Staff

Kathrin Fenner

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Prof. Dr. Kathrin Fenner

Senior scientist / group leader

Department Environmental Chemistry

About Me

I am passionate about learning how chemicals degrade in the environment and whether any hazardous transformation products are formed during degradation. The ultimate goal of my research is to develop more accurate methods to assess persistence and risk from transformation product formation in regulatory risk assessment procedures. My research focuses on the following three areas in particular.

  1. Prediction of biodegradation pathways and rates
    Current (Q)SBRs tools to predict biodegradation half-lives produce highly uncertain results and available pathway prediction tools suffer from combinatorial explosion due to a lack of methods to prioritize possible pathways. In my research, I mine biotransformation pathway and rate information to develop novel algorithms for biotransformation prediction. In parallel, my team performs bioreactor experiments with pertinent microbial communities and employ high-resolution mass spectrometry to identify transformation products to use that data to further improve biotransformation prediction
  2. Hazard and risk assessment of transformation products
    The goal of this aspect of my research is to develop models and indicators to predict and assess the environmental fate of transformation products. In collaboration with the team of Prof. B. Escher (UFZ Leipzig, Universität Tübingen) we are developing methods to estimate mixture toxicity of transformation products and their parent compound, using the strong structural resemblance to the parent compounds and what is known about parent toxicity as a guiding principle.
  3. Improved tools for persistence assessment
  4. Persistence assessment is key to all chemical legislations in Europe. In my research, I try to contribute to a critical reflection of current persistence assessment paradigms and methods. For instance, I introduced the concept of joint persistence as novel persistence indicator that accounts for transformation product formation. Currently, I am also working on a project that evaluates the value of the OECD 308 guideline for evaluation of persistence of chemicals at the sediment-water interface.

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Projects

Chemical pollution is a major threat to ecosystems and human health and current regulations seem insufficient to prevent widespread chemical contamination...

High-throughput experimental and computational tools for safe-by-design chemicals
Chemicals are released to the environment through a variety of pathways...

High-throughput biodegradation screening
Understanding and predicting the fate of synthetic chemicals under different environmental conditions is essential to evaluate their potential risk for humans and ecosystems...

enviPath plus
The increasing pollution of the environment by chemicals is a major problem.

KlarA_Prediction of the degradation of pollutants in wastewater treatment plants based on structural degradation relationships
Pesticides are major environmental pollutants. For this reason, the European Commission (EC) has imposed a stringent pesticide regulatory scheme...

ARISTO
At the Rhine monitoring station, the Basel-Stadt Environment and Energy Office (AUE Basel-Stadt) is measuring water contamination with organic micropollutants on a daily basis…

RÜS Data 2.0 - Extended data analysis of LC-HRMS time series
A large number and variety of chemicals used in households, healthcare, industry or agriculture enter our wastewater treatment plants with the domestic and industrial wastewater....

Molecular mechanisms of microbiological pollutant degradation in wastewater treatment and natural waters
When pharmaceuticals end up in the environment...

PREMIER - Prioritisation and Risk Evaluation of Medicines in the EnviRonment

enviPath

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Curriculum Vitae

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Publications

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Bosshard, J., Fenner, K., Singer, H., Anliker, S., & Gulde, R. (2024). Abwasser aus chemisch-pharmazeutischen Synthesebetrieben. Charakterisierung der Stoffeinträge in Gewässer. Aqua & Gas, 104(3), 43-49. , Institutional Repository

Abwassereinträge aus der chemisch-pharmazeutischen Industrie wirken sich messbar auf die stoffliche Belastung der ARA-Abläufe aus und hinterlassen eine hochvariable, standortspezifische Signatur. Betriebsspezifische Messkampagnen helfen den Unternehmen, ihre Einträge adäquat zu erfassen und diese mit gezielten Massnahmen abzusenken.
Hafner, J., Lorsbach, T., Schmidt, S., Brydon, L., Dost, K., Zhang, K., … Wicker, J. (2024). Advancements in biotransformation pathway prediction: enhancements, datasets, and novel functionalities in enviPath. Journal of Cheminformatics, 16(1), 93 (9 pp.). doi:10.1186/s13321-024-00881-6, Institutional Repository

Abstract: enviPath is a widely used database and prediction system for microbial biotransformation pathways of primarily xenobiotic compounds. Data and prediction system are freely available both via a web interface and a public REST API. Since its initial release in 2016, we extended the data available in enviPath and improved the performance of the prediction system and usability of the overall system. We now provide three diverse data sets, covering microbial biotransformation in different environments and under different experimental conditions. This also enabled developing a pathway prediction model that is applicable to a more diverse set of chemicals. In the prediction engine, we implemented a new evaluation tailored towards pathway prediction, which returns a more honest and holistic view on the performance. We also implemented a novel applicability domain algorithm, which allows the user to estimate how well the model will perform on their data. Finally, we improved the implementation to speed up the overall system and provide new functionality via a plugin system.
Scientific contribution: The main scientific contributions are the development of a pathway prediction model applicable to diverse chemicals, a specialized evaluation method for holistic performance assessment, and a novel applicability domain algorithm for user-specific performance estimation. The introduction of two new data sets, and the creation of links to EC classes make enviPath a unique resource in microbial biotransformation research.
Meynet, P., Joss, A., Davenport, R. J., & Fenner, K. (2024). Impact of long-term temperature shifts on activated sludge microbiome dynamics and micropollutant removal. Water Research, 258, 121790 (10 pp.). doi:10.1016/j.watres.2024.121790, Institutional Repository

Micropollutants removal efficiency strongly vary across different aerobic wastewater treatment plants, resulting in their frequent detection in surface and ground waters. Seasonal temperature variation is a major factor influencing plant performance, but it is still unclear how prolonged periods of temperature change impact microbiome and micropollutant biotransformation. This work investigates the effect of long-term temperature variation on the microbial dynamics in an activated sludge system, and the impact on micropollutant biotransformation. Sequencing batch reactors were used as model system and 4–40 °C temperature range was studied. 16S rRNA amplicon sequencing showed that temperature drives microbial structure (gDNA) and activity (RNA), rather than time, and this was stronger below 15 °C and above 25 °C. The microbial community was richest and more diverse at 20 °C, while rarer and more specific taxa became predominant over time, at more extreme temperatures. This suggested that less abundant taxa might be responsible for maintaining the biotransformation capability in the activated sludge at extreme temperatures. Micropollutant biotransformation rates mostly deviated from the classic Arrhenius model below 15 °C and above 25 °C, indicating that prolonged exposure to temperature changes leads to temperature-induced taxonomic shifts, resulting in the emerging of different sets of biotransformation pathways over different temperature ranges.
Schittich, A. R., Fenner, K., Stedmon, C. A., Xu, J., McKnight, U. S., & Smets, B. F. (2024). Coupling pathway prediction and fluorescence spectroscopy to assess the impact of auxiliary substrates on micropollutant biodegradation. Environmental Microbiology, 26(2), e16560 (18 pp.). doi:10.1111/1462-2920.16560, Institutional Repository

Some bacteria can degrade organic micropollutants (OMPs) as primary carbon sources. Due to typically low OMP concentrations, these bacteria may benefit from supplemental assimilation of natural substrates present in the pool of dissolved organic matter (DOM). The biodegradability of such auxiliary substrates and the impacts on OMP removal are tightly linked to biotransformation pathways. Here, we aimed to elucidate the biodegradability and effect of different DOM constituents for the carbofuran degrader Novosphingobium sp. KN65.2, using a novel approach that combines pathway prediction, laboratory experiments, and fluorescence spectroscopy. Pathway prediction suggested that ring hydroxylation reactions catalysed by Rieske-type dioxygenases and flavin-dependent monooxygenases determine the transformability of the 11 aromatic compounds used as model DOM constituents. Our approach further identified two groups with distinct transformation mechanisms amongst the four growth-supporting compounds selected for mixed substrate biodegradation experiments with the pesticide carbofuran (Group 1: 4-hydroxybenzoic acid, 4-hydroxybenzaldehyde; Group 2: p-coumaric acid, ferulic acid). Carbofuran biodegradation kinetics were stable in the presence of both Group 1 and Group 2 auxiliary substrates. However, Group 2 substrates would be preferable for bioremediation processes, as they showed constant biodegradation kinetics under different experimental conditions (pre-growing KN65.2 on carbofuran vs. DOM constituent). Furthermore, Group 2 substrates were utilisable by KN65.2 in the presence of a competitor (Pseudomonas fluorescens sp. P17). Our study thus presents a simple and cost-efficient approach that reveals mechanistic insights into OMP-DOM biodegradation.
Seller-Brison, C., Brison, A., Yu, Y., Robinson, S. L., & Fenner, K. (2024). Adaptation towards catabolic biodegradation of trace organic contaminants in activated sludge. Water Research, 266, 122431 (14 pp.). doi:10.1016/j.watres.2024.122431, Institutional Repository

Trace organic contaminants (TrOCs) are omnipresent in wastewater treatment plants (WWTPs), yet, their removal during wastewater treatment is oftentimes incomplete and underlying biotransformation mechanisms are not fully understood. In this study, we elucidate how different factors, including pre-exposure levels and duration, influence microbial adaptation towards catabolic TrOC biodegradation and its potential role in biological wastewater treatment. Four sequencing batch reactors (SBRs) were operated in parallel in three succeeding phases, adding and removing a selection of 26 TrOCs at different concentration levels. After each phase of SBR operation, a series of batch experiments was conducted to monitor biotransformation kinetics of those same TrOCs across various spike concentrations. For half of our test TrOCs, we detected increased biotransformation in sludge pre-exposed to TrOC concentrations ≥5 µg L−1 over a 30-day period, with most significant differences observed for the insect repellent DEET and the artificial sweetener saccharin. Accordingly, 16S rRNA amplicon sequencing revealed enrichment of taxa that have previously been linked to catabolic biodegradation of several test TrOCs, e.g., Bosea sp. and Shinella sp. for acesulfame degradation, and Pseudomonas sp. for caffeine, cyclamate, DEET, metformin, paracetamol, and isoproturon degradation. We further conducted shotgun metagenomics to query for gene products previously reported to be involved in the TrOCs’ biodegradation pathways. In the future, directed microbial adaptation may be a solution to improve bioremediation of TrOCs in contaminated environments or in WWTPs.
Tian, R., Posselt, M., Miaz, L. T., Fenner, K., & McLachlan, M. S. (2024). Influence of season on biodegradation rates in rivers. Environmental Science and Technology, 58(16), 7144-7153. doi:10.1021/acs.est.3c10541, Institutional Repository

Biodegradation plays a key role in the fate of chemicals in the environment. The variability of biodegradation in time can cause uncertainty in evaluating the environmental persistence and risk of chemicals. However, the seasonality of biodegradation in rivers has not yet been the subject of environmentally relevant testing and systematic investigation for large numbers of chemicals. In this work, we studied the biodegradation of 96 compounds during four seasons at four locations (up- and downstream of WWTPs located on two Swedish rivers). Significant seasonality (ANOVA, p < 0.05) of the first-order rate constant for primary biodegradation was observed for most compounds. Variations in pH and total bacterial cell count were not the major factors explaining the seasonality of biodegradation. Deviation from the classical Arrhenius-type behavior was observed for most of the studied compounds, which calls into question the application of this relationship to correct biodegradation rate constants for differences in environmental temperature. Similarities in magnitude and seasonality of biodegradation rate constants were observed for some groups of chemicals possessing the same functional groups. Moreover, reduced seasonality of biodegradation was observed downstream of WWTPs, while biodegradation rates of most compounds were not significantly different between up- and downstream.
Tian, R., Posselt, M., Fenner, K., & McLachlan, M. S. (2024). Variability of biodegradation rates of commercial chemicals in rivers in different regions of Europe. Environmental Science and Technology, 58(45), 20201-20210. doi:10.1021/acs.est.4c07410, Institutional Repository

Biodegradation is one of the most important processes influencing the fate of organic contaminants in the environment. Quantitative understanding of the spatial variability in environmental biodegradation is still largely uncharted territory. Here, we conducted modified OECD 309 tests to determine first-order biodegradation rate constants for 97 compounds in 18 freshwater river segments in five European countries: Sweden, Germany, Switzerland, Spain, and Greece. All but two of the compounds showed significant spatial variability in rate constants across European rivers (ANOVA, P < 0.05). The median standard deviation of the biodegradation rate constant between rivers was a factor of 3. The spatial variability was similar between pristine and contaminated river segments. The longitude, total organic carbon, and clay content of sediment were the three most significant explanatory variables for the spatial variability (redundancy analysis, P < 0.05). Similarities in the spatial pattern of biodegradation rates were observed for some groups of compounds sharing a given functional group. The pronounced spatial variability presents challenges for the use of biodegradation simulation tests to assess chemical persistence. To reflect the variability in the biodegradation rate, the modified OECD 309 test would have to be repeated with water and sediment from multiple sites.
Yu, Y., Trottmann, N. F., Schärer, M. R., Fenner, K., & Robinson, S. L. (2024). Substrate promiscuity of xenobiotic-transforming hydrolases from stream biofilms impacted by treated wastewater. Water Research, 256, 121593 (9 pp.). doi:10.1016/j.watres.2024.121593, Institutional Repository

Organic contaminants enter aquatic ecosystems from various sources, including wastewater treatment plant effluent. Freshwater biofilms play a major role in the removal of organic contaminants from receiving water bodies, but knowledge of the molecular mechanisms driving contaminant biotransformations in complex stream biofilm (periphyton) communities remains limited. Previously, we demonstrated that biofilms in experimental flume systems grown at higher ratios of treated wastewater (WW) to stream water displayed an increased biotransformation potential for a number of organic contaminants. We identified a positive correlation between WW percentage and biofilm biotransformation rates for the widely-used insect repellent, N,N-diethyl-meta-toluamide (DEET) and a number of other wastewater-borne contaminants with hydrolyzable moieties. Here, we conducted deep shotgun sequencing of flume biofilms and identified a positive correlation between WW percentage and metagenomic read abundances of DEET hydrolase (DH) homologs. To test the causality of this association, we constructed a targeted metagenomic library of DH homologs from flume biofilms. We screened our complete metagenomic library for activity with four different substrates, including DEET, and a subset thereof with 183 WW-related organic compounds. The majority of active hydrolases in the metagenomic library preferred aliphatic and aromatic ester substrates while, remarkably, only a single reference enzyme was capable of DEET hydrolysis. Of the 626 total enzyme-substrate combinations tested, approximately 5% were active enzyme-substrate pairs. Metagenomic DH family homologs revealed a broad substrate promiscuity spanning 22 different compounds when summed across all enzymes tested. We biochemically characterized the most promiscuous and active enzymes identified based on metagenomic analysis from uncultivated Rhodospirillaceae and Planctomycetaceae. In addition to characterizing new DH family enzymes, we exemplified a framework for linking metagenome-guided hypothesis generation with experimental validation. Overall, this study expands the scope of known enzymatic contaminant biotransformations for metagenomic hydrolases from WW-receiving stream biofilm communities.
Zahn, D., Arp, H. P. H., Fenner, K., Georgi, A., Hafner, J., Hale, S. E., … Reemtsma, T. (2024). Should transformation products change the way we manage chemicals?. Environmental Science and Technology, 58(18), 7710-7718. doi:10.1021/acs.est.4c00125, Institutional Repository

When chemical pollutants enter the environment, they can undergo diverse transformation processes, forming a wide range of transformation products (TPs), some of them benign and others more harmful than their precursors. To date, the majority of TPs remain largely unrecognized and unregulated, particularly as TPs are generally not part of routine chemical risk or hazard assessment. Since many TPs formed from oxidative processes are more polar than their precursors, they may be especially relevant in the context of persistent, mobile, and toxic (PMT) and very persistent and very mobile (vPvM) substances, which are two new hazard classes that have recently been established on a European level. We highlight herein that as a result, TPs deserve more attention in research, chemicals regulation, and chemicals management. This perspective summarizes the main challenges preventing a better integration of TPs in these areas: (1) the lack of reliable high-throughput TP identification methods, (2) uncertainties in TP prediction, (3) inadequately considered TP formation during (advanced) water treatment, and (4) insufficient integration and harmonization of TPs in most regulatory frameworks. A way forward to tackle these challenges and integrate TPs into chemical management is proposed.
Coll, C., Fenner, K., & Screpanti, C. (2023). Early Assessment of Biodegradability of Small Molecules to Support the Chemical Design in Agro & Pharma R&D. Chimia, 77(11), 742-749. doi:10.2533/chimia.2023.742, Institutional Repository

The use of agrochemical and pharmaceutical active ingredients is essential in our modern society. Given the increased concern and awareness of the potential risks of some chemicals, there is a growing need to align with 'green chemistry' and 'safe and sustainable by design' principles and thus to evaluate the hazards of agrochemical and pharmaceutical active ingredients in early stages of R&D. We give an overview of the current challenges and opportunities to assess the principle of biodegradability in the environment. Development of new medium/high-throughput methodologies, combining predictive tools and wet-lab experimentation are essential to design biodegradable chemicals early in the active ingredient discovery and selection process.

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Address

E-Mail: kathrin.fenner@eawag.ch
Phone: +41 58 765 5085
Fax: +41 58 765 5802
Address: Eawag
Überlandstrasse 133
8600 Dübendorf
Office: BU F18
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Expert on

biological degradation, mass spectrometry, micropollutants, organic pollutants

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Research Group

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