Doctoral Student in Environmental Bioengineering

About the role

The Environmental Microfluidics Group of Prof. Roman Stocker in the Institute of Environmental Engineering at ETH Zurich is seeking a doctoral student with an engineering background for a project on how bacterial chemotaxis accelerates plasmid transfer, including the spread of antibiotic resistance. The position is funded by a recently awarded SNSF grant and is a joint effort with Prof. Jonasz Slomka at the University of Warsaw; it is based in the professor's laboratory in Zurich.

This is a primarily experimental PhD at the interface of engineering and microbiology. The project tests whether chemotactic bacteria accumulating at microscale chemical hotspots in aquatic environments enhances plasmid spreading, and studies when, where and how strongly this occurs across different hotspots, fluid flows and bacterial strains.

Key responsibilities

• Design, build and characterize new instrumentation coupling chemotaxis assays to controlled shear systems, including mechanical design, 3D printing, control systems and integration with a fluorescence microscope.
• Run chemotaxis and conjugation experiments with bacterial donors and recipients of plasmids and various chemoattractants, learning techniques such as flow cytometry and plate-reader-based plasmid transfer quantification.
• Image and track fluorescently labeled bacteria and chemical plumes in shear flow and analyze the data with quantitative image- and data-analysis pipelines.
• Test clinically relevant bacteria and freshwater (e.g. lake) bacteria to assess the potential for chemotaxis-driven spread of resistance.
• Contribute data to mathematical models of plasmid spread.

Required profile

• MSc degree in bioengineering, mechanical engineering, mechatronics, electrical engineering, environmental engineering, physics or a related discipline.
• Fluency in English (oral and written).
• Enthusiasm for working in an interdisciplinary and international team and drive to pursue scientific excellence.
• Openness to gaining experience in the microbiology laboratory (bacterial cultures, sterile technique, plate readers, flow cytometry).

Required skills

• Preferred: practical experience in prototyping and manufacturing, e.g. CAD, 3D printing, machining.
• Preferred: experience with control systems and instrumentation, e.g. motor control, sensors, microcontrollers, and automation or data-acquisition code (Python, MATLAB, LabVIEW or similar).
• Beneficial but not necessary: microscopy, image analysis, fluid mechanics or microfluidics.

Applications must be submitted online through the university's application portal by December 15, 2026, with a CV, cover letter, transcripts, thesis copy and at least two reference letters.