Department Environmental Toxicology

Current master projects

Data base of microplastic particle optical properties based on flow cytometry


Detection and identification of microplastic particles in complex environmental samples or tissues is challenging due to the similarity in size and chemistry of natural and plastic materials in these samples. Measurement by flow cytometry and data analysis by a viSNE-based protocol developed at Eawag1,2 has proven useful to detect microplastic particles in stream biofilms, stream water, tissue and feces. viSNE. Originally developed for leukemia research, it is a tool to map high-dimensional cytometry data onto 2D while conserving high-dimensional structure and is based on the t-Distributed Stochastic Neighbor Embedding (t-SNE) algorithm3. Data is interpreted and particle types are quantified by comparison to reference data sets. Metrics for comparison include light scattering and fluorescence, which, when combined together, may provide a “fingerprint” of microplastics in complex samples. The detection limits of this approach in terms of both particle size and resolution of polymer identity are still unknown. By developing a database using a suite of known microplastic particles with various polymers, both in simple and complex media, this would provide a platform on which to analyse natural samples where unknown microplastics are present.

Proposed workflow

Within the framework of a Master’s thesis, the proposed project aims to establish a database of optical properties of microplastic particles based on flow cytometry data. Data analysis will be done by the viSNE-based protocol to characterize the detection limits in environmental samples with a focus on stream biofilms. To test the viSNE system, a relevant environmental exposure scenario will be constructed to assess microplastic particles in complex media. Stream biofilms are a potential sink for microplastic particles that sediment and interact with the extracellular polymeric substances excreted by biofilm-associated microorganisms, and thus make for an ideal proof of concept framework. Field sampling and controlled growth (setup available at Eawag) of biofilms will be realized in collaboration with Dr Ahmed Tlili/Eawag Environmental Toxicology Department. Guidance in analysis of samples by flow cytometry and data evaluation will be provided by Alexandra Kroll (Ecotox Centre). Microplastic particles from different origin (primary and secondary microplastic particles) will be selected to cover relevant sizes, aspects (e.g. spheres, fibres), polymer types, and additives in collaboration with Dr Denise Mitrano/ Eawag Process Engineering Department.

Suitable candidates for this project are expected to hold a BSc degree in biology, environmental sciences or a related discipline. For further information, please contact Alexandra Kroll, Ahmed Tlili or Denise Mitrano.   


1 Sgier L, Freiman R, Zupanic A, Kroll A. (2016) Flow cytometry combined with viSNE for the analysis of microbial biofilms and detection of microplastics. Nat Comm 7(11587).

2 Sgier, L., Merbt, S. N., Tlili, A., Kroll, A., Zupanic, A. (2018) Characterization of Aquatic Biofilms with Flow Cytometry. J Vis Exp (136), e57655, doi:10.3791/57655.

3 Amir el-AD, Davis KL, Tadmor MD, Simonds EF, Levine JH, Bendall SC, Shenfeld DK, Krishnaswamy S, Nolan GP, Pe'er D. (2013) viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia. Nat Biotechnol. 31(6):545-52.

RAINBOWflow CHIPonline:
A fish cell-based impedance sensor to monitor water quality

BACKGROUND: Biological water quality monitoring serves to assess the environmental state of water bodies to protect organisms living therein as well as to ensure safe water use by humans. Fish are one of the most sought after organisms to monitor for their survival and health because of their well-documented role in food web structures and their link to humans. Yet, water quality monitoring with fish is not only cumbersome and costly – it also consumes many fish, in fact millions every year.

METHODS: We are developing a biosensor for automated water quality testing using live fish cells (an intestinal cell line from rainbow trout) seeded on a chip with six microfluidic channels for impedance sensing. The working principle is that cells attach to the electrodes and form a monolayer covering the bottom surface of the flow-through channel. If a current is applied, the resistance can be measured and interpreted as a function of cell viability; if cells are viable there is resistance, if cells are dying, for example due to toxic compounds in the water, they detach from electrodes and resistance decreases.

AIM: This system is already functionable in the lab, but we need to adapt it to take it to the field and measure water quality on location. For this, we need to assemble a portable, miniaturized, simple impedance analyser, construct a mixing unit in which water is automatically filter-sterilised and mixed with a buffer to obtain isotonic conditions prior to exposure of cells on the chip, in a temperature-controlled system. After prototype testing in the lab we will then test and adjust the device on the LéXPLORE platform on lake Geneva from June to August 2020 ( In addition, we would like to programme the functioning of the unit so that it can be remotely controlled, with automatic analysis and visualisation of the data, which are accessible online.

This is a great opportunity to develop your engineering skills whilst working on an applied project in biology/ecotoxicology, and to get out into the field; if the RAINBOWFLOW CHIPONLINE proves operable on LéXPLORE, it should be ready to use for water quality monitoring in the field, e.g. along effluent inlets in rivers and lakes.

For further information please contact Jenny Maner. This project is being carried out in the Department Environmental Toxicology at Eawag, Dübendorf, and supervised by Prof. Philippe Renaud from the Microsystems Laboratory 4 at EPFL. It is possible to carry this project out from anywhere, with occasional visits to Eawag and EPFL.

Establishment of a CRISPR gene-editing strategy in rainbow trout cell lines

BACKGROUND: One of the main goals in the field of toxicology is the development of Adverse Outcome Pathways (AOPs): an emerging tool aimed at understanding the biochemical and signal transduction pathways that are affected when an organism is exposed to a chemical. An early step in the development of AOPs is the assessment of the toxic action of a chemical at the molecular level. The gene-editing CRISPR/Cas9 technology could help in this field by allowing scientists to specifically modify genes involved in different outcome pathways and observe how the response to the chemical exposure changes.

AIM: The aim of this Master thesis is to establish a CRISPR/Cas9 gene editing system in rainbow trout (Oncorhynchus mykiss) cell lines and use this technology in order to shed light on the molecular processes underlying the chemical action.

METHODS: Research comprises training in: (1) basic molecular biology techniques (e.g. DNA, RNA and plasmid DNA extraction, PCR) and molecular cloning strategies (e.g. Gibson assembly and E. coli transformation), (2) gene editing using the CRISPR/Cas9 system (3) how to culture, transfect and chemically expose fish cell lines (4) fluorescence microscopy and FACS analysis.

If you are eager to learn and implement new technologies and passionate about molecular biology and environmental toxicology, please contact Kristin Schirmer ( or Marina Zoppo ( This research will be performed at the department of Environmental Toxicology, Eawag, in Dübendorf.

Exploring the differences of fish cell lines in sensitivity toward chemical exposure

Background: Current environmental risk assessment for chemicals relies to a large part on experiments with fish. These tests are costly, lengthy, create large volumes of waste and are ethically questionable. In light of this unsatisfying situation, we are developing strategies to predict the impact of chemicals on fish using cell lines from different organs of fish, such as from rainbow trout. Cell line derived parameters alone or combined with computational approaches have been shown to successfully predict fish acute toxicity as well as fish growth and to improve predictions for bioaccumulation. It became apparent as well, that, indeed, cell lines from different organs respond differently to chemical exposure. Exploring such differences in more detail is therefore one of our current aims.

Aim: We offer Master thesis projects that explore the mechanisms by which fish cell lines from different organs respond to chemical exposure and what the causes of sensitivity differences are. Two hypotheses are being followed: (i) Differences stem from distinct toxicokinetic processes in the cells, particularly biotransformation; and (ii) Cells differ in their dynamic processes depending on the chemical structure and cell line origin.

Methods: Basic methods that the candidate will learn are the routine cell culture and how to work with different rainbow trout cell lines and performance of in vitro test assays upon chemical exposure. Depending on the specific project aims, expertise will be gathered in quantifying chemical uptake by the cells, biochemical and molecular effect- as well as computational analyses. 

Interested? If you are excited about this line of research, and have a background in cell biology, environmental toxicology and/or chemistry, please contact Kristin Schirmer ( or Hannah Schug ( The work will be performed at Eawag in the department of Environmental Toxicology in Dübendorf.


The impact of metal exposure on zebrafish:
Investigating the mechanism of hair cell toxicity in zebrafish larvae by behavioral, structural and molecular analysis

Metals are widespread aquatic contaminants and affect aquatic wildlife in different ways. For instance, copper ions have been shown to specifically impair hair cells of the lateral line organ in fish. These cells are sensors of hydrodynamic flows helping the fish to orient, detect predators and prey and communicate with conspecifics. As a consequence, some behavioral responses, such as e.g. rheotaxis, a natural behavioral reaction of fish to orient counter-flow in order to hold a fixed position in a stream, are severely affected in copper-exposed fish.

AIM: The aim of this Master thesis is to investigate the effects of different metals on hair-cell mediated behavior of fish and to explore the mechanism by which these cells are specifically affected.

METHODs: To tackle this question, we are using zebrafish (Danio rerio) larvae, because of several reasons: genomic resources and genetic tools are available, their transparent larval stages enable different optical techniques and their small body size allows the continuous measurement of behavior with full control of the environment.

The impact of metals on hair cells will be elucidated from different angles: 1) Behavioral tests of metal-exposed zebrafish larvae will be performed, 2) hair cell structure and metal distribution will be investigated by different staining techniques followed by bright-field or confocal imaging and 3) the molecular basis of metal transport mechanisms will be studied by whole mount in situ hybridization in zebrafish larvae, which allows to localize gene expression of relevant transporters to specific tissues such as e.g. hair cells. Gene expression will form the basis for further loss-of-function experiments. Depending on the progression, the Master thesis could be extended with such functional tests.

Up to two Master thesis can be offered about this topic, and the project can be tailored to the candidate’s interests.

Suitable candidates for this project are expected to hold a BSc degree in biology, environmental sciences or a related discipline and to have experience in laboratory work.

For further information please contact Colette vom Berg ( or Michael Burkard ( . This work will be performed at Eawag in the department of Environmental Toxicology in Dübendorf.

Impact of insecticides on the fish developing nervous system

BACKGROUND: Insecticides are extensively used in Switzerland and all over the world to control pests and pathogens in medicine, households, and agriculture. Via spray drift, leaching or run-off they find their way into the aquatic environment where they pose a risk to non-target organisms, such as fish. Toxic effects from insecticides can occur at different organizational levels and may range from easily observable lethal to very subtle behavioral effects. As most insecticides are designed to interfere with neuronal signaling, they are able to adversely affect sensory processing and motor outputs in the fish with extensive ecological consequences.

AIM: We would like to understand the causes underlying the potential locomotion defects in fishes elicited by developmental insecticide exposure. Moreover, we will investigate whether there are critical periods during the development and to what extent adverse effects can be reversed.

METHODS: We will use zebrafish larvae in this study, because behavioral responses can easily be measured and their transparent brain and body allows the use of imaging techniques for the assessment of neuronal defects. We will measure locomotor behavior of larval zebrafish, which have been exposed to insecticides during different stages of their development using a fully automated video tracking system. Neuromuscular defects will be investigated by fluorescent immunohistochemistry and confocal imaging analysis.

The candidate will learn how to 1) breed zebrafish and handle eggs and larvae; 2) measure and analyze zebrafish behavior; 3) perform fluorescent immunostainings, confocal microscopy and imaging analysis.

Suitable candidates for this project are expected to hold a BSc degree in biology, environmental sciences or a related discipline and should have a genuine interest in neuroscience.

For further information please contact Colette vom Berg ( and Sarah Könemann ( This work will be performed at Eawag in the department of Environmental Toxicology in Dübendorf.

Impact of nano- and microplastic fibers on a stream biofilm-grazer system

Particulate plastics (microplastics, fibers, and nanoplastics) are produced either intentionally for their commercial use in consumer products or unintentionally as breakdown fragments of larger synthetic materials (e.g. plastic bottles, polyester textiles, rubber tire wear). Currently, there is little information on the fate, transport and bioavailability of  nanoplastics and microplastic fibers in water bodies. Importantly, knowledge on their potential to interact with organisms and to impact food-webs is largely lacking.

AIMS: Here we aim to quantify interactions of nanoplastics and microplastic fibers with stream microbial biofilms, as well as their potential transfer from biofilms to grazers. Focus will be on examining for transgenerational effects on the snail offspring fitness. Unique metal-doped particulate plastics developed in-house will be used through all experiments, which will both expedite analysis times in determining biota-plastic burden and provide more precise and accurate quantification of plastics throughout the exposure system.

METHODS: The candidate can expect to learn (1) how to set up and maintain experimental mesocosms in a laboratory setting, (e.g. growth and sampling of biofilms and snails), (2) how to register changes in biofilm and snail biology (e.g. growth, respiration, reproduction), and (3) how to quantify particulate plastics in various media, including techniques for particle characterization (e.g. Dynamic light scattering, Nanoparticle tracking analysis, Transmission electron microscopy) and analytical chemistry (e.g. Inductively coupled plasma mass spectrometry)).

Suitable candidates for this project are expected to hold a BSc degree in biology, environmental sciences or a related discipline. For further information please contact Ahmed Tlili ( This work will be performed at Eawag (Dübendorf) in the Department of Environmental Toxicology, and in collaboration with Denise Mitrano ( in the Department of Process Engineering.


Molecular responses to herbicide exposures in stream biofilms

Stream biofilms are complex communities of algae, bacteria and fungi, which play a fundamental ecological role in aquatic ecosystems. Microorganisms composing biofilms are primary targets for herbicides, which can lead to structural and functional alterations of the community, with potential negative consequences for ecosystem functioning. Yet, molecular processes underlying functional and structural responses of biofilms to herbicides are still largely unknown.

AIM: By establishing a set of genes that are specifically regulated in biofilms upon exposure to herbicides, we aim in this project to (i) examine toxicity and adaptive cellular processes, on the transcriptome level, in aquatic biofilms and  (ii) link these processes to community functional and structural alterations.

METHODS: Candidates will learn (1) how to culture and sample biofilms both in the field and in laboratory mesocosms , (2) various techniques for gene expression (mRNA extraction and quantification, qPCR), molecular and functional diversity analyses (genomic DNA extraction and amplification, DGGE, flowcytometry), and (3) quantification of the herbicides in water and biofilms.

Suitable candidates for this project are expected to hold a BSc degree in biology, environmental sciences or a related discipline.

For further information please contact Ahmed Tlili ( This work will be performed at Eawag in the department of Environmental Toxicology in Dübendorf.



Prof. Dr. Kristin SchirmerHead of departmentTel. +41 58 765 5266Send Mail
Dr. Marc SuterDeputy Department HeadTel. +41 58 765 5479Send Mail


We are actively involved in formal course instructions and thesis supervision.


Course Title

Course Number     Persons Involved

Advanced Ecotoxicology (ETHZ)


Rik Eggen, Elisabeth Janssen,Kristin Schirmer, Marc Suter, Ahmed Tlili

Practical Course in Molecular Ecotoxicology (ETHZ)


Kristin Schirmer, Colette vom Berg, Stephan Fischer (Aquatox Solutions)

Introduction to Toxicology (ETHZ)


Rik Eggen, Melanie Erzinger, Shana Sturla

Ecotoxicology (EPFL)


Kristin Schirmer, Michael Burkhard, Julita Stadnicka

Chemistry of Aquatic Systems (ETHZ)


Lenny Winkel, Ahmed Tlili

Computational Biology and Bioinformatics Seminar (ETHZ)


Jörg Stelling, Manfred Claassen, Dagmar Iber, Tanja Stadler, Anze Zupanic

Grundlagen der Umweltchemie und Ökotoxikologie (ETHZ)


Kathrin Fenner, Juliane Hollender, Colette vom Berg

Seminar für Bachelor-Studierende: Biogeochemie (ETHZ)


Gerhard Furrer, Ruben Kretzschmar, Colette vom Berg

Division Analytical Sciences - Courses

Marc Suter is the current president of the Division Analytical Sciences (DAS) of the Swiss Chemical Society (SCS)which offers a wide range of further education courses in the fields of analytical sciences such as separation, spectroscopy, analytical applications, methods of biotechnology and life sciences as well as quality assurance and information management.

From beginners to experts, all levels of users are targeted. The courses are offered in collaboration with industrial partners to ensure the relevance of application.

A great number of courses are held at Eawag, which also hosts the DAS course office run by Esther Wolff.


The complete list of courses can be found HERE.





Esther WolffDAS course officeTel. +41 58 765 5200Send Mail
Dr. Marc SuterDeputy Department HeadTel. +41 58 765 5479Send Mail