Carbon use efficiency (CUE) describes a critical step in the terrestrial carbon cycle where microorganisms direct organic matter between anabolic and catabolic metabolism in order to balance growth with energetic demands, respectively. Because these pathways result in soil carbon either retained in the system as microbial biomass constituents or lost via mineralization, CUE is an important controller of soil carbon dynamics and CO2 efflux. CUE estimates frequently range from 0.2-0.7 for different habitats, however the information provided by many existing approaches is often unclear and potentially incompatible. Here we explore the soil processes inherent to traditional (e.g., substrate-based, biomass-based) and emerging (e.g., growth rate-based, calorimetry) CUE techniques in order to better understand the information they provide. Control (untreated) soil from the Harvard Forest Long Term Ecological Research site in Massachusetts, USA, was amended with 13C-glucose and 18O-water in laboratory mesocosms and monitored for changing rates of soil dissolved organic carbon (DOC) uptake, respiration (R), microbial biomass (MB) production, DNA synthesis, and heat (Q) flux over 96 hrs. These measurements allowed calculation of four different CUE estimates: 1) (ΔDOC – R)/ΔDOC (substrate-based), 2) Δ13C-MB/(Δ13C-MB + R) (biomass-based), 3) Δ18O-DNA/(Δ18O-DNA + R) (growth rate-based), 4) Q/R (energy-based).
Our results indicate that substrate (glucose) uptake occurs within minutes of amendment and, along with DOC, declines to pre-amendment levels within ~48 hrs. Estimates of chloroform-fumigation extraction MB used in biomass-based methods are substantially inflated as a result of rapid uptake and make substrate storage vs. biomass synthesis difficult to discern. Total DNA concentrations indicate a more typical microbial growth curve following resource addition (i.e., lag, growth, and declining phases) while 18O-DNA concentrations increased linearly throughout the 96 hr incubation period, suggesting that total DNA and 18O-DNA levels track net and gross biomass synthesis dynamics, respectively. Despite their differences, all CUE techniques were positively correlated (r > 0.4) and reveal high initial CUE at 4-8 hrs after substrate amendment (>0.8 for substrate- and biomass-based methods and ~0.15 for growth-rate based methods) that approaches zero between 24-28 hrs for all methods. These efforts will increase the transparency of microbial efficiency methods and estimates for researchers looking to choose the most appropriate technique for their scale of inquiry or use CUE estimates in modeling applications.