Microbial carbon use efficiency (CUE), a key parameter to characterize microbial carbon conversion efficiency, is assumed to be similar in soil models for different soil functional pools with varied organic matter composition and nutrient availability, that is, particulate organic matter (POM) and mineral-associated organic matter (MAOM). However, empirical studies comparing microbial CUE in POM versus MAOM are largely lacking. It is not known whether microbial CUE variance may underpin the variant behaviour (i.e. turnover and composition) of different soil functional pools.

Here we collected surface soils from 25 natural forests and grasslands with divergent edaphic properties, and compared microbial CUE in their POM versus MAOM using soil fractionation in combination with incubation using ¹⁸O-labelled water. We also quantified edaphic properties, organic matter composition, microbial community structures and the stoichiometric imbalance of nitrogen (N) and phosphorus (P) relative to carbon based on the dissolved pool relative to microbial biomass (Im_N and Im_P) to investigate variables regulating microbial CUE and its variation in POM relative to MAOM (CUE_POM/CUE_MAOM).

In contrast to our expectation, microbial CUE did not consistently differ between POM and MAOM across sites, albeit with large inter-sample variations in CUE_POM/CUE_MAOM (from 0.3 to 4.4). Although MAOM had higher substrate quality, indicated by lower ratios of soil organic carbon to total nitrogen (C/N_OM) and higher N-compounds/aromatic ratios, and higher proportions of r-strategists and fast-growing bacteria in the microbial community than POM, POM and MAOM had similar degrees of N limitation (i.e. Im_N), which was the best predictor of microbial CUE across all samples. Therefore, although MAOM harboured more N-containing compounds than POM, N limitation was not necessarily lower, leading to an overall similar microbial CUE in POM and MAOM. Nevertheless, CUE_POM/CUE_MAOM decreased with increasing P limitation in POM relative to MAOM.

Overall, our paper presents a comprehensive, empirical study comparing microbial CUE in POM and MAOM of diverse soils, and our results support the use of similar microbial CUE for POM and MAOM in soil models, but also highlight potential contrasts in microbial CUE between soil pools under strong P limitation. Such inferences deserve attention under potentially increasing P limitation induced by N deposition. This study advances our mechanistic understanding of ecological patterns and processes from the organismic to the ecosystem scale based on soil microbial physiology and different soil functional pools.