Many hard-shelled marine organisms construct their shells or skeletons from calcium carbonate. This mineral occurs naturally in a couple of different crystal structures, aragonite and calcite. Mollusk shells rely chiefly on aragonite, possibly because this was the crystal more easily precipitated from seawater at the time when mollusks first started calcifying their shells (Porter, 2007). Aragonite is also used by scleractinian corals for their skeletons, so it’s not surprising that sand in many productive coastal regions consists largely of aragonite; it’s mostly the broken, ground up shells and skeletons of corals and mollusks past.

Echinoderms, by contrast, use calcite to construct their skeletons (Raup, 1959). The hard parts of a sea urchin are relatively obvious, and both the spines and the test enclosing the body rely on calcite. The softer-looking echinoderms use it too. Starfish, brittle stars and feather stars have more flexible appendages, but these are all supported by many short segments of calcite skeleton. Even sea cucumbers have calcite ossicles embedded in their body wall.

Bryozoans (Taylor, 2012) and Calcareous sponges (Stanley and Hardie, 1998) use both calcite and aragonite, and at least some species show flexibility in which crystal they use, depending on which is favored by ambient water chemistry.

Many species of algae build with calcium carbonate too. Most red calcareous algae build calcite inside their cell membranes, while calcareous green algae usually build aragonite on the outside (Granier, 2012). These algae can be the most important habitat builders in many areas outside of the tropics (Basso, 2012).

Their aragonite tendencies may leave corals, green algae and mollusks especially vulnerable to ocean acidification. At its present concentration of carbon dioxide (CO2), the ocean is still well-supplied with the minerals needed for all organisms that use calcium carbonate to build their shells or skeletons. It has been estimated that by the year 2050, rising CO2 levels will begin to deplete the available ions below optimal levels for aragonite building (Orr et al, 2005), essentially making aragonite more soluble in seawater. This effect has also been measured in the lab on the Sea butterfly Limacina helicina, a pelagic Arctic mollusk. When raised in seawater with the predicted CO2 concentration for the year 2100, Limacina's calcification rate fell 28% (Comeau, 2009).

Different calcareous organisms are affected in different ways by changes in ocean acidification. The geological record shows a number of events in the past 300 million years when sudden very large changes in species richness occurred in some groups of calcium-carbonate builders, which is likely to be related to acidity changes in seawater (Hönisch et al, 2012). Different groups were affected to a greater or lesser degree and it appears that several factors including habitat and physiology influence which groups are more sensitive to rising acidity. For instance, some calcite-builders like sea urchins and calcareous sponges will be slightly less sensitive, since calcite crystal formation is not affected as quickly by increased CO2. However, organisms that build calcite structures with a significant dose of Magnesium ions (High Magnesium Calcite or HMC) like some red algae do, will be the most quickly affected, as HMC is even more soluble than aragonite (Basso, 2012).

There is a lot of uncertainty about how reduced ocean calcification will feedback on the changing carbon cycle globally. The process of dissolving calcium carbonate (or reducing calcification) actually uses up carbon dioxide, shifting the seawater equilibrium toward bicarbonate ion (see Encyclopedia of Earth, 2010, for review). However, the greater impact of the changes will be in the total productivity of the communities that rely on calcification and the habitat it constructs (The Royal Society, 2005). If a reef habitat is lost, the question is, what will take its place? If the new community is equally productive, it may continue to sequester organic carbon, as dead tissue sinking to the deep ocean, just as fast as the original habitat did. Of course for that scenario it should be borne in mind that natural productivity of coral reef communities is extremely high, so an equally productive one succeeding them would be very unlikely.