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Fish Gills
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Gills serve the same function in fish that lungs do in mammals̵2;taking in oxygen and giving off carbon dioxide. Gills have several rows of exposed capillaries, separated from the water by minutely thin walls. As water passes over these capillaries, they take in oxygen from the water and release carbon dioxide. Although some fish̵2;most famously sharks̵2;must swim for water to pass through the gills, most can breathe while sitting still. They open their mouths to draw in water and push it out through their gills.
Some Can't Stop
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Some fish don't have the option of taking a break if they want to keep breathing. Sharks don't have the same bone or muscle structures as other fish, and many of them can't push water through their gills unless they are moving. A shark's gills function in the same way as the gills of other fish when it comes to gas exchange, but he must open his mouth slightly while he swims so his movement can cause water to flow in and over his gills. If a shark stops swimming, it's often a sign he's not well; some species, however, such as the nurse shark, have no trouble breathing while holding still.
Other Fish at Rest
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For fish that don't require swimming to breathe, breaks are common occurrences. According to the Northeast Fisheries Science Center, fish have internal clocks that help determine when they're the most active and when they need to rest. As with mammals, these cycles typically follow a day-and-night pattern. Fish tend to find safe places to rest, such as by burrowing into the substrate at the bottom of your tank, parking near the bottom in a corner or hiding among aquarium decorations. They don't close their eyes because most fish don't have eyelids̵2;this also helps them watch for danger while they rest. You'll often see the mouth and gills of a resting fish open and close, signifying the fish is still breathing.
Disease
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Fish who suddenly become less active than normal might be suffering from a disease. Although they should be able to breathe as much as normal without swimming, take these fish out of your aquarium and put them in temporary housing until you can diagnose the problem. Watch for other signs of disease, such as dull skin, fluffy growths on the fins or skin, cloudy eyes and red or white spots on the fish's body. This might signify a problem with your aquarium water, such as too much ammonia, or your fish might need medicine to deal with an infection. Make sure the sick fish's temporary habitat has adequate filtration and aeration so he can breathe without too much effort.
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Can Fish Stop & Still Breathe?
A fish that seems to take breaks from swimming isn't necessarily sick, and he's still breathing even when resting. Most fish don't need to be moving for respiration to occur, and many enjoy resting periodically, often taking refuge among your aquarium plants or other decorations. While resting isn't usually problematic, monitor your fish carefully; a sudden change in activity level can signal a problem.