Utilizing environmental genomics to study multiple agricultural stressor impacts on stream invertebrates and ecosystem functions
Final Report Abstract
The project assessed multiple stressor effects of pesticides and fine sediment on stream invertebrates and ecosystem functioning combining genomic tools and ecological experiments. With the selected approach, we aimed to study effects at individual specimen and species level through differential gene expression analysis (RNAseq), through analysis at community level with DNA metabarcoding and at functional level studying carbon breakdown using functional assays. RNA-sequencing revealed species-specific sensitivities to chlorantraniliprole, with stronger effects on insect species compared to gammaridean amphipods. Transcriptomic analysis showed that stressor exposure generally resulted in metabolic suppression in the freshwater invertebrates, likely reflecting energy allocation to cope with environmental stress. Biotic interactions were found to interfere with organisms' ability to cope with environmental stress at the transcriptomic level. Method tests at community level revealed that quantitative DNA metabarcoding is not achievable at the moment and highlights the need for alternative quantitative assessment approaches. With respect to functional changes, we found the insecticide chlorantraniliprole and fine sediment to limit organic-matter decomposition through different pathways, affecting invertebrate density as well as microbial activity respectively. The research highlighted the importance of considering both abiotic and biotic stressor interactions when assessing the impact of insecticides in natural systems and highlights the power of linking experimental analyses with genomic tools. The project resulted in 11 peer-reviewed publications, 3 software developments, and several laboratory protocols that are now openly available.
Publications
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BOLDigger – a Python package to identify and organise sequences with the Barcode of Life Data systems. Metabarcoding and Metagenomics, 4.
Buchner, Dominik & Leese, Florian
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Invited talk for M.V. Brasseur at the Bayrische Landesanstalt für Landwirtschaft (AK Biodiversität): Insektizideffekte in Flussinsekten.
M.V. Brasseur
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Cooking small and large portions of “biodiversity‐soup”: Miniaturized DNA metabarcoding PCRs perform as good as large‐volume PCRs. Ecology and Evolution, 11(13), 9092-9099.
Buchner, Dominik; Beermann, Arne J.; Leese, Florian & Weiss, Martina
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Wet grinding of invertebrate bulk samples – a scalable and cost-efficient protocol for metabarcoding and metagenomics. Metabarcoding and Metagenomics, 5.
Buchner, Dominik; Haase, Peter & Leese, Florian
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Annual meeting of the German Society of Limnology (DGL) 2022: Multiple stressor effects of deposited fine sediment, increased salinity and reduced flow velocity on the transcriptomic landscape of G. fossarum
M.V. Brasseur
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APSCALE: advanced pipeline for simple yet comprehensive analyses of DNA metabarcoding data. Bioinformatics, 38(20), 4817-4819.
Buchner, Dominik; Macher, Till-Hendrik & Leese, Florian
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Impacts of multiple anthropogenic stressors on the transcriptional response of Gammarus fossarum in a mesocosm field experiment. BMC Genomics, 23(1).
Brasseur, Marie V.; Beermann, Arne J.; Elbrecht, Vasco; Grabner, Daniel; Peinert-Voss, Bianca; Salis, Romana; Weiss, Martina; Mayer, Christoph & Leese, Florian
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Invited talk for International Barcode of Life Webinar (iBOL). 2022. Studying the impacts of multiple stressors on freshwater biodiversity with (Meta)barcoding.
F. Leese
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Annual conference of the German Ecological Society (GfÖ) 2023. Impacts of multiple anthropogenic stressors on the transcriptional response of Gammarus fossarum in a mesocosm field experiment.
M.V. Brasseur
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Annual meeting of the German Society of Limnology (DGL). 2023. Multiple stressor effects in freshwater invertebrates – lessons learned from functional genomics.
M.V. Brasseur
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DNA-basierte Biodiversitätsanalysen im Natur- und Umweltschutz: Welche Optionen haben wir für eine Standardisierung? : eine Handlungsempfehlung aus Forschung & Praxis. BfN/VDI
Leese, F., Woppowa, L., Bálint, M., Höss, S., Krehenwinkel, H., Lötters, S., Meissner, K., Nowak, C., Rausch, P., Rduch, V., Rulik, B., Weigand, A. M., Zimmermann, J., Koschorrek, J. & Züghart, W.
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MitoGeneExtractor : Efficient extraction of mitochondrial genes from next‐generation sequencing libraries. Methods in Ecology and Evolution, 14(4), 1017-1024.
Brasseur, Marie V.; Astrin, Jonas J.; Geiger, Matthias F. & Mayer, Christoph
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Multiple stressor effects of insecticide exposure and increased fine sediment deposition on the gene expression profiles of two freshwater invertebrate species. Environmental Sciences Europe, 35(1).
Brasseur, Marie V.; Buchner, Dominik; Mack, Leoni; Schreiner, Verena C.; Schäfer, Ralf B.; Leese, Florian & Mayer, Christoph
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Predicting environmental stressor levels with machine learning: a comparison between amplicon sequencing, metagenomics, and total RNA sequencing based on taxonomically assigned data. Frontiers in Microbiology, 14.
Hempel, Christopher A.; Buchner, Dominik; Mack, Leoni; Brasseur, Marie V.; Tulpan, Dan; Leese, Florian & Steinke, Dirk
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Transcriptomic sequencing data illuminate insecticide-induced physiological stress mechanisms in aquatic non-target invertebrates. Environmental Pollution, 335, 122306.
Brasseur, Marie V.; Leese, Florian; Schäfer, Ralf B.; Schreiner, Verena C. & Mayer, Christoph
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Fine sediment and the insecticide chlorantraniliprole inhibit organic‐matter decomposition in streams through different pathways. Freshwater Biology, 69(3), 365-375.
Mack, Leoni; Buchner, Dominik; Brasseur, Marie V.; Kaijser, Willem; Leese, Florian; Piggott, Jeremy J.; Tiegs, Scott D. & Hering, Daniel
