Salinity-Associated Disintegration of Soil Multitrophic Networks Decouples Microbial Carbon Sequestration from Biotic Regulation

Soil salinization threatens agricultural sustainability and food security, especially in arid and semi-arid regions, yet how salinity gradients reshape multi-trophic networks and their associations with functional genes remain unclear. We investigated soil bacteria, fungi, protists, nematodes, and the carbon-fixation gene cbbL along a natural salinity gradient (electrical conductivity: 1.2–12.4 mS cm−1) in Karamay, Xinjiang. Salinity acted as a key environmental filter, significantly differentiating biotic communities into low- and high-salinity groups. Compared with bacteria and fungi, protists and nematodes exhibit higher sensitivity to salinity shifts from non-saline to slightly saline soils, with their Shannon diversity decreasing by 74.2% and 50.4%, respectively (p < 0.05). High salinity significantly reduced the connectivity, modularity, and robustness of soil multi-trophic co-occurrence networks, resulting in 36.8% fewer edges, 24.2% lower modularity, and diminished network robustness compared to low-salinity conditions. Crucially, salinity was associated with functional decoupling, defined as a shift in the dominant drivers of microbial carbon sequestration potential. At low salinity, biotic factors explained 94.2% of cbbL variation, whereas at high salinity abiotic factors governed 86.1%, as shown by GBM (Gradient Boosting Machine) analyses. Our findings indicate that protists and nematodes can act as early warning indicators for soil salinization, and biotic network complexity represents a core metric for assessing saline soil ecosystem stability. This study reveals salinization-induced biota–function decoupling patterns and provides insights for saline soil health assessment and biotic restoration.