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Hypercapnia and acidification

Marine organisms are more sensitive to changes in CO (carbon dioxide) levels than terrestrial organisms for a variety of reasons. CO is 28 times more soluble in water than is oxygen. Marine animals normally function with lower concentrations of CO in their bodies than land animals, as the removal of CO in air-breathing animals is impeded by the need for the gas to pass through the respiratory system's membranes (lungs ' alveolus, tracheae, and the like), even when CO diffuses more easily than oxygen. In marine organisms, relatively modest but sustained increases in CO concentrations hamper the synthesis of proteins, reduce fertilization rates, and produce deformities in calcareous hard parts. Higher concentrations of CO also result in decreased activity levels in many active marine animals, hindering their ability to obtain food. An analysis of marine fossils from the Permian's final Changhsingian stage found that marine organisms with a low tolerance for hypercapnia (high concentration of carbon dioxide) had high extinction rates, and the most tolerant organisms had very slight losses. The most vulnerable marine organisms were those that produced calcareous hard parts (from calcium carbonate) and had low metabolic rates and weak respiratory systems, notably calcareous sponges, rugose and tabulate corals, calcite -depositing brachiopods, bryozoans, and echinoderms; about 81% of such genera became extinct. Close relatives without calcareous hard parts suffered only minor losses, such as sea anemones, from which modern corals evolved. Animals with high metabolic rates, well-developed respiratory systems, and non-calcareous hard parts had negligible losses except for conodonts, in which 33% of genera died out. This pattern is also consistent with what is known about the effects of hypoxia, a shortage but not total absence of oxygen. However, hypoxia cannot have been the only killing mechanism for marine organisms. Nearly all of the continental shelf waters would have had to become severely hypoxic to account for the magnitude of the extinction, but such a catastrophe would make it difficult to explain the very selective pattern of the extinction. Mathematical models of the Late Permian and Early Triassic atmospheres show a significant but protracted decline in atmospheric oxygen levels, with no acceleration near the P–Tr boundary. Minimum atmospheric oxygen levels in the Early Triassic are never less than present-day levels and so the decline in oxygen levels does not match the temporal pattern of the extinction.

In addition, an increase in CO concentration is inevitably linked to ocean acidification, consistent with the preferential extinction of heavily calcified taxa and other signals in the rock record that suggest a more acidic ocean. The decrease in ocean pH is calculated to be up to 0.7 units. An extreme aragonite sea formed. Ocean acidification was most extreme at mid-latitudes, and the major marine transgression associated with the end-Permian extinction is believed to have devastated shallow shelf communities in conjunction with anoxia. Evidence from paralic facies spanning the Permian-Triassic boundary in western Guizhou and eastern Yunnan, however, shows a local marine transgression dominated by carbonate deposition, suggesting that ocean acidification did not occur across the entire globe and was likely limited to certain regions of the world's oceans. One study, published in Scientific Reports, concluded that widespread ocean acidification, if it did occur, was not intense enough to impede calcification and only occurred during the beginning of the extinction event. The relative success of many marine organisms that were very vulnerable to acidification has further been used to argue that acidification was not a major extinction contributor. The persistence of highly elevated carbon dioxide concentrations in the atmosphere and ocean during the Early Triassic would have impeded the recovery of biocalcifying organisms after the PTME.

Acidity generated by increased carbon dioxide concentrations in soil and sulphur dioxide dissolution in rainwater was also a kill mechanism on land. The increasing acidification of rainwater caused increased soil erosion as a result of the increased acidity of forest soils, evidenced by the increased influx of terrestrially derived organic sediments found in marine sedimentary deposits during the end-Permian extinction. Further evidence of an increase in soil acidity comes from elevated Ba/Sr ratios in earliest Triassic soils. A positive feedback loop further enhancing and prolonging soil acidification may have resulted from the decline of infaunal invertebrates like tubificids and chironomids, which remove acid metabolites from the soil. The increased abundance of vermiculitic clays in Shansi, South China coinciding with the Permian-Triassic boundary strongly suggests a sharp drop in soil pH causally related to volcanogenic emissions of carbon dioxide and sulphur dioxide. Hopane anomalies have also been interpreted as evidence of acidic soils and peats. As with many other environmental stressors, acidity on land episodically persisted well into the Triassic, stunting the recovery of terrestrial ecosystems.