The environment and the microbial community structure and function are often intimately connected. Most environments outside of the lab are physically and chemically heterogeneous, shaping and complicating the metabolisms of their resident microbial communities. On one hand, spatial variations introduce physics such as diffusive and advective transport of nutrients and byproducts. On the other hand, microbial metabolic activity can strongly effect the environment. Hence it is important to link metabolism at the cellular level to physics and chemistry at the community level.
To introduce metabolism to community-scale population dynamics, many models rely on large numbers of reaction kinetics parameters that are unmeasured, also making detailed metabolic information mostly unusable. The bioengineering community has addressed this difficulty by moving to kinetics-free formulations at the cellular level, termed flux balance analysis. To combine and connect the two scales, we propose to replace classical kinetics functions in community scale models with cell level metabolic models, and predict metabolism and how it is influenced by and influences the environment. Furthermore, our methodology permits assimilation of many types of measurement data. We will discuss the background and motivation, model development, and some numerical simulation results.