PriME Project: Elucidating Microbial Metabolic Interactions Using Metabolomic Analysis
Heterotrophic bacterial communities collectively play a fundamental role in degrading particulate organic matter in marine environments and, subsequently, in recycling elements at the global scale. Particulate organic matter in marine environments consists of fecal pellets, polysaccharides and decaying organisms. Although metabolism is at the core of this recycling, there is only a minimal understanding of how community members interact on the metabolic level. Studying metabolic exchanges will allow us to gain insight into how microbial ecosystems function, what roles are carried out by individual bacterial species, and how they may respond to environmental perturbations or resource fluctuations. Here, we aim to apply a variety of metabolomic techniques to elucidate specific metabolite exchanges of marine ecosystems and to understand the metabolic principles that contribute to the organization and function of these ecosystems. Our primary studies will focus on understanding the trophic relationships of various carbohydrate degrader and secondary consumer pairs that thrive on particulate organic matter present in marine environments. First, we will perform large numbers of conditioned media experiments, in which we measure metabolites that are excreted by degrader strains as they break down recalcitrant carbon sources, and which metabolites are used by secondary consumers for growth. Once we have identified candidate compounds, quantification of absolute concentration changes over time will allow mass balancing to separate exchange of more vitaminlike growth-promoting compounds from major exchanges of carbon and nitrogen. Finally, to demonstrate in vivo functionality we will perform pairwise (and potentially more complex) cultivations of community members with combined nutritional supplementation and 13C isotopic tracer experiments. Together, these data will allow us to identify critical pathways and metabolic capabilities of individual microbes and provide insight into their role within a microbial ecosystem.
Sammy Pontrelli graduated with a B.S./M.S. in bioengineering from Santa Clara University in 2013 and completed his Ph.D. research at the University of California, Los Angeles in chemical engineering in 2018. His Ph.D. research was under the supervision of James C. Liao. The primary focus of his research was to understand how new metabolic pathways form in response to missing essential metabolic enzymes. Other projects entailed engineering Escherichia coli for enhanced production of biofuels. Through his research experiences, Pontrelli gained a passion for science and has chosen to pursue a postdoc in Uwe Sauer’s lab at ETH Zürich as a PriME postdoctoral fellow. With hopes of a fruitful collaboration, he intends to use this opportunity to learn new skills and prepare himself for a long-term academic position in scientific research.