Master projects available in the Stocker lab

Coupling between surface- and ground-carbon cycling delineated by millifluidics: Implications for soil respiration in a changing environment

The respiratory release of carbon dioxide (CO2) from the Earth’s soil into the atmosphere is a major, yet poorly understood, flux in the global carbon cycle. Understanding soil respiration sensitivity to elevated atmospheric CO2 (eCO2) and/or climatic warming remains one of the key sources of uncertainty in projecting terrestrial carbon balance and likely future shifts in the global climate. This study aims to deepen our mechanistic understanding of hidden mechanisms neither accounted for by large-scale Earth system models nor readily quantified by field experiments. We specifically explore the role of leaf-level response to eCO2 and/or temperature in regulating soil moisture (water saving effects) and the resulting impacts on CO2 release from soil due to root and rhizomicrobial respiration.

Over the course of this project, students have the opportunity to carry out some of the following tasks as part of their Master thesis:

  • Design and fabrication of millifluidic setups resembling natural soil with microbial habitat subject to various water saturation conditions;
  • Perform experiments to visualize spatio-temporal distribution of soil water and subsurface O2 and/or CO2 gas concentrations (i.e., soil respiration hot spots) in response to changes in environmental conditions;
  • Develop a numerical model and perform simulations to study the flow field and transport through the micromodel;
  • Develop an analytical model to parametrize carbon balance dynamics under prescribed environmental conditions and determine whether (and how) the whole system could be maintained as a carbon sink.

For more information, contact Dr. Erfan Haghighi ( or Dr. Joaquin Jimenez-Martinez (

Bacterial-aerosol interactions in the aquatic surface microlayer

The goal of this Masters project is to investigate bacterial behavior in the aquatic microlayer.  The aquatic microlayer consists of the upper ~500 micrometers of ponds, lakes and oceans, and is characterized by extreme gradients in temperature, nutrient concentration and salinity, in the case of oceans.  It is a fascinating micro-environment as it represents the interface between water and air; buoyant material in the water collects there, and atmospheric material is deposited there.  The microbial and planktonic community in the microlayer, collectively known as the micro-neuston, may play a crucial role in global climate patterns and biogeochemical cycling, via accumulation of organisms and exudates (which may regulate air-sea exchange rates of climatically-relevant gases) and behavioral modes (finding and introducing nutrients available on the surface into elemental cycles).  Despite this, very little is known about the community composition of the microlayer and how bacteria and plankton live and move in this extreme environment.

The Stocker Lab has previously designed and constructed a microscopic visualization system to observe and quantify the behavior of micro-organisms in the microlayer, the characteristics of the microscale flow field, and the interaction of micro-organisms with the physical environment.  Of considerable interest is the question of bacterial chemotaxis in the microlayer, that is, the directed swimming motion of aquatic bacteria towards nutrient sources.  The goal of this project is to consider the interaction of atmospheric aerosols and microbial activity in the surface microlayer. While aerosol deposition may stimulate bacterial growth in the top layer of the ocean, there is currently no microscopic description of bacterial behavior in the microlayer in response to aerosol deposition events.

The main scientific questions are the following:

  • How do bacteria respond to surface-deposited nutrient particles? What are the time scales over which bacteria consume these transient nutrient sources?
  • What role does particle composition (e.g. organic vs. inorganic compounds) and size play in bacterial chemotaxis? What kind of particles would induce the most surface activity in bacteria?
  • In the case of sinking aerosols, would bacteria in the microlayer have privileged access to the resource by encountering the particle first?

During this project, the student will learn to culture various bacteria, conduct behavioral experiments with the microscopic imaging system, process images to extract behavioral metrics, and statistically analyze the resulting data.

For more information, please contact François Peaudecerf ( and Jeanette Wheeler (

Technology development in aquatic microbial ecology

 Aquatic microbes inhabit an ever-changing environment, where they frequently battle predators, viruses, and each other during their quest for nutrients. A key aspect of this micro scale life is the ability to sense and navigate their surroundings, and many aquatic microbes tackle this challenge through swimming informed by chemical sensing. Traditionally, researchers have struggled to observe microbial behavior in the environment, due to a number of technical hurdles. Recently the Stocker Lab has developed several tools that allow measurements of these microbial processes in unprecedented detail at the micro scale; however, our current deployment methods limit the range of habitats we can access with these new technologies. The objective of this research project is to develop and construct a deployment technology for new micro devices designed to study micro scale microbial processes in aquatic environments. Such an advance will make possible the overall goal of understanding how aquatic microorganisms access resources and thereby shape the natural and man-made systems in which they live.

The Masters project will require design and hands-on work with a number of fabrication tools, including (but not limited to) 3D printing, laser cutting, and CNC milling in order to construct new deployment platforms, based on the specific deployment environment. In addition, the student has the possibility to carry out proof of concept experiments, for example to isolate bacteria that are dominant in the selected ecosystem. These isolates could later be used in an extensive bio prospecting campaign in an effort to discover new microbial functions that may be applicable to engineered systems (i.e. drinking water quality, wastewater treatment, bio remediation), with the potential to scale-up and impact human health and well-being. Device deployment could occur in one of several systems, including lakes, rivers, soil, wastewater treatment plants, and drinking water systems.

The candidate should be familiar with prototyping techniques and have some computer-aided design experience. Although previous exposure to environmental microbiology is not a requirement, enthusiasm to develop in this area of knowledge is desirable.

During their project, the student will have the opportunity to carry out some (or all) of the following work:

  • Design and fabrication of a deployment platform for a chosen ecosystem;
  • Plan experiments to isolate key microbes involved in selected environmental processes;
  • Carry out an isolation campaign, whereby microorganisms are isolated from the environment and screened through a combination of molecular methods and microscopy.

For more information, contact Bennett Lambert (

Bacterial dispersion in groundwater

Understanding the transport of bacteria in saturated porous media is crucial for many applications in water management, ranging from the control of bio-clogging in pumping wells to the design of new bioremediation schemes for subsurface contamination. However, little is known about the spatial distribution of bacteria at the pore scale, particularly when small-scale heterogeneities – always present even in seemingly homogeneous aquifers – lead to preferential pathways for groundwater flow. In particular, the coupling of flow and motility has recently been shown to strongly affect bacterial transport, and this leads us to predict that subsurface flow may influence the dispersal of bacteria and the formation of biofilms in saturated aquifers. The specific scope of this project is to study bacterial dispersion in a sinusoidal microchannel, a simplified model that can provide great insight into the basic mechanisms that occur at the pore scale. Although natural media are in general not so simple (and certainly not periodic), the sinusoidal channel represents the simplest system to analyze the effect of the convergence and divergence of streamlines on dispersion, a mechanism that plays a central role for transport in heterogeneous porous media. Furthermore, at fracture scale, the channel model is relevant to understand the role of fracture wall roughness on transport properties.

In this project, the student will have the opportunity to learn the basics of numerical modeling and to become acquainted with microfluidic technology and optical microscopy applied to the study of bacterial transport. Flow in sinusoidal channels with different dimensions will first be studied with numerical methods (e.g., in COMSOL Multiphysics). Depending on the time available, the same geometries will then be modeled using microfluidic channels, where the transport of passive and active tracers will be visualized with an optical microscope and quantified with particle tracking techniques.

For more information, contact Eleonora Secchi ( or Roberto Rusconi (

Investigation of diel changes in buoyancy and self-assembly in the important oceanic cyanobacteria Trichodesmium

In this project, the student will have the chance to generate fundamental insights into the mechanics and ecology of the ocean’s most prominent nitrogen-fixing microorganisms, the filamentous multicellular cyanobacteria of the genus Trichodesmium, which are responsible for one quarter of global nitrogen fixation. Behavior of Trichodesmium in its natural habitat is complex: single filaments self-assemble into two major types of millimeter-scale aggregate structures that likely confer ecological advantages under certain conditions, like iron and phosphate shortage. Aggregates and single filaments can vertically migrate in the water column by changing buoyancy, but only aggregates can get as deep as 150 m, because vertical speed is dependent on aggregate size. Such behavior may allow them to scavenge for phosphate at depth during the night and photosynthesize at the surface during daylight, and may thus play a fundamental role in their contribution to nitrogen fixation.

The aim of this project is to develop an automated 24h-imaging setup that can be used to quantify diel (day-night cycle) changes in aggregation behavior (for example change in aggregate volume with time) and buoyancy (sinking/rising speed), to carry out imaging under several experimental conditions, and, depending on the time available and interests of the student, to analyze quantitatively the resulting videos.

During the project, the student will gain experience in fabrication, including laser cutting, to create a small enclosure for controlled imaging studies, handling of harmless bacterial cultures, and video imaging and analysis. After fabrication of an experimental imaging chamber, the student will carry out experiments to determine the influence of iron and phosphate concentration on buoyancy and self-assembly dynamics under different light regimes and at different stages of growth. The student should be able to work mainly independently on fabrication of the imaging chamber and optimization of the imaging itself, which will be carried out with remotely controlled digital SLR time-lapse photography, possibly involving two cameras. Quantitative video analysis will require some Matlab skills. An interest in the ecological framework of this study is desirable.

An example video showing aggregation of positively buoyant Trichodesmium in a non-optimal set up can be seen here.

For more information, contact Ulrike Pfreundt (

Groundwater on a chip: study of double porosity/permeability using microfluidics

A porous medium consists of interconnected pores (voids or cavities) in a solid material through which a fluid (liquid/gas) can flow. Often, porous media show a bimodal distribution of pore sizes, having macropore and micropore regions. Examples occur in nature in a wide range of biological (tissues, blood vessels) and inorganic (soil, sedimentary rocks) materials, with a long-standing interest for areas such as hydrology (soils and aquifers), petroleum engineering (oil/gas reservoirs), chemical engineering (filters and reactors), and bio-mechanics.

There is evidence that flow and transport processes in this type of porous medium often cannot be described using classical models, which assume uniform flow and transport, and a large number of more complex models have been proposed. The aim of this project is to develop a microfluidic device as a model of double porous media, and study fluid flow and transport experimentally and through numerical analysis.

During the project, the student will have the opportunity to carry out some of the following:

  • Design and microfabrication to develop a microfluidic device to represent a porous medium with bimodal pore size distribution;
  • Perform experiments to visualize and quantify anomalous (non-equilibrium) flow and transport through the micromodel;
  • Develop a numerical model and perform simulations to study the flow field and transport through the micromodel.

For more information, contact Mehdi Salek ( or Joaquin Jimenez-Martinez (

Chemical flow tracing: micro-optode facilitated O2 sensing in aquatic ecosystems

Fluid motion is commonly measured via particle image velocimetry (PIV), in which passive tracer particles added to the fluid (or naturally present within it) allow the visualization and quantification of flow field. While this methodology provides rich data on the physical aspects of fluid motion (e.g. streamlines, flow velocities), it does not provide information on the chemical environment. Chemical measurements, on the other hand, are usually limited to point measurements (using electrochemical or optochemical sensors) or 2D arrays (via planar optode materials), which typically fail to capture the complex and dynamic processes that are the direct result of the physical microenvironment. Thus neither approach in its present implementation can track fluid flow and the chemical microenvironment concurrently, yet such information is vital to understand microscale interactions that are dictated by the interplay between biotic and abiotic factors.

The project will tackle this problem by developing the method of ‘chemically-enabled particle image velocimetry’ (cPIV) to obtain simultaneous information on chemical microenvironments and flow fields. The student will gain hands-on experience in using O2-sensing (“micro-optode”) tracer particles in microfluidic devices, in microscopy, and in image analysis. Together, these technologies will allow the student to perform a stepwise calibration of O2-sensing particles in prescribed gas-gradients and fluid flows. This calibration procedure will involve a careful analysis of the resulting image data to infer physical and chemical processes simultaneously. Once the system is calibrated, the student will use cPIV to detect O2 heterogeneities on complex biological surface environments (for example, coral fragments) and permit a first real-time estimation of mass-transfer processes in aquatic environments.

For more information, contact Lars Behrendt (

Development of a robotic approach to study bacteria in turbulence

The aim of this project is to establish a robotic approach to directly probe the behavioral dynamics of marine microbes under the influence of turbulent stirring. The student will have the opportunity to develop and construct a device with robotic arms to stir a nutrient resource, program the robotic arm to stir the fluid at different rates and with different motion patterns, and use an existing image acquisition system to visualize the resulting bacterial population dynamics in real time. Students do not need prior knowledge in robotics, but a passion for hands-on work and fabrication is a plus. The ultimate goal is to determine how turbulence affects bacterial growth rate, which is a vital component of marine element cycles and thus one of the keystones of global climate.

For more information, contact Yutaka Yawata (