A model for Decomposition Dynamics in Soils and soil-like environments

Numerous reactions linked to carbon sequestration occur in soils and soil-like environments such as composts. Microorganisms deplete carbon resources and breathe, emitting carbon in the form of carbon dioxide. However, they also progressively die, storing carbon in the long term in the form of biological necromass. While significant progress has been made in understanding the growth and reproduction of bacteria, the mechanisms governing microbial mortality remain unclear. Current models often lack microscopic details and fail to capture the precise mechanisms behind reactions. Here we develop a new model to investigate the dynamics of microbial biomass, soil carbon, and oxygen in soil-like environments, focusing on decomposition processes. Benchmark results show cyclic patterns reminiscent of population dynamics, yet with significant differences, as population dynamics usually do not capture the dynamics of passive compounds (here carbon). Using principles from physics and chemistry, our model lays a starting point to bridge the gap between microscopic reaction dynamics and macroscopic ecology. By gaining fundamental insights into the dynamics of microorganisms and carbon in soils, we shed light on carbon flows in soils and soil-like environments such as composts. This makes it relevant in the context of ongoing climate change.