Building microbial kinetic models for environmental application: A theoretical perspective

Kinetic modeling of microbial reactions is a common tool for addressing the central environmental questions of our time, from contaminant remediation to the global carbon cycle. This review presents an overview of trait-based frameworks for modeling the kinetics of microbial reactions, with an emphasis on environmental application. I first highlight two key model assumptions: the simplification of microbial communities as ensembles of microbial functional groups and the description of microbial metabolism at a coarse-grained level with three metabolic reactions – catabolic reaction, biomass synthesis, and maintenance. Next, I aim to establish a connection between microbial rate laws and the mechanisms of metabolic reactions. For metabolic reactions limited by single substrates, the widely used rate law is the Monod equation. However, in cases where substrates are solids or nonaqueous phase liquids (NAPLs), the Contois equation and the Best equation may offer better alternatives. In microbial metabolisms limited by multiple nutrients simultaneously, two competing rate laws exist: the multiplicative rate law and Liebig's law of the minimum. Then I present two strategies for extending the modeling framework developed for laboratory cultures to natural environments. One strategy follows the multiplicative rate law and incorporates dimensionless functions to account for pH, temperature, salinity, cell density, and other environmental conditions. The other strategy focuses on the physiology of natural microbes, explicitly considering dormancy, biomass decay, and physiological acclimation. After that, I highlight recent improvements enabled by the application of molecular biology tools, ranging from functional gene-based models to metabolic models. Finally, I discuss the inherent limitations of trait-based modeling frameworks and their implications for model development and evaluation, including the gap between functional groups represented in silico and microbial communities found in natural environments, as well as the requirement of internal consistency in microbial parameter sets.