Fig. 1: Model of microbial eco-evolutionary dynamics.
a Genes on a linear genome code for specific metabolic enzymes that catalyse individual reactions of the metabolic network. To express proteins and grow, microbes require two non-substitutable building block metabolites B1 and B2 (red, blue) that do not natively occur in their environment, but can be metabolised from the single provided resource R (green) by expressing the right metabolic pathways. Active transport of metabolites across the cell membrane requires an energy metabolite E (yellow). The genome of a single microbe typically covers a small subset of the complete “chemical universe” of 59 reactions (see Methods). b Microbes compete for space and metabolites on a 45 × 45 lattice. They can reproduce in an adjacent empty space if they meet the minimal division cell size. Here, microbes NE and W of the empty space are too small to reproduce. Upon replication, genomes can mutate through gene duplication and deletion, discovery of new genes, and point mutations that can change the expression rate and kinetic parameters of individual genes. New genes can also be acquired via horizontal gene transfer from nearby microbes. Active transport of metabolites and lysis changes the composition of a microbes’ local environment.
