Let me explain really quickly

Ammonia (fish poop, un-eaten food, dead fish, dead leaf, etc.) is eaten by a less harmful bacteria called nitrites (think of this as processed ammonia) which in turn is eaten by an even less harmful bacteria called nitrates.

Fish can stand moderate levels of nitrate (the end result of ammonia and nitrite), however in high levels it can be deadly to fish.

Beneficial bacteria live in your rocks, ornaments, glass and most importantly in your filtration system. They usually live on different substrates for example: Canister filtration and a “hang on back” filtration will usually have white rock as a base for Beneficial Bacteria. Bigger systems such as Wet-Dry filters will usually have bio-balls (usually blue or black plastic balls)

So please next time you clean out your tank, take special care not to kill the beneficial bacteria. The best way to avoid this would be to leave the beneficial bacteria colony alone and preferably wet with the aquarium water.