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Quarantine is frequently recommended as a good way to prevent introducing disease into a display tank. However, in most situations where it is recommended it is simply stated that it is good and should be done but absolutely no explanation of how to quarantine properly is provided. This leads to many aquarists performing quarantines that end up causing a lot more harm than they will prevent.
The idea is that the quarantine tank is the first place new fish go so that if they are carrying any diseases they will become visible and the aquarist can treat accordingly before the fish are added to the display tank which contains many more fish that the new fish would be risking. However, disease doesn't occur because a pathogen is present, the fish have to be stressed. Very few pathogens can infect healthy, unstressed fish. These pathogens are rare in the hobbby.
The Bad Quarantine Tank:
The example of the worst quarantine tank would be something like a ten gallon that is setup when the aquarist brings fish home. The tank is filled with tap water, the filter turned on, and the fish are dumped in. There are no decorations so the fish are stressed. The tank receives no water changes for the duration of quarantine. Since the tank and its filter were uncycled the fish experience the typical ammonia and even nitrite spikes of a cycling tank, which stresses them further. The aquarist wants to see his new acquisitions and inspect for any signs of illness so provides bright lighting which also stresses the fish. In order to kill any pathogens that may be present but are not showing any signs of infection he treats the tank with an assortment of medications as a preventative measure, which also stresses the fish. All of this takes place in the matter of a week or two and then the extremely stressed fish are dumped in to the display.
As you can see this is far from a comfortable situation for any fish. Although this is the extreme and hopefully far from the average aquarist's quarantine, it is a method used by many aquarists.
The problem is that the display tank is much less stressful than the average quarantine tank. This means that the quarantine tank is much more likely to stress the fish which will cause them to get sick when most likely it would not have even shown up in the display tank at all.
Pathogens are always present. No matter how well you quarantine fish there will always be pathogens present. Even if you haven't added fish in ten years, if you stress them their immune systems will be weakened and they will get sick with something.
A true quarantine is at least 90 days after all signs of anything have gone away. This is how zoos and aquariums quarantine animals. They also provide large, proper tanks that will allow the fish to thrive during the quarantine. If two months in to quarantine a fish comes down with something the clock starts over and they have to wait another 90 days. So an aquarist doing a 14 day quarantine in a ten gallon with no decor and poor water quality is a joke.
I have added fish that I knew were sick with freshwater ich directly to display tanks because I knew that was the least stressful place for them to be. Because the tank was a better setup for them than they had been in they were no longer stressed and the ich went away without any intervention at all and no other fish got sick. I have also purchased fish from tanks where every other fish was sick. The fish I pick out and add directly to my display tanks never come down with anything, neither do any other fish in the tank.
If you control stress you will control disease. You do not have to quarantine. Buy fish from a high quality source, provide high quality food and water, and you will rarely encounter any illnesses in any of your fish.
The only exception that I would make is with tanks that house very valuable fish that are more sensitive to any stressor (such as discus) or tanks that house organisms that cannot be treated with many medications (reef tanks, freshwater stingrays, etc.). In these cases quarnatining new fish may be the best way to go, but it must be done properly. This means that the tank needs to be running with fish all the time, or have a filter that can be moved from the display tank to the quarantine tank to instantly cycle the quarantine tank (either the whole filter moves or the cartridge fits the filter in the display and the quarantine). The quarantine tank should be large enough to comfortably house the fish to be quarantined. It should receive enough water changes to keep the water quality at least as good as the display tank. Many people use the display tank's water to perform water changes on the quarantine tank, often daily. This keeps the quarantine tank's water matching that of the display, which will make the transition to the display as smooth as possible. It should be decorated enough to keep the fish comfortable and stress free. If you are quarantining bottom dwellers many hides, caves, etc should be provided and minimal light. If you are quarantining mid level swimmers then dense plants should be provided.
Do not treat with medications as a preventative tool. This stresses the fish and makes that medication ineffective when diseases do come up.
The Ideal Quarantine Tank:
The ideal quarantine tank is a tank large enough to house the fish being quarantined as if it were a display. This doesn't mean the quarantine tank has to be as large as the display, only that if the fish in question were kept in the quarantine long term it would be large enough. When the aquarist purchases new fish he fills the quarantine tank with water from the display. He also sets up a filter that has been running in the display. This could be something like a sponge filter that is run in the display when the quarantine tank is not in use, or may only be a cartridge that fits both the filter on the quarantine and the filter on the display. Even using the filter cartridge from a filter on the display in the quarantine should be enough to instantly cycle the quarantine when new fish are added. The quarantine tank should not have any lighting, at least not in the first week or two. Low light can be very effective at helping to minimize stress. Indirect light from the room should be more than adequate and allow the fish to follow a day/night cycle. During the first two weeks of quarantine the light should only be used so that the aquarist can get a good look at the fish and then turned back off. Water changes should be very frequent and use water from the display tank. This will keep the chemistry of the quarantine tank matching that of the display and make the final transition that much easier on the fish. The tank should be decorated to suit the needs of the fish being quarantined. For bottom dwellers there should be multiple hides, more than the number of fish being quarantined so that they can avoid eachother if needed. Schooling mid-dwellers should have fake plants to provide shelter. Floating plants should be provided for top-dwellers. I recommend a substrate in a quarantine tank just like any other tank. It is an important and natural part of any aquatic habitat and it can help reduce stress for any bottom-dwellers. A quarantine should last for at least 4 weeks bare minimum. Ideally it is three months. This time starts after any signs of any illness are gone. Preventative medications should not be used. Medications do stress fish and adding them as a preventative measure is just an unnecessary stressor.
A quarantine tank should be so good that it should allow fish to breed. If fish breed in quarantine it is a definite sign that the quarantine is being done the way it should be.