Fish Gill Structure and Function

How fish gills are built and how they work: filaments and lamellae, countercurrent gas exchange, ion regulation by ionocytes, ammonia excretion and gill damage caused by poor water.

What the gills do

Gills are the main respiratory organ of fish, but breathing is only one of their jobs. The same thin, blood-rich tissue also exchanges ions, water and acids with the surrounding water and gets rid of ammonia, the main nitrogenous waste of most fish. Because the gill surface is so large and so thin, it is also the organ that reacts first and most strongly to poor water quality.

Arches, filaments and lamellae

The gills sit in the walls of the pharynx, just behind the head. In bony fish they lie in a branchial chamber on each side, covered by a bony flap called the operculum, so there is a single gill opening per side. Most bony fish have five pairs of gills, though some lineages have lost a few. Sharks and rays usually have five pairs of gill slits that open straight to the outside, and some primitive sharks have six or seven.

Gill arch: a cartilaginous or bony support from which the gill tissue projects. In bony fish the gills stand free of the arch, held up by gill rays, and many species keep gill rakers on the arch.
Gill filaments: comb-like rows of tissue on each arch. Each filament carries a capillary network.
Lamellae: small folds on the filaments that multiply the surface available for exchange. Water keeps them separated, which is why the gills collapse and stop working when a fish is taken out of water.
Pseudobranch: in many bony fish, a reduced gill-like structure near the base of the operculum; in sharks it receives only blood already oxygenated by the true gills.

This large, folded surface is necessary because water holds far less oxygen than air. A litre of fresh water contains about 8 cm³ of oxygen, compared with 210 cm³ in a litre of air, and oxygen diffuses about 10,000 times more slowly in water. Water is also about 777 times denser and 100 times more viscous than air, so moving it over the gills costs energy.

Ventilation and countercurrent exchange

A bony fish takes water in through the mouth, closes valves inside the mouth, and squeezes the pharynx so that the water passes over the gills and leaves under the operculum. The operculum helps control pressure in the pharynx, so bony fish can ventilate their gills while resting. Many sharks instead rely on ram ventilation and must keep swimming forward to push water over the gills.

Inside the lamellae, blood flows in the opposite direction to the water. Because of this countercurrent arrangement, blood always meets water that holds a little more oxygen than itself, so oxygen keeps diffusing in along the whole length of the lamella. As a result, gills can extract more than 80% of the oxygen available in the water.

Ion regulation by ionocytes

A large, thin surface that lets oxygen in also lets ions and water move freely, so the gill is a central organ of osmoregulation (covered in more depth in the osmoregulation guide). Specialised cells called ionocytes, formerly called chloride cells or mitochondrion-rich cells, carry the Na⁺/K⁺-ATPase pump. Marine teleosts lose water by osmosis, drink seawater and use ionocytes to excrete excess Na⁺ and Cl⁻. Freshwater fish face the opposite problem and use their ionocytes to take ions up from the dilute water.

Ammonia excretion

Ammonia is the main end product of protein breakdown in fish and is excreted through the gills and in the faeces. The amount excreted rises with the amount of feed. Most fish are ammonotelic, meaning that ammonia is their main nitrogenous waste. The gills are the main excretion route because they have a large surface, receive the entire cardiac output, are heavily ventilated, have short diffusion distances and are in contact with a large volume of water.

For most such fish, ammonia leaves the blood mainly as un-ionised NH₃, moving down its concentration gradient into the water. This diffusion is helped by acid trapping. Expired CO₂ forms H⁺ in the boundary layer of water next to the gill, which converts NH₃ into NH₄⁺ so it cannot diffuse back. More recent work has shown that transport proteins also take part. Rhesus (Rh) glycoproteins act as ammonia channels: Rhbg sits on the blood side of gill cells and Rhcg on the water side, working together with sodium–proton exchangers and the proton pump. In zebrafish embryos, ammonia excretion rises sharply at hatching together with the expression of these Rh genes.

How water quality damages the gills

The most common way the gill responds to irritation is hyperplasia and hypertrophy of its epithelial cells. The secondary lamellae become shorter, rounded and fused, which reduces the exchange surface, and extra mucus further hinders function. The damaged gill is also more easily colonised by bacteria. Listed triggers include ammonia, nitrite, heavy metals and generally poor water quality, as well as parasites, protozoa and bacteria. Signs mainly reflect breathing difficulty: rapid opercular movement, lethargy, fish gathering near water inlets, and rising mortality.

Ammonia: only the un-ionised NH₃ fraction of total ammonia nitrogen is toxic, and that fraction rises about tenfold for each one-unit increase in pH, and also with temperature. A pond-culture extension source states that chronic exposure to un-ionised ammonia as low as 0.06 mg/L can cause gill and kidney damage and reduced growth, and that lethal short-term levels start at about 0.6 mg/L.
Nitrite: nitrite enters the blood through the gills. At the gill surface it competes with chloride for uptake. In the blood it oxidises haemoglobin to methaemoglobin, which cannot carry oxygen, so the blood turns brown and fish suffocate even in well-oxygenated water (brown blood disease). Catfish-farming guidance uses a chloride-to-nitrite ratio of at least 9:1 to block this uptake.

Specific gill infections and gas-related injury are covered in separate guides: bacterial gill disease, amoebic gill disease and gas bubble disease.