Accumulation of Soil Selenium Caused by Long-Term Foliar Spraying Reduced Soil Microbial Diversity and Enhanced Soil Denitrification in Rice Roots

Sustainable agricultural production must be aligned with environmental and biodiversity goals. Foliar selenium (Se) application can effectively increase the rice Se content; however, its long-term effects on soil microbial diversity and functional changes remain poorly understood. Therefore, we conducted a field experiment (foliar Se for 3 years), a simulation experiment (simulated foliar Se for 5 and 10 years), and a meta-analysis (effects of exogenous Se application on the soil microbial α-diversity) to evaluate the effects of foliar Se application on rice production and soil microbial communities and functions. Foliar Se application for 3 years effectively increased the grain Se content, increased soil Se and organic carbon levels, and altered root energy secretion metabolites with significant increases in glutamic acid and glutamine. Soil Se application did not affect the organic carbon content. Continuous foliar Se application for 3 years reduced the stability of the microbial community, with root exudate metabolites exerting stronger effects than Se. The meta-analysis indicated that high-concentration Se (≥0.4 mg·kg–1) significantly reduced the Shannon index of microbial communities. Treatment with Na2SeO3 (for 10 years) increased the soil Se content by 132.67% while decreasing microbial α-diversity findings that align with the meta-analysis results. However, treatment with the compound fertilizer containing Na2SeO3 (for 10 years) increased the soil Se content by 187.43% yet significantly enhancing microbial α-diversity. This discrepancy may be attributed to the oxides formed by iron and manganese ions in the compound fertilizer, which reduce the bioavailability of Se in the soil. Both field and simulation experiments confirmed that the exogenous Se application accelerated the transformation of soil organic phosphorus to an inorganic state soil available phosphorus content, which increased by 52.41% and 5.09%–72.10%, respectively. Denitrification in the soil nitrogen cycle was strengthened, and the increased abundance of norC and nosZ enhanced the possibility of N2O emissions. These results indicate that long-term foliar Se application increases the soil Se content, reduces soil microbial diversity, and strengthens microbial denitrification, which is detrimental to sustainable agricultural production.