| Summary: | Ginger soft rot is a serious soil-borne disease caused by <i>Fusarium solani</i> and <i>Fusarium oxysporum</i>, resulting in reduced crop yields. The application of common chemical fungicides is considered to be an effective method of sterilization, and therefore, they pose a serious threat to the environment and human health due to their high toxicity. Benzalkonium chloride (BAC) and benzethonium chloride (BEC) are two popular quaternary ammonium salts with a wide range of fungicidal effects. In this study, we investigated the fungicidal effects of BAC and BEC on soft rot disease of ginger as alternatives to common chemical fungicides. Two soft rot pathogens of ginger were successfully isolated from diseased ginger by using the spread plate method and sequenced as <i>F. solani</i> and <i>F. oxysporum</i> using the high-throughput fungal sequencing method. We investigated the fungicidal effects of BAC and BEC on <i>F. solani</i> and <i>F. oxysporum</i>, and we explored the antifungal mechanisms. Almost complete inactivation of spores of <i>F. solani</i> and <i>F. oxysporum</i> was observed at 100 mg/L fungicide concentration. Only a small amount of spore regrowth was observed after the inactivation treatment of spores of <i>F. solani</i> and <i>F. oxysporum</i> in soil, which proved that BAC and BEC have the potential to be used as an alternative to common chemical fungicides for soil disinfection of diseased ginger.
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