Overall biomass yield on multiple nutrient sources.

Abstract

Microorganisms primarily utilize nutrients to generate biomass and replicate. When a single nutrient source is available, the produced biomass typically increases linearly with the initial amount of that nutrient. This linear trend can be accurately predicted by "black box models", which conceptualize growth as a single chemical reaction, treating nutrients as substrates and biomass as a product. However, natural environments usually present multiple nutrient sources, prompting us to extend the black box framework to incorporate catabolism, anabolism, and biosynthesis of biomass precursors. This modification allows for the quantification of co-utilization effects among multiple nutrients on microbial biomass production. The extended model differentiates between different types of nutrients: non-degradable nutrients, which can only serve as a biomass precursor, and degradable nutrients, which can also be used as an energy source. We experimentally demonstrated using Escherichia coli that, in contrast to initial model predictions, different nutrients affect each other's utilization in a mutually dependent manner; i.e., for some combinations, the produced biomass was no longer proportional to the initial amounts of nutrients present. To account for these mutual effects within a black box framework, we phenomenologically introduced an interaction between the metabolic processes involved in utilizing the nutrient sources. This phenomenological model qualitatively captures the experimental observations and, unexpectedly, predicts that the total produced biomass is influenced not only by the combination of nutrient sources but also by their relative initial amounts - a prediction we subsequently validated experimentally. Moreover, the model identifies which metabolic processes - catabolism, anabolism, or precursor biosynthesis-is affected in each specific nutrient combination, offering insights into microbial metabolic coordination.