Differential Responses of Soil Bacterial and Fungal Communities to Simulated Nitrogen Deposition in a Temperate Wetland of Northeastern China

China has experienced a notorious increase in nitrogen (N) deposition as a result of anthropogenic activities, particularly in temperate areas. While aboveground biodiversity has been extensively studied, the impact of long-term N deposition on the diversity, composition, and function of the soil microbiome remains largely unexplored. In this study, we evaluated alterations in the diversity, composition, and function of soil bacterial and fungal communities in response to varying levels of N deposition (LN = low N addition, 40 kg N ha−1 yr−1; HN = high N addition, 80 kg N ha−1 yr−1) using Illumina MiSeq sequencing technology in a temperate natural wetland. N deposition had no discernible impact on bacterial α diversity, whereas fungal α diversity exhibited a significant decrease in response to high N addition only. Additionally, N deposition led to a notable increase in the relative abundance of the bacterial phylum Patescibacteria but a decrease in Latescibacteria. The relative abundance of Epsilonbacteraeota was highest in the unamended plots and lowest in the low N addition plots. Furthermore, N addition significantly increased the relative abundance of Ascomycota while decreasing that of Mortierellomycota, with no significant effect observed on Basidiomycota. Structural equation modeling (SEM) indicated that soil organic carbon (SOC), and total and available N were the two primary drivers shaping bacterial and fungal communities. Our study demonstrated that bacterial communities were less responsive to N addition compared to fungal communities, emphasizing the significance of simultaneously evaluating the soil microbiome in response to global changes.