Just about no "good bacteria" resides in gravel. It's mostly poo. I've done 100% gravel sand changes etc. (and also 100% water change when moving house) and never once experienced even the smallest spike - which leads me to believe it's all in the filter.
I think that most of good bacteria is in gravel. Bacteria can't attach to internal filter because of too fast flowing. I've got spike even from partial gravel change. Just wanted to point out other point of view. External filter is whole different thing. And there is no good bacteria in water, thats true.