Master projects available in the Stocker lab

Journey to the Centre of the Micro-verse: exploring formation of phytoplankton microbiomes

Keywords
Microfluidics, chemotaxis, phytoplankton, microbiomes, marine microbiology

Description
Marine microalgae (phytoplankton) are amongst the most fundamental primary producers on the planet – these microscopic organisms are responsible for over 50% of the global oxygen and carbon production despite making up only approximately 1% of the Earth’s biomass! Whilst phytoplankton constitute the basis food reservoir for larger marine organisms, they likewise exude a range of dissolved organic matter that is sought out by heterotrophic bacteria. Some bacteria can direct their motion towards these patchy nutrient sources in a process called chemotaxis. In essence, each phytoplankton cell forms the centre of its own micro-verse hosting a wide range of marine bacteria (the algae’s microbiome) who in turn also supply the host with vital vitamins and other essential nutrients. However, despite their ecological significance, such systems remain drastically understudied and establishing an understanding of the composition of such microbiomes is crucial in predicting how fundamental production processes will be affected in our climate-changing world.

In this project, we will explore if bacterial behavioural traits shape the composition of phytoplankton microbiomes. Particularly, the project will assess how cell motility and chemotaxis influence population abundance of individual species within the community. We will approach this project from an inter-disciplinary perspective, drawing on tools and techniques from engineering and biology, including custom in-house tools for chemotaxis assays, microfluidics, single-cell tracking, and sequencing. To this end, we are looking for an enthusiastic student with interest in diving into the fundamental processes of marine microorganisms. During the project, you will be trained in a range of experimental techniques and join the daily life of a world-class interdisciplinary group seeking to unravel the fundamental questions surrounding our ever-evolving oceans.

If you have any questions or wish to hear more about the project, please feel free to reach out to us!

Skills you will learn
• Algal and bacterial cultivation
• Chemotaxis assays
• PCR amplification and sequence analysis
• Microscopy
• Image analysis

Goal
Identification and characterization of motile and chemotactic members of phytoplankton microbiomes

Project start
Earliest start: March 2023
Latest end: TBD

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

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

Relevant image attachment: modified from Seymour et al. Nat Microbiol (2017)
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Contact details
Clara Martínez-Pérez and Richard Henshaw at: martinez@ifu.baug.ethz.ch, rhenshaw@ethz.ch

Impact of chemokinesis on bacteria-particle encounters

Processes controlling biogeochemical cycles are characterized by tight interactions between recycling organisms and their substrate and are therefore highly dependent on encounters between the organisms and the substrate. For example, the encounter rate between marine bacteria and sinking particles of organic matter in the ocean is of particular importance for the ocean carbon cycle. Bacteria are responsible for recycling of 50 Gt of particulate organic carbon in the ocean every year, leaving behind only 1% of the particles that sink and reach the oceans’ sediment where they remain buried and stored for millennia. To enhance particle consumption in the ocean, bacteria evolved a sophisticated toolbox, which includes hydrolytic enzymes, attachment appendages and chemokinesis (i.e. the ability of bacteria to increase their swimming speed in response to high nutrient levels). Yet, the ability of bacteria to sense plumes in the wakes of sinking particles that leak organic matter and use them to increase their encounters and therefore the consumption of organic particles requires further investigation (illustration below).

FigVision

In this thesis, the student will explore the response of bacteria exposed to chemical plumes generated in a controlled manner in a microfluidic device with the goal to evaluate if chemokinetic behavior can increase the encounter rate between bacteria and leaky sinking particles. The student will also use an existing bacteria-particle encounter model to explore the parameter space beyond the experimentally accessible range.

During the project, the student will learn how to culture bacteria, analyze their motile behavior, build microfluidic devices, master imaging techniques, and rationalize experimental observations with a model.

Knowledge of Matlab is recommended but not required.

The thesis will be supervised by Dr. Uria Alcolombri, Dr. Jonasz Słomka and Prof. Roman Stocker.
For more information, please contact Dr. Uria Alcolombri (alcolombri@ifu.baug.ethz.ch) or Dr. Jonasz Słomka (slomka@ifu.baug.ethz.ch).

“Going stealth”: how do bacteria hide for predators?

Keywords
Microfluidics, marine microbial ecology, predation

Description
The marine microbial food web, the combined trophic interactions among marine microorganisms, is the productive base of ocean ecosystems. Bacteria play important roles in these interactions: they can be both consumers of organic matter, as well as prey for mixo- and heterotrophic protists. It has been estimated that the combined cell death due to viral lysis and predation by protists roughly equals the amount of bacterial biomass production in the upper layers of the ocean. Despite this ecological importance, the precise mechanisms of predation are poorly understood, especially compared to our knowledge of bacterial growth physiology.
Bacterial use elongated filaments called flagella to swim in aquatic environments, with speeds that may reach above hundred body lengths per second. This trait is advantageous in dilute environments (swimming motility may increase encounters with nutrient hotspots) but can also be dangerous (by increased probability of encounters with predators). In addition, flagella are a known to be phagocytic activation signal by the immune cells of humans and other animals and, consequently, loss of flagellar expression is thought to act as immune evasion. However, whether possession of a flagella enhances or attenuates predation is a question that has not been studied in aquatic systems.
In this project, we would like to quantify the effect that motility and flagellation have on predation in aquatic systems. Is swimming dangerous? Or is even the possession of the flagella alone that makes them easier to detect by predators?
We offer an interdisciplinary master project to students with a background in biology, physics, chemistry, or a related field. Wet lab skills are a plus, but experience with basic bacterial and algal cell culture is not required.

Skills you will learn
• Bacterial and protist culture techniques
• Development, fabrication, and deployment of microfluidic experimental platforms
• Microscopy
• Data and image analysis using scipts (Python/Matlab)

Goal
Combination of experiments and analysis that improve our understanding of bacterial predation.

Project start
Earliest start: March 1, 2023
Latest end: TBD

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

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

Relevant image attachment
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Contact details
For more information, please contact Dr. Johannes Keegstra (keegstra@ifu.baug.ethz.ch ) or
Dr. Clara Martínez-Pérez (clperez@ethz.ch)

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.

Relevant image attachment
Bild2

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.

Relevant image attachment
Bild1
Contact details
Dr. Stefano Ugolini gugolini@ethz.ch