Ecotoxicogenomic Screening

Ecotoxicogenomic Screening for Ecotoxicological Risk Prediction

Pesticides, biocides or pharmaceuticals can display adverse effects in non-target organisms. This may threaten populations with far-reaching consequences for the ecosystem. Therefore, European legislation requires manufacturers to provide data for environmental risk assessment of active substances for registration. The commonly applied OECD tests are time and cost consuming and utilize a substantial number of animals. Thus, they are conducted only in the final stage of substance development, bearing the risk of failing registration due to adverse environmental effects. We offer an early ecotoxicological risk prediction for development compound classes based on their induced molecular changes in aquatic model organisms (see Figure 1). We have applied OMICs to identify gene expression changes as molecular biomarkers for a number of ecotoxicologically well characterized model substances covering a broad range of modes-of-action (MoA). The MoA-specific molecular signatures are linked with the corresponding adverse environmental effects and with the substance structures. The resulting data base has been used to develop targeted molecular screening approaches in order to rank members of development compound classes based on their ecotoxic potential.

Figure 1: Ecotoxicogenomic data acquisition in model organisms using transcriptomics and proteomics approaches. Created by


After uptake by environmental organisms ecotoxic compounds induce molecular events, which initiate a cascade of processes across different organizational layers finally resulting in adverse effects at the level of the organism and the population. A direct link between such molecular initiating events (MIEs) and the subsequent adverse effects is described by the Adverse Outcome Pathway (AOP) concept. As an early response to MIEs, the organism reacts by highly specific changes in gene expression and cell metabolism. That way, the active substance of a pharmaceutical with a given MoA can for example induce gene expression changes in aquatic organisms. This can lead to liver toxicity, neurotoxicity or a reduced reproductive capacity at the organism level and therefore may affect the population. In contrast, non-hazardous active substances do not induce MIEs in environmental organisms and thus do not cause adverse effects at the molecular or organism levels. Hence, highly specific changes in gene expression precede every specific adverse environmental effect. These changes can be assessed in order to obtain an early prediction of ecotoxicity (see Figure 2).


Figure 2: Adverse Outcome Pathway (AOP) concept and prediction approach using gene expression fingerprints of ecotoxic modes-of-action. Created with

Novel molecular biology and bioinformatics methods, referred to as OMICs analyses, allow for a sensitive and global detection of gene expression changes in a wide range of organisms. For several years, OMICs have been applied to assess efficacy and side effects of pharmaceutical active substances in humans. Only recently have OMICs started to be used for the identification of environmental side effects of pesticides, biocides and pharmaceuticals, consequently establishing the novel field of "ecotoxicogenomics". This development opens up new avenues for the detection of early molecular fingerprints and biomarkers in order to identify and differentiate MoA of ecotoxic substances.


We have combined recent transcriptomic and proteomic techniques with ecotoxicological approaches to generate a growing data base linking substance-specific gene expression signatures with adverse effects on the organism and the population. Therefore, aquatic model organisms such as fish larvae, water flea or algae are exposed to sublethal concentrations of reference substances in an environment based on standard OECD test guidelines (see Figure 1). The reference substances are selected to be ecotoxicologically well characterized chemicals with known adverse effects, covering a broad range of MoA. Our data base covers the substance's MoA, the adverse effects on the organism and the population as well as the OMICs-generated molecular fingerprint in aquatic non-target organisms. These data represent the basis for a screening pipeline to rank members of development compound classes based on their ecotoxic potential using a targeted OMICs approach.

Our approach aims at providing an early identification of active substance candidates with low ecotoxic potential. Hence, it supports a time and cost efficient development of environmentally friendly substances.

Selected Publications

Ayobahan, S.U., Alvincz, J., Reinwald, H., Strompen, J., Salinas, G., Schäfers, C., Eilebrecht, E., Eilebrecht, S.
Comprehensive identification of gene expression fingerprints and biomarkers of sexual endocrine disruption in zebrafish embryo
Ecotoxicology and Environmental Safety, 2023,

Essfeld, F., Reinwald, H., Salinas, G., Schäfers, C., Eilebrecht, E., Eilebrecht, S.
Transcriptomic profiling of clobetasol propionate-induced immunosuppression in challenged zebrafish embryos

(2022) Ecotoxicology and Environmental Safety.

Loll, A., Reinwald, H., Ayobahan, S.U., Göckener, B., Salinas, G., Schäfers, C., Schlich, K., Hamscher, G., Eilebrecht, S.
Short-Term Test for Toxicogenomic Analysis of Ecotoxic Modes of Action in Lemna minor

(2022) Environmental Science & Technology.

Feller, F. M.; Eilebrecht, S.; Nedielkov, R.; Yücel, O.; Alvincz, J.; Salinas, G.; Ludwig, K. C.; Möller, H.; Philipp, B.:
Investigations on the Degradation of the Bile Salt Cholate via the 9,10-Seco-Pathway Reveals the Formation of a Novel Recalcitrant Steroid Compound by a Side Reaction in Sphingobium sp. Strain
Chol11. Microorganisms 2021, 9(10), 2146,

Reinwald, H.; Alvincz, J.; Salinas, G.; Schäfers, C.; Hollert, H.; Eilebrecht, S.:
Toxicogenomic profiling after sublethal exposure to nerve- and muscle-targeting insecticides reveals cardiac and neuronal developmental effects in zebrafish embryos.

, 132746 (November 2021),

Pfaff, J.; Reinwald, H.; Ayobahan, S.; Alvincz, J.; Göckener, B.; Shomroni, O.; Salinas, G.; Düring, R.-A.; Schäfers, C.; Eilebrecht, S.:
Toxicogenomic differentiation of functional responses to fipronil and imidacloprid in Daphnia magna,
Aquatic Toxicology, 105927, Vol. 238 (September 2021)

Reinwald, H., König, A., Ayobahan, S., Alvincz, J., Göckener, B., Böhle, G., Shomroni, O., Hollert, H., Salinas, G., Schäfers, C., Eilebrecht, E., Eilebrecht, S.:
Toxicogenomic fin(ger)prints for thyroid disruption AOP refinement and biomarker identification in zebrafish embryos.
Science of the Total Environment., Article number: 143914 (December 2020 online first)
DOI: 10.1016/j.scititenv.2020.143914

Ayobahan, S.; Eilebrecht, S.; Baumann, L.; Teigeler, M.; Hollert, H.; Kalkhof, S.; Eilebrecht, E.; Schäfers, C.:
Detection of biomarkers to differentiate endocrine disruption from hepatotoxicity in zebrafish (Danio rerio) using proteomics.
Chemosphere, Article number: 124970 (2019 online first). Volume 240, February 2020
DOI: 10.1016/j.chemosphere.2019.124970

Ayobahan, S.; Eilebrecht, E.; Kotthoff, M.; Baumann, L.; Eilebrecht, S.; Teigeler, M.; Hollert, H.; Kalkhof, S.; Schäfers, C..:
A combined FSTRA-shotgun proteomics approach to identify molecular changes in zebrafish upon chemical exposure.
Scientific Reports
. Volume 9, Article number: 6599 (2019). DOI: 10.1038/s41598-019-43089-7

Brüggemann, M.; Licht, O.; Fetter, E.; Teigeler, M.; Schäfers, C.; Eilebrecht, E..:
Knotting nets: Molecular junctions of interconnecting endocrine axes identified by application of the adverse outcome pathway concept.
Environmental toxicology and chemistry
37.2 (2018): 318-328. DOI: 10.1002/etc.3995

Muth-Köhne, E.; Westphal-Settele, K.; Brückner, J.; Konradi, S.; Schiller, V.; Schäfers, C.; Teigeler, M.; Fenske, M..:
Linking the response of endocrine regulated genes to adverse effects on sex differentiation improves comprehension of aromatase inhibition in a Fish Sexual Development Test.
Aquatic Toxicology 176 (2016): 116-127. DOI: 10.1016/j.aquatox.2016.04.018