Perhaps there could simply be preset niches that NPC's in the game will compete to fill. For example set a niche for autotroph and predator. Make it so that at least, say, 34% of microbes must become autotrophs to keep the ecosystem running, while the rest become predators.
The autotrophs begin specializing and they gain chloroplasts or thermoplasts and possibly cell walls. To diversify they start developing varying agents to protect themselves.
The remaining 66% percent would evolve more agressive characteristics such as the predatory pili, toxins, engulfment, etc. Seeing as there's a lot more options for a predatorial lifestyle, we can expect a lot of diversity here.
If any of the populations fall below a certain threshold, other species would adapt to fill the empty niche. For example if all the producers suddenly died, some predators would change to get all that easy energy that is now up for grabs in the now empty autotroph spot, thus rebalancing the ecosystem.