| Summary: | Quinoa is extensively cultivated for its nutritional value, and its exceptional capacity to endure elevated salt levels presents a promising resolution to the agricultural quandaries posed by salinity stress. However, limited research has been dedicated to elucidating the correlation between alterations in the salinity soil microbial community and nitrogen transformations. To scrutinize the underlying mechanisms behind quinoa’s salt tolerance, we assessed the changes in microbial community structure and the abundance of nitrogen transformation genes across three distinct salinity thresholds (1 g·kg<sup>−1</sup>, 3 g·kg<sup>−1</sup>, and 6 g·kg<sup>−1</sup>) at two distinct time points (35 and 70 days). The results showed the positive effect of quinoa on the soil microbial community structure, including changes in key populations and its regulatory role in soil nitrogen cycling under salt stress. <i>Choroflexi</i>, <i>Acidobacteriota</i>, and <i>Myxococcota</i> were inhibited by increased salinity, while the relative abundance of <i>Bacteroidota</i> increased. <i>Proteobacteria</i> and <i>Actinobacteria</i> showed relatively stable abundances across time and salinity levels. Quinoa possesses the ability to synthesize or modify the composition of keystone species or promote the establishment of highly complex microbial networks (modularity index > 0.4) to cope with fluctuations in external salt stress environments. Furthermore, quinoa exhibited nitrogen (N) cycling by downregulating denitrification genes (<i>nirS</i>, <i>nosZ</i>), upregulating nitrification genes (Archaeal <i>amoA</i> (AOA), Bacterial <i>amoA</i> (AOB)), and stabilizing nitrogen fixation genes (<i>nifH</i>) to absorb nitrate–nitrogen (NO<sub>3</sub><sup>−</sup>_N). This study paves the way for future research on regulating quinoa, promoting soil microbial communities, and nitrogen transformation in saline environments.
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