Prothioconazole (PTC) is currently a popular triazole fungicide. In recent years, as the use of PTC has increased, there has been growing concern about its environmental and toxicological effects. Here, we studied the effect of PTC on the growth of soybean plants and further analyzed the enzyme activity and microbial community of rhizosphere soil after PTC treatment through 16S rRNA gene high-throughput sequencing and fungal ITS. Changes in structural diversity and species richness were measured using Simpson's diversity index, Shannon's diversity index and the Chao1 and ACE algorithms. The statistical t-test was applied to test whether the index values were significantly different between the two groups. The results showed that the contents of malondialdehyde (MDA) and H2O2 increased after the recommended dose of PTC, indicating that PTC has a strong toxic effect on plant growth, thus affecting the healthy growth of plants. In the presence of PTC, the species richness of fungi and bacteria decreased in all three soil types (black soil, yellow earth and red earth), and the community structure also changed significantly (the p-values were all less than 0.05). Proteobacteria, Actinomycetota, Bacteroidota and Acidobacteriota were the main bacteria, and the abundance of Acidobacteriota and Chloroflexi increased. The dominant fungal communities were Ascomycota and Mortierellomycota. The increased abundance of potentially beneficial microorganisms, such as Sphingomonadaceae, suggested that plants may be resistant to PTC stress by recruiting beneficial microorganisms. PICRUSt analysis showed that the metabolism-related functions and membrane transport pathway of rhizosphere bacterial community were inhibited after PTC stress. Spearman correlation analysis revealed a weak correlation between key fungal taxa and rhizosphere variables in the presence of PTC. Therefore, compared with those in the fungal community, the bacterial community was more likely to help plants resist PTC stress, indicating that these key fungal groups may indirectly help soybean growth under PTC stress by affecting the bacterial community.
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