From roots to residues: Tracing contrasting pathways of carbon incorporation into soil organic matter of a Mediterranean agricultural trial

Mediterranean agricultural soils are characterized by low organic matter content and high mineralization rates, making carbon stabilization a particular challenge. Here, we combined lipid biomarker analysis with compound-specific stable isotope analysis (CSIA) to trace the incorporation of maize-derived C following a crop switch from wheat (C 3 ) to maize (C 4 ). Two treatments were compared: (A) biomass+root inputs and (B) root-only inputs. Within 21 months, significant enrichment in δ 13 C was detected across compound classes, with long-chain n -alkanes, hydroxy acids and sterols showing increases of + 3 to + 6 ‰, especially in the upper 5 cm, while unsaturated fatty acids displayed minor contributions (< 1 ‰) due to rapid turnover. Aboveground residue inputs (treatment A) enhanced microbial assimilation of maize carbon in surface soils, leading to fast but short-lived incorporation, consistent with shorter bulk SOC mean residence times (MRT) of ca. 15 days compared to the root-only treatment (ca. 28 days). In contrast, root-derived inputs (treatment B) contributed to more persistent pools at depth, where bulk SOC MRTs increased up to 30 days and suberin-derived biomarkers showed pronounced environment. Bulk SOM δ 13 C showed smaller changes (< 1 ‰) than individual compounds, underscoring the value of CSIA for capturing short-term dynamics. These results demonstrate the complementary roles of aboveground residues and roots in shaping SOC turnover and stabilization. In Mediterranean soils with inherently low organic matter stability, residue management strongly mediates both the amount and persistence of new carbon, with implications for developing residue-management strategies that enhance potential pathways towards carbon stabilization in fragile Mediterranean agroecosystems. • Mediterranean soils with inherently low organic matter show rapid carbon turnover. • Lipid biomarkers are effective tracers of C 4 -derived carbon incorporation into SOC. • Above- and belowground inputs distinct SOC dynamics and microbial processing. • 13 C-enriched hydroxy acids and long-chain n -alkanes reflects microbial reworking and preservation.