Biodiversity Monitoring

Assessment of biodiversity change and ecosystem monitoring with novel tools

Biodiversity on our planet is being changed drastically due to anthropogenic activities. The effects range from the levels of intraspecific variation over changes in species and ecosystem diversity to altered interactions and ecosystem functions. Since the loss of biodiversity has also direct consequences on mankind, an accurate monitoring of the change is crucial. These data are already mandatory for some legal directives such as the Federal Nature Conservation Act, the European Habitat Directive, the European Water Framework directive or the European Marine Strategy Framework Directive. A major problem, however, is that the current monitoring is typically conducted with limited spatial and temporal resolution as well as only focusing small subsets of biodiversity.   

Molecular biodiversity assessment methods such as DNA barcoding or high-throughput DNA metabarcoding of many organisms at once, or even non-invasive assessment of unsorted environmental samples (soil, water sediment) via environmental DNA offer new approaches for the systemic monitoring of biodiversity focusing on the entire tree of life.

Concept: DNA based ecological quality assessment of streams

Our group develops such novel DNA based monitoring methods for aquatic and terrestrial organisms and evaluates the potential of an implementation in regulatory monitoring together with our partners from academia and authorities.








Blackman, R.C., Mächler, E., Altermatt, F., Arnold, A., Beja, P., Boets, P., Egeter, B., Elbrecht, V., Filipe, A.F., Jones, J.I., Macher, J.N., Majaneva, M., Martins, F.M.S., Múrria, C., Meissner, K., Pawlowski, J., Schmidt Yáñez, P.L., Zizka, V.M.A., Leese, F., Price, B., Deiner, K., 2019. Advancing the use of molecular methods for routine freshwater macroinvertebrate biomonitoring – the need for calibration experiments. MBMG 3, e34735.

Zizka, V.M.A., Geiger, M.F., Leese, F., 2020. DNA metabarcoding of stream invertebrates reveals spatio-temporal variation but consistent status class assessments in a natural and urban river. Ecological Indicators 115, 106383.

Cordier, T., Alonso‐Sáez, L., Apothéloz‐Perret‐Gentil, L., Aylagas, E., Bohan, D.A., Bouchez, A., Chariton, A., Creer, S., Frühe, L., Keck, F., Keeley, N., Laroche, O., Leese, F., Pochon, X., Stoeck, T., Pawlowski, J., Lanzén, A., 2020. Ecosystems monitoring powered by environmental genomics: a review of current strategies with an implementation roadmap. Molecular Ecology n/a.

Leese, F., Bouchez, A., Abarenkov, K., Altermatt, F., Borja, Á., Bruce, K., Ekrem, T., Čiampor, F., Čiamporová-Zaťovičová, Z., Costa, F.O., Duarte, S., Elbrecht, V., Fontaneto, D., Franc, A., Geiger, M.F., Hering, D., Kahlert, M., Kalamujić Stroil, B., Kelly, M., Keskin, E., Liska, I., Mergen, P., Meissner, K., Pawlowski, J., Penev, L., Reyjol, Y., Rotter, A., Steinke, D., van der Wal, B., Vitecek, S., Zimmermann, J., Weigand, A.M., 2018. Why We Need Sustainable Networks Bridging Countries, Disciplines, Cultures and Generations for Aquatic Biomonitoring 2.0: A Perspective Derived From the DNAqua-Net COST Action, in: Next Generation Biomonitoring: Part 1, Advances in Ecological Research. pp. 63–99.

Leese, F., Hering, D., Wägele, J.-W., 2017. Potenzial genetischer Methoden für das Biomonitoring der Wasserrahmenrichtlinie. WasserWirtschaft 7–8, 49–53.

Milošević, D., Milosavljević, A., Predić, B., Medeiros, A.S., Savić-Zdravković, D., Stojković Piperac, M., Kostić, T., Spasić, F., Leese, F., 2020. Application of deep learning in aquatic bioassessment: Towards automated identification of non-biting midges. Sci. Total Environ. 711, 135160.

Pawlowski, J., Kelly-Quinn, M., Altermatt, F., Apotheloz-Perret-Gentil, L., Beja, P., Boggero, A., Borja, A., Bouchez, A., Cordier, T., Domaizon, I., Feio, M.J., Filipe, A.F., Fornaroli, R., Graf, W., Herder, J., van der Hoorn, B., Iwan Jones, J., Sagova-Mareckova, M., Moritz, C., Barquin, J., Piggott, J.J., Pinna, M., Rimet, F., Rinkevich, B., Sousa-Santos, C., Specchia, V., Trobajo, R., Vasselon, V., Vitecek, S., Zimmerman, J., Weigand, A., Leese, F., Kahlert, M., 2018. The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems. Sci Total Environ 637–638, 1295–1310.

Zizka, V.M.A., Geiger, M.F., Leese, F., 2020. DNA metabarcoding of stream invertebrates reveals spatio-temporal variation but consistent status class assessments in a natural and urban river. Ecological Indicators 115, 106383.