Regulatory Mechanism of Carbon Fractions and Microbial Metabolism on Organic Carbon Turnover in Saline–Alkali Soils

Soil salinization is a serious threat to agricultural productivity and organic carbon cycling; however, the mechanisms by which carbon fractions and microbial metabolism regulate organic carbon sequestration remain unclear. This research investigated the effects of four sites (S1–S4) along a salinity gradient on microbial carbon metabolism, carbon fractions (particulate organic carbon, POC; mineral-associated organic carbon, MAOC), and bacterial and fungal communities in a typical saline–alkali soil. The results showed that, as the salt–alkali level increases, microbial growth, respiration, and carbon utilization efficiency (CUE) all exhibit a gradually decreasing trend, with CUE declining by 34.0% at S4 relative to S1. CUE was strongly negatively correlated with the soil pH, EC, and soluble salts, but showed a logarithmic rise with SOC, reaching a maximum of 0.47 near 8 g kg−1. Both POC and MAOC decreased alongside the salt–alkali level, the proportion of MAOC in SOC (52.04–55.02%) was significantly higher than that of POC (44.98–47.96%), and there was a significant positive linear correlation with SOC and CUE. Under high salinity, the 16S rRNA gene copy number decreased by up to 28.8%, while the ITS copy number remained stable. As the salt and alkali levels increased, bacterial Proteobacteria and Actinobacteriota showed an increasing trend, whereas fungal communities remained dominated by Ascomycota. Furthermore, correlation analyses revealed that bacterial Acidobacteriota and Proteobacteria, and fungal Basidiomycota and Chytridiomycota play crucial roles in carbon cycling. Random forest modeling (RFM) and partial least squares path modeling (PLS-PM) also revealed that saline–alkali soil properties strongly affect 16S rRNA gene abundance and microbial respiration; carbon fractions and CUE exerted a strong positive direct effect on SOC, whereas microbial respiration had a negative effect. These findings demonstrate that saline–alkali stress restricts SOC sequestration primarily by weakening microbial activity and community function, with CUE playing only an indirect role. In conclusion, enhancing the POC and MAOC pools and improving the microbial carbon turnover efficiency may be more effective strategies for mitigating carbon loss and sustaining SOC stocks in saline–alkali soils.