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.