Doctoral Student in Environmental Bioengineering

The Environmental Microfluidics Group of Prof. Roman Stocker in the Institute of Environmental Engineering is seeking a dynamic and motivated 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 the project is a joint effort with Prof.

Jonasz Slomka at the University of Warsaw. This position will be based in the laboratory of Prof. Roman Stocker.

Bacterial conjugation, the contact-dependent transfer of plasmids between cells, speeds up bacterial evolution and is a major route for the spread of antibiotic resistance in the environment, which in turn poses a global health threat. Aquatic environments are full of microscale chemical hotspots, such as the nutrient-rich 'phycosphere' around phytoplankton and sinking marine particles, and chemo tactic bacteria are known to find and accumulate rapidly at these locations.

This project will test the hypothesis that this accumulation enhances plasmid spreading in the environment, contributing to a cutting-edge view of the role of antibiotic resistance in nature.

The project seeks to study when, where and how strongly this enhancement operates across different chemical hotspots, fluid flows and bacterial strains, and what it means for the spread of antibiotic resistance among aquatic bacteria.

This is a primarily experimental PhD at the interface of engineering and microbiology. The student will:

• Design, build and characterize new instrumentation to couple existing chemotaxis assays to controlled shear systems. This includes 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 a range of chemo attractants, with the opportunity to learn and use advanced 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 in the environment.
• Contribute data to mathematical models of plasmid spread.

We are looking for a hands-on, skilled and curious engineer who loves to build new tools and is interested in using them to answer fundamental scientific questions. Ideal candidates hold an MSc degree in bioengineering, mechanical engineering, mechatronics, electrical engineering, environmental engineering, physics or a related discipline, and have some (not necessarily all) of the following skills:

• Practical experience in prototyping and manufacturing, for example CAD, 3D printing, machining (strongly preferred).
• Experience with control systems and instrumentation, for example motor control, sensors, microcontrollers, and automation or data‑acquisition code (Python, MATLAB, LabVIEW or similar) (preferred).
• Openness to gain experience in the microbiology laboratory: bacterial cultures, sterile technique, plate readers and flow cytometry.
• Familiarity with microscopy, image analysis, fluid mechanics or microfluidics (beneficial but not necessary).
• Fluency in English (oral and written), enthusiasm for working in an interdisciplinary and international team, and the drive to pursue scientific excellence (required).

You will be guided by Prof. Roman Stocker and by members of his lab with extensive experience in microbiology, experimental…