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The balance between photosynthetic organic carbon production and respiration controls atmospheric composition and climate 1 , 2 . The majority of organic carbon is respired back to carbon dioxide in the biosphere, but a small fraction escapes remineralization and is preserved over geological timescales 3 . By removing reduced carbon from Earth’s surface, this sequestration process promotes atmospheric oxygen accumulation 2 and carbon dioxide removal 1 . Two major mechanisms have been proposed to explain organic carbon preservation: selective preservation of biochemically unreactive compounds 4 , 5 and protection resulting from interactions with a mineral matrix 6 , 7 . Although both mechanisms can operate across a range of environments and timescales, their global relative importance on 1,000-year to 100,000-year timescales remains uncertain 4 . Here we present a global dataset of the distributions of organic carbon activation energy and corresponding radiocarbon ages in soils, sediments and dissolved organic carbon. We find that activation energy distributions broaden over time in all mineral-containing samples. This result requires increasing bond-strength diversity, consistent with the formation of organo-mineral bonds 8 but inconsistent with selective preservation. Radiocarbon ages further reveal that high-energy, mineral-bound organic carbon persists for millennia relative to low-energy, unbound organic carbon. Our results provide globally coherent evidence for the proposed 7 importance of mineral protection in promoting organic carbon preservation. We suggest that similar studies of bond-strength diversity in ancient sediments may reveal how and why organic carbon preservation—and thus atmospheric composition and climate—has varied over geological time. Broadening activation energy distributions and increasing radiocarbon ages reveal the global importance of mineral protection in promoting organic carbon preservation.

The reaction of atmospheric carbon dioxide (CO 2 ) with silicate rocks provides a carbon sink that helps counterbalance the release of CO 2 by volcanic degassing. However, some types of rocks contain petrogenic organic carbon, the oxidation of which adds CO 2 to the atmosphere, counteracting the drawdown by silicates. Hemingway et al. present evidence from the rapidly eroding Central Range of Taiwan showing that microbes oxidize roughly two-thirds of the petrogenic organic carbon there and that the rate of oxidation increases with the rate of erosion. Science , this issue p. 209 The oxidation of organic carbon in rapidly eroding mountain soils is microbially mediated. Lithospheric organic carbon (“petrogenic”; OC petro ) is oxidized during exhumation and subsequent erosion of mountain ranges. This process is a considerable source of carbon dioxide (CO 2 ) to the atmosphere over geologic time scales, but the mechanisms that govern oxidation rates in mountain landscapes are poorly constrained. We demonstrate that, on average, 67 ± 11% of the OC petro initially present in bedrock exhumed from the tropical, rapidly eroding Central Range of Taiwan is oxidized in soils, leading to CO 2 emissions of 6.1 to 18.6 metric tons of carbon per square kilometer per year. The molecular and isotopic evolution of bulk OC and lipid biomarkers during soil formation reveals that OC petro remineralization is microbially mediated. Rapid oxidation in mountain soils drives CO 2 emission fluxes that increase with erosion rate, thereby counteracting CO 2 drawdown by silicate weathering and biospheric OC burial.

The Paleocene-Eocene Thermal Maximum (PETM) was an abrupt global warming event associated with a large injection of carbon into the ocean-atmosphere system, as evidenced by a diagnostic carbon isotope excursion (CIE). Evidence also suggests substantial hydrologic perturbations, but details have been hampered by a lack of appropriate proxies. To address this shortcoming, here we isolate and measure the isotopic composition of hydroxyl groups (OH − ) in clay minerals from a highly expanded PETM section in the North Sea Basin, together with their bulk oxygen isotope composition. At this location, we show that hydroxyl O- and H-isotopes are less influenced than bulk values by clay compositional changes due to mixing and/or inherited signals and thus better track hydrologic variability. We find that clay OH − hydrogen-isotope values (δ 2 H OH ) decrease slowly prior to the PETM and then abruptly by ∼8‰ at the CIE onset. Coincident with an increase in relative kaolinite content, this indicates increased rainfall and weathering and implies an enhanced hydrologic cycle response to global warming, particularly during the early stages of the PETM. Subsequently, δ 2 H OH returns to pre-PETM values well before the end of the CIE, suggesting hydrologic changes in the North Sea were short-lived relative to carbon-cycle perturbations. Novel measurements of clay hydroxyl isotopic composition show an enhanced hydrological cycle during a period of intense global warming at the Paleocene-Eocene boundary 55.9 million years ago.

Selection of microorganisms in marine sediment is shaped by energy-yielding electron acceptors for respiration that are depleted in vertical succession. However, some taxa have been reported to reflect past depositional conditions suggesting they have experienced weak selection after burial. In sediments underlying the Arabian Sea oxygen minimum zone (OMZ), we performed the first metagenomic profiling of sedimentary DNA at centennial-scale resolution in the context of a multi-proxy paleoclimate reconstruction. While vertical distributions of sulfate reducing bacteria and methanogens indicate energy-based selection typical of anoxic marine sediments, 5–15% of taxa per sample exhibit depth-independent stratigraphies indicative of paleoenvironmental selection over relatively short geological timescales. Despite being vertically separated, indicator taxa deposited under OMZ conditions were more similar to one another than those deposited in bioturbated intervals under intervening higher oxygen. The genomic potential for denitrification also correlated with palaeo-OMZ proxies, independent of sediment depth and available nitrate and nitrite. However, metagenomes revealed mixed acid and Entner-Dourdoroff fermentation pathways encoded by many of the same denitrifier groups. Fermentation thus may explain the subsistence of these facultatively anaerobic microbes whose stratigraphy follows changing paleoceanographic conditions. At least for certain taxa, our analysis provides evidence of their paleoenvironmental selection over the last glacial-interglacial cycle.

Nearly all molecular oxygen (O2) on Earth is produced via oxygenic photosynthesis by plants or photosynthetically active microorganisms. Light-independent O2 production, which occurs both abiotically, e.g. through water radiolysis, or biotically, e.g. through the dismutation of nitric oxide or chlorite, has been thought to be negligible to the Earth system. However, recent work indicates that O2 is produced and consumed in dark and apparently anoxic environments at a much larger scale than assumed. Studies have shown that isotopically light O2 can accumulate in old groundwaters, that strictly aerobic microorganisms are present in many apparently anoxic habitats, and that microbes and metabolisms that can produce O2 without light are widespread and abundant in diverse ecosystems. Analysis of published metagenomic data reveals that the enzyme putatively capable of nitric oxide dismutation forms four major phylogenetic clusters and occurs in at least 16 bacterial phyla, most notably the Bacteroidota. Similarly, a re-analysis of published isotopic signatures of dissolved O2 in groundwater suggests in situ production in up to half of the studied environments. Geochemical and microbiological data support the conclusion that “dark oxygen production\" is an important and widespread yet overlooked process in apparently anoxic environments with far-reaching implications for subsurface biogeochemistry and ecology.

The mass-independent minor oxygen isotope compositions (Δ′17O) of atmospheric O₂ and CO₂ are primarily regulated by their relative partial pressures, pO₂/pCO₂. Pyrite oxidation during chemical weathering on land consumes O₂ and generates sulfate that is carried to the ocean by rivers. The Δ′17O values of marine sulfate deposits have thus been proposed to quantitatively track ancient atmospheric conditions. This proxy assumes direct O₂ incorporation into terrestrial pyrite oxidation-derived sulfate, but a mechanistic understanding of pyrite oxidation—including oxygen sources—in weathering environments remains elusive. To address this issue, we present sulfate source estimates and Δ′17O measurements from modern rivers transecting the Annapurna Himalaya, Nepal. Sulfate in high-elevation headwaters is quantitatively sourced by pyrite oxidation, but resulting Δ′17O values imply no direct tropospheric O₂ incorporation. Rather, our results necessitate incorporation of oxygen atoms from alternative, 17O-enriched sources such as reactive oxygen species. Sulfate Δ′17O decreases significantly when moving into warm, low-elevation tributaries draining the same bedrock lithology. We interpret this to reflect overprinting of the pyrite oxidation-derived Δ′17O anomaly by microbial sulfate reduction and reoxidation, consistent with previously described major sulfur and oxygen isotope relationships. The geologic application of sulfate 017O as a proxy for past pO₂/pCO₂ should consider both 1) alternative oxygen sources during pyrite oxidation and 2) secondary overprinting by microbial recycling.

Terrestrial vegetation and soils hold three times more carbon than the atmosphere. Much debate concerns how anthropogenic activity will perturb these surface reservoirs, potentially exacerbating ongoing changes to the climate system. Uncertainties specifically persist in extrapolating point-source observations to ecosystemscale budgets and fluxes, which require consideration of vertical and lateral processes on multiple temporal and spatial scales. To explore controls on organic carbon (OC) turnover at the river basin scale, we present radiocarbon (14C) ages on two groups of molecular tracers of plant-derived carbon—leaf-wax lipids and lignin phenols—from a globally distributed suite of rivers. We find significant negative relationships between the 14C age of these biomarkers and mean annual temperature and precipitation. Moreover, riverine biospheric-carbon ages scale proportionally with basinwide soil carbon turnover times and soil 14C ages, implicating OC cycling within soils as a primary control on exported biomarker ages and revealing a broad distribution of soil OC reactivities. The ubiquitous occurrence of a long-lived soil OC pool suggests soil OC is globally vulnerable to perturbations by future temperature and precipitation increase. Scaling of riverine biosphericcarbon ages with soil OC turnover shows the former can constrain the sensitivity of carbon dynamics to environmental controls on broad spatial scales. Extracting this information from fluvially dominated sedimentary sequences may inform past variations in soil OC turnover in response to anthropogenic and/or climate perturbations. In turn, monitoring riverine OC composition may help detect future climate-change–induced perturbations of soil OC turnover and stocks.

The triple oxygen isotope composition (Δ’17O) of sulfate minerals is widely used to constrain ancient atmospheric pO₂/pCO₂ and rates of gross primary production. The utility of this tool is based on amodel that sulfate oxygen carries an isotope fingerprint of tropospheric O₂ incorporated through oxidative weathering of reduced sulfur minerals, particularly pyrite. Work to date has targeted Proterozoic environments (2.5 billion to 0.542 billion years ago) where large isotope anomalies persist; younger timescale records, which would ground ancient environmental interpretation in what we know from modern Earth, are lacking. Here we present a high-resolution record of the δ 18O and Δ’17O in marine sulfate for the last 130 million years of Earth history. This record carries a Δ’17O close to 0‰, suggesting that the marine sulfate reservoir is under strict control by biogeochemical cycling (namely, microbial sulfate reduction), as these reactions follow mass-dependent fractionation. We identify no discernible contribution from atmospheric oxygen on this timescale. We interpret a steady fractional contribution of microbial sulfur cycling (terrestrial and marine) over the last 100 million years, even as global weathering rates are thought to vary considerably.

Bacterial hopanoid lipids are ubiquitous in the geologic record and serve as biomarkers for reconstructing Earth’s climatic and biogeochemical evolution. Specifically, the abundance of 2-methylhopanoids deposited during Mesozoic ocean anoxic events (OAEs) and other intervals has been interpreted to reflect proliferation of nitrogen-fixing marine cyanobacteria. However, there currently is no conclusive evidence for 2-methylhopanoid production by extant marine cyanobacteria. As an alternative explanation, here we report 2-methylhopanoid production by bacteria of the genus Nitrobacter, cosmopolitan nitrite oxidizers that inhabit nutrient-rich freshwater, brackish, and marine environments. The model organism Nitrobacter vulgaris produced only trace amounts of 2-methylhopanoids when grown in minimal medium or with added methionine, the presumed biosynthetic methyl donor. Supplementation of cultures with cobalamin (vitamin B12) increased nitrite oxidation rates and stimulated a 33-fold increase of 2-methylhopanoid abundance, indicating that the biosynthetic reaction mechanismis cobalamin dependent. Because Nitrobacter spp. cannot synthesize cobalamin, we postulate that they acquire it from organisms inhabiting a shared ecological niche—for example, ammonia-oxidizing archaea. We propose that during nutrient-rich conditions, cobalamin-based mutualism intensifies upper water column nitrification, thus promoting 2-methylhopanoid deposition. In contrast, anoxia underlying oligotrophic surface ocean conditions in restricted basins would prompt shoaling of anaerobic ammonium oxidation, leading to low observed 2-methylhopanoid abundances. The first scenario is consistent with hypotheses of enhanced nutrient loading during OAEs, while the second is consistent with the sedimentary record of Pliocene–Pleistocene Mediterranean sapropel events. We thus hypothesize that nitrogen cycling in the Pliocene–Pleistocene Mediterranean resembled modern, highly stratified basins, whereas no modern analog exists for OAEs.

Serial oxidation coupled with stable carbon and radiocarbon analysis of sequentially evolved CO2 is a promising method to characterize the relationship between organic carbon (OC) chemical composition, source, and residence time in the environment. However, observed decay profiles depend on experimental conditions and oxidation pathway. It is therefore necessary to properly assess serial oxidation kinetics before utilizing decay profiles as a measure of OC reactivity. We present a regularized inverse method to estimate the distribution of OC activation energy (E), a proxy for bond strength, using serial oxidation. Here, we apply this method to ramped temperature pyrolysis or oxidation (RPO) analysis but note that this approach is broadly applicable to any serial oxidation technique. RPO analysis directly compares thermal reactivity to isotope composition by determining the E range for OC decaying within each temperature interval over which CO2 is collected. By analyzing a decarbonated test sample at multiple masses and oven ramp rates, we show that OC decay during RPO analysis follows a superposition of parallel first-order kinetics and that resulting E distributions are independent of experimental conditions. We therefore propose the E distribution as a novel proxy to describe OC thermal reactivity and suggest that E vs. isotope relationships can provide new insight into the compositional controls on OC source and residence time.