An interview with Professor Orkun Soyer
August 2020
Orkun Soyer is a Professor in the department of Life Sciences at the University of Warwick and a member of the Microbiology Society. In this interview, he tells us more about his research which involves understanding the structure and response dynamics of biological systems from an evolutionary perspective and using these in systems and synthetic biology.
Tell us about your role and area of research.
I am leading a multi-disciplinary research group which focuses on the study of the cellular metabolism and metabolic interactions. We aim to understand the dynamics of metabolism, under different micro-environmental conditions, and how cells in a population, or across populations of different species interact metabolically. In the latter direction, we are particularly interested in microbial communities and how metabolic interactions within these systems underpin stability and spatial organisation.
Why is your research important?
Metabolism is the underpinning driver of many cellular behaviors, including growth and differentiation. While individual pathways and reactions within the metabolism are catalogued, we still lack a comprehensive system-level view of the metabolism and how it reacts to micro-environmental conditions at the single cell level. In particular, we do not understand how cells switch between different metabolic states and why under some states they excrete many metabolites. These excretions result in the formation of metabolic interactions among cells within a genetically identical population or within microbial communities composed of different species.
We use modelling approaches and experiments to study cellular metabolism and cellular micro-environments, to better understand cell physiology and emergence of cell-to-cell metabolic interactions. The former research direction is important, because understanding connections between the metabolism and cell behavior provides fundamental insights into cell biology and can allow us to better treat metabolism-linked disease conditions such as cancer.
The latter research direction is important because metabolic interactions underpin microbial communities, microbe-plants, and microbe-animal associations. A better understanding of how metabolic interactions emerge and evolve, can allow us to predict stability in these natural systems or develop synthetic, model systems composed of multiple interacting species.
What are the challenges you face in your work and how do you try to overcome them?
A key challenge in our research, and in biosciences broadly, is the ability to obtain truly quantitative measurements. This is because many systems we study are complex enough, that their key features of interest are not readily quantifiable or only quantifiable in some limited way. For example, studying metabolic interactions among microbes in a spatially organized community, requires us to measure the number of cells and metabolite levels across such spatial organisation. Such quantification is not easy and usually involves trade-offs (for example, some methods can quantify cell numbers and positions, but not in real time and without killing the cells).
To overcome these quantification challenges, we embrace collaborations with engineers, chemists, and physicists to adopt the latest measurement techniques and setups to answer biological questions. In one recent study for example, we adopted electrochemical techniques and tools, such as ultra-micro-electrodes to measure the micro-environment around individual cells. Where we can, we also aim to develop our own measurement techniques to address specific needs of our research, such as custom-designed microfluidic devices for monitoring spatial interactions among cells under different conditions, or a standardized growth rate measurement device (called MicrobeMeter) for obtaining high-resolution growth data, from strictly anaerobic microbes.
Why is it important to be a member of an organisation like the Microbiology Society?
Membership at the Society allows me to keep up to date with the latest technological developments in the field, as well as emerging research questions. It also allows me to connect with fellow researchers at the flagship Annual Conference, to get feedback on our own research, form new collaborations, and identify exciting new areas of research.
Why does microbiology matter?
Microbes have fascinating metabolic and physiological versatility. On their own, and through interactions with other microbes, this versatility gives them the ability to change their environment from micro to macro scales. Historically, this has allowed microbes to change Earth’s geochemistry and set the stage for the evolution of higher organisms. Today, these microbe-driven changes are still ongoing with macro-scale effects on climate and micro-scale effects on plant and animal growth.
It is, thus; as important as ever to be studying microbiology through a quantitative lens and with an increasing focus on physiology and interactions (among each other and with higher species). With this new focus in microbiological research, we will be able to better understand how microbes control and change their environment; predict stability of microbe-microbe, microbe-plant, and microbe-animal interactions, and perhaps even develop better microbial systems for more efficient and sustainable living.
