Colony upgrades are lost after attacking a planet, but gene strand upgrades persist until [[Black Hole]]. Modifiers provided by evolved bacteria are active depending on whether the bacteria in question is equipped. Only the effects of Dark Matter Institute technologies are always active.

*[[Red Bacteria]]

*[[Critical Hits|critical hits]]

*[[Tapping Combo|tapping combos]]

Red Bacteria is available from the beginning, but the other mechanics need to be unlocked with gene strand upgrades.