biology / geochemistry / methane / stable isotopes / numerical modeling
Methanogenic growth on methylated substrates (e.g., methanol, trimethylamine, methylsulfides) produces large carbon and hydrogen isotopic offsets between the substrates and the methane, and large-negative clumped isotopic signatures. We use the genetically-tractable methanogenic model organism Methanosarcina acetivorans to study what are the molecular mechanisms that generate these large isotopic effects, to gain a deeper understanding on this often overlooked methanogenic pathway. In this project we combine CRISPR/Cas9-based genome editting with both bulk (13C/12C and D/H) and clumped (13CH3D and 12CH2D2) isotopologue measurements.
A project in a long-term collaboration with Qusheng Jin (Univeristy of Oregon), to develop new models of microbial metabolism which include detailed reaction networks with kinetic and thermodynamic terms. These models are coupled to isotopic mass balances that allow us to predict the isotopic effects for microbial reactions as a function of their metabolic states.
Microbial production of methane from CO2 and H2 (termed “hydrogenotrophic methanogenesis”), produces methane that is substantially isotopically lighter than its substrates. The magnitude of this isotopic discrimination is dependent on the availability of the substrates. We have developed a metabolic model of hydrogenotrophic methanogenesis, and coupled it to an isotopic reaction network model. This model takes as input the concentrations of CO2, H2, and CH4, and the temperature, and its output is the isotopic fractionation for bulk carbon and hydrogen isotopes, as well as the clumped isotopologues composition (13CH3D and 12CH2D2) (Paper in Science Advances).
Microbial production of methane from methylated compounds is common in marine and freshwater sediments and is thought to contribute to ~5-10% of the annual methane emissions to the atmosphere. The disproportionation of methanol yields relatively high energy (in comparison to other methanogenic pathways) and is thus often active concurrent to other anaerobic pathways e.g., sulfate reduction. We developed a metabolic-isotopic model of methylotrophic methanogenesis, which we validate using results from our laboratory experiments.
In marine sediments, the carbon isotopic composition of methane (δ13C-CH4) is often showing strong negative excursions within the sulfate-methane interface (SMI). These excursions indicate that methane is becoming isotopically lighter in the SMI, and a common explanation for this was that cryptic methanogenic activity within the SMI produces these excursions. In a collaborative work with researchers from Bremen we found that these excursions might reflect anaerobic oxidation of methane (AOM) under sulfate-limiting conditions, which are common in the base of many SMIs. Using a combined experimental and modeling approach, we showed how reversibility of the intracellular reactions determines the δ13C-CH4, and additionally the hydrogen isotopic composition (δD-CH4), explaining the counter-intuitive preference for isotopically-heavy methane even when the entire system is far from equilibrium (Paper in Science Advances). This project was in collaboration with Gunter Wegener, Marcus Elvert, and Heidi Taubner (University of Bremen and Max Plank Institute in Bremen).
Differences in the zero-point energies of isotopically substituted molecules result in characteristic isotopic ratios under isotopic equilibrium. The isotopic equilibrium fractionation factors (EFFs) between two molecules are often complicated to measure experimentally, and various methods for calculation of these EFFs have been developed over the years. We have used different models of one of the most common methods, the Density Functional Theory (DFT), to calculate EFFs between large organic molecules. We validated our calculations for H, C, N, and O isotopes against available measured EFFs, and determined which DFT models are most accurate for these molecules (Paper in PCCP). We then used this pipeline to calculate EFFs in the anaerobic metabolism of methane. We identified the key reactions that may control the isotopic fractionation in the different methanogenic pathway and in methane oxidation (Paper in GCA). Both these projects were a collaborative effort with Mark A. Iron, a computational chemist in the Weizmann Institute of Science.