Research

Linking the physiological state of microbial communities and sediment isotope signatures Determining the response ­of microbial metabolisms to changing environments, and how this response is transcribed into isotopic signatures is crucial to understand sediment biogeochemical cycling. Current geochemical tools allow quantifying bulk cycling and molecular tools give insight into microbial communities and their metabolic potential. Both are informative, neither is sufficient to reconstruct the contribution of metabolic consortia to bulk geochemical cycling. Sediment isotopic signatures can provide such insight for modern and past microbial activity. I apply thermodynamically rooted microbial isotope models to explicitly link the physiological and environmental contributions to geochemical and isotope signatures. A good example of the power of this approach is the link that my co-authors and I established between the oxygen isotopic signature (as preserved in leftover sulfate) during microbial sulfate reduction and physiological state (cell-specific sulfate reduction rates) and environmental conditions (sulfate and sulfide levels). This link, based on a thermodynamically rooted model, allows enhancing the interpretability of sediment isotope signatures (Bertran et. al., 2020) and opens up new possibilities for tracking the secular contribution of biological processes to biogeochemical cycles (Waldeck, Bertran et. al., 2019).

Microbial net isotope effects reflect intra- and extra-cellular conditions Interpreting this duality is essential to reconstruct modern and ancient environments and ecosystems and requires a detailed calibration of intracellular dynamics. But, access to the necessary information is challenging. This can be investigated with models of microbial isotopic signatures that incorporate reaction thermodynamics. For instance, in my work, the model on the oxygen isotope signature driven by microbial sulfate reduction demonstrated the fraction of sulfate that is reset with respect to O isotopes – and is hence never reduced to sulfide – is larger than previously anticipated (Bertran et. al., 2020). In my work, I have also used similar approaches to gain a refined mechanistic understanding of MSR and MSD. Specifically, to determine the identify electron carriers in key reactions (Bertran et. al., 2018) and intracellular flux dynamics, and how these differ between the two metabolisms, producing distinct isotopic signatures and unique responses to environmental redox. Future work will use similar approaches to ground truth the MSD ecological niche through its response to extra-cellular and physiological variables coupled with high precision multiple S isotope measurements. This will calibrate the information enclosed within the MSD isotopic signal and provide a refined accounting of redox conditions in modern and past environments.

Enzymes catalyze metabolic reactions and exert control on intracellular metabolic fluxes while imparting significant kinetic isotope effects. Understanding the contribution of enzyme isotope effects and kinetics to net metabolic flux and isotopic signatures is essential. Yet, this is an underestimated feature of traditional microbial isotope models. In vitro laboratory techniques, computational simulation models, and phylogenetic tools provide unprecedented insight into the mechanism of enzymatic machineries. An enzyme structure-function-isotope signature approach provides unique insight into the governing factors of their isotopic effects and the evolutionary context of these signatures. I compared the structure of the enzyme APS reductase, found in sulfate reducers and S disproportionators, and identified structural features found in S disproportionators only, with potential consequences for enzyme regulation, redox capabilities, and substrate recognition and binding. It can be used as a marker to pinpoint evolutionary transitions between MSR and MSD (this work is currently in preparation) and updates our current understanding of their shared evolutionary histories (Bertran et. al., 2020). My future research program will test the predicted effect of inferred structural features on APS reductase functionality with crystal structure analysis and a library of mutants. This approach can be extended to other relevant enzymes, such as dissimilatory sulfite reductase and sulfate transporters.

The interpretation of both modern and paleo N cycling depends on a detailed understanding of the isotope effect of the three nitrogenase isozymes that catalyze BNF. Yet the contribution of each isozyme to net BNF, mechanism and controlling factors to net isotope effects need to be constrained. For my postdoctoral research, I am working to measure in vitro isotope effects associated with nitrogenase isozymes, which will serve to build novel quantitative models of net BNF isotope signatures and, in turn, will be placed in the context of larger scale modern and paleo N cycling. Also, the relative control of substrate N2 diffusion to and into the active site of nitrogenase compared to N2 reduction on net isotope effects is challenging to assess. For this, I am developing molecular dynamics simulations of nitrogenase to explore the mechanistic details of BNF.