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Goji berry ( Lycium barbarum  L.) is substantially dependent on nitrogen fertilizer application, which can significantly enhance fruit yield and Goji berry industrial development in Ningxia, China. This study aimed to analyze the functions of differential nitrogen application rates including low (N1), medium (N2), and high (N3) levels in soil microbial community structure (bacterial and fungal) at 2 diverse soil depths (0–20, 20–40 cm) through high-throughput sequencing technology by targeting 16S RNA gene and ITS1 &amp; ITS2 regions. All the observed physicochemical parameters exhibited significant improvement ( p  &lt; 0.05) with increased levels of nitrogen and the highest values for most parameters were observed at N2. However, pH decreased ( p  &lt; 0.05) gradually. The alpha and beta diversity analyses for bacterial and fungal communities’ metagenome displayed more similarities than differences among all groups. The top bacterial and fungal phyla and genera suggested no obvious ( p  &gt; 0.05) differences among three group treatments (N1, N2, and N3). Furthermore, the functional enrichment analysis demonstrated significant ( p  &lt; 0.05) enrichment of quorum sensing, cysteine and methionine metabolism, and transcriptional machinery for bacterial communities, while various saprotrophic functional roles for fungal communities. Conclusively, moderately reducing the use of N-supplemented fertilizers is conducive to increasing soil nitrogen utilization rate, which can contribute to sustainable agriculture practices through improved soil quality, and microbial community structure and functions.

Impact of Different Rates of Nitrogen Supplementation on Soil Physicochemical Properties and Microbial Diversity in Goji Berry