Mike, there are two concepts in play here.
One is mastering the ability to get water AND air to the root system. The other is the fact that roots "tailor" themselves to the environment they're in and cannot change once grown.
It sounds like your plant had roots that had been grown in an airier environment, then were submerged. They did not grow submerged, so suffocated, died and are now rotting.
Unlike the simple food coloring experiments we did in school, the dyed orchids are injected, not submerged.
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