Acid-resistant effectively controls pathogenic and improves plant health through metabolic interactions.

Unlabelled: is the etiological agent of Capsicum anthracnose. has traditionally been recognized as an effective biocontrol agent; however, its efficacy decreases due to soil acidification. In this study, we domesticated XY40-1 along an acid resistance gradient, resulting in a strain capable of growth at pH 4, and might adapt to acidic environments by regulating genes related to spore formation. Notably, the domesticated XY40-1 exhibits significant antagonistic activity against in acidic dual cultures and effectively reduces the disease index in . The domesticated strain employs a direct antifungal strategy under acidic conditions, with the production of amylocyclicin, regulated by , potentially serving as a primary mechanism through which combats . Conversely, under neutral conditions, domesticated focuses on bolstering its defense mechanisms by increasing the expression of , , and genes to detoxify peroxides. In addition, a dual RNA-Seq analysis comprehensively investigated the acid tolerance mechanisms and defensive responses of and the pathogenic mechanisms of , providing a foundation for the practical application of as a biocontrol agent. These findings offer important insights into the impact of soil acidification on plant disease suppression and contribute to the development of sustainable agricultural practices.

Importance: Recently, the increasing issue of soil acidification has worsened anthracnose disease in Capsicum, caused by . Our study demonstrated that can effectively inhibit the growth of . However, the molecular mechanisms underlying the interaction between and remain largely unexplored. Here, we developed an interaction system between and to explore their dynamic relationship. By employing dual RNA-Seq methods, we were able to comprehensively investigate the acid tolerance mechanisms and defense responses of , alongside the pathogenic mechanisms of . This establishes the groundwork for utilizing as an effective biocontrol agent in agriculture.