Because of the highly interdisciplinary nature of the overarching questions that drive my research, that is, understanding the evolution of microbial metabolisms and their intimate interactions with paleo-environments, a wide range of tools are necessary. These include stable isotope geochemistry, environmental observations, pure culture microbial experiments, modeling of intracellular dynamics, and construction of three-dimensional models of crucial proteins in key metabolic pathways. These tools can be expanded to other metabolic pathways. A full list of publications on these projects is available in my C.V.
Deconstructing metabolic pathways using mutants A precise knowledge of step-specific sulfur isotope effects during microbial sulfate reduction and microbial sulfur disproportionation is crucial to the interpretation of their sulfur isotopic signature. For this, it is essential to explore the cellular-level fractionation factor during specific steps of each reaction network via highly targeted experiments. This is now possible by virtue of a suite of molecular tools that allow building mutants with modified reaction networks. In my work, I have made use of the availability of such bacterial strains to further our mechanistic understanding of the biochemistry of microbial sulfate reduction, specifically during sulfite uptake and ensuing reduction. Future projects will aim at applying the same molecular tools to microbial sulfur disproportionation to further our understanding of the biochemical mechanisms underpinning this pathway.
Calibrating the disproportionation signature with pure culture experiments
Microbial sulfur disproportionation strives under narrow environmental conditions. Thus, isotopic effects consistent with microbial sulfur disproportionation will reflect specific environmental settings. I am interested in fully calibrating their effect on bacterial growth rate, geochemical signatures, and multiple sulfur isotope effects can be explored using simple pure culture experiments.
Comparative protein models
The details of the microbial sulfur disproportionation intracellular dynamics, which are at the root of its isotopic signature, are poorly understood. In a nutshell, sulfate reducers and sulfur disproportionators are biochemically undistinguishable, however sulfur disproportionating prokaryotes do not exhibit the expected metabolic plasticity, and most are incapable of reducing sulfate. I am interested in understanding whether key differences in enzymes found active in both sulfate reducing and sulfur disproportionating organisms are at the basis of the mechanistic differences between these two pathways. For this, comparative protein models of key enzymes using available protein sequences and molecular visualization software are highly informative and promising avenue. Future projects will utilize knowledge derived from these protein models to reevaluate the shared evolutionary history of microbial sulfate reduction and microbial sulfur disproportionation.
Thermodynamically informed metabolic models and extensions to oxygen isotope systems Building quantitative links between net isotope effects, bacterial physiology, and environmental conditions requires the application of sophisticated steady state isotope models. Such models have been previously built and tested for microbial sulfate reduction. The versatility of these models allows their application to a wide range of metabolic networks and isotope systems. I am interested in adapting such models to other microbial pathways, including sulfur disproportionation to refine our understanding of this pathway and the interpretability of its signature. I am also interested in extending this model to the oxygen isotope system, and utilize this signature to infer information on sedimentary microbial communities, with the ultimate goal of implementing them into sediment diagenetic models.