With the Researcher Spotlight, the Microbial Systems Initiative aims to introduce you to the breadth and diversity of research interests and potential growth opportunities on the University of Illinois at Urbana-Champaign campus. We hope that by highlighting both the researchers and their research, we can help you to learn more about and connect with your colleagues to enhance multidisciplinary research and education in microbial sciences here at Illinois.
Seppe Kuehn, an assistant professor of physics, and member of the Center for the Physics of Living Cells, completed his doctoral work in Chemical Physics at Cornell University studying non-contact friction and magnetic resonance force microscopy. His research interest in microbial systems began when he was completing postdoctoral research at the Rockefeller University. There, he pursued measurements of population dynamics in microbial communities and behavioral diversity in microbes. His current research is directed towards understanding the fundamental principles governing dynamics in complex biological systems at two levels of organization. First, his lab uses model microbial ecosystems to study stability, adaptation and function of microbial communities. Second, they study the structure of the map between genotypes and phenotypes in model microbial systems to discover the rule of adaptive evolution.
What is your research in microbial systems about?
The microbial world is a remarkable place! Hundreds or thousands of species of microbes live together in nearly every place on Earth: soil, the surface of leaves, the ocean, and in your body. What is striking to me is that these complex systems actually work – they perform myriads of metabolic functions from degrading polysaccharides to cycling carbon and nitrogen on a global scale. Even more surprising, these functional microbial communities which persist on a global scale are constantly evolving.
How has the process of evolution generated functional microbial communities in the natural world and why are they structured the way they are? In my group, we are trying to answer this question by understanding the evolutionary design principles of microbial communities. DNA sequencing technologies have revolutionized our understanding of the structure of microbial ecosystems by revealing their “parts list;” even so, we don’t yet understand how these consortia organize via the process of evolution to drive metabolic functions, interactions, and ecosystem stability. To probe those mysteries, we combine theory with sophisticated physics-style instrumentation. For example, we are constructing miniature self-sustaining closed microbial biospheres which persist indefinitely when provided only with light. These ecosystems provide model complete ecosystems, which cycle carbon, nitrogen etc. in a fashion similar to the Earth. We are working on understanding how these microbial collectives self-organize to efficiently cycle nutrients. Our hope is that these model systems can reveal key coevolved ecological interactions between microbes which allow these biospheres to persist. In a second project, we want to learn how a microbial ecology functions metabolically from the set of genes present in the community – building a map from the “metagenome” to the metabolism of the community. To address this question, we are using the process of denitrification, whereby collectives of bacteria in soil transform nitrate to di-nitrogen gas. Our goal is to predict the rates of these processes from the just a list of the genes present in the community.
Ultimately, we hope to build a predictive framework for understanding how groups of microbes act together to form functional ecosystems. Within this framework our goal is to understand how evolution has acted to shape the genomes and interactions that enable microbial communities to have such an enormous impact on life as we know it.
How are you conducting your research?
We use a variety of tools from custom instrumentation that we build ourselves (e.g. microscopes) to standard techniques such as sequencing or metabolite assays. We nearly always couple our experiments to mathematical modeling – sometimes in collaboration with a few close theory friends. The goal of modeling is to pose clear-cut, quantitative, predictions about what we can expect in our experiments. We then go back and test these predictions and iteratively refine things. This is one of the lessons we try very hard to take from physics – explain your experiments in the language of mathematics, make quantitative and testable predictions: repeat. We feel it’s a requirement to do this to make progress on any problem. Choosing the problem, on the other hand, is a much bigger challenge and one where mathematics is not such a good guide!
How does being a part of the Illinois community support and enhance your research?
Illinois is a remarkable place for the type of work that we do. The physics department at Illinois in particular is strong across the board – including in biological physics, and this gives us a like-minded community of researchers to interact with especially within the Center for the Physics of Living Cells. Since our work is crosses disciplinary boundaries we have found the Institute for Genomic Biology to be an especially stimulating and exciting place to find other collaborators – and indeed, experts who can help us as we delve into new model systems in which we are not ourselves well versed. Overall, we have an exciting group of theorists and experimentalists on campus to work with.
How will your research or work improve society or reach people?
To design and control microbial ecosystems that have particular properties would be a huge step forward in fields ranging from climate change to human health. The way we approach this problem now is largely ad hoc – using heuristics (that often work quite well!) to control processes like wastewater treatment. What we know from past successes in physics is that understanding the fundamental principles at work in any process can dramatically improve our ability to design and control those processes. So we hope to have a long term impact on understanding how processes like denitrification impact waste water treatment and agriculture.
Do you have a personal story to share or path that led to your interest in this area of study?
I did a Ph.D. in chemical physics working on magnetic resonance and friction at the nanoscale. What I liked about my doctoral work was the process of designing and building an instrument, making a very precise measurement and using theory to make sense of the result. I wanted to repeat this process, but in a discipline where I could ask fundamental questions about how nature works. I realized that most of the big problems in physics involved huge collaborations and many decades to make progress – not the benchtop “build-and-measure” approach I liked so much. So, I started reading about biology, took a few classes, and I learned how many big, wide-open, questions there are -- from evolution to physiology. The other thing I came to love about biology is its everyday-ness. It’s easy to look at an everyday phenomenon, from development to fermentation, and see how it plays out in your life from your kids to your refrigerator. This makes what we work on tangible in a way that spin-physics never quite felt.