This might be one of those ideas which sound nice on paper, but translate poorly into reality. Yes, it adds more things for the player to worry about and hence necessitates another level of consideration and management on behalf of the player: but if we make each organelle require a compound other than glucose to properly function, we could easily make the game into a mess of frustrating micro-management and unfair restriction, not even considering the burden of implementing extra elements which serve a single function and effect a single aspect of gameplay.
For your calcium carbonate exoskeleton for example; that sounds like a nice idea by itself, but of course, calcium and carbon aren’t your only worries if we make compound upkeep a significant aspect of the microbe stage. Iron-processing, hydrogen-sulfide processing, chloroplast-based, and all the other specialized organelles would need their own compounds to be maintained as well. That means you would need to not only ensure that you have enough glucose to fuel your organelles, you would also need to make sure you have enough iron, enough carbon, enough sulfate, enough calcium, and enough whatever to properly function. That just seems like a headache, if I’m being honest. You would need to constantly zip around the map and chase those clouds endlessly to fulfill your equally endless needs, and if one compound isn’t present, a whole aspect of gameplay is cut off to you. This restriction isn’t necessarily bad; making the player have important choices to decide, which dictate what strategies work or don’t, adds a good amount of depth and replayability to Thrive. Basing this restriction entirely on the environment with almost no choice or input from the player, however, doesn’t make for a fun and creative play-through, however.
I’m not saying this idea isn’t a good one or that it doesn’t have potential, but thinking about it as our traditional pursuit of a numerous amount of compound clouds doesn’t work well with Thrive.
An interpretation of this idea which works well I think would be to have certain organelles require less ATP to maintain if an environmental (non-cloud) compound is present at a sufficient level. So for example, if there’s 2-5% calcium present, it costs 5% less to maintain a carbon exoskeleton, if there’s 5-7% calcium present, it costs 10% less to maintain a carbon exoskeleton, and if there’s 7-10% calcium present, it costs 20% less energy to maintain. At the same time, we could have certain cells suffer from environmental compounds; perhaps chloroplasts could suffer a maintenance penalty if enough calcium is clogging the environment, for example. I feel that this is significant enough to effect the player’s decision making, but not in a way which takes the choice out of the player’s hands. The player could still be a plant in a calcium heavy environment; sure, it might not be smart, but it could work if they’re willing to suffer through the event and change. This interpretation of the concept I feel also connects with other pre-established concepts in Thrive, namely having compounds such as pressure, oxygen, and sunlight effect gameplay, hence allowing us a lot of flexibility in being able to induce evolutionary events. The Cambrian Explosion coincided with the increased availability of potassium in the environment in our own history; perhaps this could be reflected in Thrive, where the availability of potassium could lessen the amount of ammonia and phosphate needed for reproduction and thus trigger rapid evolution (0-5% K = No Effect, 5-10% = 5% less need for ammonia and phosphate, 10-15% = 10% less).