This paper adds to the ongoing lively debates by attempting to understand changes in the predominant types of carbonate-producing organisms during the Mesozoic–Cenozoic, while striving to minimize the uniformitarian bias. Our approach integrates estimates of changes in Ca²⁺ concentration in seawater and atmospheric CO₂, with biological evolution and ecological requirements of characteristic carbonate-producing marine communities. The underlying rationale for our approach is the fact that CO₂ is basic to both carbonates and organic matter, and that photosynthesis is a fundamental biological process responsible for both primary production of organic matter and providing chemical environments that promote calcification. Gross photosynthesis and hypercalcification are dependent largely upon sunlight, while net primary production and, e.g., subsequent burial of organic matter typically requires sources of new nutrients (N, P and trace elements). Our approach plausibly explains the changing character of carbonate production as an evolving response to changing environmental conditions driven by the geotectonic cycle, while identifying uncertainties that deserve further research.

With metazoan consumer diversity reduced by the end-Permian extinctions, excess photosynthesis by phytoplankton and microbial assemblages in surface waters, induced by moderately high CO₂ and temperature during the Early Mesozoic, supported proliferation of non-tissular metazoans (e.g., sponges) and heterotrophic bacteria at the sea floor. Metabolic activity by those microbes, especially sulfate reduction, resulted in abundant biologically-induced geochemical carbonate precipitation on and within the sea floor. For example, with the opening of Tethyan seaways during the Triassic, massive sponge/microbe boundstones (the benthic automicrite factory) formed steep, massive and thick progradational slopes and, locally, mud-mounds. As tectonic processes created shallow epicontinental seas, photosynthesis drove lime-mud precipitation in the illuminated zone of the water column. The resulting neritic lime-mud component of the shallow-water carbonate factory became predominant during the Jurassic, paralleling the increase in atmospheric pCO₂, while the decreasing importance of the benthic automicrite factory parallels the diversification of calcifying metazoans, phytoplankton and zooplankton.

With atmospheric pCO₂ declining through the Cretaceous, the potential habitats for neritic lime-mud precipitation declined. At the same time, peak oceanic Ca²⁺ concentrations promoted biotically-controlled calcification by the skeletal factory. With changes produced by extinctions and turnovers at the Cretaceous–Tertiary boundary, adaptations to decreasing Ca²⁺ and pCO₂, coupled with increasing global temperature gradients (i.e., high-latitude and deep-water cooling), and strategies that efficiently linked photosynthesis and calcification, promoted successive changes of the dominant skeletal factory through the Cenozoic: larger benthic foraminifers (protist–protist symbiosis) during the Paleogene, red algae during the Miocene and modern coral reefs (metazoan–protist symbiosis) since Late Miocene.