The ratio between the stable isotopes of carbon (¹²C/¹³C) seems to indicate that significant changes in the carbon cycle took place starting about 500,000 to 1,000,000 years before the end of the Permian Period and crossing the boundary into the Induan Age (the first age of the Triassic Period). These changes appear to coincide closely with two Permian extinction events, suggesting some cause-and-effect relationship with changes in the carbon cycle.

Several studies have suggested that changes in the carbon isotope record may indicate a disrupted biological cycle. Some scientists consider the unusually high amounts of ¹²C trapped in Permian sediments to be a result of widespread oceanic anoxia (very low levels of dissolved oxygen). They associate this anoxia with the prolonged eruption of the Siberian flood basalts (the so-called Siberian Traps), which probably led to higher levels of carbon dioxide in the atmosphere. Clouds of volcanic ash may have worsened the situation by restricting the amount of sunlight available for photosynthesis, thereby inhibiting the process of carbon fixation by plants and lowering the extraction rate of carbon dioxide from the atmosphere. In addition, high amounts of carbon dioxide may have been injected into the atmosphere by the venting of volcanic gases from the eruption of flood basalts, combined with the ignition of large coal seams, or by the burning of forests by hot lava. Other hypotheses suggest that the warming and drying of the terrestrial environments during the Permian Period reduced the amount of organic matter buried in sediments as coal or petroleum, shifting the amount of organically fixed carbon dioxide that was recycled through the atmosphere.

Population explosion of methane-producing microbes

Research in 2014 raised the possibility that the rapid blooming of archaea called Methanosarcina, which evolved the ability to manufacture methane (CH₄) near the end of the Permian Period, may have played a significant role in the dramatic rise in Earth’s ocean temperatures and changes to the planet’s carbon cycle. A sudden increase in methane in the atmosphere is thought to result in warming temperatures, ocean acidification, and other changes to the carbon cycle. Geologic evidence suggests that the uptake of carbon dioxide in the oceans and the deposition of carbon in ocean sediments near the end of the Permian was far greater than that which could have been caused by eruptions of the Siberian Traps alone. In addition, the discovery of substantial nickel deposits in China that have been dated to that time implicates the role of Methanosarcina in the Permian extinction. Nickel has been shown to be a limiting nutrient for Methanosarcina, and the substantial availability of the element, released during volcanism, near the end of the period is hypothesized to have been responsible for the population explosion of the microbe whose metabolic processes added large amounts of methane to the atmosphere.

Other potential causes

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Beyond the various temperature hypotheses and the eruptions of the Siberian flood basalts, other causes of Permian extinction events have been considered. Some authorities suspect that the Permian extinction was caused by the assembly of Pangea, a vast north-south supercontinent. It is thought that several shallow-water marine basins—the primary habitat of most marine invertebrates—were destroyed as the continental plates moved toward one another. In addition, the creation of such an extensive north-south landmass changed the courses of ocean currents and thus altered regional climates. Although these factors certainly played a role in the demise of some species, Pangea was fully assembled by the first half of the Permian, whereas the mass extinctions did not begin until the final 15 million years of the period. Other scientists contend that the Permian extinction was the result of a bolide (meteorite or comet) impact that occurred near the end of the Permian Period; however, that hypothesis is the subject of much debate.