It sounds like it may be a little late to be proposing new gameplay mechanics for the Microbe Stage, but one idea that strikes me as being potentially fun/interesting to implement (if not now, then maybe at some later point) could be horizontal gene transfer (i.e. microbes of different species swapping genetic information in order to acquire new traits); this is a very common phenomenon observed in IRL Earth prokaryotes, and it can often play an important role in their evolution.
In terms of gameplay, I could see this working something like the following:
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If a cell evolves a Perforator Pilus, it can later be upgraded into a Conjugation Pilus, which enables non-harmful exchange of genetic material between cells.
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The cell can then expend resources to enter Conjugation Mode; while in Conjugation Mode, if it bumps into another cell with its Conjugation Pilus, then each cell will receive a Plasmid carrying a random trait (e.g. an organelle, a modification to environmental tolerances, etc.) found in the other cell.
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Traits obtained via Plasmids do not cost any evolution points, and thus may be seen as a kind of “bonus trait”; however, the random nature of the traits means that they may or may not be helpful, and may even potentially be detrimental.
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Additionally, engaging in this behavior may provide a competitive advantage to other cells, rendering them better able to survive and compete for resources and/or give them abilities that enable them to directly harm the player’s cell.
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There should also probably be some limit on how often a cell can do this, either a hard cap (e.g. once per generation), or a “soft cap” in the form of just making Conjugation Mode extremely expensive to enter; otherwise, one could imagine just repeatedly doing conjugation to evolve a bunch of new traits in between generations. Alternatively, maybe the new traits won’t become available until entering the Microbe Editor.
Anyway- this seems like it might be too big/disruptive a feature to add at this stage of development, but I thought I’d bring it up just in case you guys find the idea interesting : )