ObjectiveBt toxins released from Bt plants and Bt biopesticides are potential exogenous pollutants in the environment with biocidal activity. The environmental behavior and ecological effects of Bt toxins are the focus of safety risk assessment of transgenic plants and transgenic microorganisms. Fungus is an important component of soil microbes and plays a key role in maintaining soil ecosystem stability, but the dynamic response of soil fungal communities and potential functions to exogenous Bt toxins remains unclear.MethodIn this study, the retention dynamics of Bt toxins in soils incorporated with different concentrations of Bt toxins were analyzed, and high-throughput sequencing technology of fungal 18S rRNA gene was used to analyze the effects of Bt toxins application on the soil fungal community and functional diversity.ResultThe results showed that the concentration of water-dissolved Bt toxins in soil decreased significantly with the prolongation of soil incubation time, and the amounts of water-dissolved Bt toxins in soil with initial Bt toxins concentrations of 50, 100 and 500 ng·g^-1 decreased to those of control soil on the 100th day. Both the application of Bt toxins and incubation time could significantly affect the composition of the soil fungal community, and with an increase of initial Bt toxins concentration and prolongation of soil incubation time, the difference in soil fungal community gradually widened. The application of Bt toxins increased the Shannon index of the soil fungal community, the negative correlation and modules of the association network, and thus it did not adversely affect the diversity and stability of the soil fungal community.ConclusionThe results indicate that the initial concentration of Bt toxins and its long-term effects should be of concern when assessing the environmental behavior and micro-ecological effects of Bt toxins. With the increase of Bt toxins concentration, the relative abundances of Phymatotrichopsis, Homalogastra, Geosmithia and Apiotrichum increased significantly, as well as functional genes encoding enzymes involved in protein degradation, carbon metabolism and phosphorus metabolism. It is speculated that the above-mentioned fungal taxa and potential functions were involved in the degradation and transformation process of Bt toxins in the soil. This study provides a scientific reference and theoretical basis for the ecological safety risk assessment of Bt plants, Bt recombinant biopesticides and Bt toxins.