Earlier quoted context omitted.
From a related article: "But the eco-system also uses cellular respiration to break down decaying material shed by the plant. In this part of the process, bacteria inside the soil of the bottle garden absorbs the plant's waste oxygen and releasing carbon dioxide which the growing plant can reuse."
Was this a planned hack, or does this naturally occur? My first thought was also, "Where does the CO2 come from?" I suspect this is a very fine balance - if you're off by just a little, one or the other would die. There's not much room for error in a jar.
Why would all bacteria die if there is less oxygen? I imagine the weakest bacteria would die, thereby increasing the amount of O2 per bacteria, and thus reaching equilibrium again.