1. Config→ Redox couples…
Decouple redox pairs for electron donating and accepting half reactions

2. add → Kinetic → Microbial reaction
Type out redox reaction catalyzed by the microbe
Enter thermodynamic constraints and kinetic parameters

3. Kinetics of microbially catalyzed reaction
Rate is initially biomass limited, but increases with biomass growth until thermodynamic and kinetic limitations develop.

4. Growth and decay of microbial populations
Biomass increases rapidly, then slowly declines as decay outpaces growth

5. Thermodynamic constraints on reaction
Reaction proceeds uninhibited initially but rate slows primarily due to thermodynamic limitations.

6. Two microbial populations
Identify each microbial population with a label and reaction.
Microbes can compete for common substrates or catalyze different reactions.
In this example, two different strains, (one fast, the other efficient) growing in a chemostat catalyze the same reaction. They differ in their kinetic and growth parameters.

7. Pure cultures and mixed communities
The rapidly metabolizing strain grows fastest initially, but with time is replaced by the more efficient strain.