Humans and other mammals usually convert Ammonia into carbamoyl phosphate with the enzyme carbamoyl phosphate synthase and then it is either used or expelled by various means. However, Koi and other fish lack the mechanism so they excrete it directly into the water. About 60% comes from the gills and about 40% comes from their solid waste. Ammonia buildup in the water is very irritating on a Koi's gills.
There are many reasons for Ammonia buildup, uncycled filters, over feeding, overloading a filter, new Koi additions to a pond ect. Water will take on a cloudy look and it will smell fishy. Long term exposure will cause harm to a Koi's internal organs. Ammonia levels can be brought down with large water changes, additional filtration, and certain chemicals. Ammonia is converted into the less toxic Nitrite by the bacteria, Nitrosamonas. pH can contribute to the toxicity of Ammonia too, if the pH in a pond is lower than 7.0, it will transform the toxic Ammonia (NH3) into harmless ionized Ammonia (NH4).
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