Anaerobic oxidation of methane coupled with sulphate reduction: high concentration of methanotrophic archaea might be responsible for low stable isotope fractionation factors in methane

2021 ◽  
pp. 1-16
Author(s):  
Vasily A. Vavilin ◽  
Lyudmila Y. Lokshina ◽  
Sergey V. Rytov
Keyword(s):  
Stable Isotope ◽  
Isotope Fractionation ◽  
Sulphate Reduction ◽  
Anaerobic Oxidation Of Methane ◽  
Anaerobic Oxidation ◽  
High Concentration ◽  
Oxidation Of Methane ◽  
Stable Isotope Fractionation ◽  
Fractionation Factors

scholarly journals Theoretical Estimates of Equilibrium Carbon and Hydrogen Isotope Effects in Microbial Methane Production and Anaerobic Oxidation of Methane

2020 ◽  
Author(s):  
Jonathan Gropp ◽  
Mark Iron ◽  
Itay Halevy
Keyword(s):  
Isotopic Composition ◽  
Methane Production ◽  
Isotope Fractionation ◽  
Isotope Effects ◽  
Anaerobic Oxidation Of Methane ◽  
Anaerobic Oxidation ◽  
Oxidation Of Methane ◽  
Production And Consumption ◽  
Fractionation Factors ◽  
Equilibrium Fractionation

Microbial production and consumption of methane are widespread in natural and artificial environments, with important economic and climatic implications. Attempts to use the isotopic composition of methane to constrain its sources are complicated by incomplete understanding of the mechanisms of variation in methane's isotopic composition. Knowledge of the equilibrium isotope fractionations among the large organic intracellular intermediates in the microbial pathways of methane production and consumption must form the basis of any exploration of the mechanisms of isotopic variation, but estimates of these equilibrium isotope fractionations are currently unavailable. To address this gap, we calculated the equilibrium isotopic fractionation of carbon (<sup>13</sup>C/<sup>12</sup>C) and hydrogen (D/H) isotopes among compounds in anaerobic methane metabolisms, as well as the abundance of multiple isotope substitutions ("clumping," e.g., <sup>13</sup>C--D) in these compounds. The Density Functional Theory calculations employed the M06-L/def2-TZVP level of theory and the SMD implicit solvation model, which we have recently optimized for large organic molecules and tested against measured equilibrium isotope fractionations. The computed <sup>13</sup>beta and <sup>2</sup>beta values decrease with decreasing average oxidation state of the carbon atom in the molecules, resulting in a preference for enrichment of the molecules with more oxidized carbon in <sup>13</sup>C and D. Using the computed $\beta$ values, we calculated the equilibrium isotope fractionation factors in the prominent methanogenesis pathways (hydrogenotrophic, methylotrophic and acetoclastic) and in the pathway for anaerobic oxidation of methane (AOM) over a temperature range of 0-700 degrees Celsius. Our calculated equilibrium fractionation factors compare favorably with experimental constrains, where available, and we used them to investigate the relation between the apparent isotope fractionation during methanogenesis and AOM and the thermodynamic drive for these reactions. We show that a detailed map of the equilibrium fractionation factors along these metabolic pathways allows an evaluation of the contribution of equilibrium and kinetic isotope effects to apparent isotope fractionations observed in laboratory, natural and artificial settings. The comprehensive set of equilibrium isotope fractionation factors calculated in this study provides a firm basis for future explorations of isotope effects in methane metabolism.

scholarly journals Theoretical Estimates of Equilibrium Carbon and Hydrogen Isotope Effects in Microbial Methane Production and Anaerobic Oxidation of Methane

2020 ◽  
Author(s):  
Jonathan Gropp ◽  
Mark Iron ◽  
Itay Halevy
Keyword(s):  
Isotopic Composition ◽  
Methane Production ◽  
Isotope Fractionation ◽  
Isotope Effects ◽  
Anaerobic Oxidation Of Methane ◽  
Anaerobic Oxidation ◽  
Oxidation Of Methane ◽  
Production And Consumption ◽  
Fractionation Factors ◽  
Equilibrium Fractionation

Microbial production and consumption of methane are widespread in natural and artificial environments, with important economic and climatic implications. Attempts to use the isotopic composition of methane to constrain its sources are complicated by incomplete understanding of the mechanisms of variation in methane's isotopic composition. Knowledge of the equilibrium isotope fractionations among the large organic intracellular intermediates in the microbial pathways of methane production and consumption must form the basis of any exploration of the mechanisms of isotopic variation, but estimates of these equilibrium isotope fractionations are currently unavailable. To address this gap, we calculated the equilibrium isotopic fractionation of carbon (<sup>13</sup>C/<sup>12</sup>C) and hydrogen (D/H) isotopes among compounds in anaerobic methane metabolisms, as well as the abundance of multiple isotope substitutions ("clumping," e.g., <sup>13</sup>C--D) in these compounds. The Density Functional Theory calculations employed the M06-L/def2-TZVP level of theory and the SMD implicit solvation model, which we have recently optimized for large organic molecules and tested against measured equilibrium isotope fractionations. The computed <sup>13</sup>beta and <sup>2</sup>beta values decrease with decreasing average oxidation state of the carbon atom in the molecules, resulting in a preference for enrichment of the molecules with more oxidized carbon in <sup>13</sup>C and D. Using the computed $\beta$ values, we calculated the equilibrium isotope fractionation factors in the prominent methanogenesis pathways (hydrogenotrophic, methylotrophic and acetoclastic) and in the pathway for anaerobic oxidation of methane (AOM) over a temperature range of 0-700 degrees Celsius. Our calculated equilibrium fractionation factors compare favorably with experimental constrains, where available, and we used them to investigate the relation between the apparent isotope fractionation during methanogenesis and AOM and the thermodynamic drive for these reactions. We show that a detailed map of the equilibrium fractionation factors along these metabolic pathways allows an evaluation of the contribution of equilibrium and kinetic isotope effects to apparent isotope fractionations observed in laboratory, natural and artificial settings. The comprehensive set of equilibrium isotope fractionation factors calculated in this study provides a firm basis for future explorations of isotope effects in methane metabolism.

scholarly journals Theoretical Estimates of Equilibrium Carbon and Hydrogen Isotope Effects in Microbial Methane Production and Anaerobic Oxidation of Methane

2020 ◽  
Author(s):  
Jonathan Gropp ◽  
Mark Iron ◽  
Itay Halevy
Keyword(s):  
Isotopic Composition ◽  
Methane Production ◽  
Isotope Fractionation ◽  
Isotope Effects ◽  
Anaerobic Oxidation Of Methane ◽  
Anaerobic Oxidation ◽  
Oxidation Of Methane ◽  
Production And Consumption ◽  
Fractionation Factors ◽  
Equilibrium Fractionation

Microbial production and consumption of methane are widespread in natural and artificial environments, with important economic and climatic implications. Attempts to use the isotopic composition of methane to constrain its sources are complicated by incomplete understanding of the mechanisms of variation in methane's isotopic composition. Knowledge of the equilibrium isotope fractionations among the large organic intracellular intermediates in the microbial pathways of methane production and consumption must form the basis of any exploration of the mechanisms of isotopic variation, but estimates of these equilibrium isotope fractionations are currently unavailable. To address this gap, we calculated the equilibrium isotopic fractionation of carbon (<sup>13</sup>C/<sup>12</sup>C) and hydrogen (D/H) isotopes among compounds in anaerobic methane metabolisms, as well as the abundance of multiple isotope substitutions ("clumping," e.g., <sup>13</sup>C--D) in these compounds. The Density Functional Theory calculations employed the M06-L/def2-TZVP level of theory and the SMD implicit solvation model, which we have recently optimized for large organic molecules and tested against measured equilibrium isotope fractionations. The computed <sup>13</sup>beta and <sup>2</sup>beta values decrease with decreasing average oxidation state of the carbon atom in the molecules, resulting in a preference for enrichment of the molecules with more oxidized carbon in <sup>13</sup>C and D. Using the computed $\beta$ values, we calculated the equilibrium isotope fractionation factors in the prominent methanogenesis pathways (hydrogenotrophic, methylotrophic and acetoclastic) and in the pathway for anaerobic oxidation of methane (AOM) over a temperature range of 0-700 degrees Celsius. Our calculated equilibrium fractionation factors compare favorably with experimental constrains, where available, and we used them to investigate the relation between the apparent isotope fractionation during methanogenesis and AOM and the thermodynamic drive for these reactions. We show that a detailed map of the equilibrium fractionation factors along these metabolic pathways allows an evaluation of the contribution of equilibrium and kinetic isotope effects to apparent isotope fractionations observed in laboratory, natural and artificial settings. The comprehensive set of equilibrium isotope fractionation factors calculated in this study provides a firm basis for future explorations of isotope effects in methane metabolism.

scholarly journals Theoretical Estimates of Equilibrium Carbon and Hydrogen Isotope Effects in Microbial Methane Production and Anaerobic Oxidation of Methane

2020 ◽  
Author(s):  
Jonathan Gropp ◽  
Mark Iron ◽  
Itay Halevy
Keyword(s):  
Isotopic Composition ◽  
Methane Production ◽  
Isotope Fractionation ◽  
Isotope Effects ◽  
Anaerobic Oxidation Of Methane ◽  
Anaerobic Oxidation ◽  
Oxidation Of Methane ◽  
Production And Consumption ◽  
Fractionation Factors ◽  
Equilibrium Fractionation

Microbial production and consumption of methane are widespread in natural and artificial environments, with important economic and climatic implications. Attempts to use the isotopic composition of methane to constrain its sources are complicated by incomplete understanding of the mechanisms of variation in methane's isotopic composition. Knowledge of the equilibrium isotope fractionations among the large organic intracellular intermediates in the microbial pathways of methane production and consumption must form the basis of any exploration of the mechanisms of isotopic variation, but estimates of these equilibrium isotope fractionations are currently unavailable. To address this gap, we calculated the equilibrium isotopic fractionation of carbon (<sup>13</sup>C/<sup>12</sup>C) and hydrogen (D/H) isotopes among compounds in anaerobic methane metabolisms, as well as the abundance of multiple isotope substitutions ("clumping," e.g., <sup>13</sup>C--D) in these compounds. The Density Functional Theory calculations employed the M06-L/def2-TZVP level of theory and the SMD implicit solvation model, which we have recently optimized for large organic molecules and tested against measured equilibrium isotope fractionations. The computed <sup>13</sup>beta and <sup>2</sup>beta values decrease with decreasing average oxidation state of the carbon atom in the molecules, resulting in a preference for enrichment of the molecules with more oxidized carbon in <sup>13</sup>C and D. Using the computed $\beta$ values, we calculated the equilibrium isotope fractionation factors in the prominent methanogenesis pathways (hydrogenotrophic, methylotrophic and acetoclastic) and in the pathway for anaerobic oxidation of methane (AOM) over a temperature range of 0-700 degrees Celsius. Our calculated equilibrium fractionation factors compare favorably with experimental constrains, where available, and we used them to investigate the relation between the apparent isotope fractionation during methanogenesis and AOM and the thermodynamic drive for these reactions. We show that a detailed map of the equilibrium fractionation factors along these metabolic pathways allows an evaluation of the contribution of equilibrium and kinetic isotope effects to apparent isotope fractionations observed in laboratory, natural and artificial settings. The comprehensive set of equilibrium isotope fractionation factors calculated in this study provides a firm basis for future explorations of isotope effects in methane metabolism.

scholarly journals Improved quantification of microbial CH<sub>4</sub> oxidation efficiency in Arctic wetland soils using carbon isotope fractionation

2012 ◽  
Vol 9 (12) ◽  
pp. 16999-17035 ◽  
Author(s):  
I. Preuss ◽  
C. Knoblauch ◽  
J. Gebert ◽  
E.-M. Pfeiffer
Keyword(s):  
Stable Isotope ◽  
Isotope Fractionation ◽  
Wetland Soils ◽  
Tundra Soils ◽  
Ch4 Oxidation ◽  
Stable Isotope Fractionation ◽  
Oxidation Efficiency ◽  
Water Saturated ◽  
Fractionation Factors

Abstract. Permafrost-affected tundra soils are significant sources of the climate-relevant trace gas methane (CH4). The observed accelerated warming of the Arctic will cause a deeper permafrost thawing followed by increased carbon mineralization and CH4 formation in water saturated tundra soils which might cause a positive feedback to climate change. Aerobic CH4 oxidation is regarded as the key process reducing CH4 emissions from wetlands, but quantification of turnover rates has remained difficult so far. The application of carbon stable isotope fractionation enables the in situ quantification of CH4 oxidation efficiency in arctic wetland soils. The aim of the current study is to quantify CH4 oxidation efficiency in permafrost-affected tundra soils in Russia's Lena River Delta based on stable isotope signatures of CH4. Therefore, depth profiles of CH4 concentrations and δ13CH4-signatures were measured and the fractionation factors for the processes of oxidation (αox) and diffusion (αdiff) were determined. Most previous studies employing stable isotope fractionation for the quantification of CH4 oxidation in soils of other habitats (e.g. landfill cover soils) have assumed a gas transport dominated by advection (αtrans = 1). In tundra soils, however, diffusion is the main gas transport mechanism, aside from ebullition. Hence, diffusive stable isotope fractionation has to be considered. For the first time, the stable isotope fractionation of CH4 diffusion through water-saturated soils was determined with an αdiff = 1.001 ± 0.000 (n = 3). CH4 stable isotope fractionation during diffusion through air-filled pores of the investigated polygonal tundra soils was αdiff = 1.013 ± 0.003 (n = 18). Furthermore, it was found that αox differs widely between sites and horizons (mean αox, = 1.017 ± 0.009) and needs to be determined individually. The impact of both fractionation factors on the quantification of CH4 oxidation was analyzed by considering both the potential diffusion rate under saturated and unsaturated conditions and potential oxidation rates. For a submerged organic rich soil, the data indicate a CH4 oxidation efficiency of 50% at the anaerobic-aerobic interface in the upper horizon. The improved in situ quantification of CH4 oxidation in wetlands enables a better assessment of current and potential CH4 sources and sinks in permafrost affected ecosystems and their potential strengths in response to global warming.

scholarly journals Improved quantification of microbial CH<sub>4</sub> oxidation efficiency in arctic wetland soils using carbon isotope fractionation

2013 ◽  
Vol 10 (4) ◽  
pp. 2539-2552 ◽  
Author(s):  
I. Preuss ◽  
C. Knoblauch ◽  
J. Gebert ◽  
E.-M. Pfeiffer
Keyword(s):  
Stable Isotope ◽  
Isotope Fractionation ◽  
Wetland Soils ◽  
Tundra Soils ◽  
Ch4 Oxidation ◽  
Stable Isotope Fractionation ◽  
Oxidation Efficiency ◽  
Water Saturated ◽  
Fractionation Factors

Abstract. Permafrost-affected tundra soils are significant sources of the climate-relevant trace gas methane (CH4). The observed accelerated warming of the arctic will cause deeper permafrost thawing, followed by increased carbon mineralization and CH4 formation in water-saturated tundra soils, thus creating a positive feedback to climate change. Aerobic CH4 oxidation is regarded as the key process reducing CH4 emissions from wetlands, but quantification of turnover rates has remained difficult so far. The application of carbon stable isotope fractionation enables the in situ quantification of CH4 oxidation efficiency in arctic wetland soils. The aim of the current study is to quantify CH4 oxidation efficiency in permafrost-affected tundra soils in Russia's Lena River delta based on stable isotope signatures of CH4. Therefore, depth profiles of CH4 concentrations and δ13CH4 signatures were measured and the fractionation factors for the processes of oxidation (αox) and diffusion (αdiff) were determined. Most previous studies employing stable isotope fractionation for the quantification of CH4 oxidation in soils of other habitats (such as landfill cover soils) have assumed a gas transport dominated by advection (αtrans = 1). In tundra soils, however, diffusion is the main gas transport mechanism and diffusive stable isotope fractionation should be considered alongside oxidative fractionation. For the first time, the stable isotope fractionation of CH4 diffusion through water-saturated soils was determined with an αdiff = 1.001 &amp;pm; 0.000 (n = 3). CH4 stable isotope fractionation during diffusion through air-filled pores of the investigated polygonal tundra soils was αdiff = 1.013 &amp;pm; 0.003 (n = 18). Furthermore, it was found that αox differs widely between sites and horizons (mean αox = 1.017 ± 0.009) and needs to be determined on a case by case basis. The impact of both fractionation factors on the quantification of CH4 oxidation was analyzed by considering both the potential diffusion rate under saturated and unsaturated conditions and potential oxidation rates. For a submerged, organic-rich soil, the data indicate a CH4 oxidation efficiency of 50% at the anaerobic–aerobic interface in the upper horizon. The improved in situ quantification of CH4 oxidation in wetlands enables a better assessment of current and potential CH4 sources and sinks in permafrost-affected ecosystems and their potential strengths in response to global warming.

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