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Methyl groups are found in numerous biogenic and synthetic materials including geologically preserved materials such as wood. The carbon and hydrogen isotope compositions of methyl groups are used as tracers in biogeochemical cycles, as paleothermometers, and to determine the hydrogen isotopic composition of ancient rain. Here we present analyses of resolved 13C–D (13CH2D) and D–D (12CHD2) clumped isotope compositions of methyl groups as new variables for the study of methyl groups in the present and past. We first present chemical methods to extract, purify, and derivatize methyl groups from methoxyl (R–O–CH3) groups as CH3F and CH3Cl, and high-resolution mass spectrometric techniques to determine the clumped isotope compositions of these species. We achieve precisions for 13C–D clumping of ±0.25‰ and D–D clumping of ±2.5‰. We anchor our clumped isotopic measurements to a thermodynamic reference frame by first calculating the theoretical temperature dependences of 13C–D and D–D clumping in CH3Cl, then placing our measurements onto this reference frame through experimental internal isotopic equilibration of CH3Cl at 200 °C. Finally, we provide and analyze an initial dataset of clumped 13C–D and D–D compositions of methyl groups from various commercial/synthetic monomers and environmental woods. We observe ranges in clumped isotope compositions of ∼11‰ in 13C–D and ∼48‰ in D–D, and systematic differences within these ranges between methyl groups from commercial monomers and wood. Specifically, commercial clumped 13C–D compositions are between 0 and 3‰, which correspond to apparent equilibrium temperatures between 170 °C and the infinite temperature limit. In contrast, the clumped 13C–D compositions of wood methoxyl groups are distinctively high (9.50–11.25‰) and 3–6‰ higher than would be expected if formed in internal isotopic equilibrium at Earth-surface temperatures. Commercial/synthetic methyl and wood methoxyl clumped D–D compositions are also distinct: −5 to +13‰ in commercial monomers vs. −35 to −8‰ in wood—such negative values cannot result from formation in isotopic equilibrium and require kinetic processes to have occurred. These results indicate that wood methoxyl groups are formed out of isotopic equilibrium and that clumped isotope compositions of methyl groups may be useful tracers of methyl group sources and sinks in the environment. For instance, isotopic clumping in methyl groups may be useful for understanding controls on isotopic clumping in methane produced by methylotrophic methanogens.

Methane is produced and consumed via numerous microbial and chemical reactions in atmospheric, hydrothermal, and magmatic reactions. The stable isotopic composition of methane has been used extensively for decades to constrain the source of methane in the environment. A recently introduced isotopic parameter used to study the formation temperature and formational conditions of methane is the measurement of molecules of methane with multiple rare, heavy isotopes ("clumped") such as 13CH3D and 12CH2D2. In order to place methane-clumped isotope measurements into a thermodynamic reference frame that allows calculations of clumped isotope-based temperatures (geothermometry) and comparison between laboratories, all past studies have calibrated their measurements using a combination of experiment and theory based on the temperature dependence of clumped isotopologue distributions for isotopically equilibrated systems. These have previously been performed at relatively high temperatures (>150 °C). Given that many natural occurrences of methane form below these temperatures, previous calibrations require extrapolation when calculating clumped isotope-based temperatures outside of this calibration range. We provide a new experimental calibration of the relative equilibrium abundances of 13CH3D and 12CH2D2 from 1 to 500 °C using a combination of γ-Al2O3- and Ni-based catalysts and compare them to new theoretical computations using Path Integral Monte Carlo (PIMC) methods and find 1:1 agreement (within ±1 standard error) for the observed temperature dependence of clumping between experiment and theory over this range. This demonstrates that measurements, experiments, and theory agree from 1 to 500 °C, providing confidence in the overall approaches. Polynomial fits to PIMC computations, which are considered the most rigorous theoretical approach available, are given as follows (valid T ≥ 270 K): Δ13CH3D ≅ 1000 × ln(K13CH3D) = (1.47348 × 1019)/T7 - (2.08648 × 1017)/T6 + (1.19810 × 1015)/T5 - (3.54757 × 1012)/T4 + (5.54476 × 109)/T3 - (3.49294 × 106)/T2 + (8.89370 × 102)/T and Δ12CH2D2 ≅ 1000 × ln(8/3K12CH2D2) = -(9.67634 × 1015)/T6 + (1.71917 × 1014)/T5 - (1.24819 × 1012)/T4 + (4.30283 × 109)/T3 - (4.48660 × 106)/T2 + (1.86258 × 103)/T. We additionally compare PIMC computations to those performed utilizing traditional approaches that are the basis of most previous calibrations (Bigeleisen, Mayer, and Urey model, BMU) and discuss the potential sources of error in the BMU model relative to PIMC computations.

18O/16O and 17O/16O ratios of atmospheric and dissolved oceanic O2 are used as biogeochemical tracers of photosynthesis and respiration. Critical to this approach is a quantitative understanding of the isotopic fractionations associated with production, consumption, and transport of O2 in the ocean both at the surface and at depth. We made measurements of isotopic fractionations associated with O2 respiration by E. coli. Our study included wild-type strains and mutants with only a single respiratory O2 reductase in their electron transport chains (either a heme-copper oxygen reductase or a bd oxygen reductase). We tested two common assumptions made in interpretations of O2 isotope variations and in isotope-enabled models of the O2 cycle: (i) laboratory-measured respiratory 18O/16O isotopic fractionation factors (18α) of microorganisms are independent of environmental and experimental conditions including temperature, carbon source, and growth rate; And (ii) the respiratory ‘mass law’ exponent, θ, between 18O/16O and 17O/16O, 17α = (18α)θ, is universal for aerobic respiration. Results demonstrated that experimental temperatures have an effect on both 18α and θ for aerobic respiration. Specifically, lowering temperatures from 37 to 15 °C decreased the absolute magnitude of 18α by 0.0025 (2.5‰), and caused the mass law slope to decrease by 0.005. We propose a possible biochemical basis for these variations using a model of O2 reduction that incorporates two isotopically discriminating steps: the reversible binding and unbinding of O2 to a terminal reductase, and the irreversible reduction of that O2 to water. Finally, we cast our results in a one-dimensional isopycnal reaction-advection-diffusion model, which demonstrates that enigmatic δ18O and Δ17O variations of dissolved O2 in the dark ocean can be understood by invoking the observed temperature dependence of these isotope effects.

The measurement of multiply isotopically substituted (‘clumped isotope’) carbonate groups provides a way to reconstruct past mineral formation temperatures. However, dissolution-reprecipitation (i.e., recrystallization) reactions, which commonly occur during sedimentary burial, can alter a sample's clumped-isotope composition such that it partially or wholly reflects deeper burial temperatures. Here we derive a quantitative model of diagenesis to explore how diagenesis alters carbonate clumped-isotope values. We apply the model to a new dataset from deep-sea sediments taken from Ocean Drilling Project site 807 in the equatorial Pacific. This dataset is used to ground truth the model. We demonstrate that the use of the model with accompanying carbonate clumped-isotope and carbonate δ18O values provides new constraints on both the diagenetic history of deep-sea settings as well as past equatorial sea-surface temperatures. Specifically, the combination of the diagenetic model and data support previous work that indicates equatorial sea-surface temperatures were warmer in the Paleogene as compared to today. We then explore whether the model is applicable to shallow-water settings commonly preserved in the rock record. Using a previously published dataset from the Bahamas, we demonstrate that the model captures the main trends of the data as a function of burial depth and thus appears applicable to a range of depositional settings.

Oxygen self-diffusion in calcite and many other minerals is considerably faster under wet conditions relative to dry conditions. Here we investigate whether this “water effect” also holds true for solid-state isotope exchange reactions that alter the abundance of carbonate groups with multiple rare isotopes (‘clumped’ isotope groups) via the process of solid-state bond reordering. We present clumped-isotope reordering rates for optical calcite heated under wet, high-pressure (100 MPa) conditions. We observe only modest increases in reordering rates under such conditions compared with rates for the same material reacted in dry CO2 under low-pressure conditions. Activation energies under wet, high-pressure conditions are indistinguishable from those for dry, low-pressure conditions, while rate constants are resolvably higher (up to ∼3 times) for wet, high-pressure relative to dry, low-pressure conditions in most of our interpretations of experimental results. This contrasts with the water effect for oxygen self-diffusion in calcite, which is associated with lower activation energies, and diffusion coefficients that are ≥103 times higher compared with dry (pure CO2) conditions in the temperature range of this study (385–450 °C). The water effect for clumped-isotopes leads to calculated apparent equilibrium temperatures (“blocking temperatures”) for typical geological cooling rates that are only a few degrees higher than those for dry conditions, while O self-diffusion blocking temperatures in calcite grains are ∼150–200 °C lower in wet conditions compared with dry conditions. Since clumped-isotope reordering is a distributed process that occurs throughout the mineral volume, our clumped-isotope results support the suggestion of Labotka et al. (2011) that the water effect in calcite does not involve major changes in bulk (volume) diffusivity, but rather is primarily a surface phenomenon that facilitates oxygen exchange between the calcite surface and external fluids. We explore the mechanism(s) by which clumped isotope reordering rates may be modestly increased under wet, high-pressure conditions, including changes in defect concentrations in the near surface environment due to reactions at the water–mineral interface, and lattice deformation resulting from pressurization of samples.

Carbonates form ubiquitously throughout the history of deposition, burial, and uplift of basins. As such, they potentially record the environmental conditions at the time of formation. Carbonate clumped isotopes provide the temperature of precipitation but can be internally reordered if the host rock is exposed to elevated temperatures over geologic time scales. Here, we exploited this kinetic behavior by analyzing multiple generations of cements that capture the range of environments experienced by the El Abra Formation from eastern Mexico. From this, we developed a quantitative diagenetic history for these different phases of cementation. We observed a 70 °C range in clumped isotope temperatures from 64 °C to 134 °C for these cements, which is not compatible with their inferred precipitation environments. This suggests that bond reordering occurred during burial but did not fully reorder all cements to a common apparent temperature. We reconstructed original cement growth temperatures and the isotopic signature of the parent fluids to show that precipitation from a marine pore fluid began at 125 Ma, contemporaneous with deposition, and continued throughout burial to temperatures of at least 138 °C at 42 Ma. We show that precipitation of equant cements, which occluded 90% of the pore space, was coincident with Laramide-related burial to depths greater than 3800 m. A U-Pb age of diagenetic calcite of 77.1 ± 3.6 Ma provides independent support for our estimates of the absolute timing of precipitation of two distinct phases of the paragenesis. This is the first demonstration of the utility of integrating U-Pb age dating with reordered clumped isotope temperatures to provide quantitative constraints on the time-temperature history of cementation. Such information may ultimately lead to advances in our understanding of the formational environments and geological processes that drive diagenesis in carbonates for temperatures below the clumped isotope "blocking temperature".

Multiply isotopically substituted molecules (‘clumped’ isotopologues) can be used as geothermometers because their proportions at isotopic equilibrium relative to a random distribution of isotopes amongst all isotopologues are functions of temperature. This has allowed measurements of clumped-isotope abundances to be used to constrain formation temperatures of several natural materials. However, kinetic processes during generation, modification, or transport of natural materials can also affect their clumped-isotope compositions. Herein, we show that methane generated experimentally by closed-system hydrous pyrolysis of shale or nonhydrous pyrolysis of coal yields clumped-isotope compositions consistent with an equilibrium distribution of isotopologues under some experimental conditions (temperature–time conditions corresponding to ‘low,’ ‘mature,’ and ‘over-mature’ stages of catagenesis), but can have non-equilibrium (i.e., kinetically controlled) distributions under other experimental conditions (‘high’ to ‘over-mature’ stages), particularly for pyrolysis of coal. Non-equilibrium compositions, when present, lead the measured proportions of clumped species to be lower than expected for equilibrium at the experimental temperature, and in some cases to be lower than a random distribution of isotopes (i.e., negative Δ18 values). We propose that the consistency with equilibrium for methane formed by relatively low temperature pyrolysis reflects local reversibility of isotope exchange reactions involving a reactant or transition state species during demethylation of one or more components of kerogen. Non-equilibrium clumped-isotope compositions occur under conditions where 'secondary’ cracking of retained oil in shale or wet gas hydrocarbons (C2-5, especially ethane) in coal is prominent. We suggest these non-equilibrium isotopic compositions are the result of the expression of kinetic isotope effects during the irreversible generation of methane from an alkyl precursor. Other interpretations are also explored. These findings provide new insights into the chemistry of thermogenic methane generation, and may provide an explanation of the elevated apparent temperatures recorded by the methane clumped-isotope thermometer in some natural gases. However, it remains unknown if the laboratory experiments capture the processes that occur at the longer time and lower temperatures of natural gas formation.

Methane clumped-isotope compositions provide a new approach to understanding the formational conditions of methane from both biogenic and thermogenic sources. Under some conditions, these compositions can be used to reconstruct the formational temperatures of the gas, and this capability can be applied to common subsets of both biogenic and thermogenic systems. Additionally, there are examples in which clumped-isotope compositions do not reflect gas-formation temperatures but instead mixing effects and kinetic phenomena; such kinetic effects also occur in common and recognizable subtypes of biogenic and thermogenic gases. Here we review the use of methane clumped-isotope measurements for understanding the origin of methane in the subsurface. We review methane clumped-isotope measurements from numerous biogenic and thermogenic natural gas reservoirs.We then place these measurements in the context of common frameworks for identifying the formational conditions of methane including the use of methane δ13C and δD values and C1/C2-3 ratios. Finally, we propose a framework for how methane clumped isotopes can be used to identify the origin of methane accumulations.

The isotopic composition of methane is of longstanding geochemical interest, with important implications for understanding petroleum systems, atmospheric greenhouse gas concentrations, the global carbon cycle, and life in extreme environments. Recent analytical developments focusing on multiply substituted isotopologues (‘clumped isotopes’) are opening a valuable new window into methane geochemistry. When methane forms in internal isotopic equilibrium, clumped isotopes can provide a direct record of formation temperature, making this property particularly valuable for identifying different methane origins. However, it has also become clear that in certain settings methane clumped isotope measurements record kinetic rather than equilibrium isotope effects. Here we present a substantially expanded dataset of methane clumped isotope analyses, and provide a synthesis of the current interpretive framework for this parameter. In general, clumped isotope measurements indicate plausible formation temperatures for abiotic, thermogenic, and microbial methane in many geological environments, which is encouraging for the further development of this measurement as a geothermometer, and as a tracer for the source of natural gas reservoirs and emissions. We also highlight, however, instances where clumped isotope derived temperatures are higher than expected, and discuss possible factors that could distort equilibrium formation temperature signals. In microbial methane from freshwater ecosystems, in particular, clumped isotope values appear to be controlled by kinetic effects, and may ultimately be useful to study methanogen metabolism.

Exhumation and accompanying retrograde metamorphism alter the compositions and textures of metamorphic rocks through deformation, mineral–mineral reactions, water–rock reactions, and diffusion-controlled intra- and inter-mineral atomic mobility. Here, we demonstrate that these processes are recorded in the clumped- and single-isotope (δ13C and δ18O) compositions of marbles, which can be used to constrain retrograde metamorphic histories. We collected 27 calcite and dolomite marbles along a transect from the rim to the center of the metamorphic core-complex of Naxos (Greece), and analyzed their carbonate single- and clumped-isotope compositions. The majority of Δ47 values of whole-rock samples are consistent with exhumation- controlled cooling of the metamorphic complex. However, the data also reveal that water–rock interaction, deformation driven recrystallization and thermal shock associated with hydrothermal alteration may considerably impact the overall distribution of Δ47 values. We analyzed specific carbonate fabrics influenced by deformation and fluid–rock reaction to study how these processes register in the carbonate clumped-isotope system. Δ47 values of domains drilled from a calcite marble show a bimodal distribution. Low Δ47 values correspond to an apparent temperature of 260 °C and are common in static fabrics; high Δ47 values correspond to an apparent temperature of 200 °C and are common in dynamically recrystallized fabrics. We suggest that the low Δ47 values reflect diffusion-controlled isotopic reordering during cooling, whereas high Δ47 values reflect isotopic reordering driven by dynamic recrystallization. We further studied the mechanism by which dynamic recrystallization may alter Δ47 values by controlled heating experiments. Results show no significant difference between laboratory reactions rates in the static and dynamic fabrics, consistent with a mineral-extrinsic mechanism, in which slip along crystal planes was associated with atomic-scale isotopic reordering in the calcite lattice. An intrinsic mechanism (enhanced isotopic reordering rate in deformed minerals) is contraindicated by these experiments. We suggest that Δ47 values of dynamically recrystallized fabrics that form below the diffusion-controlled blocking-temperature for calcite constrain the temperature of deformation. We find that Δ47-based temperatures of static fabrics from Naxos marbles are ∼60–80 °C higher than commonly observed in slowly cooled metamorphic rocks, and would suggest cooling rates of ∼105°CMyr−1. A similar thermal history is inferred for dolomite marbles from the core vicinity, which preserve apparent temperatures up to 200 °C higher than a typical blocking temperature (∼300 °C). This finding could be explained by a hydrothermal event driving a brief thermal pulse and locally resetting Δ47 values. Rapid cooling of the core-complex region is consistent with a compilation of published cooling ages and a new apatite U–Th/He age, associating the thermal event with the emplacement of a granodiorite pluton at ∼12 Ma.

The Athel silicilyte is an enigmatic, hundreds of meters thick, finely laminated quartz deposit, in which silica precipitated in deep water (>~100-200 m) at the Ediacaran-Cambrian boundary in the South Oman Salt Basin. In contrast, Meso-Neoproterozoic sinks for marine silica were dominantly restricted to peritidal settings. The silicilyte is known to contain sterane biomarkers for demosponges, which today are benthic, obligately aerobic organisms. However, the basin has previously been described as permanently sulfidic and time-equivalent shallow-water carbonate platform and evaporitic facies lack silica. The Athel silicilyte thus represents a unique and poorly understood depositional system with implications for late Ediacaran marine chemistry and paleoecology. To address these issues, we made petrographic observations, analyzed biomarkers in the solvent-extractable bitumen, and measured whole-rock iron speciation and oxygen and silicon isotopes. These data indicate that the silicilyte is a distinct rock type both in its sedimentology and geochemistry and in the original biology present as compared to other facies from the same time period in Oman. The depositional environment of the silicilyte, as compared to the bounding shales, appears to have been more reducing at depth in sediments and possibly bottom waters with a significantly different biological community contributing to the preserved biomarkers. We propose a conceptual model for this system in which deeper, nutrient-rich waters mixed with surface seawater via episodic mixing, which stimulated primary production. The silica nucleated on this organic matter and then sank to the seafloor, forming the silicilyte in a sediment-starved system. We propose that the silicilyte may represent a type of environment that existed elsewhere during the Neoproterozoic. These environments may have represented an important locus for silica removal from the oceans.

The history of atmospheric O2 partial pressures (Po2) is inextricably linked to the coevolution of life and Earth's biogeochemical cycles. Reconstructions of past Po2 rely on models and proxies but often markedly disagree. We present a record of Po2 reconstructed using O2/N2 ratios from ancient air trapped in ice. This record indicates that Po2 declined by 7 per mil (0.7%) over the past 800,000 years, requiring that O2 sinks were ~2% larger than sources. This decline is consistent with changes in burial and weathering fluxes of organic carbon and pyrite driven by either Neogene cooling or increasing Pleistocene erosion rates. The 800,000-year record of steady average carbon dioxide partial pressures (Pco2) but declining Po2 provides distinctive evidence that a silicate weathering feedback stabilizes Pco2 on million-year time scales.

Methane is a potent greenhouse gas, and there are concerns that its natural emissions from the Arctic could act as a substantial positive feedback to anthropogenic global warming. Determining the sources of methane emissions and the biogeochemical processes controlling them is important for understanding present and future Arctic contributions to atmospheric methane budgets. Here we apply measurements of multiply-substituted isotopologues, or clumped isotopes, of methane as a new tool to identify the origins of ebullitive fluxes in Alaska, Sweden and the Arctic Ocean. When methane forms in isotopic equilibrium, clumped isotope measurements indicate the formation temperature. In some microbial methane, however, non-equilibrium isotope effects, probably related to the kinetics of methanogenesis, lead to low clumped isotope values. We identify four categories of emissions in the studied samples: thermogenic methane, deep subsurface or marine microbial methane formed in isotopic equilibrium, freshwater microbial methane with non-equilibrium clumped isotope values, and mixtures of deep and shallow methane (i.e., combinations of the first three end members). Mixing between deep and shallow methane sources produces a non-linear variation in clumped isotope values with mixing proportion that provides new constraints for the formation environment of the mixing end-members. Analyses of microbial methane emitted from lakes, as well as a methanol-consuming methanogen pure culture, support the hypothesis that non-equilibrium clumped isotope values are controlled, in part, by kinetic isotope effects induced during enzymatic reactions involved in methanogenesis. Our results indicate that these kinetic isotope effects vary widely in microbial methane produced in Arctic lake sediments, with non-equilibrium δ18 values spanning a range of more than 5‰.

The isotopic composition of apatites from sedimentary phosphorite deposits has been used previously to reconstruct ancient conditions on the surface of the Earth. However, questions remain as to whether these minerals retain their original isotopic composition or are modified during burial and lithification. To better understand how apatites in phosphorites form and are diagenetically modified, we present new isotopic measurements of δ18O values and clumped-isotope-based (δ47) temperatures of carbonate groups in apatites from phosphorites from the past 265 million years. We compare these measurements to previously measured δ18O values of phosphate groups from the same apatites. These results indicate that the isotopic composition of many of the apatites do not record environmental conditions during formation but instead diagenetic conditions. To understand these results, we construct a model that describes the consequences of diagenetic modification of phosphorites as functions of the environmental conditions (i.e., temperature and δ18O values of the fluids) during initial precipitation and subsequent diagenesis. This model captures the basic features of the dataset and indicates that clumped-isotope-based temperatures provide additional quantitative constraints on both the formational environment of the apatites and subsequent diagenetic modification. Importantly, the combination of the model with the data indicates that the δ18O values and clumped-isotope temperatures recorded by phosphorites do not record either formation or diagenetic temperatures, but rather represent an integrated history that includes both the formation and diagenetic modification of the apatites.

Sources of methane to sedimentary environments are commonly identified and quantified using the stable isotopic compositions of methane. The methane "clumped-isotope geothermometer", based on the measurement of multiply substituted methane isotopologues (13CH3D and 12CH2D2), shows promise in adding new constraints to the sources and formational environments of both biogenic and thermogenic methane. However, questions remain about how this geothermometer behaves in systems with mixtures of biogenic and thermogenic gases and different biogenic environments. We have applied the methane clumped-isotope thermometer to a mixed biogenic-thermogenic system (Antrim Shale, USA) and to biogenic gas from gas seeps (Santa Barbara and Santa Monica Basin, USA), a pond on the Caltech campus, and methanogens grown in pure culture. We demonstrate that clumped-isotope based temperatures add new quantitative constraints to the relative amounts of biogenic vs. thermogenic gases in the Antrim Shale indicating a larger proportion (~50%) of thermogenic gas in the system than previously thought. Additionally, we find that the clumped-isotope temperature of biogenic methane appears related to the environmental settings in which the gas forms. In systems where methane generation rates appear to be slow (e.g., the Antrim Shale and gas seeps), microbial methane forms in or near both internal isotopic equilibrium and hydrogen-isotope equilibrium with environmental waters. In systems where methane forms rapidly, microbial methane is neither in internal isotopic equilibrium nor hydrogen-isotope equilibrium with environmental waters. A quantitative model of microbial methanogenesis that incorporates isotopes is proposed to explain these results.

Carbonate clumped-isotope geothermometry is a tool used to reconstruct formation or (re)equilibration temperatures of carbonate bearing minerals, including carbonate groups substituted into apatite. It is based on the preference for isotopologues with multiple heavy isotopes (for example,13C16O218O2- groups) to be more abundant at equilibrium than would be expected if all isotopes were randomly distributed amongst all carbonate groups. Because this preference is only a function of temperature, excesses of multiply substituted species can be used to calculate formation temperatures without knowledge of the isotopic composition of water from which the mineral precipitated or other phases with which it may have equilibrated. However, the measured temperature could be modified after mineral growth if exchange of isotopes amongst carbonate groups within the mineral has occurred through internal isotope-exchange reactions. Because these exchange reactions occur through thermally activated processes, their rates depend on temperature and increase at higher temperatures. Thus internal isotope-exchange reactions could lead to effective reequilibration at high temperatures, overprinting the original temperatures recorded during mineral growth. We measured clumped-isotope temperatures in carbonate bearing minerals (including apatites) from several carbonatites to constrain the kinetics of these internal isotope-exchange reactions. We observe two key trends for clumped-isotope temperatures in carbonatites: (i) clumped-isotope temperatures of apatites and carbonate-bearing minerals decrease with increasing intrusion depth and (ii) apatites record lower clumped-isotope temperatures than carbonate minerals from the same intrusion. We additionally conducted heating experiments at different temperatures to derive the temperature dependence for the rate constants that describe the alteration of clumped-isotope temperatures with time in calcites and apatites. We find that calcites exhibit complex kinetics as has been seen in previous studies. To quantify these results, we constructed a model that incorporates both diffusion of isotopes through the crystal lattice and isotope-exchange reactions between adjacent carbonate groups. We tested this model through comparison to previous measurements of optical calcites and brachiopods and to samples with known cooling histories and find that the model is able to reasonably capture kinetic data from previous experiments and the observed clumped-isotope temperatures of calcites assuming geologically reasonable cooling rates. A similar model for apatite over-predicts the observed clumped-isotope temperatures found in natural samples; we hypothesize this discrepancy is the result of annealing of radiation damage in our experiments, which lowers the diffusivity and rate of isotope exchange of carbonate groups compared to damaged natural samples. Finally, we constructed models to explore how heating can alter recorded clumped-isotope temperatures. Our model predicts that samples change in clumped-isotope temperatures in two stages. The first stage changes the recorded clumped isotope temperatures by

The chemical compositions of island arc basalts (IAB) reflect contributions from the mantle as well as fluids and melts from the subducting slab. Addition of radiogenic seawater Sr to oceanic crust through hydrothermal alteration and subsequent subduction is often invoked to explain elevated 87 Sr/ 86 Sr signatures in modern IAB. However, changes in the 87 Sr/ 86 Sr of island arc magmatic rocks through time has not been investigated, limiting our understanding of the factors influencing the Sr budgets of arcs throughout Earth's history. To address this, we compiled 87 Sr/ 86 Sr values from island arc magmatic rocks ranging in age from modern to Paleoproterozoic, only including data from island arc localities that best preserve initial magmatic 87 Sr/ 86 Sr. Median initial 87 Sr/ 86 Sr values are consistently elevated compared to depleted mantle 87 Sr/ 86 Sr over this period, indicating persistent enrichment in radiogenic Sr in island arcs. Moreover, the elevation in island arc 87 Sr/ 86 Sr relative to the depleted mantle is variable. A notable rise in island arc 87 Sr/ 86 Sr during the late Neoproterozoic coincides with a steep increase in seawater 87 Sr/ 86 Sr and Sr concentration. To investigate this potential connectivity, we modeled the 87 Sr/ 86 Sr of island arc magmas between 0 and 830 Ma with inputs of depleted mantle 87 Sr/ 86 Sr, seawater 87 Sr/ 86 Sr, and seawater Sr concentration. The model reproduces the overall trajectory of the compiled data. We interpret the observed temporal variation in island arc 87 Sr/ 86 Sr values and its close association with fluctuations in seawater chemistry as evidence that changes in marine geochemistry have strongly influenced the Sr isotopic record of island arc magmas over time., Competing Interests: Competing interests statement:The authors declare no competing interest.

Photorespiration can limit gross primary productivity in terrestrial plants. The rate of photorespiration relative to carbon fixation increases with temperature and decreases with atmospheric [CO 2 ]. However, the extent to which this rate varies in the environment is unclear. Here, we introduce a proxy for relative photorespiration rate based on the clumped isotopic composition of methoxyl groups ( R -O-CH 3 ) in wood. Most methoxyl C-H bonds are formed either during photorespiration or the Calvin cycle and thus their isotopic composition may be sensitive to the mixing ratio of these pathways. In water-replete growing conditions, we find that the abundance of the clumped isotopologue 13 CH 2 D correlates with temperature (18-28 °C) and atmospheric [CO 2 ] (280-1000 ppm), consistent with a common dependence on relative photorespiration rate. When applied to a global dataset of wood, we observe global trends of isotopic clumping with climate and water availability. Clumped isotopic compositions are similar across environments with temperatures below ~18 °C. Above ~18 °C, clumped isotopic compositions in water-limited and water-replete trees increasingly diverge. We propose that trees from hotter climates photorespire substantially more than trees from cooler climates. How increased photorespiration is managed depends on water availability: water-replete trees export more photorespiratory metabolites to lignin whereas water-limited trees either export fewer overall or direct more to other sinks that mitigate water stress. These disparate trends indicate contrasting responses of photorespiration rate (and thus gross primary productivity) to a future high-[CO 2 ] world. This work enables reconstructing photorespiration rates in the geologic past using fossil wood.

Carbonate mud represents one of the most important geochemical archives for reconstructing ancient climatic, environmental, and evolutionary change from the rock record. Mud also represents a major sink in the global carbon cycle. Yet, there remains no consensus about how and where carbonate mud is formed. Here, we present stable isotope and trace-element data from carbonate constituents in the Bahamas, including ooids, corals, foraminifera, and algae. We use geochemical fingerprinting to demonstrate that carbonate mud cannot be sourced from the abrasion and mixture of any combination of these macroscopic grains. Instead, an inverse Bayesian mixing model requires the presence of an additional aragonite source. We posit that this source represents a direct seawater precipitate. We use geological and geochemical data to show that "whitings" are unlikely to be the dominant source of this precipitate and, instead, present a model for mud precipitation on the bank margins that can explain the geographical distribution, clumped-isotope thermometry, and stable isotope signature of carbonate mud. Next, we address the enigma of why mud and ooids are so abundant in the Bahamas, yet so rare in the rest of the world: Mediterranean outflow feeds the Bahamas with the most alkaline waters in the modern ocean (>99.7th-percentile). Such high alkalinity appears to be a prerequisite for the nonskeletal carbonate factory because, when Mediterranean outflow was reduced in the Miocene, Bahamian carbonate export ceased for 3-million-years. Finally, we show how shutting off and turning on the shallow carbonate factory can send ripples through the global climate system.

A rise in atmospheric O 2 levels between 800 and 400 Ma is thought to have oxygenated the deep oceans, ushered in modern biogeochemical cycles, and led to the diversification of animals. Over the same time interval, marine sulfate concentrations are also thought to have increased to near-modern levels. We present compiled data that indicate Phanerozoic island arc igneous rocks are more oxidized (Fe 3+ /ΣFe ratios are elevated by 0.12) vs. Precambrian equivalents. We propose this elevation is due to increases in deep-ocean O 2 and marine sulfate concentrations between 800 and 400 Ma, which oxidized oceanic crust on the seafloor. Once subducted, this material oxidized the subarc mantle, increasing the redox state of island arc parental melts, and thus igneous island arc rocks. We test this using independently compiled V/Sc ratios, which are also an igneous oxybarometer. Average V/Sc ratios of Phanerozoic island arc rocks are elevated (by +1.1) compared with Precambrian equivalents, consistent with our proposal for an increase in the redox state of the subarc mantle between 800 and 400 Ma based on Fe 3+ /ΣFe ratios. This work provides evidence that the more oxidized nature of island arc vs. midocean-ridge basalts is related to the subduction of material oxidized at the Earth's surface to the subarc mantle. It also indicates that the rise of atmospheric O 2 and marine sulfate to near-modern levels by the late Paleozoic influenced not only surface biogeochemical cycles and animal diversification but also influenced the redox state of island arc rocks, which are building blocks of continental crust., Competing Interests: The authors declare no conflict of interest.

The million-year variability of the marine nitrogen cycle is poorly understood. Before 57 million years (Ma) ago, the 15 N/ 14 N ratio (δ 15 N) of foraminifera shell-bound organic matter from three sediment cores was high, indicating expanded water column suboxia and denitrification. Between 57 and 50 Ma ago, δ 15 N declined by 13 to 16 per mil in the North Pacific and by 3 to 8 per mil in the Atlantic. The decline preceded global cooling and appears to have coincided with the early stages of the Asia-India collision. Warm, salty intermediate-depth water forming along the Tethys Sea margins may have caused the expanded suboxia, ending with the collision. From 50 to 35 Ma ago, δ 15 N was lower than modern values, suggesting widespread sedimentary denitrification on broad continental shelves. δ 15 N rose at 35 Ma ago, as ice sheets grew, sea level fell, and continental shelves narrowed., (Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

The oxygenation of the deep ocean in the geological past has been associated with a rise in the partial pressure of atmospheric molecular oxygen (O 2 ) to near-present levels and the emergence of modern marine biogeochemical cycles. It has also been linked to the origination and diversification of early animals. It is generally thought that the deep ocean was largely anoxic from about 2,500 to 800 million years ago, with estimates of the occurrence of deep-ocean oxygenation and the linked increase in the partial pressure of atmospheric oxygen to levels sufficient for this oxygenation ranging from about 800 to 400 million years ago. Deep-ocean dissolved oxygen concentrations over this interval are typically estimated using geochemical signatures preserved in ancient continental shelf or slope sediments, which only indirectly reflect the geochemical state of the deep ocean. Here we present a record that more directly reflects deep-ocean oxygen concentrations, based on the ratio of Fe 3+ to total Fe in hydrothermally altered basalts formed in ocean basins. Our data allow for quantitative estimates of deep-ocean dissolved oxygen concentrations from 3.5 billion years ago to 14 million years ago and suggest that deep-ocean oxygenation occurred in the Phanerozoic (541 million years ago to the present) and potentially not until the late Palaeozoic (less than 420 million years ago).

Methane is an important greenhouse gas and energy resource generated dominantly by methanogens at low temperatures and through the breakdown of organic molecules at high temperatures. However, methane-formation temperatures in nature are often poorly constrained. We measured formation temperatures of thermogenic and biogenic methane using a "clumped isotope" technique. Thermogenic gases yield formation temperatures between 157° and 221°C, within the nominal gas window, and biogenic gases yield formation temperatures consistent with their comparatively lower-temperature formational environments (<50°C). In systems where gases have migrated and other proxies for gas-generation temperature yield ambiguous results, methane clumped-isotope temperatures distinguish among and allow for independent tests of possible gas-formation models., (Copyright © 2014, American Association for the Advancement of Science.)

The zinc finger protein EVI1 is causally associated with acute myeloid leukemogenesis, and inhibition of its function with a small molecule therapeutic may provide effective therapy for EVI1-expressing leukemias. In this paper we describe the development of a pyrrole-imidazole polyamide to specifically block EVI1 binding to DNA. We first identify essential domains for leukemogenesis through structure-function studies on both EVI1 and the t(3;21)(q26;q22)-derived RUNX1-MDS1-EVI1 (RME) protein, which revealed that DNA binding to the cognate motif GACAAGATA via the first of two zinc finger domains (ZF1, encompassing fingers 1-7) is essential transforming activity. To inhibit DNA binding via ZF1, we synthesized a pyrrole-imidazole polyamide 1, designed to bind to a subsite within the GACAAGATA motif and thereby block EVI1 binding. DNase I footprinting and electromobility shift assays revealed a specific and high affinity interaction between polyamide 1 and the GACAAGATA motif. In an in vivo CAT reporter assay using NIH-3T3-derived cell line with a chromosome-embedded tet-inducible EVI1-VP16 as well as an EVI1-responsive reporter, polyamide 1 completely blocked EVI1-responsive reporter activity. Growth of a leukemic cell line bearing overexpressed EVI1 was also inhibited by treatment with polyamide 1, while a control cell line lacking EVI1 was not. Finally, colony formation by RME was attenuated by polyamide 1 in a serial replating assay. These studies provide evidence that a cell permeable small molecule may effectively block the activity of a leukemogenic transcription factor and provide a valuable tool to dissect critical functions of EVI1 in leukemogenesis.

Molecular oxygen (O(2)) is the second most abundant gas in the Earth's atmosphere, but in many natural environments, its concentration is reduced to low or even undetectable levels. Although low-oxygen-adapted organisms define the ecology of low-oxygen environments, their capabilities are not fully known. These capabilities also provide a framework for reconstructing a critical period in the history of life, because low, but not negligible, atmospheric oxygen levels could have persisted before the "Great Oxidation" of the Earth's surface about 2.3 to 2.4 billion years ago. Here, we show that Escherichia coli K-12, chosen for its well-understood biochemistry, rapid growth rate, and low-oxygen-affinity terminal oxidase, grows at oxygen levels of ≤ 3 nM, two to three orders of magnitude lower than previously observed for aerobes. Our study expands both the environmental range and temporal history of aerobic organisms.