Individual Based Model Links Thermodynamics, Chemical Speciation and Environmental Conditions to Microbial Growth

Area of Science:

• Microbial Ecology
• Biochemical Engineering
• Computational Biology

Background:

• Individual based models (IbM) require enhanced biological and physical credibility to transition from research to engineering tools.
• Thermodynamic principles offer predictive power in microbial ecology but necessitate models incorporating pH and chemical speciation.
• Physical credibility requires plausible mechanics and environmental connectivity.

Purpose of the Study:

• To present an individual based model integrating thermodynamics, pH, chemical speciation, and environmental conditions for microbial growth.
• To demonstrate the model's application in simulating microbial communities with up to 5·10^5 individuals.
• To evaluate the impact of thermodynamic and environmental factors on microbial community dynamics.

Main Methods:

• Development of a novel individual based model (IbM) incorporating thermodynamic principles, pH, and chemical speciation.
• Simulation of a two functional group nitrification model.
• Simulation of a three functional group anaerobic microbial community.

Main Results:

• In nitrification models, pH and environmental coupling significantly influenced simulation outcomes.
• In anaerobic communities, spatial arrangements and methane production were strongly dependent on thermodynamic and reactor coupling.
• The model successfully linked thermodynamics, pH, and environmental conditions to microbial growth in complex communities.

Conclusions:

• Integrating thermodynamics, pH, chemical speciation, and environmental conditions is crucial for developing credible IbM for engineered biological systems.
• Further development is needed for calculating specific uptake rates and enabling longer simulations with larger models.
• A common, fast, and modular platform is essential for future innovations in IbM development and application.