Department Environmental Chemistry

Environmental Fate Modeling

The research group Environmental Fate Modeling investigates microbial biotransformation in natural and engineered systems relevant for water quality. Our aim is to develop predictive models for use in contemporary chemical risk assessment. We combine experimental work and data mining to develop novel tools for the prediction of stable transformation products and chemical persistence.

In our experimental work, we investigate the biotransformation of structurally diverse micropollutants in natural communities. We determine rates and products of biotransformation using modern analytical methods and simultaneously characterize the microbial communities in terms of their active functions using molecular biology tools. In our data-driven work, we collect and curate existing biotransformation data ( We then apply methods from Bayesian statistics and cheminformatics to the data to develop improved algorithms for predicting transformation products and biotransformation half-lives in different environmental settings.

Team leader & Contact

Prof. Dr. Kathrin Fenner Senior scientist / group leader Tel. +41 58 765 5085 Send Mail

Latest publications

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
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
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
Escher, B. I.; Altenburger, R.; Blüher, M.; Colbourne, J. K.; Ebinghaus, R.; Fantke, P.; Hein, M.; Köck, W.; Kümmerer, K.; Leipold, S.; Li, X.; Scheringer, M.; Scholz, S.; Schloter, M.; Schweizer, P. J.; Tal, T.; Tetko, I.; Traidl-Hoffmann, C.; Wick, L. Y.; Fenner, K. (2023) Modernizing persistence–bioaccumulation–toxicity (PBT) assessment with high throughput animal-free methods, Archives of Toxicology, 97, 1267-1283, doi:10.1007/s00204-023-03485-5, Institutional Repository
Hafner, J.; Fenner, K.; Scheidegger, A. (2023) Systematic handling of environmental fate data for model development - illustrated for the case of biodegradation half-life data, Environmental Science and Technology Letters, 10(10), 859-864, doi:10.1021/acs.estlett.3c00526, Institutional Repository
Seller, C.; Varga, L.; Börgardts, E.; Vogler, B.; Janssen, E.; Singer, H.; Fenner, K.; Honti, M. (2023) Do biotransformation data from laboratory experiments reflect micropollutant degradation in a large river basin?, Water Research, 235, 119908 (13 pp.), doi:10.1016/j.watres.2023.119908, Institutional Repository
Zhang, K.; Fenner, K. (2023) enviRule: an end-to-end system for automatic extraction of reaction patterns from environmental contaminant biotransformation pathways, Bioinformatics, 39(7), btad407 (8 pp.), doi:10.1093/bioinformatics/btad407, Institutional Repository
Achermann, S.; Falås, P.; Joss, A.; Mansfeldt, C.; Men, Y.; Vogler, B.; Fenner, K. (2018) Trends in micropollutant biotransformation along a solids retention time gradient, Environmental Science and Technology, 52(20), 11601-11611, doi:10.1021/acs.est.8b02763, Institutional Repository
Wang, Y.; Lai, A.; Latino, D.; Fenner, K.; Helbling, D. E. (2018) Evaluating the environmental parameters that determine aerobic biodegradation half-lives of pesticides in soil with a multivariable approach, Chemosphere, 209, 430-438, doi:10.1016/j.chemosphere.2018.06.077, Institutional Repository
Achermann, S.; Bianco, V.; Mansfeldt, C. B.; Vogler, B.; Kolvenbach, B. A.; Corvini, P. F. X.; Fenner, K. (2018) Biotransformation of sulfonamide antibiotics in activated sludge: the formation of pterin-conjugates leads to sustained risk, Environmental Science and Technology, 52(11), 6265-6274, doi:10.1021/acs.est.7b06716, Institutional Repository
Gulde, R.; Anliker, S.; Kohler, H.-P. E.; Fenner, K. (2018) Ion trapping of amines in protozoa: a novel removal mechanism for micropollutants in activated sludge, Environmental Science and Technology, 52(1), 52-60, doi:10.1021/acs.est.7b03556, Institutional Repository
Latino, D. A. R. S.; Wicker, J.; Gütlein, M.; Schmid, E.; Kramer, S.; Fenner, K. (2017) Eawag-Soil in enviPath: a new resource for exploring regulatory pesticide soil biodegradation pathways and half-life data, Environmental Science: Processes and Impacts, 19(3), 449-464, doi:10.1039/C6EM00697C, Institutional Repository
Wicker, J.; Lorsbach, T.; Gütlein, M.; Schmid, E.; Latino, D.; Kramer, S.; Fenner, K. (2016) enviPath – the environmental contaminant biotransformation pathway resource, Nucleic Acids Research, 44(D1), D502-D508, doi:10.1093/nar/gkv1229, Institutional Repository
Gulde, R.; Meier, U.; Schymanski, E. L.; Kohler, H.-P. E.; Helbling, D. E.; Derrer, S.; Rentsch, D.; Fenner, K. (2016) Systematic exploration of biotransformation reactions of amine-containing micropollutants in activated sludge, Environmental Science and Technology, 50(6), 2908-2920, doi:10.1021/acs.est.5b05186, Institutional Repository

External collaborators

Dr. Emanuel Schmid, SIS, ETH Zürich

Dr. Paola Meynet, academic guest, University Newcastle


Team members

Albert Anguera Sempere Research Assistant: Chemical Data Science Tel. +41 58 765 5119 Send Mail
Janis Anthamatten Bachelor student Tel. +41 58 765 6767 Send Mail
Elia Ceppi Research collaborator Tel. +41 58 765 6808 Send Mail
Dr. José Cordero PostDoc Tel. +41 58 765 5785 Send Mail
Dr. Jasmin Hafner Postdoctoral scientist Tel. Send Mail
Chiel Kaal PhD student Tel. +41 58 765 5543 Send Mail
Martina Kalt PhD student Tel. +41 58 765 5956 Send Mail
Sarah Mayer Master student Tel. +41 58 765 5762 Send Mail
Nicolas Mueller Research Assistant Tel. +41 58 765 6496 Send Mail
Dr. Sarah Partanen Postdoctoral Scientist Tel. +41 58 765 5336 Send Mail
Athira Shankar Research Collaborator Tel. +41 58 765 6431 Send Mail
Dr. Yaochun Yu Postdoctoral scientist Tel. +41 58 765 5695 Send Mail

Ongoing projects

Understanding and predicting the fate of synthetic chemicals under different environmental conditions is essential to evaluate their potential risk for humans and ecosystems...
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....
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…
Pesticides are major environmental pollutants. For this reason, the European Commission (EC) has imposed a stringent pesticide regulatory scheme...
Reading biotransformation half-lives of agrochemicals across different compartments...

Terminated projects

In regulatory hazard and risk assessment chemical persistence is assessed through a tiered system of degradation studies.
Predicting environment-specific biotransformation of chemical contaminants
Biodegradation simulation tests are an essential element of environmental risk assessment in most chemical regulations.
A large variety of micropollutants, from pesticides, pharmaceuticals to personal care products, can reach surface waters through the effluent of wastewater treatments plants or leaching off agricultural soils.