Model projections predict tropical forests will experience longer periods of drought and more intense precipitation cycles under a changing climate. Such transitions have implications for structure-function relationships within microbial communities. We examine how throughfall exclusion might reshape prokaryotic and fungal communities across four lowland forests in Panama with a wide variation in mean annual precipitation and soil fertility. Four sites were established across a 1000 mm span in Mean Annual Precipitation (MAP: 2335–3421 mm). We expected microbial communities at sites with lower MAP to be less sensitive to throughfall exclusion than sites with higher MAP and fungal communities to be more resistant to disturbance than prokaryotes. At each location, partial throughfall exclusion structures were established over 10 × 10 m plots to reduce direct precipitation input. After short-term (∼3–9 months) throughfall exclusion, prokaryotic communities showed no change in composition. However, prolonged (12–18 months) throughfall exclusion resulted in divergent prokaryotic community responses, reflecting MAP and soil fertility. We observed the emergence of a “drought microbiome” within infertile sites, whereby the community structure of the experimental throughfall exclusion plots at the lower MAP sites diverged from their respective control sites and converged towards overlapping assemblages. Furthermore, under throughfall exclusion, taxa increasing in relative abundance at the wettest site reflected that endemic to control plots at the lowest MAP site, suggesting a shift toward communities with life-history traits selected for under a lower MAP. By contrast, fungal community composition across sites was resilient to throughfall exclusion; however, biomass diverged in response to throughfall exclusion, increasing at two sites while decreasing in the other two. Broadly, our results suggest that microbial communities' sensitivity to frequent drying and rewetting periods in tropical forest soils will depend on climate history and soil fertility, with infertile sites likely to respond readily to changes in precipitation.

High carbon isotope values (δ13CCH4 > −40‰) have widely been used as evidence that methane in alkaline rock-hosted fluids was formed abiotically, particularly in serpentinizing systems. However, isotope fractionation during microbial methanogenesis is relatively understudied at high pH. We isolated a hydrogenotrophic Methanobacterium sp. from hyperalkaline subsurface fluids in the Samail ophiolite to assess how carbon and hydrogen isotope values of CH4 varied depending upon pH and carbonate mineral source (NaHCO3 or CaCO3). The hydrogen isotope fractionation αH20/CH4 (1.46–1.66) did not vary across pH. In contrast, the expressed carbon isotope fractionation, αCO2/CH4, ranged from 1.028 to 1.089. Carbon isotope fractionation increased with pH, reaching a maximum 13C depletion of −85‰. However, the 13C depletion significantly diminished at pH ≥ 9 for CaCO3-amended experiments, generating δ13CCH4 as high as −28‰. To evaluate the large variability in δ13CCH4, we developed a steady-state model to assess how the rates of carbonate dissolution, cellular uptake of CO2 and irreversible CH4 production can affect the net isotope fractionation during methanogenesis. Methanobacterium sp. can produce highly depleted δ13CCH4 in simulated alkaline serpentinizing fluids when dissolved inorganic carbon levels are high and methanogenesis rates are slow. However, small carbon isotope fractionation occurs when rates of carbonate dissolution are slower than cellular uptake, leading to relatively high δ13CCH4 values (>∼−35‰) that are traditionally interpreted to be purely “abiotic”. Thus, microbial CH4 can be produced in carbon-limited mafic and ultramafic rock-hosted environments on Earth and potentially other planetary bodies, but it may be difficult to isotopically identify biogenic methane when mineral carbonates are the dominant carbon source.

Transport from the soil surface to groundwater is commonly mediated through deeper portions of the vadose zone and capillary fringe, where variations in temperature and water saturation strongly influence biogeochemical processes. This technical note describes a sediment column design that allows laboratory simulation of thermal and hydrologic conditions found in many field settings. Temperature control is particularly important because room temperature is not representative of most subsurface environments. A 2.0-m-tall column was capable of simulating profiles with temperatures ranging from 3 to 22°C, encompassing the full range of seasonal temperature variation observed in the deep vadose zone and capillary fringe of a semiarid floodplain in western Colorado. The water table was varied within the lower 0.8-m section of the column, and profiles of water content and matric potential were measured. Vadose zone CO2 collected from depth-distributed gas samplers under representative seasonal conditions reflected the influences of temperature and water table depth on microbial respiration. Thus, realistic subsurface biogeochemical dynamics can be simulated in the laboratory through establishing column profiles that represent seasonal thermal and hydrologic conditions.

The hydrogen isotopic composition of methane (CH4) is used as a fingerprint of gas origins. Exchange of hydrogen isotopes between CH4 and liquid water has been proposed to occur in both low- and high-temperature settings. However, despite environmental evidence for hydrogen isotope exchange between CH4 and liquid water, there are few experimental constraints on the kinetics of this process. We present results from hydrothermal experiments conducted to constrain the kinetics of hydrogen isotope exchange between CH4 and supercritical water. Seven isothermal experiments were performed over a temperature range of 376–420 °C in which deuterium-enriched water and CH4 were reacted in flexible gold reaction cell systems. Rates of exchange were determined by measuring the change in the δD of CH4 over the time course of an experiment. Regression of derived second order rate constants (kr) vs. 1000/T (i.e., an Arrhenius plot) yields the following equation: ln(kr) = −17.32 (±4.08, 1 s.e.) × 1000/T + 3.19 (±6.01, 1 s.e.) (units of kr of sec−1 [mol/L]−1), equivalent to an activation energy of 144.0 ± 33.9 kJ/mol (1 s.e.). These results indicate that without catalysts, CH4 will not exchange hydrogen isotopes with liquid water on a timescale shorter than the age of the Earth (i.e., billions of years) at temperatures below 100–125 °C. Exchange at or below these temperatures is thought to occur due to the activity of life, and thus hydrogen isotopic equilibrium between methane and water may be a biosignature at low temperatures on Earth (in the present or the past) and on other planetary bodies. At temperatures ranging from 125 to 200 °C, hydrogen isotope exchange between CH4 and liquid water can occur on timescales of millions to hundreds of thousands of years, indicating that in thermogenic natural gas systems CH4 may isotopically equilibrate with water and achieve equilibrium isotopic compositions. Finally, the kinetics indicate that in deep-sea hydrothermal systems, the hydrogen (and thus clumped) isotopic composition of CH4 is likely set by formation and/or storage conditions isolated from the active flow regime. The determined kinetics indicate that once methane is entrained in circulating fluids, the expected time-temperature pathways are insufficient for measurable hydrogen isotope exchange between CH4 and water to occur.

Arctic wetlands are currently net sources of atmospheric CH4 . Due to their complex biogeochemical controls and high spatial and temporal variability, current net CH4 emissions and gross CH4 processes have been difficult to quantify, and their predicted responses to climate change remain uncertain. We investigated CH4 production, oxidation, and surface emissions in Arctic polygon tundra, across a wet-to-dry permafrost degradation gradient from low-centered (intact) to flat- and high-centered (degraded) polygons. From 3 microtopographic positions (polygon centers, rims, and troughs) along the permafrost degradation gradient, we measured surface CH4 and CO2 fluxes, concentrations and stable isotope compositions of CH4 and DIC at three depths in the soil, and soil moisture and temperature. More degraded sites had lower CH4 emissions, a different primary methanogenic pathway, and greater CH4 oxidation than did intact permafrost sites, to a greater degree than soil moisture or temperature could explain. Surface CH4 flux decreased from 64 nmol m(-2)  s(-1) in intact polygons to 7 nmol m(-2)  s(-1) in degraded polygons, and stable isotope signatures of CH4 and DIC showed that acetate cleavage dominated CH4 production in low-centered polygons, while CO2 reduction was the primary pathway in degraded polygons. We see evidence that differences in water flow and vegetation between intact and degraded polygons contributed to these observations. In contrast to many previous studies, these findings document a mechanism whereby permafrost degradation can lead to local decreases in tundra CH4 emissions.

Shales contain high levels of organic carbon (OC) and represent a large fraction of the Earth's reduced carbon stocks. While recent evidence suggests that shale-derived OC may be actively cycled in riverine systems, this process is poorly understood and not currently considered in global C models. Through the use of sediment density fractionations, extractions, radiocarbon measurements, and chemical characterization, we provide information on the abundance, chemistry, and mobility of shale-derived OC in floodplain sediments of a shale-rich mountainous watershed. The heavy fraction of the sediment, representing mineral-associated OC, is the largest (84 ± 6% of TOC) and oldest (Δ14C values −224 to −853‰) OC pool. Evidence of shale-derived OC is observed in all sediment C pools (i.e., occluded light fraction, water-soluble, and pyrophosphate-extractable) except the free light fraction, which is entirely modern. Relatively consistent chemistry was observed across samples for extracted and density-separated OC, despite wide ranges of Δ14C values. Carbon spectroscopy revealed that floodplain sediments had a higher degree of functionalized aromatic groups and lower carbonate content compared to shale collected nearby, consistent with chemical alteration and mixing with other C sources in the floodplain. We estimate that approximately 23–34% of sediment OC is derived from shale, with implications for other shale-derived elements (e.g., N). This study demonstrates the important contribution of shale-OC, particularly in environments with low litter inputs. The large impact of radiocarbon-dead shale-OC, which has a thermally altered chemical structure distinct from plant litter, on Δ14C values and reactivity of sediment-OC must be considered.

C₁ metabolism in plants is known to be involved in photorespiration, nitrogen and amino acid metabolism, as well as methylation and biosynthesis of metabolites and biopolymers. Although the flux of carbon through the C₁ pathway is thought to be large, its intermediates are difficult to measure and relatively little is known about this potentially ubiquitous pathway. In this study, we evaluated the C₁ pathway and its integration with the central metabolism using aqueous solutions of ¹³C-labeled C₁ and C₂ intermediates delivered to branches of the tropical species Inga edulis via the transpiration stream. Delivery of [¹³C]methanol and [¹³C]formaldehyde rapidly stimulated leaf emissions of [¹³C]methanol, [¹³C]formaldehyde, [¹³C]formic acid, and ¹³CO₂, confirming the existence of the C1 pathway and rapid interconversion between methanol and formaldehyde. However, while [¹³C]formate solutions stimulated emissions of ¹³CO₂, emissions of [¹³C]methanol or [¹³C]formaldehyde were not detected, suggesting that once oxidation to formate occurs it is rapidly oxidized to CO₂ within chloroplasts. ¹³C-labeling of isoprene, a known photosynthetic product, was linearly related to ¹³CO₂ across C₁ and C₂ ([¹³C₂]acetate and [2-¹³C]glycine) substrates, consistent with reassimilation of C₁, respiratory, and photorespiratory CO₂. Moreover, [¹³C]methanol and [¹³C]formaldehyde induced a quantitative labeling of both carbon atoms of acetic acid emissions, possibly through the rapid turnover of the chloroplastic acetyl-CoA pool via glycolate oxidation. The results support a role of the C₁ pathway to provide an alternative carbon source for glycine methylation in photorespiration, enhance CO₂ concentrations within chloroplasts, and produce key C₂ intermediates (e.g., acetyl-CoA) central to anabolic and catabolic metabolism.

Organic matter deposits in alluvial aquifers have been shown to result in the formation of naturally reduced zones (NRZs), which can modulate aquifer redox status and influence the speciation and mobility of metals, affecting groundwater geochemistry. In this study, we sought to better understand how natural organic matter fuels microbial communities within anoxic biogeochemical hot spots (NRZs) in a shallow alluvial aquifer at the Rifle (CO) site. We conducted a 20-day microcosm experiment in which NRZ sediments, which were enriched in buried woody plant material, served as the sole source of electron donors and microorganisms. The microcosms were constructed and incubated under anaerobic conditions in serum bottles with an initial N₂ headspace and were sampled every 5 days for metagenome and metatranscriptome profiles in combination with biogeochemical measurements. Biogeochemical data indicated that the decomposition of native organic matter occurred in different phases, beginning with mineralization of dissolved organic matter (DOM) to CO₂ during the first week of incubation, followed by a pulse of acetogenesis that dominated carbon flux after 2 weeks. A pulse of methanogenesis co-occurred with acetogenesis, but only accounted for a small fraction of carbon flux. The depletion of DOM over time was strongly correlated with increases in expression of many genes associated with heterotrophy (e.g., amino acid, fatty acid, and carbohydrate metabolism) belonging to a Hydrogenophaga strain that accounted for a relatively large percentage (~8%) of the metatranscriptome. This Hydrogenophaga strain also expressed genes indicative of chemolithoautotrophy, including CO₂ fixation, H₂ oxidation, S-compound oxidation, and denitrification. The pulse of acetogenesis appears to have been collectively catalyzed by a number of different organisms and metabolisms, most prominently pyruvate:ferredoxin oxidoreductase. Unexpected genes were identified among the most highly expressed (>98th percentile) transcripts, including acetone carboxylase and cell-wall-associated hydrolases with unknown substrates (numerous lesser expressed cell-wall-associated hydrolases targeted peptidoglycan). Many of the most highly expressed hydrolases belonged to a Ca. Bathyarchaeota strain and may have been associated with recycling of bacterial biomass. Overall, these results highlight the complex nature of organic matter transformation in NRZs and the microbial metabolic pathways that interact to mediate redox status and elemental cycling.

The stable isotopic composition of methane (CH4) is commonly used to fingerprint natural gas origins. Over the past 50 years, there have been numerous proposals that both microbial and thermogenic CH4 can form in or later attain hydrogen isotopic equilibrium with water (H2O) and carbon isotopic equilibrium with carbon dioxide (CO2). Evaluation of such proposals requires knowledge of the equilibrium fractionation factors between CH4 and H2O or CO2 at the temperatures where microbial and thermogenic CH4 form in or are found in the environment, which is generally less than 200 °C. Experimental determinations of these fractionation factors are only available above 200 °C, requiring extrapolation of these results beyond the calibrated range or the use of theoretical calculations at lower temperatures. Here, we provide a calibration of the equilibrium hydrogen isotopic fractionation factor for CH4 and hydrogen gas (H2) (DαCH4(g)–H2(g)) based on experiments using γ-Al2O3 and Ni catalysts from 3 to 200 °C. Results were regressed as a 2nd order polynomial of 1000 × lnDαCH4(g)–H2(g) vs. 1/T (K−1) yielding: 1000×lnDαCH4(g)-H2(g)=[Formula presented]+[Formula presented]-179.48 We combine this calibration with previous experimental determinations of hydrogen isotope equilibrium between H2, H2O(g), and H2O(l) and we provide an interpolatable experimental calibration of 1000 × lnDαCH4(g)–H2O(l) from 3 to 200 °C. Our resulting 4th order polynomial is the following equation: 1000×lnDαCH4(g)-H2Ol=-[Formula presented]+[Formula presented]-[Formula presented]+[Formula presented]-382.05 At 3 °C, the value from our calibration differs by 93‰ relative to what would be calculated based on the extrapolation of the only experimental calibration currently available to temperatures below its calibrated range (lowest temperature of 200 °C; Horibe and Craig, 1995). We additionally provide new theoretical estimates of hydrogen isotopic equilibrium between CH4(g), H2(g), and H2O(g) and carbon isotopic equilibrium between CH4(g) and CO2(g) using Path Integral Monte Carlo (PIMC) calculations. Our PIMC calculations for hydrogen isotopic equilibrium between CH4 and H2 agree 1:1 with our experiments. Finally, we compile carbon and hydrogen isotopic measurements of CH4, CO2, and H2O from various environmental systems and compare observed differences between carbon and hydrogen isotopes to those expected based on isotopic equilibrium. We find that isotopic compositions of some microbial gases from marine sedimentary, coalbed, and shale environments are consistent with those expected for CH4–H2O(l) hydrogen and CH4–CO2 carbon isotopic equilibrium. In contrast, microbial terrestrial and pure culture gases are not consistent with both CH4–H2O(l) hydrogen and CH4–CO2 carbon isotopic equilibrium. These results are explained qualitatively using previously developed conceptual models that link free energy gradients available to microorganisms to the degree that their enzymes can promote isotope-exchange reactions between CH4, CO2, and H2O.

The weathering of shale exerts an important control on the hydrochemical fluxes to river systems, thus influencing the global carbon, nutrient, and geochemical cycles. However, the quantitative understanding of shale weathering and its impact on global biogeochemical cycles remains inadequate due to the complex interplay between hydrological, biogeochemical, and physical processes. In this study, we develop a novel modeling approach to quantitatively interpret the long-term chemical weathering of shale occurring since the last glaciation period (15,000 years) leading to the present geochemical conditions. The model explicitly considers processes occurring across multiple phases and involved in the weathering, including: (i) the infiltration of meteoric water, (ii) the interactions between the water and the mineral assemblage via dissolution/precipitation reactions, (iii) the microbially-mediated oxidation of organic matter, (iv) the evolution of porosity induced by mineral reactions, and (v) the exchange of gases between the subsurface and the atmosphere. To implement and test our model, we conduct this study at a well-instrumented hillslope underlain by Mancos Shale and located at the East River study site, Western Colorado. Consistent with field observations, the model successfully reproduces the stratified weathering front, the complex spatial distribution of organic carbon, and the gaseous emissions of carbon dioxide from the subsurface. Model simulations show that aerobic respiration exerts a fundamental control on the weathering of shale. While previous studies have highlighted the diffusion of oxygen from the atmosphere as the primary mechanism for shale weathering, our model simulations demonstrate that aerobic respiration limits the propagation of oxygen in the shallow subsurface, and thereby inhibits the dissolution of pyrite at depth. Aerobic respiration is particularly favored in the top soil horizon due to the constant flux of oxygen from the atmosphere, the replenishment of fresh litter/plant-derived organic matter, and to a lesser extent the presence of fossil shale-associated organic matter. The acidic pore water generated through aerobic respiration within the shallow subsurface is transported to greater depths, where it sustains the dissolution of carbonate (dolomite in this example). Overall, our results demonstrate that the evolution of pyrite and carbonate depletion fronts are significantly different, and primarily depend on the ability of microorganisms to carry out microbial respiration and the various transport pathways of reactants controlling the mineral reactions under partially saturated conditions.