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.

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.

The analysis of mass 47 isotopologues of CO2 (mainly 13C18O16O) is established as a constraint on sources and sinks of environmental CO2, complementary to δ13C and δ18O constraints, and forms the basis of the carbonate clumped isotope thermometer. This measurement is commonly reported using the δ47 value - a measure of the enrichment of doubly substituted CO2 relative to a stochastic isotopic distribution. Values of δ47 for thermodynamically equilibrated CO2 approach 0 (a random distribution) at high temperatures (≥ several hundred degrees C), and increase with decreasing temperature, to ≈0.9% at 25°C. While the thermodynamic properties of doubly substituted isotopologues of CO2 (and, similarly, carbonate species) are relatively well understood, there are few published constraints on their kinetics of isotopic exchange. This issue is relevant to understanding both natural processes (e.g., photosynthesis, respiration, air-sea or air-groundwater exchange, CO2 degassing from aqueous solutions, and possibly gas-sorbate exchange on cold planetary surfaces like Mars), and laboratory handling of CO2 samples for δ47 analysis (e.g., re-equilibration in the presence of liquid water, water ice or water adsorbed on glass or metal surfaces). We present the results of an experimental study of the kinetics of isotopic exchange, including changes in δ47 value, of CO2 exposed to liquid water between 5 and 37°C. Aliquots of CO2 gas were first heated to reach a nearly random distribution of its isotopologues and then exposed at low pressure for controlled periods of time to large excesses of liquid water in sealed glass containers. Containers were held at 5, 25 and 37°C and durations of exchange ranging from 5min to 7days. To avoid the formation of a boundary layer that might slow exchange, the tubes were vigorously shaken during the period of exchange. At the end of each experiment, reaction vessels were flash frozen in liquid nitrogen. CO2 gas was then recovered from the head space of the reaction vessel, purified and analyzed for its δ47, δ13C and δ18O by gas source isotope ratio mass spectrometry. Equilibrium was reached for both δ18O and δ47 after durations of a few hours to tens of hours. δ18O values at equilibrium were consistent with known fractionation factors for the CO2-H2O system. The evolution of δ18O and δ47 with experiment duration were consistent with first-order reactions, with rate constants equal to each other (within error), averaging 0.19h-1 at 5°C, 0.38h-1 at 25°C and 0.65h-1 at 37°C. We calculate an activation energy for this isotopic exchange reaction of 26.2kJ/mol. By comparison, Mills and Urey (1940) measured the rate of 18O exchange between CO2(aq) and water to have a rate of 11h-1 at 25°C and an activation energy of 71.7kJ/mol. Our finding of a slower rate and lower activation energy is consistent with the rate limiting step of our experiment being the CO2(g)-CO2(aq) exchange, even when samples are shaken during the partial equilibration. Our results broadly resemble those from the study of (Affek, 2013), though this prior study found a lower rate constant for δ47. We propose that the difference is due to analytical uncertainties and explore the theoretical consequences of unequal reaction rates between 12C18O16O and 13C18O16O with a forward model.

The mechanism and environmental controls on soil hydrogen (H₂) uptake are not well understood but are essential for understanding the atmospheric H₂ budget. Field observations of soil H₂ uptake are limited, and here we present the results from a series of measurements in forest, desert, and marsh ecosystems in southern California. We measured soil H₂ fluxes using flux chambers from September 2004 to July 2005. Mean H₂ flux rates and standard deviations were −7.9 + −4.2, −7.6 + −5.3 and −7.5 + −3.4 nmol m⁻² s⁻¹ for the forest, desert, and marsh, respectively (corresponding to deposition velocities of 0.063 + −0.029, 0.051 + −0.036, 0.035 + −0.013 cm s⁻¹). Soil profile measurements showed that H₂ mixing ratios were between 3% and 51% of atmospheric levels at 10 cm and that the penetration of H₂ into deeper soil layers increased with soil drying. Soil removal experiments in the forest demonstrated that the litter layer did not actively consume H₂, the removal of this layer increased uptake by deeper soil layers, and the exposure of subsurface soil layers to ambient atmospheric H₂ levels substantially increased their rate of uptake. Similar soil removal experiments at the desert site showed that extremely dry surface soils did not consume H₂ and that fluxes at the surface increased when these inactive layers were removed. We present a model of soil H₂ fluxes and show that the diffusivity of soils, along with the vertical distribution of layers that actively consume H₂ regulate surface fluxes. We found that soil organic matter, CO₂ fluxes, and ecosystem type were not strong controllers of H₂ uptake. Our experiments highlight H₂ diffusion into soils as an important limit on fluxes and that minimum moisture level is needed to initiate microbial uptake.

The soil sink of molecular hydrogen is the largest and most uncertain term in the global atmospheric H₂ budget. Lack of information about the mechanisms regulating this sink limits our ability to predict how atmospheric H₂ may respond to future changes in climate or anthropogenic emissions. Here we present the results from a series of laboratory experiments designed to systematically evaluate and describe the temperature and soil moisture dependence of H₂ uptake by soils from boreal forest and desert ecosystems. We observed substantial H₂ uptake between −4°C and 0°C, a broad temperature optimum between 20°C and 30°C, a soil moisture optimum at approximately 20% saturation, and inhibition of uptake at both low and high soil moisture. A sigmoidal function described the temperature response of H₂ uptake by soils between −15°C and 40°C. Based on our results, we present a framework for a model of the soil H₂ sink.

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.

Processes in upper-crustal magma reservoirs such as recharge, magma mixing, recycling of previously crystallized material, and eruption affect both the physical state and the chemical composition of magmas. A growing body of evidence shows that crystals in intermediate or silicic volcanic rocks preserve records of these processes that may be obscured due to mixing in the liquid fraction of magmas. Fewer studies have focused on crystals in basaltic lavas, but these show evidence for a more subtle, but still rich record of magmatic processes. We present new 238U–230Th–226Ra data for plagioclase, combined with δ18O and trace-element measurements of the same crystal populations, from basalts erupted at Krafla Volcanic Center, Iceland. These data document the presence of multiple crystal populations within each sample, with chemical and oxygen isotope heterogeneity at a variety of scales: within individual crystals, between crystals in a given population, between crystal populations within the same sample, and between crystals in lavas erupted from different vents during the same eruption. Comparison to whole-rock or groundmass data shows that the majority of macroscopic crystals are not in trace-element or oxygen isotope equilibrium with their host liquids. The most likely explanation for these data is that the macroscopic crystals originated within a highly heterogeneous crystal mush in the shallow magma reservoir system. U-series and diffusion data indicate that the crystals (and therefore the mush) formed recently (likely within a few thousand years of eruption, and with a maximum age of 8–9 ka), and that the crystals resided in their host magma prior to eruption for decades to a few centuries at most. These data, in conjunction with other recent studies, suggest a model where erupted Icelandic magmas are the result of diverse magmas entering the crust, followed by complex interactions between melts and previously crystallized material at all crustal levels.

Abstract Considerable technical developments over the past half century have enabled widespread application of electronic tags to the study of animals in the wild, including in freshwater environments. We review the constraints associated with freshwater telemetry and biologging and the technical developments relevant to their use. Technical constraints for tracking animals are often influenced by the characteristics of the animals being studied and the environment they inhabit. Collectively, they influence which and how technologies can be used and their relative effectiveness. Although radio telemetry has historically been the most commonly used technology in freshwater, passive integrated transponder (PIT) technology, acoustic telemetry and biologgers are becoming more popular. Most telemetry studies have focused on fish, although an increasing number have focused on other taxa, such as turtles, crustaceans and molluscs. Key technical developments for freshwater systems include: miniaturization of tags for tracking small-size life stages and species, fixed stations and coded tags for tracking large samples of animals over long distances and large temporal scales, inexpensive PIT systems that enable mass tagging to yield population- and community-level relevant sample sizes, incorporation of sensors into electronic tags, validation of tag attachment procedures with a focus on maintaining animal welfare, incorporation of different techniques (for example, genetics, stable isotopes) and peripheral technologies (for example, geographic information systems, hydroacoustics), development of novel analytical techniques, and extensive international collaboration. Innovations are still needed in tag miniaturization, data analysis and visualization, and in tracking animals over larger spatial scales (for example, pelagic areas of lakes) and in challenging environments (for example, large dynamic floodplain systems, under ice). There seems to be a particular need for adapting various global positioning system and satellite tagging approaches to freshwater. Electronic tagging provides a mechanism to collect detailed information from imperilled animals and species that have no direct economic value. Current and future advances will continue to improve our knowledge of the natural history of aquatic animals and ecological processes in freshwater ecosystems while facilitating evidence-based resource management and conservation.

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.

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".