A microfluidic investigation of spatial arrangement of microorganisms in a biofilm for sustainable light-driven wastewater treatmentTitle


Biofilm, phototrophic biofilms, mass transfer in porous media, fluorescence in situ hybridization (FISH), microscopy, microfluidics


The activated sludge process is a biological method for treating sewage or industrial wastewater. It involves aeration and uses biological flocs mainly composed of bacteria. In the past decade, engineering bacteria to form spherical, compact biofilms known as granules, instead of loose flocs, has revolutionized wastewater treatment. Granules enhance the settling times of activated sludge, reducing area and cost requirements by 75% and 25%, respectively. However, conventional aerobic granular sludge technology demands high levels of O2 (up to 70% of operational costs) and results in significant CO2 emissions. Recently, photogranules have gained attention for their potential to achieve sustainable wastewater treatment. Photogranules combine heterotrophic bacteria with phototrophic microorganisms like microalgae and filamentous cyanobacteria. Phototrophs can produce the O2needed by heterotrophs while consuming the CO2 they generate. In addition, phototrophs often produce valuable biopolymers in higher yields than aerobic granules, leading to a great resource-recovery potential from wastewater.

To harness their full potential, it is important to delve into the structure and function of phototrophic biofilms. Biofilms have a complex architecture, consisting of bacterial cells within extracellular polymeric substances like polysaccharides. Biofilms have viscoelastic properties and their structure evolves through the interplay of microbial growth and fluid flow. To date, the relationship between fluid flow and biofilm growth has been studied in microfluidic channels with single bacterial species. However, in nature, diverse microorganisms often coexist within biofilms and are arranged into distinct layers (see attached figure from ref 3), influenced by the structure of the porous medium, light availability, and nutrient consumption rates.

In this project, the MSc student will explore the competition for space and nutrients among different microorganisms within a phototrophic biofilm by studying mass transfer within the porous biofilm matrix. Using biofilm grown in a microfluidic channel, the location of the different microorganisms will be detected by fluorescence in situ microscopy (FISH), and mass transfer will be quantified using a combination of microfluidic experiments, biofilm rheology, and numerical modelling, using the methodology presented in refs 1 and 2.


  1. Kurz, D. L. et al., PNAS 119, e2122202119 (2022).
  2. Kurz, , D. L. et al., Environ. Sci. Technol. (2023) doi:10.1021/acs.est.2c08890.
  3. Javed, M. A. & Hassan, A. A. Microbial mats and its significance in biofuel production. in Basic Research Advancement for Algal Biofuels Production (eds. Srivastava, N. & Mishra, P. K.) 59–75 (Springer, 2023).

Skills you will learn

  • Culture of bacteria and microalgae
  • Microfluidics and optical microscopy
  • Bulk rheometry
  • Image analysis


The aim of this project is to study the relationship between mass transfer in the porous biofilm matrix and the location of the different species within the biofilm. The fundamental understanding gained in this work will later be used to optimize the growth of phototrophic species and biofilm formation in a photobioreactor, allowing sustainable wastewater treatment.

Project start

Earliest start: preferably Jan 01, 2025, but can be discussed. 

Relevant image 


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

Project type

The project can be adapted for a Master thesis or a Master project. 

Contact details

Dr. Eleonora Secchi (esecchi@ethz.ch)