Carbonate concretions that include marine organisms such as ammonites or even the full body of a fish are abundant in Cretaceous shales of the Magdalena Valley of Colombia, South America. The occurrence of carbonate concretions in central basin shale facies is common not only throughout the Cretaceous of the lengthy Andean geo-syncline but also in similar facies throughout the world. The concretions are of syngenetic or early diagenetic origin. They formed soon after deposition, when the now compact muds were plastic enough to flow in around them. The fish and other organisms calcified rapidly, and the enveloping concretions developed sufficiently early to arrest extreme decomposition and to withstand compression from the many thousands of pounds of subsequent overburden.

The central-basin environments in which most carbonate concretion-bearing shales were deposited were not favorable to carbonate deposition. Such environments are stagnant and so are charged with carbon dioxide while the pH is too low for calcium carbonate deposition. However, an alkalinity adequate for such deposition in calcium-ion-rich waters may be locally created by the ammonia that evolves rapidly with decomposition of proteinaceous (nitrogen-bearing) organic matter.

Similarly, limited decomposition, mainly anaerobic, of organic matter that impregnates deeper basinal muds may create enough alkalinity to free calcium carbonate from the lime-bearing solutions permeating the muds. This may account for calcareous shales in basins where pure limestones are restricted to the aerated shallow flank, shelf, or lesser bottom-high areas.

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