You treat whatever tank has the sick fish in.
Fungus, bacteria and protozoans are completely different organisms that affect fish and other animals, including people, reptiles, amphibians and birds. There are also yeast and viruses that affect most creatures. All these organisms are tiny and require a microscope to see the individual creature, but when they have spread over a large area, you can identify the main type of infection just by looking at it.
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There are lots of good bacteria that live in and on us (and in and on our fish). The good bacteria help control yeast and fungus from infecting our bodies, and good bacteria in our digestive tract help us digest food and get more nutrients out of the food. Some good bacteria produce vitamins and chemicals to help our body function properly.
There are also bad bacteria and these are the ones that kill fish and other creatures. The fish in the picture has a bacterial infection caused by one of the species of bad bacteria.
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There are a number of different types of fungus that can infect fish and other creatures. The most commonly encountered fungus in fish tanks is Saprolegnia, which infects open wounds and looks like white fluff sticking up from the fish.
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There is a microscopic world on our bodies and fish's bodies. These microscopic organisms are at war with each other and compete for space. Yeast is tiny and common on terrestrial animals but not common on fish. Some bacteria eat the yeast and help control it.
A lot of good viruses hunt down and kill bacteria and help keep the bacteria under control. Some viruses are bad and cause the common cold and flu.
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There are protozoans that infect people's and fish's digestive tract (intestine). They are normally bad protozoans and cause a number of health issues and can kill people and animals (and fish).
There are protozoans that infect the outside of fish and can kill the fish if not treated. Whitespot, Velvet, Costia, Chilodonella and Trichodina are all external protozoans that affect fish. Whitespot is the most commonly seen.