A new approach to continuous monitoring of carbon use efficiency and biosynthesis in soil microbes from measurement of CO₂ and O₂

Abstract. Soils comprise the largest terrestrial carbon pool. Therefore, understanding processes that control soil carbon stabilization and release is vital to improving our understanding of the global carbon cycle.  Heterotrophic respiration is the main pathway by which soil organic carbon is returned to the atmosphere, however not all carbon utilized by heterotrophs shares this fate, as some portion is retained in the soil as biomass and biosynthesized extracellular compounds. The fraction of carbon consumed by microbes that is used for biomass growth (the carbon use efficiency or CUE) is an important variable controlling soil carbon stocks but is difficult to measure. Here we show that CUE can be continuously monitored in laboratory glucose-amended soil incubations by measuring CO₂ and O₂ gas concentrations, allowing instantaneous estimates of microbial biomass growth. We derive a theoretical relationship between the respiratory quotient (RQ), the ratio of carbon dioxide produced to oxygen consumed during respiration, and CUE that recognizes the influence of both substrate and biosynthesized product oxidation states on RQ. Assuming the biosynthesized product has the stoichiometry of an average microbe, and that the substrate is primarily the glucose used for amendment, we measure RQ and use our theoretical relationship to calculate CUE, and from that, biomass production. Extractions of microbial biomass carbon at the end of the experiments reveal minimal net increases in standing biomass across all amended treatments, suggesting that much of this newly produced biomass is likely converted to necromass as substrate availability declines and this results in a net storage of new soil organic matter. Carbon budgets compiled from measurements of relevant pools account for the amended carbon and suggest that with larger carbon amendments, increases in C : N ratios lead to increases in the relative portion of the amendment acutely lost from the soil. These findings demonstrate that soil RQ values may be used to monitor changes in CUE and that studies which monitor soil RQ values should consider CUE as a key factor when changes in RQ are observed, for instance, with changing environmental conditions or changes in production of plant derived compounds. This new approach may be leveraged to provide information on the storage of soil organic matter. These findings demonstrate how measurements of soil RQ may be leveraged to understand soil carbon transformations, specifically the fate of fresh carbon inputs.