Department Environmental Chemistry

Open master thesis topics 2020

Analysis of antibiotics in sewage sludge and compost using LC-MS/MS

Preferred starting date: Mid 2020

Antibiotics are widely used pharmaceuticals that pose a risk to the aquatic environment and through antibiotic resistance potentially also to human health. Antibiotics usually end up in wastewater treatment plants (WWTPs) where parts of them are degraded. However, relevant concentrations can still enter the environment via the treated water or via sludge that is used in many countries as agricultural soil amendment.

In Switzerland, the agricultural use of sewage sludge has been banned. However, it I discussed to what extent residues from composting toilets (often mixtures of feces and sawdust) are permitted to be used as fertilizer. The number of public composting toilets in Switzerland is increasing and the potential environmental risks of their residues need to be assessed.

Hence, in this study we investigate sludge samples of WWTPs for selected antibiotics to investigate per capita fluxes for Switzerland. Furthermore, levels of antibiotics in fecal compost samples are determined and compared to sludge levels. The results will contribute to assessing the risk of using sludge or fecal compost for agricultural purposes.

In this project, the student is able to develop comprehensive skills related to the chemical analysis of trace organic pollutants in complex sample matrices.

  • Method optimization/validation for the analysis of selected antibiotics in sewage sludge and compost
  • Sample preparation of sludge and compost samples (extraction and clean-up procedures)
  • Chemical analysis of processed samples with LC-MS/MS
  • Statistical analysis, evaluation of mass flows and data interpretation

Supervision by: Lena Schinkel, Christa McArdell, Juliane Hollender and Michael Berg



Evaluation of organic micropollutant abatement in advanced wastewater treatment

Starting date: as soon as possible

Short description:

The presence of micropollutants in treated wastewater is of increasing concern, due to their release and potential impacts to organisms in receiving waters and drinking water resources downstream of wastewater treatment plants (WWTPs). The new Swiss water protection act implemented as of January 2016 aims at reducing the concentrations of these compounds through advanced wastewater treatment. Ozonation and treatment with powdered activated carbon (PAC) are the methods of choice to reach a sufficient abatement of micropollutants. However, the application of granular activated carbon (GAC) and the combination of ozonation with activated carbon treatment are currently under investigation to evaluate their potential to fulfill the requirements of the new water protection act.

Within the context of the SCREEN-O3TP project, samples have been collected from three WWTPs with GAC and PAC treatment, with and without a pre-treatment with ozone. The aim of this master’s thesis is to quantify the abatement of known micropollutants during advanced wastewater treatment and compare these efficiencies among the different study locations. Also known ozonation transformation products will be evaluated for their fate in GAC and PAC post-treatments. The student will learn how to conduct a quantitative target and qualitative suspect screening for measurement acquired with liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS). He/she will also become acquainted with up-to-date wastewater treatment technologies applied in full scale in Swiss WWTPs. Since all measurements are already done, this master thesis does not involve lab work, but insight can be gained.

Keywords: LC-HRMS, advanced wastewater treatment, target and suspect screening, ozonation transformation products

Supervisors: Christa McArdell & Jennifer Schollee

Does enzyme evolution generated through changes of substrate specificity induce different O2 activation pathways

Preferred start date: Spring 2020

Short Description:

The faulty oxygenation of xenobiotic compounds leads to the formation of reactive oxygen species (ROS) after O2 activation. Those ROS are thought to promote mutations that ultimately lead to the adaptation of exposed microorganisms and their enzymatic machinery to new carbon sources.
In this master thesis we will test this hypothesis by assessing several biochemical indicators for O2 activation and substrate specificity using a microbial strain that has evolved through a substrate adaption processes.

To that end, we will work with Acidovorax sp. strain JS42 as well as mutant strains which were generated by switching from 2-nitrotoluene to 3-nitrotoluene as source of carbon and energy. This selection process has led to enzymes with enhanced affinity for the new substrate compared to the wild type enzyme. While mutations are documented by changes in amino acid residues, information on the efficiency of substrate oxygenation, O2 uncoupling, and the type of activated O2 species are lacking and will be provided in this work. 

Links: Project flyier (; Group webpage (

Supervision: Thomas Hofstetter (, Charlotte Bopp (

Oxygenation efficiency of nitroarene dioxygenases

Preferred start date: August 2019

Short Description:

Iron-containing oxygenases catalyse the initial step of the most important biodegradation reactions of aromatic pollutants but can also give rise to oxidative stress upon faulty oxidation reactions. Despite their importance for microbial contaminant metabolism, their catalytic mechanisms are poorly understood. With the study proposed in this master thesis, we aim at understanding basic aspects of the active site chemistry of Rieske non-heme ferrous iron dioxygenases that lead to both ``good'' results, that is pollutant degradation, and ``bad'' side effects through the generation of toxic reactive oxygen species. Using dioxygenases that are capable of oxygenating nitroaromatic compounds, we plan to establish quantitative relationships for the ``efficiency'' with which these enzymes incorporate molecular O2 into the aromatic contaminants vs. the amount of O2 that ends up in reactive oxygen species. We hypothesize that the degree of such O2 uncoupling is correlated with the expression of the kinetic isotope effect for the hydroxylation of the aromatic substrate. This hypothesis will be tested with measurements of mass- and electron balances as well as a characterization of enzyme kinetics. 

Links: Project flyier (; Group webpage (

Supervision: Thomas Hofstetter (, Charlotte Bopp (

Effect-based toxicity tests with cyanobacterial toxins

Starting date possible in August 2020

Our ecosystems and drinking water resources are vulnerable not only to anthropogenic pollutants but also to natural toxins. Among the diverse array of known natural toxins, those produced by aquatic organisms such as cyanobacteria (blue green “algae”) are of particular concern to the integrity and safety of water resources due to their direct release in to surface waters during lytic cell death. Given that cyanobacteria are known to produce a diverse mixture of potentially toxic metabolites, strategies are now required to assess which, if any, of the known and emerging cyanobacterial metabolites, in particular those belonging to the family of molecules termed cyanopeptides, truly pose a toxicological risk to global drinking water resources.

In this thesis project – which is jointly hosted by the Environmental Chemistry and Toxicology departments of Eawag - the student will directly contribute to advancing understanding of the toxicological risks posed by emerging cyanobacterial metabolites. To achieve this goal, the student learn how to culture cyanobacteria, extract and purify secondary metabolites (preparative liquid chromatography, ultraviolet-visible spectroscopy and mass spectrometry). The student will then perform toxicological assessments with the purified compounds and mixtures using the internationally accepted zebrafish embryo assay (monitoring of survival, morphological changes by microscopy). We are particularly interested in sublethal effects to evaluate neurotoxicity. Therefore, the student will participate in monitoring behavioral responses to different sensory stimuli. Therefore, students should have a joint interest in toxicological and environmental chemistry, comfortable in reading and communicating in English and be curious and motivated.

In this thesis project, the student will learn about 

  • Cyanobacterial culturing and metabolite production
  • Preparative chromatography and mass spectrometry
  • Zebrafish embryo model tests (dose-response, mixture effects, microscopy, behavioral analysis)
  • Statistical data evaluation

For a successful thesis, you should 

  • have strong interest in environmental toxicology 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: cyanobacteria, toxins, toxicity, zebrafish 

Advisors: Dr. Martin Jones (primary), Dr. Colette vom Berg, Dr. Elisabeth Janssen

Please contact: or

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

Starting date:  as soon as possible

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

LC-Orbitrap-MS is a powerful tool to analyze micropollutants in environmental samples such as wastewater effluent. However, it is often difficult to pinpoint to the most environmentally important signal. Through combination with ICP-MS-MS one could obtain further information on the content and distribution of the elements S, Br, Cl and I, which are often associated with high toxicity. This valuable information is then used to prioritize and identify novel emerging contaminants.

In this Masterthesis we aim to combine ICP-MS and Orbitrap MS by developing a suitable mobile LC-system and optimization of both mass spectrometry methods. The established method will be applied to industrial wastewater to locate polluted hotspots and identify novel contaminants of concern.

We encourage Students with a strong background in analytical chemistry or some experience with one of the two mass spectrometers to apply. During your time at EAWAG you will get hands on experience on two cutting-edge mass spectrometers (Orbitrap and ICP-MS/MS) and learn valuable skills of data analysis and in depth understanding of high resolution mass spectrometry and its potential for structure elucidation.

Key Tasks:

  • Method development and independent hands-on experience on ICP-MS and LC-Orbitrap-MS, two state of the art powerful mass spectrometers
  • Application to real samples from an industrial wastewater treatment plant
  • Identification of chromatographic hot spots and structure elucidation of interesting peaks by high-resolution tandem mass spectrometry


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