Microbial pathways of plant-derived carbon differ between root and residue inputs in degraded Mediterranean soils

Rapid organic matter mineralization and low carbon (C) inputs in Mediterranean agroecosystems may alter microbial C utilization pathways and soil organic carbon (SOC) formation compared with temperate systems. We investigated microbial C assimilation, turnover, and SOC incorporation in an organic matter–depleted Calcaric Cambisol following a 5-year C₃–C₄ vegetation shift (wheat to maize) under Mediterranean conditions. Two post-harvest treatments were applied: (i) combined aboveground litter plus roots, and (ii) root-only inputs. Over five years, maize-derived C (C₄) progressively contributed to SOC, with higher incorporation under combined inputs (up to 30%) than root-only inputs (up to 25%). SOC mean residence time (MRT) was shorter under combined inputs (12 years) than root-only inputs (17 years), indicating faster C cycling driven by a broader substrate spectrum. Total microbial biomass, assessed via phospholipid fatty acids (PLFAs), approximately doubled under both maize treatments relative to the control, with root-only inputs promoting higher fungal biomass. Compound-specific δ¹³C analysis showed differential microbial C use: with greater fungal incorporation of C4-derived carbon under root-only inputs and higher bacterial incorporation under combined biomass and root inputs. Microbial turnover times based on PLFAs ranged from 10 to 35 days. Fungal biomarkers showed shorter turnover times (10–12 days) than bacterial biomarkers (17–35 days), indicating faster cycling of fungal-associated C pools. Bacterial turnover was slower under root-only inputs, whereas fungal turnover remained stable across treatments. These functional differences in microbial C assimilation and turnover govern SOC dynamics, highlighting the importance of plant input type in regulating C persistence in Mediterranean agroecosystems.