Collaborative Research: Merging Metabolomics and Isotope Biogeochemistry as a New Approach for Quantitative Flux Analysis of Environmental Carbon Metabolism

Carbon isotopes serve as important tracers of metabolism in both the biological and earth sciences. Earth scientists have long used subtle variations in the natural abundance of the stable isotope carbon-13 in biomolecules to draw inferences about organismal or biochemical origins, and metabolic carbon fluxes. In systems biology, the metabolomics approach employs the addition of carbon-13 tracers to cultures, followed by monitoring of labeled metabolites to quantify carbon fluxes through metabolic pathways. However, a key drawback is that this approach is only feasible for organisms cultivated in the lab, where relatively high levels of isotope tracer can be achieved. Similar information is potentially available in the natural-abundance distribution of carbon isotopes, as they are modulated by kinetic isotope effects that accompany most metabolic reactions. Retrieving this information requires a specialized style of mass spectrometry that is already available in isotope geochemistry labs; as well as new metabolic models that account for all of the relevant fluxes and isotope effects. The latter is tractable but as-yet unproven. This project will leverage the unique collaboration between an isotope geochemist (at Caltech) and a systems biologist (at Northwestern) to combine these two approaches to develop and validate a new algorithm for measuring rates and types of metabolism in organisms, based on natural abundances of the carbon-13 isotope. The goal of this project is to build and validate the newly developed algorithm for aerobic and anaerobic heterotrophic bacteria, using both conventional (13C-tracer) and natural-abundance measurements as constraints. The success of this project would greatly expand our ability to quantify metabolic fluxes in organisms collected from the environment, as well as to predict their stable isotope signatures. This new ability could have many important applications, including improved understanding of how many microbes function in the environment, as well as marine and soil food webs, fisheries, and the carbon cycle. The project will provide training of graduate students at Caltech and Northwestern, and involve the partnerships of respective institutions with educational activities with local middle-school and high-school students. . This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.