Soil salinity is a growing threat to agricultural sustainability, particularly in arid and semi-arid regions. Understanding how salinity affects soil organic matter (OM) is critical for improving land management and maintaining soil health. This study addresses these challenges by exploring the molecular-level impact of salinity on OM dynamics. Salinity exerts a depth-dependent influence on lignin and microbial lipid biomarkers, which are used to trace plant inputs and microbial activity, respectively. For lignin biomarkers, in the surface layer (0–20 cm), higher salinity levels are associated with increased Syringyl/Vanillyl (S/V) and Cinnamyl/Vanillyl (C/V) ratios, suggesting enhanced preservation of syringyl (S) and cinnamyl (C) units. In the middle layer (−20 to −60 cm), higher salinity correlates with elevated SVC (total lignin phenols), Acid/aldehyde (Ad/Al) ratios, and other markers of selective lignin degradation. For lipid biomarkers, salinity modulates microbial adaptation and turnover, as seen in variations in i17 (iso-C17), a17 (anteiso-C17), and unsaturation indices such as C16:1/C16, reflecting Gram-positive and Gram-negative bacterial activity. These trends indicate that salinity stress alters microbial lipid profiles, leading to reduced turnover and enhanced preservation in deeper, more anoxic environments. Principal Component Analysis (PCA) revealed depth- and salinity-driven patterns that distinguish between surface microbial transformations and deep-layer molecular preservation. Correlation analysis of Principal Components (PCs) with salinity revealed that higher salinity favored molecular stability in deeper layers, while lower salinity was associated with microbial transformations in surface layers. These findings underscore salinity’s critical role in OM stabilization and turnover, and provide a molecular framework to guide sustainable management of saline soils.

Understanding how soil organic matter (SOM) responds to agricultural management at the molecular scale remains a central challenge, particularly in semi-arid Mediterranean systems where long-term monitoring is limited, and soils face marked seasonal fluctuations, salinity constraints, and sustained cultivation pressure. In this study, lignin and lipid biomarkers were combined to provide complementary views of SOM dynamics in the agricultural soils of Oued Rhiou (Algeria), enabling the simultaneous assessment of plant-derived inputs, microbial processing, and stabilization pathways under cultivation and subsequent rest periods. Depth-dependent patterns showed that lignin indicators responded strongly to shifts between crop residue inputs and root-derived material, while lipid proxies captured changes in microbial activity, biosynthesis, and OM stabilization. Surface soils exhibited enhanced microbial turnover during cultivation, whereas deeper layers were characterized by selective preservation of recalcitrant compounds. Principal Component Analysis (PCA) further highlighted these processes by distinguishing vegetation-driven variability from microbial reworking patterns, with subset analyses (lignin-only and lipid-only) providing clearer explanatory power than the combined dataset. Collectively, the findings underscore the importance of integrating rest periods into agricultural cycles to promote SOM stabilization, highlight the complementarity of lignin and lipid proxies for deciphering SOM transformation pathways, and offer molecular-level insights that can guide sustainable soil management strategies aimed at balancing productivity, soil resilience, and long-term carbon sequestration.