Microfluidic investigation of bacterial interactions in the leaf microbiome


Microfluidics, microscopy, plant biology, biophysics, environmental microbiology, phyllosphere

The leaf microbiome, the community of bacteria that live in and on plant leaves, makes a fundamental contribution to how plants interact with pathogenic bacteria and with the environment, and so plays a central role in plant health and disease. Yet little is known about how this bacterial community survives on leaves, from coping with constant drying cycles to regulation of nutrient sharing, and so we lack the basic understanding to know how we might manipulate the microbiome to improve plant health. We are currently developing and deploying microfluidic systems to investigate interactions in the microbiome by monitoring and tracking strains on real leaves as well as in artificial environments designed to pair them and observe interactions. The student working on this project will have the chance to employ microfluidic systems, microscopy tracking as well as standard microbiology techniques to discover novel interactions or biophysical principles governing the life of bacteria on leaves. This is a project for a student who wants to work at the interface of biophysics, environmental engineering and plant biology. Join us!

Skills you will learn

  • Development, fabrication, and deployment of microfluidic experimental platforms
  • Microbiology techniques related to leaf bacteria (bacteria culture, supernatant analyses, etc.)
  • Microscopy (Fluorescence and Confocal)
  • Image analysis (Python)


To screen a collection of natural isolates from leaves for potential interactions, monitor their growth patterns in space and time and correlate them with physical aspects . There is flexibility for the student to suggest complementary experiments using the microfluidic platform.

Project start



Environmental Microfluidics Laboratory, IfU, D-BAUG (ETH Zurich, Hoenggerberg campus)

Project type

This project can be adapted for Master Thesis or Master Project.

Contact details

Dr. Stefano Ugolini gugolini@ethz.ch