Mechanistic mathematical models of microbial growth in bioreactors and in natural soils: Explanation of complex phenomena

The paper summarizes the development of so-called synthetic chemostat model (SCM) simulating complex dynamic behavior of microorganisms. The basic SCM represents microbial growth as a conversion of exosubstrate into cell macromolecules via pool of intermediates. The “quality” of biomass is characterized by scalar variable r. This variable denotes a relative amount of inducible cell constituents which provide intensive growth and display positive correlation with growth rate (RNA, ribosomal proteins, respiratory enzymes, etc.). Basic SCM (four differential equations) was able to simulate both steady-state growth and transient dynamics of such well studied microorganisms as Pseudomonas and Enterobacteria. To describe the behavior of other organisms having unconventional life strategy (sporeforming bacteria, K-selected and oligotrophic microorganisms), the basic SCM was augmented to different degree by incorporating additional state variables (reserve compounds, prospore compartment, signal metabolic products, etc.). The competition of 2–5 species for a common limiting substrate and growth of one population on several substrates were simulated by enlarged model containing up to 22 differential equations. Application of SCM in physiological and ecological studies provided mechanistic interpretation of many unusual aspects of microbial behavior both in vitro and in situ.