- no ideas for population control, you'll get unlimited source of useless bacteria liquid (yes, bacteria colony is liquid in my vision).
- no ideas for reactions except realistic ones I put into OP.
1. You could make population growth a bell-curve function instead of a linear one, that way once the population reaches a certain threshold growth will stagnate until the population goes down again. This also have the benefit of being kinda sorta realistic. It also still allows the player to pump out the bacteria, if they so choose, but also doesn't force them to.
2. My pleasure.
- Dirt gives some of the most versatile but also inefficient bacteria, capable of consuming almost anything with even a silver of organic matter in it and turning it into biomass. This includes: Wood, dirt, (leaves behind sand as a byproduct) all foods and crops, seeds, saplings, leaves, meat, scrap, etc. They also take a LOT of negligence to kill accidentally, as they go into a dormant state when not fed rather then starving. They'll still loose most of the population, but enough will remain that they can spring back qiuickly and easily. Basically, these are great if you essentially want an alternative to the recycler for organic things, but if you want to power your base with bacteria you should probably look elsewhere.
A few example mutations these could have would be yielding clay as a byproduct from dirt, or consuming sand and organic matter and turning it into dirt.
- Grass gives bacteria which are better for specialized, efficient energy production from plant matter. These have high biomass yields, especially once you start to specialize them to a specific food type, but are fragile, with high sensitivity to starvation, temperature fluctuations, competition, basically everything.
A few example mutations would be higher yields from specific plants, such as only oak saplings or spruce wood logs, as well as some by products from specific plants which are applicable, such as water from cacti.
- Netherrack gives access to bacterial strains which consume netherrack and/or less efficiently sulfer, and produce lava. These could also have some special requirement conditions, such as requiring the player to turn the fermenter's temperature up to 11, thus making it require more power or they might only be capable of surviving in the nether.
There could also be specialist/mutation-only strains which produce certain nether-specific resources either in addition to lava, or as a replacement. Some examples: a strain that consumes redstone or gold + sulfer/netherrack, and produces glowstone. A strain which produces mercury as a by-product from netherrack, at the cost of less lava. Or strains which distil coal, gold, or redstone from netherrack more efficiently then a centrifuge, but at the cost of less or none of the other resources.
There could also be species which consume lava instead, and produce resources from it, such as the centrifuge products more energy-efficiently or with higher yield, or they could produce netherrack.
- Ores could have a very low chance of giving bacteria whose unique biology makes them need that ore's products to live. This makes them very efficient at extracting metals from ores, which can be used to your advantage to increase ore yields by centrifuging/electrolyzing the metal out of the bacteria after letting them do their work, though it does take time and you loose any byproducts that the ore might have given in the Industrial Grinder. These bacteria also have the advantage of being very well adapted to long periods of stavation, making them almost completely unaffected by starvation but they are also slow to multiply, making them easily out-competed.
These could almost be considered mutations unto themselves, but some mutations they could have are allowing extraction of metals from stone/cobblestone, or specialists in yielding more of the ore's byproducts, at the cost of primary metal yield.
I could continue, if you'd like. There's still Endstone.