Scientific profile

I am a microbial ecologist with expertise in microbial bioinformatics and data analysis, especially for amplicon sequencing and metagenomics. In my PhD and postdoc work, I have conducted field experiments and guided lab experiments to uncover insights from the field experiments, supported by computational analysis. I am generally interested in how climatic conditions and anthropogenic impact shape soil and plant microbial communities, in terms of composition and functionality, and how microbes and their interactions can improve sustainable agriculture by boosting crop performance with a negligible impact on soil health. In addition, I often provide my computational expertise to projects focused on the dissemination of antibiotic resistance in the environment. My work at UFZ and iDIV primarily focuses on the ecology of soil viruses under different land-use management and climate conditions.

Work Experience

August 2025–Currently, Postdoctoral Researcher (UFZ/iDiv) at Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany.

December 2022–July 2025, Postdoctoral Researcher at Julius Kühn-Institut, Braunschweig, Germany.

September 2021–September 2022, Research Assistant at Aarhus University, Aarhus, Denmark

August 2019–August 2021, Research Assistant at Technische Universität Dresden, Department of Environmental Sciences, Institute for Hydrobiology, Dresden, Germany

August 2016–August 2019, Marie Curie Fellow (ANSWER-ITN) at Technische Universität Dresden, Department of Environmental Sciences, Institute for Hydrobiology, Dresden, Germany

Education

March 2017–March 2022, Doctor of Philosophy (PhD)
Technische Universität Dresden, Department of Hydrosciences, Institute for Hydrobiology, Dresden, Germany

Title of the dissertation: The impact of treated wastewater irrigation on the dissemination of antibiotic resistance in soil, subsoil and groundwater environments. Awarded with summa cum laude.
Supervisor: Prof. Thomas U. Berendonk

November 2013–June 2016, Master of Science (MSc) in Applied Genetics and Biotechnology Aristotle University of Thessaloniki, Faculty of Science, Department of Biology, University Campus, Thessaloniki,Greece,

Title of the graduation thesis: Isolation of microorganisms from wastewater sludge capable to degrade N-acyl-homoserine lactone and investigation of their role in the increase of efficiency membrane bioreactor treating wastewater. Grade: 10/10.
Supervisors: Prof. Minas Yiangou and Prof. Petros Samaras.

September 2007–July 2012, Bachelor of Science (BSc) in Biochemistry and Biotechnology. University of Thessaly, School of Health sciences, Department of Biochemistry and Biotechnology, Larissa, Greece

Title of the graduation thesis: Detection of Mutations in Mitochondrial tRNA Genes in Normal Individuals and Patients with Alzheimer’s Disease. Grade: 10/10.
Supervisor: Dr. Aimilia Zifa

Peer Review Publications

• Gschwind R., Bonnet M., Abramova A., Jarquín-Díaz V.H., Wenne M., Löber U., Godron N., Kampouris I.D., Tskhay F., Nahid F., Debroucker C., Bui-Hai M., el Aiba I., Klümper U., Berendonk T.U., Forslund-Startceva S.K., Zahra R., Bengtsson-Palme J., Ruppé E. (2026) Cefiderocol resistance genes identified in environmental samples using functional metagenomics. ISME J 20. https://doi.org/10.1093/ismejo/wrag010
• Francioli, D., Kampouris, I. D., Kuhl-Nagel, T., Babin, D., Sommermann, L., Behr, J. H., Chowdhury, S. P., Zrenner, R., Moradtalab, N., Schloter, M., Geistlinger, J., Ludewig, U., Neumann, G., Smalla, K., & Grosch, R. (2025). Microbial inoculants modulate the rhizosphere microbiome, alleviate plant stress responses, and enhance maize growth at field scale. Genome Biology 2025 26:1, 26(1), 1–29. https://doi.org/10.1186/S13059-025-03621-7
• Kampouris, I. D., Kuhl-Nagel, T., Behr, J. H., Sommermann, L., Babin, D., Francioli, D., Zrenner, R., Kublik, S., Schloter, M., Ludewig, U., Smalla, K., Neumann, G., Grosch, R., & Geistlinger, J. (2025). Selective recruitment of beneficial microbes in the rhizosphere of maize affected by microbial inoculants, farming practice, and seasonal variations. Environmental Microbiome, 20(1), 1–20. https://doi.org/10.1186/S40793-025-00729-Y
• Raab, M., Schütz, L., Sommermann, L., Babin, D., Kampouris, I., Francioli, D., Grosch, R., Neumann, G., Deubel, A., Geistlinger, J., Bade, K., & Rozhon, W. (2025). Two decades long-term field trial data on fertilization, tillage, and crop rotation focusing on soil microbes. Scientific Data , 12(1). https://doi.org/10.1038/s41597-025-05314-z
• Soufi, L., Kampouris, I. D., Lüneberg, K., Heyde, B. J., Pulami, D., Glaeser, S. P., Siebe, C., Siemens, J., Smalla, K., Grohmann, E., & Gallego, S. (2025). Wastewater-borne pollutants influenced antibiotic resistance genes and mobile genetic elements in the soil without affecting the bacterial community composition in a changing wastewater irrigation system. Journal of Hazardous Materials, 494. https://doi.org/10.1016/j.jhazmat.2025.138680
• Cerecetto, V., Leoni, C., Jurburg, S.D., Kampouris, I.D., Smalla, K., Babin, D., 2024. Pasture-crop rotations modulate the soil and rhizosphere microbiota and preserve soil structure supporting oat cultivation in the Pampa biome. Soil Biol. Biochem. 195, 109451. https://doi.org/10.1016/j.soilbio.2024.109451
• Alygizakis, N., Ng, K., Čirka, Ľ., Berendonk, T., Cerqueira, F., Cytryn, E., Deviller, G., Fortunato, G., Iakovides, I.C., Kampouris, I.D., Michael-Kordatou, I., Lai, F.Y., Lundy, L., Manaia, C.M., Marano, R.B.M., Paulus, G.K., Piña, B., Radu, E., Rizzo, L., Ślipko, K., Kreuzinger, N., Thomaidis, N.S., Ugolini, V., Vaz-Moreira, I., Slobodnik, J., Fatta-Kassinos, D., 2024. Making waves: The NORMAN antibiotic resistant bacteria and resistance genes database (NORMAN ARB&ARG)–An invitation for collaboration to tackle antibiotic resistance. Water Res. 257, 121689. https://doi.org/10.1016/j.watres.2024.121689
• Behr, J.H., Kampouris, I.D., Babin, D., Sommermann, L., Francioli, D., Kuhl-nagel, T., Chowdhury, S.P., Geistlinger, J., Smalla, K., Neumann, G., 2023. Bene fi cial microbial consortium improves winter rye performance by modulating bacterial communities in the rhizosphere and enhancing plant nutrient acquisition 1–17. https://doi.org/10.3389/fpls.2023.1232288
• Kampouris, I.D., Gründger G.F., Christensen J.F., Greer C.W., Kjeldsen K.U., Boone W., Meire L., Rysgaard S., Vergeynst L. 2022. Long-term patterns of hydrocarbon biodegradation and bacterial community composition in epipelagic and mesopelagic zones of an Arctic fjord J. Hazard. 446, 130656. https://doi.org/10.1016/j.jhazmat.2022.130656
• Kampouris, I.D., Klümper, U., Kramer, L., Sorum, H., Wedekind, H., Berendonk, T.U., 2022. Dissemination of antibiotic resistance in antibiotic-free recirculating aquaculture systems. J. Hazard. Mater. Adv. 8, 100201. https://doi.org/10.1016/j.hazadv.2022.100201
• Kampouris, I.D., Alygizakis, N., Klümper, U., Agrawal, S., Lackner, S., Cacace, D., Kunze, S., Thomaidis, N.S., Slobdonik, J., Berendonk, T.U., 2022. Elevated levels of antibiotic resistance in groundwater during treated wastewater irrigation associated with infiltration and accumulation of antibiotic residues. J. Hazard. Mater. 423, 127155. https://doi.org/10.1016/j.jhazmat.2021.127155
• Kampouris, I.D., Agrawal, S., Orschler, L., Cacace, D., Kunze, S., Berendonk, T.U., Klümper, U., 2021. Antibiotic resistance gene load and irrigation intensity determine the impact of wastewater irrigation on antimicrobial resistance in the soil microbiome. Water Res. 116818. https://doi.org/10.1016/j.watres.2021.116818
• Kampouris, I.D., Klümper, U., Agrawal, S., Orschler, L., Cacace, D., Kunze, S., Berendonk, T.U., 2021. Treated wastewater irrigation promotes the spread of antibiotic resistance into subsoil pore-water. Environ. Int. 146. https://doi.org/10.1016/j.envint.2020.106190
• Kampouris, I.D., Karayannakidis, P.D., Banti, D.C., Sakoula, D., Konstantinidis, D., Yiangou, M., Samaras, P.E., 2018. Evaluation of a novel quorum quenching strain for MBR biofouling mitigation. Water Res. 143, 56–65. https://doi.org/10.1016/j.watres.2018.06.030
• Alygizakis, N.A., Urík, J., Beretsou, V.G., Kampouris, I., Galani, A., Oswaldova, M., Berendonk, T., Oswald, P., Thomaidis, N.S., Slobodnik, J., Vrana, B., Fatta-Kassinos, D., 2020. Evaluation of chemical and biological contaminants of emerging concern in treated wastewater intended for agricultural reuse. Environ. Int. 138, 105597. https://doi.org/10.1016/j.envint.2020.105597
• Manaia, C.M., Rocha, J., Scaccia, N., Marano, R., Radu, E., Biancullo, F., Cerqueira, F., Fortunato, G., Iakovides, I.C., Zammit, I., Kampouris, I., Vaz-Moreira, I., Nunes, O.C., 2018. Antibiotic resistance in wastewater treatment plants: Tackling the black box. Environ. Int. 115, 312–324. https://doi.org/10.1016/j.envint.2018.03.044
• Rocha, J., Cacace, D., Kampouris, I., Guilloteau, H., Jäger, T., Marano, R.B.M., Karaolia, P., Manaia, C.M., Merlin, C., Fatta-Kassinos, D., Cytryn, E., Berendonk, T.U., Schwartz, T., 2020. Inter-laboratory calibration of quantitative analyses of antibiotic resistance genes. J. Environ. Chem. Eng. 8, 102214. https://doi.org/10.1016/j.jece.2018.02.022