Methane seep carbonates yield clumped isotope signatures out of equilibrium with formation temperatures

Resolving and correcting for kinetic biases on methane seep paleotemperature using carbonate ∆47/∆48 analysis

Methane-derived authigenic carbonate often constitutes the sole remaining record of relic methane seeps. The clumped (∆47) and oxygen isotopic composition of seep carbonates often yield inaccurate temperatures, attributed to kinetic isotope effects and modification of seawater isotope composition by hydrate water. Here, we analyzed the dual-clumped isotope (∆47/∆48) composition of authigenic carbonate from a modern methane seep. We demonstrate that aragonite forms closest to isotopic equilibrium such that its ∆47 can directly yield the correct formational temperature, whereas calcite is unambiguously biased by kinetic isotope effects. Numerical models show that the observed bias in the isotopic composition arises from rate-limiting dehydration/dehydroxylation of HCO3- alongside diffusive fractionation, which can be corrected for with analysis of carbonate ∆47/∆48 values. We demonstrate the utility of dual-clumped isotope analysis for studying seep carbonates, as it reveals the origin and magnitude of kinetic biases and can be used to reconstruct paleotemperature and seawater δ18O.

Microbially induced precipitation of silica by anaerobic methane-oxidizing consortia and implications for microbial fossil preservation

Authigenic carbonate minerals can preserve biosignatures of microbial anaerobic oxidation of methane (AOM) in the rock record. It is not currently known whether the microorganisms that mediate sulfate-coupled AOM-often occurring as multicelled consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB)-are preserved as microfossils. Electron microscopy of ANME-SRB consortia in methane seep sediments has shown that these microorganisms can be associated with silicate minerals such as clays [Chen et al., Sci. Rep. 4, 1-9 (2014)], but the biogenicity of these phases, their geochemical composition, and their potential preservation in the rock record is poorly constrained. Long-term laboratory AOM enrichment cultures in sediment-free artificial seawater [Yu et al., Appl. Environ. Microbiol. 88, e02109-21 (2022)] resulted in precipitation of amorphous silicate particles (~200 nm) within clusters of exopolymer-rich AOM consortia from media undersaturated with respect to silica, suggestive of a microbially mediated process. The use of techniques like correlative fluorescence in situ hybridization (FISH), scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDS), and nanoscale secondary ion mass spectrometry (nanoSIMS) on AOM consortia from methane seep authigenic carbonates and sediments further revealed that they are enveloped in a silica-rich phase similar to the mineral phase on ANME-SRB consortia in enrichment cultures. Like in cyanobacteria [Moore et al., Geology 48, 862-866 (2020)], the Si-rich phases on ANME-SRB consortia identified here may enhance their preservation as microfossils. The morphology of these silica-rich precipitates, consistent with amorphous-type clay-like spheroids formed within organic assemblages, provides an additional mineralogical signature that may assist in the search for structural remnants of microbial consortia in rocks which formed in methane-rich environments from Earth and other planetary bodies.

Density functional theory and ab initio molecular dynamics reveal atomistic mechanisms for carbonate clumped isotope reordering

Carbon (¹³C) and oxygen (¹⁸O) isotopes in carbonates form clumped isotope species inversely correlated with temperature, providing a valuable paleothermometer for sedimentary carbonates and fossils. However, this signal resets ("reorders") with increasing temperature after burial. Research on reordering kinetics has characterized reordering rates and hypothesized the effects of impurities and trapped water, but the atomistic mechanism remains obscure. This work studies carbonate-clumped isotope reordering in calcite via first-principles simulations. We developed an atomistic view of the isotope exchange reaction between carbonate pairs in calcite, discovering a preferred configuration and elucidating how Mg²⁺ substitution and Ca²⁺ vacancies lower the free energy of activation (ΔA^‡) compared to pristine calcite. Regarding water-assisted isotopic exchange, the H⁺-O coordination distorts the transition state configuration and reduces ΔA^‡. We proposed a water-mediated exchange mechanism showing the lowest ΔA^‡ involving a reaction pathway with a hydroxylated four-coordinated carbon atom, confirming that internal water facilitates clumped isotope reordering.

Microbial Denitrification: Active Site and Reaction Path Models Predict New Isotopic Fingerprints

The study of isotopic fingerprints in nitrate (δ15N, δ18O, Δ17O) has enabled pivotal insights into the global nitrogen cycle and revealed new knowledge gaps. Measuring populations of isotopic homologs of intact NO3 - ions (isotopologues) shows promise to advance the understanding of nitrogen cycling processes; however, we need new theory and predictions to guide laboratory experiments and field studies. We investigated the hypothesis that the isotopic composition of the residual nitrate pool is controlled by the N-O bond-breaking step in Nar dissimilatory nitrate reductase using molecular models of the enzyme active sites and associated kinetic isotope effects (KIEs). We integrated the molecular model results into reaction path models representing the reduction of nitrate under either closed-system or steady-state conditions. The predicted intrinsic KIE (15ε and 18ε) of the Nar active site matches observed fractionations in both culture and environmental studies. This is what would be expected if the isotopic composition of marine nitrate were controlled by dissimilatory nitrate reduction by Nar. For a closed system, the molecular models predict a pronounced negative 15N-18O clumping anomaly in residual nitrate. This signal could encode information about the amount of nitrate consumed in a closed system and thus constrain initial nitrate concentration and its isotopic composition. Similar clumped isotope anomalies can potentially be used to distinguish whether a system is open or closed to new nitrate addition. These mechanistic predictions can be tested and refined in combination with emerging ESI-Orbitrap measurements.

Characterization of Compound-Specific Chlorine Isotopologue Distributions of Polychlorinated Organic Compounds by GC-HRMS for Source Identification

Distributions of chlorine isotopologues are potentially a fingerprint feature of organochlorines. However, the exact distributions remain little known. This study measured compound-specific chlorine isotopologue distributions of six polychlorinated organic compounds (POCs) for source identification. Complete chlorine isotopologues of POCs were detected by gas chromatography coupled to high-resolution mass spectrometry. The measured relative abundances (A_meas), theoretical relative abundances (A_theo), and relative variations between A_meas and A_theo (ΔA) of chlorine isotopologues were determined. These ΔA values were applied to characterize differences in isotopologue distribution patterns, and the ΔA patterns directly illustrated the distribution characteristics. Perchloroethylene (PCE) and trichloroethylene (TCE) from two manufacturers were chosen as model analytes to develop and validate the analytical method, including precision, concentration dependency, and temporal drift. The ΔA values of isotopologues of the PCE and TCE chemicals were from -82.5 to 19.9‰ with standard deviations (SDs) of 0.3-16.9‰. In addition, the ΔA values of the first three isotopologues (with 0-2 ³⁷Cl atoms) were from -15.5 to 19.9‰ with SDs of 0.3-1.6‰, showing sufficient precisions. No concentration dependency and temporal drift of ΔA were observed. The method has been successfully applied to source identification for PCE and TCE in commercial chemicals and plastic materials, and four polychlorinated biphenyls in chemicals and sediments, demonstrating that the ΔA values and ΔA patterns were discernable for POCs from different sources. This study demonstrates that compound-specific chlorine isotopologue distributions of POCs are differentiable and measurable, proposing a novel approach to perform fingerprinting analysis for the distributions, which is anticipated to facilitate source identification for organochlorine pollutants.

Carbonate facies-specific stable isotope data record climate, hydrology, and microbial communities in Great Salt Lake, UT

Organic and inorganic stable isotopes of lacustrine carbonate sediments are commonly used in reconstructions of ancient terrestrial ecosystems and environments. Microbial activity and local hydrological inputs can alter porewater chemistry (e.g., pH, alkalinity) and isotopic composition (e.g., δ¹⁸ O_water , δ¹³ C_DIC ), which in turn has the potential to impact the stable isotopic compositions recorded and preserved in lithified carbonate. The fingerprint these syngenetic processes have on lacustrine carbonate facies is yet unknown, however, and thus, reconstructions based on stable isotopes may misinterpret diagenetic records as broader climate signals. Here, we characterize geochemical and stable isotopic variability of carbonate minerals, organic matter, and water within one modern lake that has known microbial influences (e.g., microbial mats and microbialite carbonate) and combine these data with the context provided by 16S rRNA amplicon sequencing community profiles. Specifically, we measure oxygen, carbon, and clumped isotopic compositions of carbonate sediments (δ¹⁸ O_carb , δ¹³ C_carb , ∆₄₇ ), as well as carbon isotopic compositions of bulk organic matter (δ¹³ C_org ) and dissolved inorganic carbon (DIC; δ¹³ C_DIC ) of lake and porewater in Great Salt Lake, Utah from five sites and three seasons. We find that facies equivalent to ooid grainstones provide time-averaged records of lake chemistry that reflect minimal alteration by microbial activity, whereas microbialite, intraclasts, and carbonate mud show greater alteration by local microbial influence and hydrology. Further, we find at least one occurrence of ∆₄₇ isotopic disequilibrium likely driven by local microbial metabolism during authigenic carbonate precipitation. The remainder of the carbonate materials (primarily ooids, grain coatings, mud, and intraclasts) yield clumped isotope temperatures (T(∆₄₇ )), δ¹⁸ O_carb , and calculated δ¹⁸ O_water in isotopic equilibrium with ambient water and temperature at the time and site of carbonate precipitation. Our findings suggest that it is possible and necessary to leverage diverse carbonate facies across one sedimentary horizon to reconstruct regional hydroclimate and evaporation-precipitation balance, as well as identify microbially mediated carbonate formation.

Methane Derived Authigenic Carbonate (MDAC) Aragonite Cemented Quaternary Hardground from a Methane Cold Seep, Rathlin Basin, Northern Ireland: δ13C and δ18O Isotopes, Environment, Porosity and Permeability

A block of sandstone retrieved by divers from near Rathlin Island, Co. Antrim, Northern Ireland, represents an aragonite cemented sand formed during the Quaternary. Strongly negative δ13C of the aragonite cement (−50 to −60‰ δ13C) indicates that the hardground was formed by the anaerobic oxidation of methane (AOM), resulting in the formation of a methane-derived authigenic carbonate (MDAC) hardground. Such hardgrounds have previously been recorded as forming extensive pavements in deeper waters in the mid Irish Sea (e.g., Croker Carbonate Slabs), although the latter also contains high-magnesium calcite. Sand was initially deposited as part of a storm lag deposit, with a reworked bivalve and gastropod fauna. This sand was then colonised by a probable crustacean fauna, producing horizontal open dwelling burrows (Thalassinoides). After aragonite cementation, the hardground was colonised by boring bivalves, with slightly negatively elevated levels of δ13C. Finally, the hardground was colonised by an encrusting fauna (bryozoans, calcareous algae and serpulids), by then in warmer seas. Continued depleted levels of δ13C present within the encrusting fauna (−1 to −5‰ δ13C) indicate continued methane generation and seepage, which may still be active to the present day, and to the possibility of shallow gas reserves. The δ18O values change between macro-infauna vs. encrusters, indicating a warming in water temperature, reflecting glacial and post-glacial environments. The aragonite cemented sandstone has a highly variable porosity, with large vugs (open burrows and borings), smaller mouldic porosity within gastropods and bivalves and complex micro-porosity associated with acicular aragonite cements. Overall permeability was recorded at the 2.5 to 23 Darcies level, reflecting the highly variable vuggy porosity, although matrix permeability was around 100 mD and controlled by the MDAC fabric. Actual permeability will likely be controlled by the extent to which larger pores are interconnected. The sea around the Rathlin Island area contains a diverse fauna, which is worthy of future study in the context of cold seep and MDAC pavement formation.

Effects of different constants and standards on the reproducibility of carbonate clumped isotope (Δ47 ) measurements: Insights from a long-term dataset

RATIONALE

Carbonate clumped isotope (Δ₄₇ ) thermometry examines the temperature-dependent excess abundance of the ¹³ C-¹⁸ O bond in the carbonate lattice. Inconsistent temperature calibrations and standard values have been reported among laboratories, which has led to the use of equilibrated gases and carbonate standards for standardization. Furthermore, different acid fractionation factors and isotopic parameter sets have been proposed for improving inter-laboratory data comparability. However, few long-term datasets have been generated to explore the effects of these factors on the long-term reproducibility of Δ₄₇ data within a laboratory.

METHODS

Four standards (ISTB-1, NBS-19, GBWO4416, and GB04417) were analyzed as unknowns by isotope ratio mass spectrometry from 2015 to 2019. The values of Δ₄₇ were calibrated using the ETH standards. We investigated the Assonov, Brand, and Gonfiantini isotope parameter sets for carbon and oxygen isotopes, as well as two correction schemes of equilibrated gas and carbonate standardization, using the same sample measurements to determine which procedures enhanced reproducibility. ISTB-1 (calcite) and ZK312-346W (dolomite) were measured to determine the 90°C acid fractionation factor.

RESULTS

The corrected 90°C acid fractionation factors are 0.076 ± 0.008‰ for ISTB-1 and 0.077 ± 0.009‰ for ZK312-346W. The choice of isotope parameter set had no significant influence on final Δ₄₇ values in this study. However, using the Assonov parameters to calculate Δ₄₇ values improved the reproducibility of the results. The use of carbonate standards improved reproducibility through time compared with the use of equilibrated gases for standardization.

CONCLUSIONS

At 90°C, the acid fractionation factors of calcite and dolomite are statistically indistinguishable. We find an insignificant effect from changing the isotope parameter set, suggesting that the choice of isotope parameter set among laboratories is not a major factor affecting inter-laboratory reproducibility. We find that using carbonate standards improved the reproducibility of results, suggesting that the use of carbonate standards may help to achieve inter-laboratory comparability of results in future studies.

Micro-Raman Study of Thermal Transformations of Sulfide and Oxysalt Minerals Based on the Heat Induced by Laser

The minerals in the hydrothermal and cold seep system form at different temperatures and show responses to the laser power to varying degrees. Here, we focus on the heat-induced by laser to study thermal transformations of the chalcopyrite, covellite, pyrite, barite, and aragonite based on Raman spectroscopy. Chalcopyrite mainly transforms into hematite, and covellite mainly transforms into chalcocite with the increase of laser power. Interestingly, comparing with the previous study, the pyrite can transform to the marcasite firstly, and form hematite finally. We also find that high-temperature opaque chalcopyrite is more likely to occur thermal transformations due to the smaller absolute energy difference (|ΔE1|) based on the frontier orbital theory. In contrast, the oxysalt minerals won’t transform into new components under high laser power. However, the structure of the barite has been destroyed by the high laser power, while the more transparent aragonite is not affected by the high laser power due to the laser penetrates through the transparent aragonite crystal and causes little heat absorption. Finally, we established the minimum laser power densities for thermal transformations of these minerals formed under different environments. The above study provides a simple way to study the thermal transformations of minerals by the local heat-induced by laser and also enlightens us to identify the minerals phases precisely.

Evidences for Paleo-Gas Hydrate Occurrence: What We Can Infer for the Miocene of the Northern Apennines (Italy)

The occurrence of seep-carbonates associated with shallow gas hydrates is increasingly documented in modern continental margins but in fossil sediments the recognition of gas hydrates is still challenging for the lack of unequivocal proxies. Here, we combined multiple field and geochemical indicators for paleo-gas hydrate occurrence based on present-day analogues to investigate fossil seeps located in the northern Apennines. We recognized clathrite-like structures such as thin-layered, spongy and vuggy textures and microbreccias. Non-gravitational cementation fabrics and pinch-out terminations in cavities within the seep-carbonate deposits are ascribed to irregularly oriented dissociation of gas hydrates. Additional evidences for paleo-gas hydrates are provided by the large dimensions of seep-carbonate masses and by the association with sedimentary instability in the host sediments. We report heavy oxygen isotopic values in the examined seep-carbonates up to +6‰ that are indicative of a contribution of isotopically heavier fluids released by gas hydrate decomposition. The calculation of the stability field of methane hydrates for the northern Apennine wedge-foredeep system during the Miocene indicated the potential occurrence of shallow gas hydrates in the upper few tens of meters of sedimentary column.

Characterization of Carbonate Crust from a Recently Discovered Methane Seep on the North Atlantic Continental Margin of the USA

This study is focused on mineralogical and chemical characterization of an authigenic carbonate rock (crust) collected at a recently discovered cold seep on the US North Atlantic continental margin. X-ray diffraction (XRD) and scanning electron microscopy (SEM) indicate that the carbonate rock is composed of microcrystalline aragonite cement, white acicular aragonite crystals (AcAr), equant quartz crystals, small microcrystalline aluminosilicates, and trace amounts of iron sulfide microcrystals. Element/calcium ratios were measured with laser ablation inductively-coupled plasma mass spectrometry (LA-ICP-MS) using a calcite standard, which was prepared by annealing USGS certified carbonate powder (MACS-3). The occurrence of microscopic, non-carbonate inclusions precluded evaluation of trace elements in the aragonite cement, but allowed for in situ analysis of AcAr crystals. Carbon and oxygen isotopes were analyzed via isotope ratio mass spectrometry (IRMS) and expressed as δ13C and δ18O. Low δ13C values suggest that aragonite grew as a result of anaerobic oxidation of methane and observed δ18O values indicate that the temperature of aragonite crystallization was 1.7–1.9 °C.

Carbonate formation in salt dome cap rocks by microbial anaerobic oxidation of methane

Major hydrocarbon accumulations occur in traps associated with salt domes. Whereas some of these hydrocarbons remain to be extracted for economic use, significant amounts have degraded in the subsurface, yielding mineral precipitates as byproducts. Salt domes of the Gulf of Mexico Basin typically exhibit extensive deposits of carbonate that form as cap rock atop salt structures. Despite previous efforts to model cap rock formation, the details of subsurface reactions (including the role of microorganisms) remain largely unknown. Here we show that cap rock mineral precipitation occurred via closed-system sulfate reduction, as indicated by new sulfur isotope data. 13C-depleted carbonate carbon isotope compositions and low clumped isotope-derived carbonate formation temperatures indicate that microbial, sulfate-dependent, anaerobic oxidation of methane (AOM) contributed to carbonate formation. These findings suggest that AOM serves as an unrecognized methane sink that reduces methane emissions in salt dome settings perhaps associated with an extensive, deep subsurface biosphere.

Oxygen isotope composition of the Phanerozoic ocean and a possible solution to the dolomite problem

The ¹⁸O/¹⁶O of calcite fossils increased by ∼8‰ between the Cambrian and present. It has long been controversial whether this change reflects evolution in the δ¹⁸O of seawater, or a decrease in ocean temperatures, or greater extents of diagenesis of older strata. Here, we present measurements of the oxygen and ‟clumped" isotope compositions of Phanerozoic dolomites and compare these data with published oxygen isotope studies of carbonate rocks. We show that the δ¹⁸O values of dolomites and calcite fossils of similar age overlap one another, suggesting they are controlled by similar processes. Clumped isotope measurements of Cambrian to Pleistocene dolomites imply crystallization temperatures of 15-158 °C and parent waters having δ¹⁸O_VSMOW values from -2 to +12‰. These data are consistent with dolomitization through sediment/rock reaction with seawater and diagenetically modified seawater, over timescales of 100 My, and suggest that, like dolomite, temporal variations of the calcite fossil δ¹⁸O record are largely driven by diagenetic alteration. We find no evidence that Phanerozoic seawater was significantly lower in δ¹⁸O than preglacial Cenozoic seawater. Thus, the fluxes of oxygen-isotope exchange associated with weathering and hydrothermal alteration reactions have remained stable throughout the Phanerozoic, despite major tectonic, climatic and biologic perturbations. This stability implies that a long-term feedback exists between the global rates of seafloor spreading and weathering. We note that massive dolomites have crystallized in pre-Cenozoic units at temperatures >40 °C. Since Cenozoic platforms generally have not reached such conditions, their thermal immaturity could explain their paucity of dolomites.