Department Environmental Chemistry

Open master thesis topics 2019

Micropollutant distribution dynamics in a small creek:
From water to aquatic invertebrates

Starting Date: Autumn 2019/Spring 2020

Short Description:

The number of chemicals reaching surface waters from agricultural, industrial and personal use is steadily increasing. This can lead to effects on non-target organisms living in the aquatic environment. While for most of the compounds lab studies exist that analyse the uptake into and the effect onto aquatic organisms, it has been shown that there are strong deviation when compared to data collected in the field. For example is the internal concentration of the neonicotinoid pesticides in gammarid species around a 100fold higher than expected based on the measured water concentration and bioaccumulation factors determined in lab studies.

In this project, the temporal dynamics of the micropollution distribution into the most relevant compartments of a small creek (water, sediments, biofilms, detritus and Gammarus invertebrates) are analysed.  

Depending on the interests of the applicant and the starting data, the master thesis can focus on different stages of the analytical process.

Some possibilities:

- Target analysis of a few priority compound in one compartment, including sample work-up, LC-MSMS measurement and target screening.

- Target/Suspect screening for non-priority compounds in pre-measured sample of different compartments and analysis of the distribution dynamics.

-  Suspect/Non-target screening for possible transformation products in premeasured samples. (Only with later start of project)

keywords: LC-HRMS, pesticides, target/suspect screening, bioaccumulation, exposure dynamics

contacts: and

Analysing abiotic transformation of micropollutants across different sediment-water test systems

Starting Date: Between July and September 2019

To date, it remains impossible to fully prevent bioactive and therefore potentially harmful substances, such as pharmaceuticals and pesticides, from entering the aquatic environment. Some pathways through which those pollutants reach surface waters are hardly controllable, e.g. agricultural runoff. The manufacturing and use of chemicals, however, could be controlled more easily. From the regulatory side, there are testing guidelines in place that dictate to assess the transformation potential of chemicals that may enter surface waters prior to their registration on the market. However, there is scientific consensus that transformation kinetics observed in those regulatory studies do not directly project into compound behaviour in the environment. A thorough understanding of relevant system-specific differences that govern the transferability from laboratory to field systems is still missing. This Master Thesis is embedded in the context of a project that targets the connection between a substance’s persistence measured in different regulatory water-sediment test systems and its fate in the environment.  

We follow the dissipation of 44 micropollutants, mostly pharmaceuticals and pesticides, in various laboratory test systems. We then use the observed concentration-time series to estimate transformation rate constants. The ultimate goal is to generate substance-specific and therefore system-independent parameters that can be used to predict transformation kinetics in rivers based on experimental data from lab studies.  

For surface water bodies, the fate and transport of individual compounds is controlled by complex interactions between abiotic and biotic processes such as hydrolysis, direct and indirect phototransformation, microbial biotransformation and sorption. While we are currently investigating biotransformation in running experiments, we are missing information on the abiotic transformation pathways of our target compounds. To close this knowledge gap, we are seeking a student who will perform sorption and phototransformation experiments in the lab.  

Briefly, sorption experiments will be carried out with two different sediments in various solids-to-water ratios at two micropollutant concentration levels representative of lab and field conditions. Samples will then be analysed for solid-sorbed and dissolved compound concentrations using liquid chromatography - mass spectrometry (LC-MS/MS). A sun-simulator will be used to determine direct and indirect phototransformation in samples containing the investigated micropollutant mixture and different contents of dissolved organic matter. In addition to this experimental work, a thorough literature study on previous research on sorption and phototransformation behaviour will be necessary to bring the results in context with existing data.  

We encourage motivated master students with a background in environmental science, analytical chemistry, or related fields to apply. During your time at Eawag, you will perform independent lab work and acquire skills in sample preparation, LC-MS/MS analysis and potentially simple kinetic modelling.  

Keywords: micropollutants, sorption, phototransformation, LC-MS/MS

Advisors: Carolin Seller, Dr. Elisabeth Janssen, Prof. Dr. Kathrin Fenner

Contact: or



Identification of Natural Toxins from cyanobacteria by high resolution mass spectrometry

Starting Date: from June 2019 or later

Our ecosystems and drinking water resources are not only vulnerable towards anthropogenic pollutants. Natural toxins present an additional threat for which we still lack comprehensive risk assessment and management plans. Among the natural toxins from various kingdoms, those produced by aquatic organisms, such as cyanobacteria have a direct entry into our water resources. Cyanobacterial bloom events conquered freshwater resources across the globe, yet the potential risk of many cyanobacterial metabolites remains mostly unknown. Only microcystins, one class of cyanopeptides, have been studied intensively and the wealth of evidence regarding exposure concentrations and toxicity led to their inclusion in risk management frameworks for water quality. However, cyanobacteria produce an incredible diversity of hundreds of cyanopeptides beyond the class of microcystins. The question arises, whether the other cyanopeptides are in fact of no human and ecological concern or whether these compounds merely received (too) little attention thus far.

In this project the student will investigate the production of various cyanotoxins. Briefly, the student will compare the cyanopeptides produced in laboratory cultures to those produced in cyanobacteria in real lake samples. Depending on the period of the thesis work, the student will be involved in taking local lake samples where cyanobacteria bloom in the summer and early fall season. The effect on the toxin production by different growth condition in the field and in the laboratory will be compared. The samples will be analyzed by liquid chromatography with high resolution tandem mass spectrometry. To identify specific toxins, the student will use a data processing workflow established in our group. 

In this Thesis project, the student will learn about 

  • identification and analytical measurement of cyanotoxins (LC-MS/MS, data processing)
  • cultivation of cyanobacteria in the laboratory (sterile work, inoculation)
  • presence of cyanotoxins in local lakes (lake sampling, sample preparation)
  • research environment at the Environmental Chemistry Department at Eawag
  • project planning, experimental routine and data interpretation, writing and presentation skills

For a successful thesis, you should

  • have strong interest in analytical chemistry and environmental science
  • ideally have first experience (practical courses, internships) regarding laboratory work
  • be proficient in speaking and writing in English
  • be enthusiastic and motivated

Keywords: cyanotoxins, production dynamics, LC-MS/MS

Advisors: Dr. Martin Jones, Dr. Elisabeth Janssen

contact: or

Assessing inactivation rates of extracellular enyzmes in surface waters

Starting Date: as soon as possible

Various organisms including bacteria and algae produce extracellular enzymes. These extracellular enzymes are also referred to as “master recyclers” as they turn over vast amounts of organic matter in surface waters, driving carbon and nutrient cycling. The enzymes are released by heterotrophic microorganisms to the environment via active secretion or cell lysis. Once released, extracellular enzymes are exposed to numerous environmental factors that can lead to their inactivation. The activity of an enzyme depends critically on the integrity of its macromolecular structure. Inactivation of extracellular enzymes and therefore changes in their structure need to be better understood to predict their impacts on biogeochemical cycles. Besides studying transformation processed driven by microbes and light, the enzymes can also be inactivated by changing environmental conditions and chemicals that act as inhibitors.

In this Thesis project, the student will learn about mechanisms that inactivate critically important extracellular enzymes in our surface waters. Briefly, the student will work with model enzymes and enzymes from natural biofilms. The student will use colorimetric activity assays to follow the functioning of the enzymes and then test the stability of these enzymes under different solution condition (pH, temperature, etc.) and in the presence of inhibitors. Here, the student will test whether a group of cyclic peptides can inhibit these enzymes including natural toxins produced by cyanobacteria and peptide-based pharmaceuticals.

In this Thesis project, the student will learn about 

  • enzymatic activity assays (HPLC, colorimetric plate reader assays, kinetic rates)
  • dose response batch tests (IC50 values, mixture effects)
  • research environment at the Environmental Chemistry Department at Eawag
  • project planning, experimental routine and data interpretation, writing and presentation skills

For a successful thesis, you should 

  • have strong interest in environmental science and chemistry
  • ideally have first experience (practical courses, internships) regarding laboratory work
  • be proficient in speaking and writing in English
  • be enthusiastic and motivated

Keywords: enyzmes, inactivation rates, inhibition by toxins and pharmaceuticals

Advisors: Christine Egli, Dr. Elisabeth Janssen


Identification of ozonation transformation products during wastewater treatment

Starting date: as soon as possible

Short description:

Ozonation is increasingly applied for the abatement of micropollutants, such as pharmaceuticals and personal care products, during drinking water and wastewater treatment. However, the micropollutants are not fully mineralized but ozonation transformation products (OTPs) are formed. Persistent OTPs might enter the aquatic environment with the effluent of wastewater treatment plants. However, it can be hypothesized that OTPs are better biodegradable during biological post-treatment as their parent micropolluants. Unfortunately, up to now only a few single substance studies are available that test this hypothesis. 


Within the TRANSFO3RM project, laboratory-based ozonation batch experiments with mixtures of micropollutants were performed and measured with liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS) to identify OTP signals. These OTPs were screened for in samples of both a full-scale wastewater and a pilot drinking water treatment plant with biological post-treatment after ozonation. Within this project, the following topics can be tackled for the master thesis, I) differentiation between persistent and biodegradable OTP peaks , II) behavior of biodegradable OTPs over the sandfilter III) structure elucidation of prioritized OTPs, or IV) identification and structure elucidation of persistent OTPs entering the aquatic environment after wastewater treatment. The exact topic of the thesis can be discussed together with the master student depending on her / his interests. Since all experiments are already performed, this master thesis does not involve lab work, but insight can be gained. 

keywords:   LC-HRMS, wastewater treatment with ozone, suspect screening, structure elucidation, (lab work already finished)


Pollution fingerprint of waste water – development of a novel combinatory approach linking LC-ICP-MS and LC-Orbitrap

keywords:   LC-HRMS, LC-ICPMS, non-target screening, industrial and   municipal wastewater


Enzyme mechanisms of oxidative pollutant biodegradation

keywords: Isotope analysis (GC/IRMS, LC/IRMS), protein purification, enzymatic adaptation, reactive oxygen species


Application of effect-directed analysis for the identification of genotoxic byproducts potentially formed during ozonation of wastewater

Starting date: January or February 2020

keywords: wastewater treatment, ozonation, genotoxicity, suspect and non-target screening, effect-directed analysis


Bioaccumulation in stream biofilms

Keywords: Bioaccumulation, sorption, pesticides, pharmaceuticals, field work, extraction, microorganisms

Description: Natural stream biofilms are composed of algae, bacteria, fungi and small protozoan species, which are embedded in an extracellular polymeric matrix. Such riverine biofilms are among the most important and dominant microbial life-forms within streams and rivers, regulating crucial ecosystem processes as, e.g., ecosystem respiration. They also contribute to bioremediation of aquatic habitats by removing anthropogenic pollutants from the water through biotransformation and sorption. However, so far, there are only few studies addressing bioaccumulation of small polar organic micropollutants in biofilms. In previous experiments done in our group, evidence was found that certain compounds tend to bioaccumulate in stream biofilms. However, the mechanisms involved in this process are not fully understood.

This project aims to get more insight in the process of bioaccumulation of polar organic micropollutants in stream biofilms and to close the existing knowledge gaps. 

Project: The project will consist of three major parts: I) Based on previous experiments, the student will develop an experimental protocol to differentiate between sorption (extracellular) and bioaccumulation (intracellular) in stream biofilms. To do so, the biofilm matrix will be split into large, eukaryotic cells, small, prokaryotic cells and extracellular polymeric substances. Those three different compartments will then be used to do bioaccumulation experiments. II) The student will test bioaccumulation in standardized lab experiments with a set of polar and ionizable organic micropollutants. This part of the project is planned to be conducted with pure algae cultures, in order to investigate the potential of algal sorption/bioaccumulation. III) In a last step, the student will carry out a field sampling campaign in order to evaluate bioaccumulation in natural streams.

The MSc student will learn how to properly plan and set up an experiment, will gain knowledge in sophisticated analytical methods (HPLC-HRMS), and learn how to handle and evaluate large chemical and biological datasets.

Advisors: Werner Desiante, Prof. Dr. Kathrin Fenner

Contact: or

Designing and comparing experimental set-ups to study biotransformation in river biofilms

Keywords: Field work, native stream biofilm, artificial substrates, development of experimental setup, pesticides, pharmaceuticals, microorganisms

Description: Stream biofilms consisting of bacteria, algae and other microorganisms play an essential role in aquatic ecosystems. They have been shown to possess the ability to reduce the concentrations of chemical pollutants via e.g. biotransformation, usually demonstrated in controlled laboratory experiments. Naturally, stream biofilms grow on rocks and pebbles, but also on any other submerged surfaces. In order to evaluate processes, such as, e.g., biotransformation, in a consistent way, it is crucial to develop experimental setups that allow for reproducible research. Therefore, stream biofilms that are used for laboratory experiments are often grown on artificial substrates like, e.g., glass plates. In order to increase the biomass/volume ratio, those biofilms are then usually suspended in water, instead of using them in their attached form. Regardless, the consequences of such modifications from the natural appearance are not well investigated. Also, it is not well understood if results gained with such modified systems still can be translated back to behavior in the natural environment.

This project addresses those knowledge gaps by i) developing test systems that are more representative of naturally grown biofilms than the ones used so far, ii) doing biotransformation experiments with the newly developed systems and iii) comparing the results to a standardized testing system.

Project: One goal of this project is the development of an experimental setup that allows using stream biofilms in their native form, i.e. on a solid surface (glass slide, stones/pebbles) in contrast to suspending the biofilms. This experimental system will then be used to assess biotransformation of a mixture of environmentally relevant polar organic micropollutants. To do so, test reactors will be spiked with a set of micropollutants and the decrease of these pollutants will be monitored over time by means of high-performance liquid chromatography-high resolution mass spectrometry (HPLC-HRMS). Finally the outcomes of the different experimental setups will be evaluated (i.e. glass vs. stone vs. suspension). The MSc student will learn how to properly plan and set up an experiment, will gain knowledge in sophisticated analytical methods, and learns how to handle and evaluate large chemical datasets.

Advisors: Werner Desiante, Prof. Dr. Kathrin Fenner

Contact: or