Using the Calorespirometric Ratio to investigate the metabolism of a growing microbial community dominated by Firmicutes in glucose-amended soil

Soil microorganisms rely on coupled fluxes of carbon and energy from the decomposition of organic substrates to fuel their maintenance and growth requirements. This complex coupling depends on environmental conditions as well as the specific metabolic reactions carried out by the microbial community, but our understanding of the principles governing these dynamics is still limited. The joint analysis of both matter and energy fluxes and in particular the linkage of the microbial carbon and energy use efficiencies (CUE and EUE) during substrate turnover have the potential to elucidate the underlying metabolic pathways. However, such evaluations remain rare.

In this study, we present measurements of heat and CO₂ release from soil after batch input of glucose along with estimates of microbial biomass and community composition. The results reveal a temporal variation in the ratio of heat to CO₂ release (Calorespirometric Ratio, CR) that is inconsistent with simple aerobic decomposition of the substrate. In addition, we find that the dynamics are dominated by the growth of Firmicutes, whose relative abundance increases from 2 percent of initial biomass to almost 50 percent over the course of the incubation.

To interpret these findings, we developed a dynamic model of carbon and energy fluxes during growth on glucose. The model simulates aerobic respiration as well as anaerobic fermentation to lactate and acetate depending on the time-varying availability of O₂ and accounts for activation of the microbial population after initial dormancy. Model simulations capture the complex experimental CR pattern and suggest a gradual depletion of available O₂ and a concurrent shift to anaerobic pathways as the main driver of the dynamics. Given the widespread adaptation to anaerobic conditions found in prevalent members of the Firmicutes, this interpretation is consistent with the observed dominance of the phylum. Notably, model variants of lower complexity that do not include fermentation or increasing microbial activity fail to appropriately reproduce the measured CR and biomass.

These results highlight the potential of the joint analysis of matter and energy fluxes in a combined experimental and modeling approach. The evolution of CR over time revealed the presence of complex dynamics even in the simple case of glucose-amended soil samples and provided constraints on the metabolic processes behind those dynamics that align with the available biomass and community composition estimates. By considering the balance of multiple metabolic pathways as well as the concept of microbial activity, our findings offer a more detailed description of temporal microbial carbon and energy use that goes beyond the assumption of constant CUE and EUE. Such an approach will be essential for the investigation of more complicated transformations of organic matter in soil.