources of antifungal metabolites for agriculture and pharmaceuticals, but discovery efforts have focused largely on Streptomyces , leaving other genera underexplored. This study demonstrates that Saccharomonospora , a rare actinomycete genus, produces antifungal metabolites active against major Fusarium pathogens and harbors largely uncharacterized biosynthetic gene clusters, indicating a reservoir of novel chemistry. These findings establish Saccharomonospora as a promising yet underutilized resource for discovering new antifungal agents, expanding the toolkit for sustainable plant disease management beyond traditional actinomycete sources.