The Lomagundi (2.22–2.1 Ga) positive carbon isotope excursion in shallow-marine sedimentary carbonates has been associated with the rise in atmospheric oxygen, but subsequent studies have demonstrated that the carbon isotope excursion was preceded by the rise in atmospheric oxygen. The amount of oxygen released to the exosphere during the Lomagundi excursion is constrained by the average global fractionation between inorganic and organic carbon, which is poorly characterized. Because dissolved inorganic and organic carbon reservoirs were arguably larger in the Paleoproterozoic ocean, at a time of lower solar luminosity and lower ocean redox state, decoupling between these two variables might be expected. We determined carbon isotope values of carbonate and organic matter in carbonates and shales of the Silverton Formation, South Africa and in the correlative Sengoma Argillite Formation, near the border in Botswana. These units were deposited between 2.22 and 2.06 Ga along the margin of the Kaapvaal Craton in an open-marine deltaic setting and experienced lower greenschist facies metamorphism. The prodelta to offshore marine shales are overlain by a subtidal carbonate sequence. Carbonates exhibit elevated 13C values ranging from 8.3 to 11.2‰ vs. VPDB consistent with deposition during the Lomagundi positive excursion. The total organic carbon (TOC) contents range from 0.01 to 0.6% and δ 13C values range from − 24.8 to − 13.9‰. Thus, the isotopic fractionation between organic and carbonate carbon was on average 30.3 ± 2.8‰ ( n = 32) in the shallow-marine environment. The underlying Sengoma shales have highly variable TOC contents (0.14 to 21.94%) and δ 13C values (− 33.7 to − 20.8‰) with an average of − 27.0 ± 3.0‰ ( n = 50). Considering that the shales were also deposited during the Lomagundi excursion, and taking δ 13C values of the overlying carbonates as representative of the δ 13C value of dissolved inorganic carbon during shale deposition, a carbon isotope fractionation as large as ~ 37‰ appears to characterize the production of bulk organic matter in the deeper part of the Pretoria Basin at that time. This enhanced fractionation relative to that observed in shallow-water environments likely reflects heterotrophic (secondary) and chemotrophic productivity at and below a pronounced redoxcline, consistent with the euxinic conditions inferred from independent evidence for the deeper part of the Pretoria Basin. Greater variability in organic carbon vs. carbonate carbon isotopic values on the shallow-marine carbonate platform suggests that the carbon cycling was dominated by a large dissolved inorganic carbon reservoir during the Lomagundi excursion. Our study suggests that in contrast to the Late Neoproterozoic and Phanerozoic, when carbon isotope fractionation between carbonate and organic carbon in the open ocean was mostly controlled by primary producers, in the Paleoproterozoic redox-stratified ocean heterotrophic and chemotrophic productivity overprinted a signal of primary productivity below the redoxcline. This strong imprint of heterotrophic and chemotrophic productivity on organic carbon isotope records complicates the reconstruction of spatial patterns and secular trends in the δ 13C values of dissolved inorganic carbon in the Paleoproterozoic seawater.
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