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.

Ah, here's a summary of the various things that went wrong, including details about the concrete: http://biology.kenyon.edu/slonc/bio3/2000projects/carroll_d_... .

It doesn't mention fungus, but does talk about other ecosystem problems (the pollinating insects died out, the morning glories took over, etc.).