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Microbial coal-bed methane is an important economic resource and source of a potent greenhouse gas, but controls on its formation are poorly understood. To test whether the microbial degradability of coal limits microbial methane, we monitored methoxyl group demethylation—a reaction that feeds methanogenesis—in a global sample suite ranging in maturity from wood to bituminous coal. Carbon isotopic compositions of residual methoxyl groups were inconsistent with a thermal reaction, instead implying a substrate-limited biologic process. This suggests that deep biosphere communities participated in transforming plant matter to coal on geologic time scales and that methoxyl abundance influences coal-bed methane yield. Carbon isotopic enrichments resulting from microbial methylotrophy also explain an enigmatic offset in the carbon-13 content of microbial methane from coals and conventional hydrocarbon deposits.

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 extensi...

Dolomite clumped isotope compositions are indispensable for determining the temperatures and fluid sources of dolomitizing environments, but can be misleading if they have modified since formation. Carbonate Δ_(47) values are susceptible to resetting by recrystallization during diagenesis, and, even in the absence of dissolution and reprecipitation reactions, alteration by solid-state reordering during prolonged residences at elevated temperatures. In order to understand the potential of dolomite Δ_(47) values to preserve the conditions of dolomitizationin ancient sections, the kinetic parameters of solid-state reordering in this phase must be determined. We heated mm-sized crystals of near-stoichiometric dolomite in a Rene-type cold seal apparatus at temperatures between 409 and 717 °C for 0.1–450 h. In order to prevent the decarbonation of dolomite to calcite, periclase, and CO_2 at these conditions, the system was pressurized with CO_2 to 0.45–0.8 kbar. Over the course of 31 temperature-time points and 128 individual Δ_(47) measurements of powdered dolomite crystals from these points, we observed the evolution of dolomite Δ_(47) values from the initial (unheated) composition of the crystals (0.452 ± 0.004‰, corresponding to a formation temperature of ∼145 °C) towards high-temperature equilibrium distributions. Complete re-equilibration occurred in the 563–717 °C experiments. As with previous heating experiments using calcite and apatite, dolomite Δ_(47) exhibited complex reordering behavior inadequately described by first-order Arrhenian-style models. Instead, we fit the data using two published models for clumped isotope reordering: the transient defect/equilibrium defect model of Henkes et al. (2014), and the exchange-diffusion model of Stolper and Eiler (2015). For both models, we found optimal reordering parameters by using global least-squares minimization algorithms and estimated uncertainties on these fits with a Monte Carlo scheme that resampled individual Δ_(47) measurements and re-fit the dataset of these new mean values. Because the exact Δ_(47)–T relationship between 250 and 800 °C is uncertain, we repeated these fitting exercises using three published high-temperature Δ_(47)–T calibrations. Regardless of calibration choice, dolomite Δ_(47) rate constants determined using both models are resolvably slower than those of calcite and apatite, and predict that high-grade dolomite crystals should preserve apparent equilibrium blocking temperatures of between ∼210 and 300 °C during cooling on geologic timescales. Best agreement between model predictions and natural dolomite marbles was found when using the exchange-diffusion model and the ab initio Δ_(63)–T calibration of Schauble et al. (2006), projected into the Δ_(47) reference frame by Bonifacie et al. (2017). Therefore, we recommend modeling dolomite Δ_(47) reordering using the exchange-diffusion model and this parameter set. In simple heating scenarios, the two models disagree. The transient defect/equilibrium defect model suggests that dolomite fabrics resist detectable reordering at ambient temperatures as high as 180 °C for tens of millions of years, while the exchange-diffusion model predicts incipient partial reordering perhaps as low as 150 °C. In either case, barring later recrystallization, dolomite Δ_(47) values should be faithful recorders of the conditions of dolomitization in sedimentary sections buried no hotter than ∼150 °C for tens of millions of years.

Stable isotope compositions of biologically cycled elements encode information about the interaction between life and environment. On Earth, geochemical biomarkers have been used to probe the extent, nature, and activity of modern and ancient organisms. However, extracting biological information from stable isotopic compositions requires untangling the interconnected nature of the Earth’s biogeochemical system, and must be viewed through the lens of evolving metabolisms on an evolving planet. In this chapter, we provide an introduction to isotope geobiology and to the geobiological history of Earth. We discuss the isotope biogeochemistry of the biologically essential elements carbon, nitrogen and sulfur, and we summarize their distribution on the modern Earth as an interconnected network of isotopically fractionated reservoirs with contrasting residence times. We show how this framework can be used to explore the evolution of life and environments on the ancient Earth, which is our closest accessible analogue for an extraterrestrial planet.

The release of long‐stored carbon from thawed permafrost could fuel increased methanogenesis in northern lakes, but it remains unclear whether old carbon substrates released from permafrost are metabolized as rapidly by methanogenic microbial communities as recently produced organic carbon. Here, we apply methane (CH₄) clumped isotope (Δ₁₈) and ¹⁴C measurements to test whether rates of methanogenesis are related to carbon substrate age. Results from culture experiments indicate that Δ₁₈ values are negatively correlated with CH₄ production rate. Measurements of ebullition samples from thermokarst lakes in Alaska and glacial lakes in Sweden indicate strong negative correlations between CH₄ Δ₁₈ and the fraction modern carbon. These correlations imply that CH₄ derived from older carbon substrates is produced relatively slowly. Relative rates of methanogenesis, as inferred from Δ₁₈ values, are not positively correlated with CH₄ flux estimates, highlighting the likely importance of environmental variables other than CH₄ production rates in controlling ebullition fluxes.

Organic compounds are ubiquitous in the Earth's surface, sediments and many rocks, and preserve records of geological, geochemical and biological history; they are also critical natural resources and major environmental pollutants. The naturally occurring stable isotopes of volatile elements (D, ^(13)C, ^(15)N, ^(17,18)O, ^(33,34,36)S) provide one way of studying the origin, evolution and migration of geological organic compounds. The study of bulk stable isotope compositions (i.e. averaged across all possible molecular isotopic forms) is well established and widely practised, but frequently results in non-unique interpretations. Increasingly, researchers are reading the organic isotopic record with greater depth and specificity by characterizing stable isotope ‘structures’ – the proportions of site-specific and multiply substituted isotopologues that contribute to the total rare-isotope inventory of each compound. Most of the technologies for measuring stable isotope structures of organic molecules have been only recently developed and to date have been applied only in an exploratory way. Nevertheless, recent advances have demonstrated that molecular isotopic structures provide distinctive records of biosynthetic origins, conditions and mechanisms of chemical transformation during burial, and forensic fingerprints of exceptional specificity. This paper provides a review of this young field, which is organized to follow the evolution of molecular isotopic structure from biosynthesis, through diagenesis, catagenesis and metamorphism.

Several technologies are being developed to examine the intramolecular isotopic structures of molecules (i.e., site-specific and multiple substitution), but limitations in sample size and type or (for mass spectrometry) resolution have so far prevented the creation of a general technique. We have now demonstrated the capacity for precise and accurate study of molecular isotopic contents and structures by Fourier transform mass spectrometry, using instruments containing a Thermo Scientific™ Orbitrap™ mass analyzer, here the Thermo Scientific Q Exactive GC™ and Q Exactive HF™ instruments. Orbitrap mass analyzers achieve mass resolutions in the range ∼250,000–1 M (FWHM) in the mass range of greatest interest to studies of molecular isotopic structure, 50–200 amu. This allows for resolution of many nearly isobaric interferences for compounds containing H, C, N, O and/or S. In this paper we show that internal and external experimental reproducibilities of isotope ratio analyses using the Orbitrap analysis can conform to shot-noise limits down to levels of tenths of per mil (1SE), with similar accuracy when standardized to reference materials. Precision reaches ±0.015‰ for exceptionally long integrations. Such measurements do not call for modifications to the ion optics of the Q Exactive instruments, but do require specially designed sample introduction devices to permit sample/standard comparison and long integration times. The sensitivity of the Q Exactive instruments permit analysis of sub-nanomolar samples and quantification of multiply-substituted species. Site-specific capabilities arise from the fact that mass spectra of molecular analytes commonly contain diverse fragment ion species, each of which samples a specific sub-set of molecular sites.

The timing, extent and driving mechanisms of burial, uplift and exhumation of the Colorado Plateau, and the carving of the Grand Canyon have been at the center of a long-standing controversy. Here, we develop a new approach to constrain burial and exhumation histories of sedimentary basins from the distributions of ‘clumped’ isotope compositions in carbonate minerals. We apply this approach to constrain peak-burial temperatures and infer the extent of peak sediment overburden and total exhumation of the Colorado Plateau at several sites extending from the Plateau's southwestern margin to its interior. Our constraints are broadly consistent with independent reconstructions of thermal history from low-temperature thermochronometry and oil-maturation indices. Together these data suggest that ∼3 km of rocks have been removed by erosion across the Plateau. This inferred prior extent of sediment overburden is consistent with the presence of a ∼1 km deep canyon at the Upper Gorge of the Grand Canyon during the Early Eocene, and therefore with topography at that time similar to today. Combined with the published record of partial exhumation—based on apatite-thermochronometry and stratigraphic constraints—we find that 63-83% of the total exhumation of the southwestern Plateau occurred prior to the Neogene. This is consistent with Sevier-Laramide contractional tectonism and/or pre-Neogene modification of the Colorado Plateau lithosphere driving uplift there. In contrast, apatite thermochronometry suggests that in the interior plateau, ∼50% of the total exhumation has occurred after the integration of the Colorado River – indicating a much younger source for uplift and the exhumation there. Considering recent suggestions that efficient exhumation of the Plateau by escarpment-retreat is associated with the incision of the drainage system, early exhumation of the Lower Gorge and Grand Wash segments of the Grand Canyon is consistent with the pre-Neogene carving of these segments, followed by relative stability of the base level.

Clumped isotope compositions of slowly-cooled calcite and dolomite marbles record apparent equilibrium temperatures of roughly 150-200 °C and 300-350 °C, respectively. Because clumped isotope compositions are sensitive to the details of T-t path within these intervals, measurements of the Δ_(47) values of coexisting calcite and dolomite can place new constraints on thermal history of low-grade metamorphic rocks over a large portion of the upper crust (from ∼5 to ∼15 km depth). We studied the clumped isotope geochemistry of coexisting calcite and dolomite in marbles from the Notch Peak contact metamorphic aureole, Utah. Here, flat-lying limestones were intruded by a pluton, producing a regular, zoned metamorphic aureole. Calcite Δ_(47) temperatures are uniform, 156 ± 12 ˚C (2σ s.e.), across rocks varying from high-grade marbles that exceeded 500 °C to nominally unmetamorphosed limestones >5 km from the intrusion. This result appears to require that the temperature far from the pluton was close to this value; an ambient temperature just 20 ˚C lower would not have permitted substantial re-equilibration, and should have preserved depositional or early diagenetic Δ_(47) values several km from the pluton. Combining this result with depth constraints from overlying strata suggests the country rock here had an average regional geotherm of 22.3–27.4 ˚C/km from the late Jurassic Period until at least the middle Paleogene Period. Dolomite Δ_(47) in all samples above the talc+tremolite-in isograd record apparent equilibrium temperatures of 328^(+13)_(-12) °C (1σ s.e.), consistent with the apparent equilibrium blocking temperature we expect for cooling from peak metamorphic conditions. At greater distances, dolomite Δ_(47) records temperatures of peak (anchi)metamorphism or pre-metamorphic diagenetic conditions. The interface between these domains is the location of the 330 ˚C isotherm associated with intrusion. Multiple-phase clumped isotope measurements are complemented by bulk δ^(13)C and δ^(18)O dolomite-calcite thermometry. These isotopic exchange thermometers are largely consistent with peak temperatures in all samples within 4 km of the contact, indicating that metamorphic recrystallization can occur even in samples too low-grade to produce growth of conventional metamorphic index minerals (i.e., talc and tremolite). Altogether, this work demonstrates the potential of these methods to quantify the conditions of metamorphism at sub-greenschist facies.

The southern Sierra Nevada foothills, central California (USA), expose a fossil pre–40 Ma bedrock pediment which we call the southern Sierra Nevada pediment. We document this landscape with multiple types of data, and also report new apatite ^4He/^3He, (U-Th)/He, and zircon (U-Th)/He data from the pediment that significantly expand the spatial extent of southern Sierra low-temperature thermochronology data westward into the foothills. Applying recently published thermal modeling software for thermochronologic data, which uses a transdimensional Bayesian Monte Carlo Markov chain statistical approach, we tightly constrain the thermal history of the southern Sierra Nevada pediment. Integrating this thermal history with numerous previously published data sets from across the southern Sierra, we present a chronology of tectonic and landscape evolution of the southern Sierra Nevada. For the first time we cover the entire width of the range, integrate the numerous published data sets into a single coherent geologic story, and link each phase of this story to a potential mechanism. Modeling results are consistent with a three-phase cooling history for the southern Sierra Nevada pediment. Rapid exhumation ca. 95–85 Ma resulted in cooling to between 55 °C and 100 °C. Following this, slow cooling to surface conditions occurred from 85 Ma to 40 Ma at rates consistent with those estimated for the axial southern Sierra during the same time period by previous studies. Little if any additional cooling occurred post–40 Ma. We hypothesize that a thin sedimentary cover protected the 40 Ma bedrock landscape through much of the last 40 m.y., and that this cover eroded away post–10 Ma, re-exhuming the southern Sierra Nevada pediment as a fossil pre–40 Ma landscape. Each of these three phases of cooling links to a distinct tectonic or geomorphic regime, including the profound rapid exhumation of the southern Sierra Nevada–Mojave segment of the Cretaceous arc due to subduction of a large oceanic plateau, the formation of the low-relief landscape of the high-elevation areas of the southern Sierra Nevada with more limited tectonic forcing, and Eocene activity on the Western Sierra Fault System.

The clumped isotope compositions of carbonate minerals are subject to alteration at elevated temperatures. Understanding the mechanism of solid-state reordering in carbonate minerals is important in our interpretations of past climates and the thermal history of rocks. The kinetics of solid-state isotope reordering has been previously studied through controlled heating experiments of calcite, dolomite and apatite. Here we further explore this issue through controlled heating experiments on aragonite. We find that Δ47 values generally decrease during heating of aragonite, but increase by 0.05–0.15‰ as aragonite starts to transform into calcite. We argue that this finding is consistent with the presence of an intermediate pool of immediately adjacent singly-substituted carbonate ion isotopologues (‘pairs’), which back-react to form clumped isotopologues during aragonite to calcite transformation, revealing the existence of kinetically preferred isotope exchange pathways. Our results reinforce the ‘reaction-diffusion’ model as the mechanism for solid-state clumped isotope reordering in carbonate minerals. Our experiments also reveal that the reordering kinetics in aragonite is faster than in calcite and dolomite, making its clumped isotope composition highly susceptible to alteration during early diagenesis, even before conversion to calcite. publishedVersion

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 (δ^(13)C and δ^(18)O) 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 Δ_(47) 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 Δ_(47) 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. Δ_(47) values of domains drilled from a calcite marble show a bimodal distribution. Low Δ_(47_ values correspond to an apparent temperature of 260 °C and are common in static fabrics; high Δ_(47) values correspond to an apparent temperature of 200 °C and are common in dynamically recrystallized fabrics. We suggest that the low Δ_(47) values reflect diffusion-controlled isotopic reordering during cooling, whereas high Δ_(47) values reflect isotopic reordering driven by dynamic recrystallization. We further studied the mechanism by which dynamic recrystallization may alter Δ_(47) 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 Δ_(47) values of dynamically recrystallized fabrics that form below the diffusion-controlled blocking-temperature for calcite constrain the temperature of deformation. We find that Δ_(47)-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 ∼10^5°C Myr^(−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 Δ_(47) 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.