I thought the biggest problem was the concrete. That is, soil microbes produced excess CO2, which would have been okay because the plants should have been able to photosynthesize it to O2, but instead the excess carbon dioxide reacted with the concrete, thus reducing the O2 levels.
If you're ever in Tucson, you should go for a tour. It's a fascinating place, and they've repurposed the facility to do a lot of worthwhile and interesting science.
I can't see how decaying plant matter would provide enough CO2 to keep the larger greenery healthy. Perhaps the original soil had an exceptional amount, but it would take time for it to break down; plants can empty a container such as that of CO2 in a day or so.