Carbon and energy use efficiency of soil microorganisms unfolding over time

We live in a time of unprecedented global change. Understanding its causes and predicting its consequences are challenges of utmost urgency. In a clash of scales, the future of the global climate system depends in no small part on the activity of the microscopic organisms that inhabit the soils beneath us. They mediate the future of the world's soil organic matter stocks, the single largest terrestrial pool of organic carbon on the planet. Consequently, enormous scientific effort has been invested to unravel the details of soil microbial carbon cycling and carbon use efficiency. Yet, the spatial and temporal heterogeneity of the soil environment and the interactions of many physical, chemical, and biological processes across scales continue to limit our mechanistic understanding of the system. This thesis contributed to the recent endeavor of establishing a bioenergetic framework for the description of microbial carbon cycling in soil based on thermodynamic principles. Specifically, microbial-explicit process-based models were employed to investigate the coupling between carbon and energy fluxes during soil microbial growth. This involved the theoretical analysis of dynamic model behavior as well as model calibration using specific datasets to facilitate the interpretation of experimental observations. The results revealed a close correspondence between microbial carbon and energy use efficiency in accordance with thermodynamic predictions. In particular, the models accurately captured the complex temporal patterns in microbial efficiency after the addition of labile substrates. Based on these simulations, the effects of oxygen and nutrient limitation, soil organic matter utilization, and microbial maintenance on the dynamics of microbial growth in several experiments could be disentangled and quantified. The calorespirometric ratio of heat to CO2 release proved to be a particularly valuable tool for such analyses of experimental data and for the generation of falsifiable hypotheses. In terms of process-based modeling, the explicit incorporation of heat dynamics presented the most important novelty. It was instrumental to both the model calibration and the analytical utility of the models. The strengths, weaknesses, and possible extensions of the approaches presented in this thesis are discussed to highlight promising options for future research. Overall, the thesis demonstrated the feasibility and utility of microbial-explicit process-based modeling for the analysis of coupled carbon and energy flows in the soil system.