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Question: Why can't fish breathe out of water?
Let's first clarify a few things about breathing. First, I'll use the broadest definition of air breathing, which is simply the intake of O2 from air and the release of CO2. Second, no matter whether gills, lungs, skin, or other body locations are used for air breathing, oxygen must first be dissolved in water, and so all respiratory surfaces must be kept moist, which isn't usually a problem for fish. Third, getting oxygen from air instead of water isn't a bad idea, for air has about 30 times more oxygen than the same amount of water. It is therefore surprising that the vast majority of fishes will suffocate in air, even if they stay moist.
The original question of why some fish can breathe out of water is best broken down into two questions: why do some fish apparently need to live out of water for long periods, and what special structures permit air breathing. The answer to the first question becomes apparent when one studies those fishes able to breathe air – essentially all of them live in shallow, freshwater habitats that occasionally dry up and expose the fish to dehydration, crowding and reduced oxygen, loss of food, and intense predation. The ability to breathe out of water and move overland in search of better streams and pools, or to move into the bottom mud of dried up habitats until rains fill these habitats again, has obvious advantages. Ocean fishes are not exposed to these dangers, nor can they breathe air.
So what are the innovations for air breathing in fish? When typical fish are removed from water, air surrounds the gills, the gills collapse against one another, and oxygen from either water or air can't reach most of the gill membranes. The fish suffocate. Some fish such as the walking catfish from Southeast Asia have extra gill supports that prevent collapse, which allows the fish to breath air using the gills. To keep the gills moist, the fish walk only on rainy nights. The Climbing Perch of India is even more specialized. It has a separate pouch next to the gill chamber that is filled with air gulped from the pond surface. This perch has grown so efficient at getting extra oxygen in this manner that it will suffocate in water if not allowed to gulp air, even in oxygen rich water. These perch can live many days in damp clay pots, ensuring a fresh food supply for natives of the Malayan Peninsula.
Yet another innovation for air breathing is having thin, moist skin for gas exchange, as seen in American and European eels. These body breathers slither snake like in grass from one stream to another at night. Additional innovators include the lungfish that breathe air drawn into lung-like air bladders, and the Giant Loach of Europe that actually swallows air and breathes through the stomach. So, some fish have acquired adaptations for air breathing to allow movement over land when living gets tough at home. Movement on land isn't easy for a fish, but that's another story.
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