PhD Position on “Bacterial dynamics in heterogeneous landscapes” in Zürich

100%, Zurich, fixed-term

The Environmental Microfluidics Group of Prof. Roman Stocker in the Institute of Environmental Engineering is seeking a dynamic and motivated doctoral student for a project on bacterial dynamics in heterogeneous landscapes. The position is funded by the Innovative Training Network (ITN) PHYMOT and will be based in the laboratory of Prof. Roman Stocker (ETH).

The life of motile bacteria is characterized by a relentless search for nutrient sources, which in the ocean take the form of particulate matter such as marine snow, plumes and filaments of dissolved organic matter being exuded by phytoplankton cells, or gels. The interaction kinetics between bacteria and resources in the ocean ultimately set the pace of the biological pump, which is the rate of carbon sequestration to the deep ocean. Bacteria rely on chemotaxis, the process of detecting chemical gradients and modifying motility in response, to navigate chemical seascapes. A great amount of research has been devoted to the molecular pathways of chemotaxis and its characterization in simplified scenarios, such as steady, linear gradients. However much less is known on how chemotaxis is effective under ecological relevant environments, in particular the ephemeral nutrient sources bacteria encounter in the ocean.

In this project, the PhD candidate will aim to mimic under laboratory settings these types of ecological dynamics taking place in the ocean. He/she will develop a bacterial arena by using microfluidics tools to generate controlled, dynamic pulses of nutrients delivered at the microscale and to simultaneously observe bacterial dynamics from behavioral through to reproductive timescales. The student will perform live 3D imaging of swimming cells through Digital Holographic Microscopy (DHM) to characterize single-cell and population-scale movement of bacteria chasing nutrient pulses. Compared to previous approaches, DHM imaging in combination with differential fluorescence labeling, will offer the prospect to achieve much longer bacterial tracks and will reveal the behavioral and metabolic strategies bacteria implement to gain resources under temporally varying and spatially structured nutrient landscapes. The student will have the unique opportunity to learn, develop and apply a range of cutting-edge experimental techniques, including Digital Holographic Microscopy and microfluidic technology, state-of-the-art image analysis, and exposure to biophysical modeling of bacterial chemotaxis and growth.

The successful candidate will have a background in biophysics, engineering, or biology with a strong quantitative inclination and a desire to work experimentally at the interface between biophysics, microbiology and microbial ecology. The student will work in a highly interdisciplinary, cutting-edge, fast-paced research environment, to interact with researchers from many different disciplines, to gain skills in a number of technologies, to learn about fundamental biophysical and ecological processes in microorganisms, and to interact with world-class collaborators within the ITN PHYMOT. The ability to work independently, but also to interact and collaborate within a team, will be great assets.

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