A novel microbial duel strategy for isolating antifungal subcommunities from soil

Fusarium is a major soil-borne fungal pathogen worldwide, causing significant agricultural losses. Chemical control methods pose environmental risks, making microbial-mediated biocontrol an urgent alternative. However, current approaches rely on omics data to analyze and predict antifungal communities, lacking a direct method to isolate these functional subgroups from soil. In this study, we developed a novel “microbial duel” strategy that reduces community complexity while maintaining antifungal activity, enabling the direct isolation of antifungal subcommunities. By imposing carbon-deficient conditions, Fusarium was used as a selective pressure to screen for subcommunities with strong antifungal properties. Following two rounds of artificial selection, the number of dominant genera decreased from 28 in the original soil sample, representing 46.05 % of the community, to 13–14 genera in the R2 subcommunities, which accounted for nearly 95 % of the total abundance. Species richness decreased by over 90 % during this process, along with a significant reduction in diversity, indicating the substantial simplification of the community. The most effective subcommunity reduced Fusarium by 83.06 % in microplate assays and by 75.41 % in soil environments, confirming robust antifungal activity under different conditions. The isolated subcommunities demonstrated structural flexibility across different environments, with stable "killer" species, including Pedobacter , Pseudomonas , and Variovorax , consistently present in all groups, while decomposer species showed more variability. For the first time, we successfully isolated antifungal subcommunities at the community level from soil, providing a promising method for obtaining functional subgroups from complex microbiota with broad potential applications. • Novel approach effectively isolates antifungal subcommunities from soil. • Isolated subcommunities show reduced complexity but high antifungal activity. • Microbes in isolated subcommunities can be divided into "killer" or "decomposer". • Isolated subcommunities exhibit robust antifungal activity in soil environments.