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.
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Data availability
The raw data of 16S, ITS2, and 18S have been stored in the NCBI database under the accession numbers PRJNA842502, PRJNA1057538 and PRJNA1057773, respectively.
Code availability
R code used for data analysis has been deposited in the Figshare database (https://doi.org/10.6084/m9.figshare.25907878).
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Acknowledgements
This work was supported by the National Natural Science Foundation Project of China (Nos. U1906223, 42007208), Youth Innovation Team of Shandong Provincial Department of Science and Technology (No. 2022KJ333), Shandong Provincial Natural Science Foundation, China (No. ZR2020QD084), Funds of the Shandong “Double Tops” Program. We thank Zhaojing Zhang of Shandong University, Qingdao, China for helping us in the physical and chemical determination of soil samples.
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Mengyue Sun: study conception and design, conduct study, data collection and analysis, writing—original draft. Mingcong Li: study conception and design, conduct study, supervision, writing—review & editing. Baohua Xie: field simulation experiment platform management, project administration, funding acquisition. Guangshan Wei: methodology, writing—review & editing. Yuqi Zhou: methodology, writing—review & editing. Wenxi Zhou: writing—review & editing. Wenchong Shi: writing—review & editing. Guangxuan Han: field simulation experiment platform management, sample collection. Ye Deng: supervision, project administration, funding acquisition, writing—review & editing. Zheng Gao: conceptualization, supervision, project administration, funding acquisition, writing—review & editing.
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Sun, M., Li, M., Xie, B. et al. Heterogeneous responses of soil microbial communities and functions in coastal wetlands to long-term nitrogen deposition. npj Biofilms Microbiomes (2026). https://doi.org/10.1038/s41522-026-00947-3
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DOI: https://doi.org/10.1038/s41522-026-00947-3
