Don't worry this post isn't going to be full of calculus!
So when going about making a list of Microbe Biomes it's interesting to think about in what ways they can be different, other than visually. The Wayward Admiral has some really interesting suggestions in this thread, It's interesting to think how these might actually be different in the game.
Sunlight: High, Medium or Low
Hydrogen Sulfide: Is it present?
Oxygen, Nitrogen, Carbon Dioxide, Ammonia, Phosphates concentrations. I suppose different concentrations of these would allow different species to do well.
Heat: The problem here is that nothing is actually heat dependent yet. So maybe if there is a Thermoplast then fine but otherwise temperature is, currently, not factored in. Maybe heat could be damaging to the microbe introducing some sort of terrain?
Currents: What does this mean? Does it mean some amount of flow which moves the cell around? Does it make agent based warfare harder? How does it work? If everything is in the same flow is that the same as no flow at all (like being in a moving Galilean frame)?
Salinity: Currently Salinity doesn't affect anything. It might if we go with the osmotic pressure cell wall health system.
Plant Life: Presumably the microbe stage is set before the evolution of plants and so there won't be any?
I had been assuming all the patches would be accessible from each other. So you would always be in one connected ocean. However does that mean you could go up rivers and into lakes as well? Why not?
I love the idea of the Abyss and the Cynobacterial Mat. Would we want several types of Bacterial Scenery?
Also there is the possibility of spatial arrangement of patches. So for example sometimes one patch could be directly below another from which "material" (not sure exactly what) could descend to it. Also maybe material from a patch high up a river could descend to the estuary at the bottom of it.
Because everything is in 2D we have a nice chance to make quite a lot of different patches without too much difficulty for the player to explore. Also what about some sort of procedural system? If we can identify the variables could we not just generate random patches? (So you might get high sunlight, high ammonia, no current, for example, without knowing to what that corresponded to).