New Multi-Omics Study Reveals How Streptomyces avermitilis SM12 Suppresses devastating Fusarium Diseases

A newly released study has uncovered the multi-layered antifungal strategies of Streptomyces avermitilis SM12, a promising microbial agent with potential to combat Fusarium solani and Fusarium oxysporum—two notorious pathogens responsible for major crop losses worldwide.

Using an integrated genomic, transcriptomic, and metabolomic (multi-omics) approach, researchers identified 39 biosynthetic gene clusters (BGCs) in the SM12 strain, including nine directly linked to antimicrobial compound synthesis. Particularly noteworthy is a BGC with strong similarity to the oligomycin biosynthetic pathway, a compound already known for potent antifungal activity.

Antifungal Metabolites Identified

Metabolomic profiling revealed several key antifungal compounds produced by SM12, including:

Oligomycin
Phthoxazolin
Ectoine
2,3-Hexanedione (a volatile antifungal compound)

These metabolites were confirmed by LC–MS and HS–SPME–GC–MS analysis. The cell-free supernatant collected after four days of fermentation significantly inhibited the growth of both F. solani and F. oxysporum. Further in vitro tests validated the strong antifungal activity of oligomycin, ectoine, and 2,3-hexanedione.

How SM12 Coordinates Its Antifungal Response

Time-series transcriptomics showed that the oligomycin and phthoxazolin BGCs become highly active during the peak antifungal production phase. These transcriptional patterns matched the metabolite accumulation profiles, illustrating a tightly regulated system that synchronizes antifungal molecule production with growth phase.

The study also identified post-transcriptional and translational regulatory mechanisms, revealing that metabolite levels don’t always directly reflect gene expression levels—an important factor for future biocontrol optimization.

A Strong Candidate for Sustainable Agriculture

This multi-omics analysis provides one of the most detailed mechanistic insights to date on how a Streptomyces strain suppresses plant pathogens. By mapping gene-to-metabolite relationships, the study highlights how SM12’s chemical arsenal makes it a potent biocontrol agent.

With rising global interest in microbial alternatives to chemical fungicides, Streptomyces avermitilis SM12 stands out as an excellent candidate for development into a sustainable biocontrol product.

Reference

Ma, X., Jia, C., Su, J., Lu, W., Zheng, R., & Yue, S. (2025). Dynamicomic analysis reveals the biocontrol activity of a Streptomyces avermitilis SM12 against Fusarium spp. Pesticide Biochemistry and Physiology, 106822. https://doi.org/10.1016/j.pestbp.2025.106822