Surface ocean waters generally have oxygen concentrations close to equilibrium with the Earth's atmosphere. In general, colder waters hold more oxygen than warmer waters. As this water moves out of the mixed layer into the thermocline it is exposed to a rain of organic matter from above. Aerobic bacteria feed on this organic matter; oxygen is used as part of the bacterial metabolic process lowering its concentration within the water. Therefore, the concentration of oxygen in deep water is dependent on the amount of oxygen it had when it was at the surface minus depletion by deep sea organisms.
The downward flux of organic matter decreases sharply with depth, with 80-90% being consumed in the top 1000m. The deep ocean thus has higher oxygen because rates of oxygen consumption are low compared with the supply of cold, oxygen-rich deep waters from polar regions. In the surface layers, oxygen is supplied by exchange with the atmosphere. Depths in between, however, have higher rates of oxygen consumption and (as discussed below) lower rates of advective supply of oxygen-rich waters.
The distribution of the open-ocean oxygen minimum zones is controlled by the large-scale ocean circulation. Essentially, waters that are part of the wind-driven subtropical gyre circulations are rapidly exchanged with the surface and never acquire a strong oxygen deficit. However, along the equatorial edge of the gyres, one finds a stagnant pool of water which has no direct connection to the ocean surface. As a result these "shadow zones" have very low oxygen concentrations-even though in regions such as the Eastern Tropical North Pacific there may relatively little organic matter falling from the surface.
For those organisms, like the Vampire Squid, who live in the oxygen minimum zone, special adaptations are needed to either make do with lesser amounts of oxygen or to extract oxygen from the water more efficiently. One strategy used by some classes of bacteria in the oxygen minimum zones is to use nitrate rather than oxygen, thus drawing down the concentrations of this important nutrient. The oxygen minimum zones thus play an important role in regulating the productivity and ecological community structure of the global ocean (Deutsch et al., 2007).