In the interim my posting, I've been reading a couple books from my list about Biosphere 2, and have been thinking about habitat breathing.

One way in which Biosphere 2 was designed to breathe, in the sense of regulating CO2 and O2, was through the controlled dormancy of its savanna biome. The grasslands were used to increase or decrease photosynthetic O2 production simply by watering.  This seems to me a very desirable way to moderate O2 levels, but I think would require some more quantifiable understanding than what I currently have.

Another of the key design features of Biosphere 2 was its "lungs", great bellows that helped to equalize pressure between the outside and inside of the enclosure. When air is heated, it expands. The Biosphere 2 enclosure is situatated within Earth's (aka Biosphere 1's) atmosphere, where the pressure varies with the weather. Without these lungs, Biosphere 2's glass would have shattered under pressure, and even without shattering, small leaks would be accelerated by pressure differentials. 

It occurs to me that a second possible use for lungs (not really explored by B2 to my knowledge) might to promote condensation or precipitation by dropping the pressure on command. Clearly, the structure must be designed to withstand the pressure differential. For most off-Earth designs this would naturally need to be the case anyway- expanding into vacuum would be trivial (where the worst case pressure differential is at compressed state). An undersea habitat would have the opposite problem (with the worst case pressure differential at the expanded state).

Additionally, a third potential use of lungs would be to create wind internal to the habitat. Again, this is not how the Biosphere 2 ones were designed to work, but I understand that the airlocks going into the lungs can be rather windy. Wind would useful to keep air from stagnating, and minimize need for fans to circulate air.

Biosphere 2's lungs are comprised of an expandable rubber membrane that rises along with the temperature, and a large metal counterweight that pulls the membrane back down and forces air back into the facility at night when temperatures drop. The system was designed to maintain a slight positive pressure, so that no outside air would ever seep in, but some could escape in the event of leaks.  My understanding is that this was determined largely to keep any critics at bay, but the gradual loss of air would also more accurately simulate conditions in space where this would inevitably be true as well. Losses were about 8% per year. I would imagine that with age, the leaking has gotten worse. Note, however that the ISS leaks at more than 20% per year. So without replenishment, presumably the astronauts would be breathing vacuum within only a few years. Clearly, hermeticity is something that will need to be vastly improved on for any isolated long term space habitats.