Mengyue Sun, Mingcong Li, Baohua Xie, Guangshan Wei, Yuqi Zhou, Wenxi Zhou, Wenchong Shi, Guangxuan Han, Ye Deng & Zheng Gao

Abstract

Global nitrogen (N) deposition, a major consequence of climate change, has profound impacts on soil microbes, yet comparative studies investigating the effects of different N types and levels on diverse soil microorganisms and their ecological functions remain scarce. Here, we conducted a 7-year simulated N deposition with multiple levels (Low, Medium, High) and multiple forms (NH4NO3, NH4Cl, KNO3), combining amplicon sequencing, QMEC chips and ¹⁵N isotope tracing to analyze their impacts on soil microbial communities of prokaryotes, fungi and Cercozoa, elemental cycling, and N transformation. The results showed that N forms dominated Cercozoa and prokaryote community structures (P < 0.05) but not fungi. High NH₄⁺-N deposition significantly reduced microbial resistance (P < 0.05), while NO₃--N deposition enhanced prokaryote-Cercozoa bipartite network stability and linearly increased community resistance (P < 0.05), supporting the ecological phenomenon of “Interdependence Leading to Enhanced Resilience”. Elevated N deposition increased microbial diversity but inhibited key C / N cycling genes (e.g., pmoA, hzsB, nirK2, and nirS1) and N transformation (P < 0.05), raising CH₄ emission and soil N enrichment risks. In conclusion, this study provides scientific support for mitigating N deposition impacts and advancing environmental sustainability.

Paper Linkage:https://doi.org/10.1038/s41522-026-00947-3