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Carbon and chlorine isotope effects for biotransformation of chloroform by different microbes show significant variability. Reductive dehalogenases (RDase) enzymes contain different cobamides, affecting substrate preferences, growth yields, and dechlorination rates and extent. We investigate the role of cobamide type on carbon and chlorine isotopic signals observed during reductive dechlorination of chloroform by the RDase CfrA. Microcosm experiments with two subcultures of a Dehalobacter‐containing culture expressing CfrA—one with exogenous cobamide (Vitamin B12, B12+) and one without (to drive native cobamide production)—resulted in a markedly smaller carbon isotope enrichment factor (εC, bulk) for B12− (−22.1 ± 1.9‰) compared to B12+ (−26.8 ± 3.2‰). Both cultures exhibited significant chlorine isotope fractionation, and although a lower εCl, bulk was observed for B12− (−6.17 ± 0.72‰) compared to B12+ (−6.86 ± 0.77‰) cultures, these values are not statistically different. Importantly, dual‐isotope plots produced identical slopes of ΛCl/C (ΛCl/C, B12+ = 3.41 ± 0.15, ΛCl/C, B12− = 3.39 ± 0.15), suggesting the same reaction mechanism is involved in both experiments, independent of the lower cobamide bases. A nonisotopically fractionating masking effect may explain the smaller fractionations observed for the B12− containing culture. The presence of vitamin B12 has a significant effect on carbon isotope effects, consistent with an isotope masking effect. We interpret this in the context of predicted enzyme structures.

Carbon and chlorine isotope effects for biotransformation of chloroform by different microbes show significant variability. Reductive dehalogenases (RDase) enzymes contain different cobamides, affecting substrate preferences, growth yields, and dechlorination rates and extent. We investigate the role of cobamide type on carbon and chlorine isotopic signals observed during reductive dechlorination of chloroform by the RDase CfrA. Microcosm experiments with two subcultures of a Dehalobacter-containing culture expressing CfrA-one with exogenous cobamide (Vitamin B , B12 ) and one without (to drive native cobamide production)-resulted in a markedly smaller carbon isotope enrichment factor (ε ) for B12 (-22.1 ± 1.9‰) compared to B12 (-26.8 ± 3.2‰). Both cultures exhibited significant chlorine isotope fractionation, and although a lower ε was observed for B12 (-6.17 ± 0.72‰) compared to B12 (-6.86 ± 0.77‰) cultures, these values are not statistically different. Importantly, dual-isotope plots produced identical slopes of Λ (Λ  = 3.41 ± 0.15, Λ - = 3.39 ± 0.15), suggesting the same reaction mechanism is involved in both experiments, independent of the lower cobamide bases. A nonisotopically fractionating masking effect may explain the smaller fractionations observed for the B12 containing culture.

Helium, nitrogen and hydrogen are continually generated within the deep continental crust 1 – 9 . Conceptual degassing models for quiescent continental crust are dominated by an assumption that these gases are dissolved in water, and that vertical transport in shallower sedimentary systems is by diffusion within water-filled pore space (for example, refs. 7 , 8 ). Gas-phase exsolution is crucial for concentrating helium and forming a societal resource. Here we show that crustal nitrogen from the crystalline basement alone—degassing at a steady state in proportion to crustal helium-4 generation—can reach sufficient concentrations at the base of some sedimentary basins to form a free gas phase. Using a gas diffusion model coupled with sedimentary basin evolution, we demonstrate, using a classic intracratonic sedimentary basin (Williston Basin, North America), that crustal nitrogen reaches saturation and forms a gas phase; in this basin, as early as about 140 million years ago. Helium partitions into this gas phase. This gas formation mechanism accounts for the observed primary nitrogen–helium gas discovered in the basal sedimentary lithology of this and other basins, predicts co-occurrence of crustal gas-phase hydrogen, and reduces the flux of helium into overlying strata by about 30 per cent because of phase solubility buffering. Identification of this gas phase formation mechanism provides a quantitative insight to assess the helium and hydrogen resource potential in similar intracontinental sedimentary basins found worldwide. A modelling study shows that crustal nitrogen from the crystalline basement can reach sufficient concentrations in some sedimentary basins to form a free gas phase, into which helium partitions.

SignificanceMicroorganisms can oxidize hydrocarbons anaerobically, but the detection and quantification of this process in natural settings remains difficult, impeding reliable estimation of these processes at the global scale. We have used the technique of position-specific isotope analysis of propane and show that anaerobic biological degradation of propane leads to a specific signature that differs from that of propane produced from thermal decomposition of higher hydrocarbons. When applied to natural gas reservoirs, we show that anaerobic bacterial oxidation of propane can be detected and quantified, which is not the case with the use of conventional methods. Our findings are thus of importance for the detection of subsurface biology, for the understanding of the carbon cycle, and more broadly for environmental sciences. Microbial anaerobic oxidation of hydrocarbons is a key process potentially involved in a myriad of geological and biochemical environments yet has remained notoriously difficult to identify and quantify in natural environments. We performed position-specific carbon isotope analysis of propane from cracking and incubation experiments. Anaerobic bacterial oxidation of propane leads to a pronounced and previously unidentified 13C enrichment in the central position of propane, which contrasts with the isotope signature associated with the thermogenic process. This distinctive signature allows the detection and quantification of anaerobic oxidation of hydrocarbons in diverse natural gas reservoirs and suggests that this process may be more widespread than previously thought. Position-specific isotope analysis can elucidate the fate of natural gas hydrocarbons and provide insight into a major but previously cryptic process controlling the biogeochemical cycling of globally significant greenhouse gases.

Subsurface lithoautotrophic microbial ecosystems (SLiMEs) under oligotrophic conditions are typically supported by H₂. Methanogens and sulfate reducers, and the respective energy processes, are thought to be the dominant players and have been the research foci. Recent investigations showed that, in some deep, fluid-filled fractures in the Witwatersrand Basin, South Africa, methanogens contribute <5% of the total DNA and appear to produce sufficient CH₄ to support the rest of the diverse community. This paradoxical situation reflects our lack of knowledge about the in situ metabolic diversity and the overall ecological trophic structure of SLiMEs. Here, we show the active metabolic processes and interactions in one of these communities by combining metatranscriptomic assemblies, metaproteomic and stable isotopic data, and thermodynamic modeling. Dominating the active community are four autotrophic β-proteobacterial genera that are capable of oxidizing sulfur by denitrification, a process that was previously unnoticed in the deep subsurface. They co-occur with sulfate reducers, anaerobic methane oxidizers, and methanogens, which each comprise <5% of the total community. Syntrophic interactions between these microbial groups remove thermodynamic bottlenecks and enable diverse metabolic reactions to occur under the oligotrophic conditions that dominate in the subsurface. The dominance of sulfur oxidizers is explained by the availability of electron donors and acceptors to these microorganisms and the ability of sulfur-oxidizing denitrifiers to gain energy through concomitant S and H₂ oxidation. We demonstrate that SLiMEs support taxonomically and metabolically diverse microorganisms, which, through developing syntrophic partnerships, overcome thermodynamic barriers imposed by the environmental conditions in the deep subsurface.

Abstract Reductive dehalogenases (RDases) are corrinoid-dependent enzymes that reductively dehalogenate organohalides in respiratory processes. By comparing isotope effects in biotically catalyzed reactions to reference experiments with abiotic corrinoid catalysts, compound-specific isotope analysis (CSIA) has been shown to yield valuable insights into enzyme mechanisms and kinetics, including RDases. Here, we report isotopic fractionation (ε) during biotransformation of chloroform (CF) for carbon (εC = -1.52 ± 0.34‰) and chlorine (εCl = -1.84 ± 0.19‰), corresponding to a ΛC/Cl value of 1.13 ± 0.35. These results are highly suppressed compared to isotope effects observed both during CF biotransformation by another organism with a highly similar RDase (>95% sequence identity) at the amino acid level, and to those observed during abiotic dehalogenation of CF. Amino acid differences occur at four locations within the two different RDases’ active sites, and this study examines whether these differences potentially affect the observed εC, εCl, and ΛC/Cl. Structural protein models approximating the locations of the residues elucidate possible controls on reaction mechanisms and/or substrate binding efficiency. These four locations are not conserved among other chloroalkane reducing RDases with high amino acid similarity (>90%), suggesting that these locations may be important in determining isotope fractionation within this homologous group of RDases. This study investigates the relationship between active site amino acid sequences with carbon and chlorine isotope fractionation for chlorinated alkane biotransformation by reductive dehalogenases..

Methane is a key component in the global carbon cycle, with a wide range of anthropogenic and natural sources. Although isotopic compositions of methane have traditionally aided source identification, the abundance of its multiply substituted \"clumped\" isotopologues (for example, 13CH3D) has recently emerged as a proxy for determining methane-formation temperatures. However, the effect of biological processes on methane's clumped isotopologue signature is poorly constrained. We show that methanogenesis proceeding at relatively high rates in cattle, surface environments, and laboratory cultures exerts kinetic control on 13CH3D abundances and results in anomalously elevated formation-temperature estimates. We demonstrate quantitatively that H2 availability accounts for this effect. Clumped methane thermometry can therefore provide constraints on the generation of methane in diverse settings, including continental serpentinization sites and ancient, deep groundwaters.

Identifying the origin of primordial volatiles in the Earth's mantle provides a critical test between models that advocate magma-ocean equilibration with an early massive solar-nebula atmosphere and those that require subduction of volatiles implanted in late accreting material. Here we show that neon isotopes in the convecting mantle, resolved in magmatic CO 2 well gases, are consistent with a volatile source related to solar corpuscular irradiation of accreting material. This contrasts with recent results that indicated a solar-nebula origin for neon in mantle plume material, which is thought to be sampling the deep mantle. Neon isotope heterogeneity in different mantle sources suggests that models in which the plume source supplies the convecting mantle with its volatile inventory require revision. Although higher than accepted noble gas concentrations in the convecting mantle may reduce the need for a deep mantle volatile flux, any such flux must be dominated by the neon (and helium) isotopic signature of late accreting material. Gone to Earth New noble gas data from volcanic gases reveal how volatiles (compounds and elements such as water and nitrogen that are gases at high temperatures at atmospheric pressure) were incorporated into the Earth during its early history. The neon isotope measurements suggest that the primordial volatiles were implanted by solar wind into dust or small planetesimals before they coalesced to form the Earth. Previous models had proposed equilibration between a planetary wide magma ocean and the Earth's early atmosphere as the dominant source. The new data also provide insight into how the Earth's mantle has evolved since accretion.

Distinguishing biotic compounds from abiotic ones is important in resource geology, biogeochemistry, and the search for life in the universe. Stable isotopes have traditionally been used to discriminate the origins of organic materials, with particular focus on hydrocarbons. However, despite extensive efforts, unequivocal distinction of abiotic hydrocarbons remains challenging. Recent development of clumped-isotope analysis provides more robust information because it is independent of the stable isotopic composition of the starting material. Here, we report data from a 13 C- 13 C clumped-isotope analysis of ethane and demonstrate that the abiotically-synthesized ethane shows distinctively low 13 C- 13 C abundances compared to thermogenic ethane. A collision frequency model predicts the observed low 13 C- 13 C abundances (anti-clumping) in ethane produced from methyl radical recombination. In contrast, thermogenic ethane presumably exhibits near stochastic 13 C- 13 C distribution inherited from the biological precursor, which undergoes C-C bond cleavage/recombination during metabolism. Further, we find an exceptionally high 13 C- 13 C signature in ethane remaining after microbial oxidation. In summary, the approach distinguishes between thermogenic, microbially altered, and abiotic hydrocarbons. The 13 C- 13 C signature can provide an important step forward for discrimination of the origin of organic molecules on Earth and in extra-terrestrial environments. Distinguishing biotic compounds from abiotic ones is critical to the search for life in the universe. Here, the authors demonstrate that the abiotic ethane has distinctively low 13C-13C abundances compared to biotic ethane.

Ice sheets are currently ignored in global methane budgets 1 , 2 . Although ice sheets have been proposed to contain large reserves of methane that may contribute to a rise in atmospheric methane concentration if released during periods of rapid ice retreat 3 , 4 , no data exist on the current methane footprint of ice sheets. Here we find that subglacially produced methane is rapidly driven to the ice margin by the efficient drainage system of a subglacial catchment of the Greenland ice sheet. We report the continuous export of methane-supersaturated waters (CH 4(aq) ) from the ice-sheet bed during the melt season. Pulses of high CH 4(aq) concentration coincide with supraglacially forced subglacial flushing events, confirming a subglacial source and highlighting the influence of melt on methane export. Sustained methane fluxes over the melt season are indicative of subglacial methane reserves that exceed methane export, with an estimated 6.3 tonnes (discharge-weighted mean; range from 2.4 to 11 tonnes) of CH 4(aq) transported laterally from the ice-sheet bed. Stable-isotope analyses reveal a microbial origin for methane, probably from a mixture of inorganic and ancient organic carbon buried beneath the ice. We show that subglacial hydrology is crucial for controlling methane fluxes from the ice sheet, with efficient drainage limiting the extent of methane oxidation 5 to about 17 per cent of methane exported. Atmospheric evasion is the main methane sink once runoff reaches the ice margin, with estimated diffusive fluxes (4.4 to 28 millimoles of CH 4 per square metre per day) rivalling that of major world rivers 6 . Overall, our results indicate that ice sheets overlie extensive, biologically active methanogenic wetlands and that high rates of methane export to the atmosphere can occur via efficient subglacial drainage pathways. Our findings suggest that such environments have been previously underappreciated and should be considered in Earth’s methane budget. Subglacially produced methane of microbial origin is flushed to the ice margin of the Greenland ice sheet by meltwater, contributing to a previously unaccounted for methane flux to the atmosphere.