Overall biomass yield on multiple nutrient sources

Abstract

Abstract Microorganisms utilize nutrients primarily to generate biomass and replicate. When a single nutrient source is available, the produced biomass increases linearly with the initial amount of the available nutrient. This linear trend can be predicted to high accuracy by “black box models” that consider growth as a single chemical reaction with nutrients as substrates and biomass as a product. Since natural environments typically feature multiple nutrients, we extended the black box framework to include catabolism, anabolism, and biosynthesis of biomass precursors to quantify co-utilization of multiple nutrients on microbial biomass production. The model differentiates between different types of nutrients: degradable nutrients that first must be catabolized before they can be used from non-degradable nutrients that can only be used as a biomass precursor. Experimentally, we demonstrated that contradictory to the model predictions, there is a mutual effect between different nutrients on Escherichia coli’s nutrient utilization, where the ability to utilize one is affected by the other; i.e., for some combinations the produced biomass was no longer linear to the initial amount of nutrients. To capture such mutual effects with a black box model, we phenomenologically added an interaction between the metabolic processes used in utilizing the nutrient sources. The phenomenological model qualitatively captures the experimental observations and, unexpectedly, predicts that the produced biomass does not only depend on the combination of nutrient sources but also on their relative initial amounts – a prediction we validated experimentally. Moreover, the model predicts which metabolic processes – catabolism, anabolism, or precursor biosynthesis – is affected in each nutrient combination.