Minute quantities of metallic elements are present in solution in seawater and also occur in marine invertebrate skeletons, though not in the same proportions as in the surrounding water. Magnesium and strontium are the most frequently occurring trace elements in reef skeletons and are measured in parts per thousand, but barium, manganese, and iron are also present and can be measured in parts per million. In Pacific corals 2.17 parts per million of uranium have been found, in Florida coral 2.36–2.95 parts per million. Strontium is concentrated in aragonitic skeletons and magnesium in calcitic skeletons. Coral aragonite has a higher strontium content than (some) molluscan aragonite. The magnesium content in the calcite of coralline algae is high, and that of barnacle shells is low (11.5 parts per thousand). By identifying these trace elements and their degree of assimilation in different organisms, sediments formed predominantly of coral skeletal detritus can be distinguished from sediment derived chiefly from mollusks or coralline algae.

Atomic absorption spectrophotometry has shown that ultratraces of metals are present in the aragonite skeleton of the hydrozoan coral Millepora from a reef flat on the Coral Sea Plateau off Queensland. These are, in parts per billion: lead (100), copper (71), cadmium (23), cobalt (17), nickel (1,480), iron (507), and zinc (507).

Another aspect of reef geochemistry is the carbon and oxygen isotopic composition of coral skeletons and shells. Determination of the number of carbon isotopes present provides a method of assessing the age of a sample, and determinations of oxygen isotopes present are useful in indicating water temperature changes that occurred during the period of growth of the reef.

Winds, currents, temperature, and salinity

Winds and currents are important in shaping individual reefs and in determining the orientation, shape, and position of the coral sand cays, or “low islands,” that develop on reefs. Currents are primarily those generated by the prevailing winds, but, in areas where the tidal range is great, tidal effects may become paramount.

Cays may be round, oval (or boat-shaped), or irregular in outline. They originate when sediment is lifted from the reef surface and carried leeward by waves or tidal currents and then deposited where the water velocity is reduced abruptly. Thus, they commonly form on the more protected leeward end of the reef. Wind action at low tide on these deposits may build dunes above the high-water mark. Beach rock may form by carbonate cementation of grains in deposits lying between tide levels. It then acts as a stabilizing factor. Storm waves may drive forward coral fragments derived from staghorn corals growing on the windward slopes of the reef, forming shingle banks; successive superposed banks may thus be formed. The shingle on the banks may become cemented and thus add considerable stability to the cay, as does the growth of vegetation. Hurricanes, however, may carve back the shorelines of even stabilized cays. Huge, isolated boulders of coral or coral limestone are fairly common along reef margins. Some may be remnants of a once-emergent reef platform; others are hurricane or storm jetsam.

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Coral reefs are best developed where the mean annual surface water temperatures are approximately 23–25 °C (73–77 °F). No significant reefs occur where such temperatures fall below about 18 °C (about 64 °F), although a few reef coral species can exist in temperatures considerably below this. Seasonal temperature differences on any one reef are usually slight, as are differences due to depths of water or situation on the reef.

Seawater of normal oceanic salinity (between 30 and 40 parts per thousand), to which corals are restricted, is normally supersaturated in calcium carbonate (CaCO₃), so that adequate ionized calcium (Ca²⁺) is available for the skeleton-forming process. Floods of fresh water may destroy life on inshore fringing reefs. A luxuriant reef on Stone Island near Bowen, Queens., Austrl., was killed to a depth of 3 metres (about 10 feet) below mean tide level by a week of cyclonic rains during which 90.7 cm (about 36 inches) of rain coincided with full-moon spring tides.

Biological factors

The most significant biological determinant of reef accumulation is the presence of zooxanthellae in the living tissues of all reef corals and of many massive-shelled mollusks (Tridacnidae) and other shelled invertebrates, as well as in the soft-bodied hydrozoans, scyphozoans, and anthozoans. Zooxanthellae are now known to represent the vegetative stages of dinoflagellate algae, and their association with reef corals is symbiotic—i.e., mutually helpful. In temperate seas they occur only occasionally. Their profusion in reef animals is no doubt connected with the greater light intensity and radiant energy of reef waters, for, like other plantlike protists, zooxanthellae require sunlight for photosynthesis. They remove at the source part of the carbon dioxide, together with nitrogen, phosphorus, and sulfur, produced by metabolic breakdown within the coral and which would otherwise be excreted by the corals. They greatly aid in the formation of the coral skeleton by increasing the speed with which the carbon dioxide produced in coral metabolism is removed and the speed with which the skeletal calcium carbonate is formed. Corals also may gain some nutrient from their zooxanthellae, but they probably do not need the oxygen produced during photosynthesis.

The biological productivity of reefs is an important area of research. A constant supply of food in the form of zooplankton is essential to reef corals, which are carnivorous. The zooplankton supply is dependent on an adequate phytoplankton supply, and the phytoplankton in turn require an adequate supply of plant nutrients dissolved in the water. An atoll in the open ocean may be compared to an oasis in a desert, as a localized centre of high productivity. In the warm, well-lit, and well-mixed lagoon waters there is a rapid turnover of the endemic planktonic (floating or swimming) and benthic (bottom-dwelling) population, perhaps 12.5 times per year. Carbonate skeletal matter is accumulated perhaps 1,000 times faster on the summit of an atoll than in the surrounding depths.