Make redundant food webs. Increase diversity gradually. If you can't provide a physical function, you need to simulate it. The atmosphere communicates the state of the whole system. In the end our interest in fashioning new closed systems rests on concocting second examples of living closed systems so that we may generalize their behavior and understand the system of Earth, our home.
Closed systems are a particularly intense variety of coevolution.
Pouring shrimp into a flask and pinching off the throat of the flask is like putting a chameleon in a mirrored bottle and pinching closed the entrance. The chameleon responds to the image it has generated, just as the shrimp responds to the atmosphere it has generated. This isolation, like the isolation in terrestrial evolution, breeds variety and marked differences. But eventually all closed systems are opened or at least leak. We can be certain that whatever artificial closed systems we fabricate will sooner or later be opened.