Exogenous organic carbon inputs drive a temporal shift in microbial carbon use efficiency from chemical constraints to microbial adaptation

Soil microbial carbon use efficiency (CUE) regulates whether assimilated carbon (C) is retained in microbial biomass or lost through respiration, thereby influencing soil C cycling under long-term nutrient management. Two widespread nutrient-input pathways can alter this balance in different ways: inorganic nitrogen (N) addition primarily supplies mineral nutrients, whereas exogenous organic C inputs alter substrate supply, nutrient context, and the costs of processing complex organic materials. We therefore used N addition as a benchmark pathway to test whether microbial CUE is more sensitive to experimental duration under inputs that alter substrate complexity than under inputs that primarily relieve nutrient limitation. Using 250 paired observations from 52 field experiments, we quantified the main and interactive effects of input rate and experimental duration on microbial CUE using hierarchical meta-analysis and linear mixed-effects models. Both N addition and exogenous organic C inputs increased microbial CUE by 8.6% and 29.4%, respectively. However, microbial CUE under N addition showed no significant interaction between input rate and experimental duration. In contrast, exogenous organic C inputs showed a significant rate–duration interaction and a biphasic response over time, with weaker or negative responses in shorter-duration experiments (≤ 24 years) and stronger positive responses in longer-duration experiments (> 24 years), particularly at higher input rates. Around 24 years, the dominant correlates of microbial CUE under exogenous organic C inputs shifted from short-term chemical and stoichiometric correlates, especially the response ratio of total N and changes in soil pH, toward microbial biomass C and mean annual temperature. These results suggest that the correlates of microbial CUE under sustained exogenous organic C inputs shift with experimental duration. Our results highlight the importance of incorporating experimental duration into biogeochemical models of soil C cycling and evaluations of long-term soil C dynamics under sustained nutrient inputs and global change.