Fractionation of stable carbon isotopes during anaerobic production and degradation of propionate in defined microbial cultures

In many anoxic environments propionate is, after acetate, the second most important fermentation product, being degraded further to finally result in CH₄ production. In principle, isotope discrimination can be used to assess the path of organic matter degradation to acetate, CO₂ and CH₄. However, nothing is known about the isotope fractionation in primary and secondary fermentation steps involving propionate, although it is an important precursor of acetate. We therefore studied the degradation of propionate with a syntrophic coculture of Syntrophobacter fumaroxidans and Methanobacterium formicicum. The isotope enrichment factor for propionate degradation to acetate, CO₂ and CH₄ was almost negligible (ε_prop 0.9‰). The fermentative production of propionate was studied in cultures with Opitutus terrae growing on pectin, xylan and starch. These polysaccharides were fermented to acetate, succinate, propionate, H₂ and CO₂. While the δ¹³C value of the initially produced propionate was similar to that of the organic substrates (ca. −28 to −25‰), the δ¹³C value of the other fermentation products was higher. The δ¹³C values of all products generally decreased during the course of fermentation. Finally, a small depletion in ¹³C (ca. 6‰) with respect to the organic substrate was observed for propionate, while the other fermentation products where slightly enriched. Overall, stable carbon isotope discrimination was small during both fermentative production and consumption of propionate in the anaerobic microbial cultures, so that propionate turnover probably only marginally affects isotope fractionation during anaerobic degradation of organic matter.     

Quantification of carbon flow from stable isotope fractionation in rice field soils with different organic matter content

Rice fields are an important source for the greenhouse gas methane produced by acetoclastic and hydrogenotrophic methanogenesis. Fractionation of ¹³C/¹²C can in principle be used to quantify the relative contribution of these pathways, but our knowledge of isotopic fractionation during reduction of CO₂ and turnover of acetate in different methanogenic environments is still scarce. We therefore measured δ¹³C signatures in two types of anoxic Italian rice field soils, one with high and one with low degradable organic matter (OM) content. Both soils were incubated in the presence and absence of methyl fluoride, a specific inhibitor of acetoclastic methanogenesis. Optimization of methyl fluoride concentration resulted in complete inhibition of acetoclastic methanogenesis. CH₄ was then exclusively produced by hydrogenotrophic methanogenesis, allowing determination of the isotopic signatures and fractionation factors specific for this methanogenic pathway. Acetate, which was then no longer consumed, accumulated and was used for determination of the isotopic signature of the fermentatively produced acetate (both total acetate and methyl carbon of acetate). Hence, all isotopic signatures, including fractionation factors were determined for the methanogenic soil. These data, were then used for computation of the relative contribution of the two methanogenic pathways. In the high OM soil, the contribution of acetoclastic methanogenesis to total CH₄ production increased simultaneously with decreasing acetate concentration. In the low OM soil, methanogenesis from H₂/CO₂ was clearly greater than theoretically expected. Furthermore, isotope fractionation of hydrogenotrophic methanogenesis indicated that the in situ energy status of methanogens strongly depended on the availability of organic carbon in the rice field soil system. Collectively, our data show that the study of isotopic fractionation in methanogenic environments allows a deeper insight into the ongoing processes, which may be quite different in the same ecosystem with different content of degradable OM.     

Stable carbon isotope discrimination in rice field soil during acetate turnover by syntrophic acetate oxidation or acetoclastic methanogenesis

Rice fields are an important source for the greenhouse gas methane. In Italian rice field soil CH₄ is produced either by hydrogenotrophic and acetoclastic methanogenesis, or by hydrogenotrophic methanogenesis and syntrophic acetate oxidation when temperatures are below and above about 40-45 °C, respectively. In order to see whether these acetate consumption pathways differently discriminate the stable carbon isotopes of acetate, we measured the δ¹³C of total acetate and acetate-methyl as well as the δ¹³C of CO₂ and CH₄ in rice field soil that had been pre-incubated at 45 °C and then shifted to different temperatures between 25 and 50 °C. Acetate transiently accumulated to about 6 mM, which is about one-third of the amount of CH₄ produced, irrespective of the incubation temperature and the CH₄ production pathway involved. However, the patterns of δ¹³C of the CH₄ and CO₂ produced were different at low (25, 30, 35 °C) versus high (40, 45, 50 °C) temperatures. These patterns were consistent with CH₄ being exclusively formed by hydrogenotrophic methanogenesis at high temperatures, and by a combination of acetoclastic and hydrogenotrophic methanogenesis at low temperatures. The patterns of δ¹³C of total acetate and acetate-methyl were also different at high versus low temperatures, indicating the involvement of different pathways of production and consumption of acetate at the two temperature regimes. Isotope fractionation during consumption of the methyl group of acetate was more pronounced at low (α = 1.010-1.025) than at high (α = 1.0-1.01) temperatures indicating that acetoclastic methanogenesis exhibits a stronger isotope effect than syntrophic acetate oxidation. Small amounts of propionate also transiently accumulated and were analyzed for δ¹³C. The δ¹³C values slightly increased (by about 10‰) during production and consumption of propionate, but were not affected by incubation temperature. Collectively, our results showed distinct isotope discrimination for different paths of acetate (and propionate) production and consumption, albeit differences were only small, and discrimination between methanogenic and syntrophic acetate consumption in nature may be difficult to detect.     

Carbon and hydrogen isotope fractionation by moderately thermophilic methanogens

A series of laboratory studies were conducted to increase understanding of stable carbon (¹³C/¹²C) and hydrogen (D/H) isotope fractionation arising from methanogenesis by moderately thermophilic acetate- and hydrogen-consuming methanogens. Studies of the aceticlastic reaction were conducted with two closely related strains of Methanosaeta thermophila. Results demonstrate a carbon isotope fractionation of only 7‰ (α = 1.007) between the methyl position of acetate and the resulting methane. Methane formed by this process is enriched in ¹³C when compared with other natural sources of methane; the magnitude of this isotope effect raises the possibility that methane produced at elevated temperature by the aceticlastic reaction could be mistaken for thermogenic methane based on carbon isotopic content. Studies of H₂/CO₂ methanogenesis were conducted with Methanothermobacter marburgensis. The fractionation of carbon isotopes between CO₂ and CH₄ was found to range from 22 to 58‰ (1.023 ≤ α ≤ 1.064). Greater fractionation was associated with low levels of molecular hydrogen and steady-state metabolism. The fractionation of hydrogen isotopes between source H₂O and CH₄ was found to range from 127 to 275‰ (1.16 ≤ α ≤ 1.43). Fractionation was dependent on growth phase with greater fractionation associated with later growth stages. The maximum observed fractionation factor was 1.43, independent of the δD-H₂ supplied to the culture. Fractionation was positively correlated with temperature and/or metabolic rate. Results demonstrate significant variability in both hydrogen and carbon isotope fractionation during methanogenesis from H₂/CO₂. The relatively small fractionation associated with deuterium during H₂/CO₂ methanogenesis provides an explanation for the relatively enriched deuterium content of biogenic natural gas originating from a variety of thermal environments. Results from these experiments are used to develop a hypothesis that differential reversibility in the enzymatic steps of the H₂/CO₂ pathway gives rise to variability in the observed carbon isotope fractionation. Results are further used to constrain the overall efficiency of electron consumption by way of the hydrogenase system in M. marburgensis, which is calculated to be less than 55%.     

Carbon isotope fractionation of Thermoanaerobacter kivui in different growth media and at different total inorganic carbon concentration

Chemolithotrophic homoacetogenic bacteria apparently express a characteristic stable carbon isotope fractionation and may contribute significantly to acetate production in anoxic environments. However, fractionation factors (ε) in bacterial cultures have rarely been determined and the effect of substrate availability has not been assessed. We therefore studied the kinetic carbon isotope effect in cultures of Thermoanaerobacter kivui grown at 55 °C. The fractionation factor in HCO₃⁻ buffered medium was ca. 15‰ more negative than that in PO₄³⁻ buffered medium. To test whether the difference was caused by the initial substrate ratio of H₂ and total inorganic carbon (TIC; 0.5 in HCO₃⁻ vs. 4.0 in PO₄³⁻ buffered medium), T. kivui was grown in either [3-(N-morpholino) propanesulfonic acid, MOPS] buffered or PO₄³⁻ buffered media with different HCO₃⁻ concentration. Indeed, the fractionation factor became more negative with increasing HCO₃⁻ concentration and decreasing H₂/TIC ratio. While pH had only a small effect, the fractionation was generally more negative in MOPS buffered than in phosphate buffered media, indicating that the buffer system also affected fractionation. Collectively, the results show that substrate availability and other environmental factors affect the magnitude of isotope fractionation during acetate production by chemolithotrophic homoacetogenesis.     

Stable carbon isotope composition and concentrations of CO2 and CH4 in the deep catotelm of a peat bog

Vertical profiles of concentration and C-isotopic composition of dissolved methane and carbon dioxide were observed over 26 months in the catotelm of a deep (6.5 m) peat bog in Switzerland. The dissolved concentrations of these gases increase with depth while CO₂ predominates over CH₄ (CO₂ ca. 5 times CH₄). This pattern can be reproduced by a reaction-advection-ebullition model, where CO₂ and CH₄ are formed in a ratio of 1:1. The less soluble methane is preferentially lost via outgassing (bubbles). The isotopic fractionation between CO₂ and CH₄ also increases with depth, with α_C values ranging from 1.045 to 1.075. The isotopic composition of the gases traces the passage of respiration-derived CO₂ (from the near surface) through a shallow zone with methanogenesis of low isotopic fractionation (splitting of fermentation-derived acetate). This solution then moves through the catotelm, where methanogenesis occurs by CO₂ reduction (large isotopic fractionation). In the upper part of the catotelm the C-13-depleted respiration-derived CO₂ pool buffers the isotopic composition of CO₂; the δ¹³C of CO₂ increases only slowly. At the same time strongly depleted CH₄ is formed as CO₂ reduction consumes the depleted CO₂. In the lower part of the catotelm, the respiration-derived CO₂ and shallow CH₄ become less important and CO₂ reduction is the dominant source of CO₂ and CH₄. Now, the δ¹³C values of both gases increase until equilibrium is reached with respect to the isotopic composition of the substrate. Thus, the δ¹³C values of methane reach a minimum at intermediate depth, and the deep methane has δ¹³C values comparable to shallow methane. A simple mixing model for the isotopic evolution is suggested. Only minor changes of the observed patterns of methanogenesis (in terms of concentration and isotopic composition) occur over the seasons. The most pronounced of these is a slightly higher rate of acetate splitting in spring.     

The influence of carbon source on abiotic organic synthesis and carbon isotope fractionation under hydrothermal conditions

A series of laboratory experiments were performed to investigate the relative contributions of CO and other single-carbon compounds to abiotic synthesis of organic compounds in hydrothermal environments. Experiments were conducted by heating aqueous solutions of CO, CO₂, HCOOH, or CH₄ at 250 °C under reducing conditions, and observing production of CH₄ and other hydrocarbons. Native Fe was included in the experiments as a source of H₂ through reaction with water and as a potential catalyst. Experiments with CO or HCOOH as the carbon source resulted in rapid generation of CH₄ and other hydrocarbons that closely resembled typical products of Fischer-Tropsch organic synthesis. In contrast, experiments using CO₂ or CH₄ as the carbon source yielded no detectable hydrocarbon products. Carbon isotope measurements of reaction products from the CO experiments indicate that the CH₄ and other hydrocarbons were substantially depleted in ¹³C, with CH₄ δ¹³C values 30 to 34‰ lighter than the initial CO. Most of the fractionation apparently occurs during attachment of CO to the catalyst surface and subsequent reduction to surface-bound methylene. The initial step in polymerization of these methylene units to form hydrocarbons involves a small, positive fractionation, so that ethane and ethene are slightly enriched in ¹³C relative to CH₄. However, subsequent addition of carbon molecules to the growing hydrocarbon chain proceeds with no net observable fractionation, so that the isotopic compositions of the C₃₊ light hydrocarbons are controlled by isotopic mass balance. This result is consistent with a previously proposed model for carbon isotopic patterns of light hydrocarbons in natural samples. The abundance and isotopic composition of light hydrocarbons produced with HCOOH as the carbon source were similar to those generated with CO, but the isotopic compositions of non-volatile hydrocarbons diverged, suggesting that the higher hydrocarbons were formed by different mechanisms in the CO and HCOOH experiments. The experiments indicate that CO, and possibly HCOOH, may be critical intermediates in the abiotic formation of organic compounds in geologic environments, and suggest that the low levels of these compounds present in most hydrothermal systems could represent a bottleneck restricting the extent of abiotic organic synthesis in some circumstances.     

Variable carbon isotope fractionation expressed by aerobic CH4-oxidizing bacteria

Carbon isotope fractionation factors reported for aerobic bacterial oxidation of CH₄(α_CH4-CO2) range from 1.003 to 1.039. In a series of experiments designed to monitor changes in the carbon isotopic fractionation of CH₄ by Type I and Type II methanotrophic bacteria, we found that the magnitude of fractionation was largely due to the first oxidation step catalyzed by methane monooxygenase (MMO). The most important factor that modulates the (α_CH4-CH3OH) is the fraction of the total CH₄ oxidized per unit time, which strongly correlates to the cell density of the growth cultures under constant flow conditions. At cell densities of less than 0.1 g/L, fractionation factors greater than 1.03 were observed, whereas at cell densities greater than 0.5 g/L the fractionation factors decreased to as low as 1.002. At low cell densities, low concentrations of MMO limit the amount of CH₄ oxidized, while at higher cell densities, the overall rates of CH₄ oxidation increase sufficiently that diffusion of CH₄ from the gaseous to dissolved state and into the cells is likely the rate-determining step. Thus, the residual CH₄ is more fractionated at low cell densities, when only a small fraction of the total CH₄ has been oxidized, than at high cell densities, when up to 40% of the influent CH₄ has been utilized. Therefore, since Rayleigh distillation behavior is not observed, δ¹³C values of the residual CH₄ cannot be used to infer the amount oxidized in either laboratory or field-studies. The measured (α_CH4-CH3OH) was the same for both Type I and Type II methanotrophs expressing particulate or soluble MMO. However, large differences in the δ¹³C values of biomass produced by the two types of methanotrophs were observed. Methylosinus trichosporium OB3b (Type II) produced biomass with δ¹³C values about 15‰ higher than the dissimilated CO₂, whereas Methylomonas methanica (Type I) produced biomass with δ¹³C values only about 6‰ higher than the CO₂. These effects were independent of the magnitude of the initial carbon isotope fractionation caused by MMO and were relatively constant despite changing ratios of assimilatory to dissimilatory carbon transformation by the organisms. This suggests that the difference in biomass carbon isotopes is primarily due to differences in the fractionation effect at the formaldehyde branch point in the metabolic pathway, rather than assimilation of CO₂ by Type II methanotrophs.     

Anomalous carbon isotope fractionation between atmospheric CO2 and dissolved inorganic carbon induced by intense photosynthesis

A stable isotope mass-balance of dissolved inorganic carbon during a blue-green algae bloom in a softwater lake demonstrates that at low partial pressure of carbon dioxide there must be a large net negative carbon isotope fractionation between atmospheric CO₂ and the CO₂ absorbed by lake water at pH = 9.5. The net fractionation of CO₂(g) with respect to HCO⁻₃ was about −13%. compared with about +8%. for water at equilibrium with atmospheric CO₂ at pH ≈ 7. Chemical enhancement of CO₂ invasion at high pH by the reaction CO₂ + OH⁻→ HCO⁻₃ at large apparent film thicknesses may result in carbon isotope fractionation approaching that for a hydroxide solution. This phenomenon, coupled with a decrease in the photosynthetic fractionation, forced the surface water of a softwater lake to achieve increasingly negative δ¹³C values during an algal bloom, which is in the opposite sense to the trend that results from photosynthesis under less extreme conditions. This and other similar systems must operate under non-equilibrium (kinetic) conditions, causing a large kinetic fractionation during CO₂ invasion at pH > 8 and relatively large film thicknesses (i.e., low wind stress).     

Temporal change of C-isotope signatures and methanogenic pathways in rice field soil incubated anoxically at different temperatures

Production of CH₄ and CO₂ was quantified in anoxically incubated soil samples taken from an Italian rice field. The rates increased with temperature between 10 and 37°C. The δ¹³C of the accumulated CO₂, CH₄ and acetate changed with time in a systematic way. The data were used in mass balance equations to constrain isotopic fractionation factors and pathways of CH₄ production. The calculations were further constrained by the determination of ¹⁴CH₄ production from ¹⁴CO₂ at steady state. At 50°C, CH₄ was exclusively produced from CO₂, indicating a fractionation factor of α_CO2/CH4 = 1.073. Between 10 and 37°C, the results showed a temporal change in the methanogenic pathway. A relatively high (40-60%) CO₂-derived fraction of CH₄ production in the beginning was followed by a phase in which contribution of CO₂-derived CH₄ decreased to low (<15%) values, and ultimately by the steady state phase in which values increased to <40% (the theoretically expected value). The rate of change from one phase to the next increased with temperature. Incubation temperature had a strong effect on the overall fractionation of ¹³C during the formation and consumption of acetate, with stronger fractionation at low than at high temperature. The results further showed that, especially at low temperatures, fractionation occurred during acetate turnover and acetoclastic methanogenesis, despite the fact that steady-state conditions caused (apparent) substrate-limitation.     

Carbon and hydrogen isotopic compositions of products of open-system catalytic hydrogenation of CO2: Implications for abiogenic hydrocarbons in Earth’s crust

This paper reports the isotope effects in an open-system Fischer-Tropsch type (FTT) synthesis, with implications for the origin of natural abiogenic hydrocarbons. The starting form of carbon was CO₂, with carbon and hydrogen isotopic compositions measured for products of catalytic hydrogenation of CO₂ on iron and cobalt catalysts (FTCO₂-Fe and FTCO₂-Co) at 350 and 245 °C, respectively, and 10 MPa. The carbon isotopic composition of the resulting saturated hydrocarbons (alkanes) as a function of carbon number shows a positive trend for both FTCO₂-Fe and FTCO₂-Co, with a fractionation of 2-4‰ and 3-6‰ between CH₄ and C₂H₆ over the Fe and Co catalysts, respectively. The unsaturated hydrocarbons (alkenes) do not show any trend. A strong kinetic isotope fractionation (>40‰) occurred between CO₂ and CH₄ in both experiments. The hydrogen isotope fractionation between alkanes appeared to be similar to that found in natural (thermogenic and biogenic) gases, with enrichment in deuterium of longer hydrocarbon chains; the dominant H/D fractionation occurred between CH₄ and C₂H₆. Alkenes in the products of the FTCO₂-Fe reaction are enriched in deuterium (∼50‰) and do not show any trend versus carbon number. We suggest that other than FTT reactions or a simple mixing are responsible for the occurrence of the inverse isotopic trends in both δ¹³C and δD found in light hydrocarbons in some terrestrial environments and meteorites.     

Isotopic signatures of CH4 and higher hydrocarbon gases from Precambrian Shield sites: A model for abiogenic polymerization of hydrocarbons

Previous studies of methane and higher hydrocarbon gases in Precambrian Shield rocks in Canada and the Witwatersrand Basin of South Africa identified two major gas types. Paleometeoric waters were dominated by hydrocarbon gases with compositional and isotopic characteristics consistent with production by methanogens utilizing the CO₂ reduction pathway. In contrast the deepest, most saline fracture waters contained gases that did not resemble the products of microbial methanogenesis and were dominated by both high concentrations of H₂ gas, and CH₄ and higher hydrocarbon gases with isotopic signatures attributed to abiogenic processes of water-rock reaction in these high rock/water ratio, hydrogeologically-isolated fracture waters. Based on new data obtained for the higher hydrocarbon gases in particular, a model is proposed to account for carbon isotope variation between CH₄ and the higher hydrocarbon gases (specifically ethane, propane, butane, and pentane) consistent with abiogenic polymerization. Values of δ¹³C for CH₄ and the higher hydrocarbon gases predicted by the model are shown to match proposed abiogenic hydrocarbon gas end-members identified at five field sites (two in Canada and three in South Africa) suggesting that the carbon isotope patterns between the hydrocarbon homologs reflect the reaction mechanism. In addition, the δ²H isotope data for these gases are shown to be out of isotopic equilibrium, suggesting the consistent apparent fractionation observed between the hydrocarbon homologs may also reflect reaction mechanisms involved in the formation of the gases. Recent experimental and field studies of proposed abiogenic hydrocarbons such as those found at mid-ocean spreading centers and off-axis hydrothermal fields such as Lost City have begun to focus not only on the origin of CH₄, but on the compositional and isotopic information contained in the higher hydrocarbon gases. The model explored in this paper suggests that while the extent of fractionation in the first step in the hydrocarbon synthesis reaction chain may vary as a function of different reaction parameters, δ¹³C values for the higher hydrocarbon gases may be predicted by a simple mass balance model from the δ¹³C values of the lower molecular weight precursors, consistent with abiogenic polymerization. Integration of isotopic data for the higher hydrocarbon gases in addition to CH₄ may be critical for delineation of the origin of the hydrocarbons and investigation of formation mechanisms.     

Geochemical implications of induced changes in C13 fractionation by blue-green algae

The photosynthetic fractionation of carbon isotopes by blue-green algae in laboratory culture is dependent in a non-linear fashion on the CO₂ concentration in the feed gas. For the three species tested, the minimum fractionation occurred at a CO₂ concentration of 0.2% in air and was approximately zero for the two marine species tested. Enrichment of C¹² in the reduced carbon is not an inevitable result of photosynthetic carbon fixation. Temperature and pH had no detectable effect on fractionation. The maximum fractionation observed in the laboratory cultures or in recent blue-green algal mats was 18‰. Differences in the isotope ratio of coexisting oxidized and reduced carbon in Precambrian stromatolites are as great as 31‰. Present carbon isotopic evidence is not consistent with the idea that blue-green algae were major contributors to the organic matter in Precambrian sediments.     

The stable carbon isotope biogeochemistry of acetate and other dissolved carbon species in deep subseafloor sediments at the northern Cascadia Margin

Ocean drilling has revealed the existence of vast microbial populations in the deep subseafloor, but to date little is known about their metabolic activities. To better understand the biogeochemical processes in the deep biosphere, we investigate the stable carbon isotope chemistry of acetate and other carbon-bearing metabolites in sediment pore-waters. Acetate is a key metabolite in the cycling of carbon in anoxic sediments. Its stable carbon isotopic composition provides information on the metabolic processes dominating acetate turnover in situ. This study reports our findings for a methane-rich site at the northern Cascadia Margin (NE Pacific) where Expedition 311 of the Integrated Ocean Drilling Program (IODP) sampled the upper 190 m of sediment. At Site U1329, δ¹³C values of acetate span a wide range from −46.0‰ to −11.0‰ vs. VPDB and change systematically with sediment depth. In contrast, δ¹³C values of both the bulk dissolved organic carbon (DOC) (−21.6 ± 1.3‰ vs. VPDB) and the low-molecular-weight compound lactate (−20.9 ± 1.8‰ vs. VPDB) show little variability. These species are interpreted to represent the carbon isotopic composition of fermentation products. Relative to DOC, acetate is up to 23.1‰ depleted and up to 9.1‰ enriched in ¹³C. Broadly, ¹³C-depletions of acetate relative to DOC indicate flux of carbon from acetogenesis into the acetate pool while ¹³C-enrichments of pore-water acetate relative to DOC suggest consumption of acetate by acetoclastic methanogenesis. Isotopic relationships between acetate and lactate or DOC provide new information on the carbon flow and the presence and activity of specific functional microbial communities in distinct biogeochemical horizons of the sediment. In particular, they suggest that acetogenic CO₂-reduction can coexist with methanogenic CO₂-reduction, a notion contrary to the hypothesis that hydrogen levels are controlled by the thermodynamically most favorable electron-accepting process. Further, the isotopic relationship suggests a relative increase in acetate flow to acetoclastic methanogenesis with depth although its contribution to total methanogenesis is probably small. Our study demonstrates how the stable carbon isotope biogeochemistry of acetate can be used to identify pathways of microbial carbon turnover in subsurface environments. Our observations also raise new questions regarding the factors controlling acetate turnover in marine sediments.     

Volatile fatty acid cycling in organic-rich marine sediments

Volatile fatty acid (VFA) apparent turnover rates were determined by measuring whole sediment VFA concentrations and the corresponding reaction rate constants. The following ranges of VFA concentrations were measured in Cape Lookout Bight, N.C. sediments (μmole·l_s^?1): acetate 54–660, propionate 1–24, butyrate <0.5–22, iso-butyrate <0.5–6. Apparent turnover rates measured over a one-year period ranged from 18–600 μmole·l_s^?1·h^?1 for acetate and 0.7–7 μmole·l_s^?1·h^?1 for the carboxyl carbon of propionate. Methane production was observed only with acetate and only in sulfatedepleted sediments; total acetate turnover attained approximately the same maximum value in both sulfate-reducing and sulfate-depleted sediments.Apparent turnover rates for acetate and propionate appeared to be controlled by similar factors: in sulfate-reducing (surface) sediments the turnover rates were stimulated by autumn storm-mediated deposition/resuspension events; in deeper sulfate-depleted sediments the turnover rates followed changes in the ambient temperature. Changes in VFA poolsizes were proportionally much larger than changes in corresponding rate constants. The ratio of CO₂ to CH₄ produced from acetate vs. depth suggested that non-methanogenic bacteria accounted for 60% of the acetate turnover in sulfate-depleted sediments.VFA concentrations were much lower in N.C. continental slope mud than in Cape Lookout sediments; acetate was the only VFA detectable throughout the top 40 cm of the slope sediments. The estimated production rate of CO₂ from acetate decreased rapidly with depth. The surface rate was approximately 20 times less than that measured at similar temperatures in sulfate-reducing Cape Lookout sediments.     

A comparison of isotope fractionation of carbon and hydrogen from paddy field rice roots and soil bacterial enrichments during CO2/H2 methanogenesis

To better understand the isotope biogeochemistry of paddy field CH₄, we investigated carbon and hydrogen isotope fractionation during CO₂ reduction by a methanogenic community enriched from California paddy field soil and rice plants. Results from analyses of terminal restriction fragment length polymorphism (T-RFLP) and sequences of the archaeal small-subunit (SSU) rRNA-encoding genes (rDNA) showed a difference in methanogenic community structure between the soil (dominated by Methanobacteriaceae) and roots (dominated by Methanospirillaceae) which was essentially the same for sampling dates 15 and 99 days after flooding (DAF). CO₂/H₂ methanogenesis by these microbial communities produced CH₄ with different isotope ratios and fractionation factors (α factors). The carbon isotope α factors in an open system with a continuous supply of 0.5% H₂ were 1.050 ± 0.002 and 1.057 ± 0.001 for soil and root enrichment cultures at 15 DAF, and 1.052 ± 0.0.002 and 1.059 ± 0.002 for soil and root enrichment cultures at 99 DAF, respectively. These α factors are similar to, but distinct from values previously obtained from cultures of mesophilic methanogens and are larger than calculated values (1.045) for paddy soil. Fractionation of hydrogen isotopes was also studied in a closed system under 80% H₂. The difference in α factors between soil and root enrichment cultures remained clear. The hydrogen isotope fractionations between culture water and the product CH₄ were −327 ± 14‰ and −319 ± 18‰ for soil enrichments, and −389 ± 17‰ and −382 ± 21‰ for root enrichments at 15 DAF and 99 DAF, respectively.     

BRYOCARB: A process-based model of thallose liverwort carbon isotope fractionation in response to CO2, O2, light and temperature

Evidence from laboratory experiments indicates that fractionation against the heavy stable isotope of carbon (Δ¹³C) by bryophytes (liverworts and mosses) is strongly dependent on atmospheric CO₂. This physiological response may therefore provide the basis for developing a new terrestrial CO₂ proxy [Fletcher, B.J., Beerling, D.J., Brentnall, S.J., Royer, D.L., 2005. Fossil bryophytes as recorders of ancient CO₂ levels: experimental evidence and a Cretaceous case study. Global Biogeochem. Cycles19, GB3012]. Here, we establish a theoretical basis for the proxy by developing an extended model of bryophyte carbon isotope fractionation (BRYOCARB) that integrates the biochemical theory of photosynthetic CO₂ assimilation with controls on CO₂ supply by diffusion from the atmosphere. The BRYOCARB model is evaluated against measurements of the response of liverwort photosynthesis and Δ¹³C to variations in atmospheric O₂, temperature and irradiance at different CO₂ concentrations. We show that the bryophyte proxy is at least as sensitive to variations in atmosphere CO₂ as the two other leading carbon isotope-based approaches to estimating palaeo-CO₂ levels (δ¹³C of phytoplankton and of paleosols). Mathematical inversion of BRYOCARB provides a mechanistic means of estimating atmospheric CO₂ levels from fossil bryophyte carbon that can explicitly account for the effects of past differences in O₂ and climate.     

The effect of iron availability on the regulation of inorganic carbon acquisition in the coccolithophore Emiliania huxleyi and the significance of cellular compartmentation for stable carbon isotope fractionation

Iron is limiting phytoplankton productivity in large parts of today’s oceans, the so-called HNLC (high nutrient low chlorophyll) areas. It is a key component in photosynthesis during which inorganic carbon fixation in most phytoplankton species is sustained by so-called carbon concentrating mechanisms (CCMs). Here we investigate CCM regulation in the coccolithophore Emiliania huxleyi in response to varying degrees of iron limitation by means of membrane-inlet mass spectrometry. Compared to iron replete conditions rates of both active CO₂ and uptake were markedly reduced under iron limitation leading to significantly diminished growth rates. Moreover, there was a concomitant decrease in CCM efficiency, reflected in an increased CO₂ loss from the cell in relation to carbon fixation. Under such conditions higher values for carbon isotope fractionation (?_p) would be expected. However, direct measurements of ?_p showed that carbon isotope fractionation was insensitive to changes in growth rates and CCM activity. This can be explained by concomitant changes in internal DIC fluxes in and out of the chloroplast as demonstrated with a simple cell model comprising two compartments. Thus, carbon isotope fractionation reflects the ability of phytoplankton to actively control their inorganic carbon acquisition depending on environmental conditions. The insensitivity of carbon isotope fractionation to changes in the availability of iron could be of interest for paleoreconstructions in the HNLC areas of today’s oceans.     

Experimental investigation on the carbon isotope fractionation of methane during gas migration by diffusion through sedimentary rocks at elevated temperature and pressure

Molecular transport (diffusion) of methane in water-saturated sedimentary rocks results in carbon isotope fractionation. In order to quantify the diffusive isotope fractionation effect and its dependence on total organic carbon (TOC) content, experimental measurements have been performed on three natural shale samples with TOC values ranging from 0.3 to 5.74%. The experiments were conducted at 90°C and fluid pressures of 9 MPa (90 bar). Based on the instantaneous and cumulative composition of the diffused methane, effective diffusion coefficients of the ¹²CH₄ and ¹³CH₄ species, respectively, have been calculated.Compared with the carbon isotopic composition of the source methane (δ¹³C₁ = −39.1‰), a significant depletion of the heavier carbon isotope (¹³C) in the diffused methane was observed for all three shales. The degree of depletion is highest during the initial non-steady state of the diffusion process. It then gradually decreases and reaches a constant difference (Δ δ = δ¹³C_diff −δ¹³C_source) when approaching the steady-state. The degree of the isotopic fractionation of methane due to molecular diffusion increases with the TOC content of the shales. The carbon isotope fractionation of methane during molecular migration results practically exclusively from differences in molecular mobility (effective diffusion coefficients) of the ¹²CH₄ and ¹³CH₄ entities. No measurable solubility fractionation was observed.The experimental isotope-specific diffusion data were used in two hypothetical scenarios to illustrate the extent of isotopic fractionation to be expected as a result of molecular transport in geological systems with shales of different TOC contents. The first scenario considers the progression of a diffusion front from a constant source (gas reservoir) into a homogeneous “semi-infinite” shale caprock over a period of 10 Ma.In the second example, gas diffusion across a 100 m caprock sequence is analyzed in terms of absolute quantities and isotope fractionation effects. The examples demonstrate that methane losses by molecular diffusion are small in comparison with the contents of commercial size gas accumulations. The degree of isotopic fractionation is related inversely to the quantity of diffused gas so that strong fractionation effects are only observed for relatively small portions of gas.The experimental data can be readily used in numerical basin analysis to examine the effects of diffusion-related isotopic fractionation on the composition of natural gas reservoirs.