The Environmental Microfluidics Lab

Master projects available in the Stocker lab

Biophysics of bacteria-phytoplankton interactions

Keywords
Biophysics, bacterial motility, chemotaxis, microbial ecology, encounter rates, numerical simulations

Description
Interactions between bacteria and phytoplankton cells constitute a major pathway for the flux of organic matter in oceanic biogeochemical cycles. The ability of bacteria to swim and respond to chemical cues (a process known as chemotaxis) is recognized as a crucial driver of these interactions, but quantitative estimates are lacking. We have developed a highly customizable package for simulations of bacterial motility and chemotaxis, to systematically explore the effect of various physical properties on such interactions, informing future modelling approaches. The student working on this proposal will design numerical experiments representing idealistic yet ecologically meaningful scenarios to understand the fundamental physical principles regulating bacteria-phytoplankton interactions.

Skills you will learn
• Physical modelling of biological systems
• Agent-based modelling
• Data analysis
• High-performance computing (ideally using the Julia language, but the student is free to choose different languages if they wish)

Goal
Perform agent-based simulations of bacteria-phytoplankton systems, investigating how different physical properties (bacterial speed, swimming strategy, phytoplankton shape and size…) modulate uptake and interaction rates. There is flexibility for the student to suggest complementary studies.

Project start
Anytime

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

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

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Contact details
Riccardo Foffi: rfoffi@ethz.ch
Dr. Jonasz Słomka: slomka@ifu.baug.ethz.ch

Quantifying the Relevance of Fine-Scale Hydraulics for Fish Stranding from Field Experiments

Keywords
Hydropeaking, Ecohydraulics, Stranding, Particle Image Velocimetry, Larval Fish

Description
Stranding occurs under hydropeaking conditions when fish are exposed to emerging riverbanks and bars. Laboratory and field experiments examined the impact of different biotic and abiotic variables on the number of stranded fish. However, these experiments are unable to address hydraulic variables varying strongly within the study site. Such fine-scale hydraulic changes may carry important cues for fish to detect a receding water line and relocate in time. Hence, by quantifying fine-scale hydraulics at the stranding location of fish we can address open scientific questions: What (hydraulic) conditions affect the stranding rate? Which variables should be considered to describe stranding risk?
Stranding experiments with wild brown trout larvae were conducted at the Hasliaare River in 2019 and 2021: A known number of larvae were released at high flow in a confined area at the riverbank. Here, not only the number but also the precise location of stranded larvae was documented. Additionally, biotic and abiotic variables potentially governing stranding were recorded. However, the relation between stranding location and local hydraulic conditions remains unknown.

Skills you will learn
The project will apply state-of-the-art techniques to quantify hydraulic variables, such as Particle Image Velocimetry, and advanced statistical analysis. It further enhances the student’s knowledge of fish ecology and movement behavior.

Goal
The goal of the Master Project is to quantify the hydraulic variables with high resolution from the raw data and to statistically assess their relevance for stranding.

Project start
From September 2023 on

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

Labels
This project is also available as a Master Thesis with an extended statistical analysis.

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Contact details
Joël Wittmann joelw@ethz.ch
Dr. Luiz Silva lumartins@ethz.ch

How often do bacteria exchange genes in aquatic environments?

Keywords
Bacterial encounters, bacterial conjugation, fluid mechanics, fluorescence microscopy, (machine learning)

Description
Bacteria evolve rapidly because they can share genes not only vertically, from parents to offspring during division, but also horizontally, directly between each other. This ability to speedily exchange genes drives the evolution of life on Earth. It also drives the spread of antimicrobial resistance in pathogenic bacteria, a major emerging public health hazard that could cause 10 million deaths each year by 2050. Conjugation, a key horizontal gene transfer mechanism, involves two steps (see figure). First, an encounter between bacteria needs to occur to establish direct cell–cell contact. Second, transfer of genetic material, such as a resistance-carrying plasmid, takes place through a pilus, a ‘syringe’ through which the material is injected from the donor cell to the recipient cell. Crucially, both steps need to be quantified to accurately characterize conjugation and thus the spread of genetic information. However, to date, these two steps have been treated as one. As a result, it remains unknown whether high or low gene transfer rates originate from frequent encounters or an efficient conjugation mechanism, making it challenging to predict the rates with which genes spread in microbial ecosystems.
In this thesis, the student will carry out experiments to measure the key missing parameter that characterizes gene exchange between bacteria, the probability that a bacterium-bacterium encounter results in a gene (plasmid) exchange. The student will carefully mix two bacterial strains in a fluid using a rheometer to control cell-cell encounters, and use fluorescence microscopy backed up with machine learning to count how many gene transfer events occurred (see figure). During the project, the student will learn how to culture bacteria, perform conjugation experiments and investigate the impact of fluid mixing on the rates of gene exchange between bacteria.

Goal
The finalization of the development of a method to measure the frequency of bacterial conjugation events as a function of the conjugation rate and its application in varying conditions.

Skills you will learn
• Culture and grow bacteria
• Handling of a rheometer
• Performing of conjugation experiments
• Fluorescence microscopy
• Microscopy image analysis
• Critical thinking and protocol optimization

Project start
Earliest start: 19.09.2023
Latest end: 22.12.2023 (Master Project), 21.06.2024 (Master Thesis)

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

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

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Contact details
The thesis will be supervised by Dr. Jonasz Słomka and Prof. Roman Stocker and will be carried out at the Institute of Environmental Engineering.
For more information, please contact Dr. Jonasz Słomka (slomka@ifu.baug.ethz.ch).

How does turbulence control the size of aggregates of Trichodesmium, a key ocean fertilizer?

Keywords
Cyanobacteria, microbial ecology, colony formation in flow, experiments

Description
Trichodesmium, a globally distributed filamentous marine cyanobacterium, can perform nitrogen fixation to fertilize and thus sustain life in nutrient-poor regions of the oceans. Occasionally, it can form large-scale surface blooms spanning tens of thousands of square kilometers. Crucial to its success in colonizing global oceans is its ability to live either as individual filaments or as aggregates of filaments. This dual lifestyle enables Trichodesmium to adapt to changing environments, but it remains unclear what environmental factors control the size of aggregates.

Goal
Aggregates form when turbulence and buoyancy bring individual filaments together by encounters, but turbulence may also break aggregates apart. In this project, the student will perform experiments to study how encounters and fragmentation in turbulence control the size of emerging aggregates. The goal is to expose Trichodesmium cultures to controlled mixing levels and observe, through microscopic imaging, how mixing impacts aggregation.

Skills you will learn
During the project, the student will learn how to culture Trichodesmium, use a rheometer as a precise mixing device that mimics ocean turbulence, and perform image analysis (in (MATLAB or Phyton)) to extract aggregate size spectra.

Project start
01.09.2023 – 30.06.2024

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

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

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Applying a novel microfluidic membrane device to the characterization of biofilm hydraulic resistance

Keywords
Microfluidics, optical microscopy, biophysics, environmental microbiology

Description
Microbial biofilms are communities of bacteria encased within a self-secreted extracellular matrix (ECM). The composition and microstructure of ECM determine biofilm water permeability. Within water treatment systems, such as micro and ultrafiltration membrane filtration, biofilm dramatically increases hydraulic resistance, causing severe energy losses. To improve water filtration systems, we require a systematic understanding of how ECM hydraulic resistance varies as a function of hydrostatic pressure.
Using a novel microfluidic platform, which enables simultaneous monitoring of ECM secretion and hydraulic resistance, you will perform a series of high throughput experiments to reveal the relationship between hydrostatic pressure, biofilm hydraulic resistance, and ECM secretion. Are you a motivated student who wish to work on the interface of biophysics and environmental engineering? Join us!

Skills you will learn
• Development, fabrication, and deployment of microfluidic experimental platforms
• Bacterial culture technique
• Microscopy (Fluorescence and Confocal)
• Image analysis (Python)

Goal
To compile a dataset of hydraulic resistances and structural properties of bacterial biofilms using a library of biofilm ECM mutants. There is flexibility for the student to suggest complementary experiments using the microfluidic platform.

Project start
Earliest start
Latest end

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

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

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Contact details
Dr. Sam Charlton, charlton@ethz.ch, Dr. Eleonora Secchi, esecchi@ethz.ch

Microfluidic investigation of bacterial interactions in the leaf microbiome

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

Description
The leaf microbiome is a fundamental component playing a role in plant health and disease. Little is known on the principles regulating how bacteria live on leaves, from the constant hydration/drying cycles, to nutrient sharing and interactions. We are currently developing and deploying microfluidic systems to investigate these aspects in more detail 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 proposal will have the chance to employ microfluidic systems, microscopy tracking as well as standard microbiology techniques to discover novel interactions or biophysical principle driving the life of bacteria on leaves. This is a project for student who wish to work on 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)

Goal
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
Earliest start: Anytime
Latest end:

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

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

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Contact details
Dr. Stefano Ugolini gugolini@ethz.ch