We have developed a new kinetic model to study how microbial dynamics are affected by the heterogeneity in the physical structure of the environment and by different strategies for hydrolysis of polymeric carbon. The hybrid model represented the dynamics of substrates and enzymes using a continuum representation and the dynamics of the cells were modeled individually. Individual-based biological model allowed us to explicitly simulate microbial diversity, and to model cell physiology as regulated via optimal allocation of cellular resources to enzyme synthesis, control of growth rate by protein synthesis capacity, and shifts to dormancy. This model was developed to study how microbial community functioning is influenced by local environmental conditions in heterogeneous media such as soil and by the functional attributes of individual microbes. Microbial community dynamics were simulated at two spatial scales: micro-pores that resemble 6-20-μm size portions of the soil physical structure and in 111-μm size soil aggregates with a random pore structure. Different strategies for acquisition of carbon from polymeric cellulose were investigated. Bacteria that express membrane-associated hydrolase had different growth and survival dynamics in soil pores than bacteria that release extracellular hydrolases. The kinetic differences suggested different functional niches for these two microbe types in cellulose utilization. Our model predicted an emergent behavior in which co-existence of membrane-associated hydrolase and extracellular hydrolases releasing organisms led to higher cellulose utilization efficiency and reduced stochasticity. Our analysis indicated that their co-existence mutually benefits these organisms, where basal cellulose degradation activity by membrane-associated hydrolase-expressing cells shortened the soluble hydrolase buildup time and, when enzyme buildup allowed for cellulose degradation to be fast enough to sustain exponential growth, all the organisms in the community shared the soluble carbon product and grew together. Although pore geometry affected the kinetics of cellulose degradation, the patterns observed for the bacterial community dynamics in the 6-20 μm-sized micro-pores were relevant to the dynamics in the more complex 111-μm-sized porous soil aggregates, implying that micro-scale studies can be useful approximations to aggregate scale studies when local effects on microbial dynamics are studied. As shown with examples in this study, various functional niches of the bacterial communities can be investigated using complex predictive mathematical models where the role of key environmental aspects such as the heterogeneous three-dimensional structure, functional niches of the community members, and environmental biochemical processes are directly connected to microbial metabolism and maintenance in an integrated model.