Electron bifurcation mechanism and homoacetogenesis explain products yields in mixed culture anaerobic fermentations

Anaerobic fermentation of organic wastes using microbial mixed cultures is a promising avenue to treat residues and obtain added-value products. However, the process has some important limitations that prevented so far any industrial application. One of the main issues is that we are not able to predict reliably the product spectrum (i.e. the stoichiometry of the process) because the complex microbial community behaviour is not completely understood. To address this issue, in this work we propose a new metabolic network of glucose fermentation by microbial mixed cultures that incorporates electron bifurcation and homoacetogenesis. Our methodology uses NADH balances to analyse published experimental data and evaluate the new stoichiometry proposed. Our results prove for the first time the inclusion of electron bifurcation in the metabolic network as a better description of the experimental results. Homoacetogenesis has been used to explain the discrepancies between observed and theoretically predicted yields of gaseous H2 and CO2 and it appears as the best solution among other options studied. Overall, this work supports the consideration of electron bifurcation as an important biochemical mechanism in microbial mixed cultures fermentations and underlines the importance of considering homoacetogenesis when analysing anaerobic fermentations

New individual-based model links microbial growth to the energy available in the environment

A new individual-based model is presented in which we aim to describe microbial growth constrained by the environmental conditions at each point of a 2D space. The model is characterized for a full description of the physico-chemistry of the system and uses thermodynamics to approximate the microbial growth. The growth parameters are estimated using the information of the surroundings and it employs only first principles instead of relying on measurements at the population level. This allows ab initio approximation of the growth parameters, and therefore directly links microbial growth and environmental conditions. For this reason, the model is characterised for its flexibility. We test the model in three very different scenarios: anaerobic digestion, aerobic heterotrophic growth and nitrification. Due to its flexibility, rigorous thermodynamic calculations and the possibility to estimate the parameters ab initio, the model will be further used to hypothesize the presence of new functional groups or microbial species not yet discovered and to model complex microbial populations not well understood. Moreover, it can be used to study the rules that control microbial evolution or/and immigration

Study of the competition between complete nitrification by a single organism and ammonia- and nitrite-oxidizing bacteria

Complete nitrification by only one microorganism has been recently experimentally discovered. However, it was theoretically predicted almost 10 years ago by hypothesizing that complete nitrifiers are yield strategist that have a metabolic advantage to survive in biofilms. In this work, we study the competition for ammonia between complete nitrifiers and the canonical division of labour between ammonia and nitrite oxidizing bacteria in biofilms by using an individual based model. The model calculates the maximum growth yield using thermodynamics to evaluate the limitation in growth for each functional group in each position of the computational domain. Our results suggest that the trade-off between growth yield and growth rate in ammonia oxidizing bacteria and in complete nitrifiers is not significant as to observe a clear advantage for complete nitrifiers existence in biofilms