I'm a total amateur when it comes to chemistry so take this with a grain of salt, but I do have experience with nitrogen in a closed system...

The first thing that happens when nitrogen is depleted is a collapse of beneficial bacteria colonies. The bacteria that converts free ammonia into nitrite is the first to go, and shortly after, the colony converting nitrite to nitrate - the more usable form of nitrogen - follows. Finally, the plants that rely on these nitrates to grow begin to die off, creating a new source of ammonia in the closed system. The ammonia kills off vulnerable microfauna, leading to even more ammonia buildup and less potential food sources. Depending on the severity of the collapse, the cascade can continue all the way up to the macro fauna. In response to the newly available nitrogen in the form of ammonia from decomposed organics, however, the beneficial bacteria colonies will reestablish. Surviving microfauna will begin to decompose the dying plants and new growth will start to emerge once enough nitrates are again being produced. The new plant growth removes nitrates from the system, the surviving macro fauna reproduces and the system starts working its way back to stability.

But to get to this point, you still need an external source of nitrogen. Fertilizers, foods that the fauna can process into waste, etc. We're lucky in that nitrogen is available in extreme abundance, but I think you're definitely asking the right questions here.