Microbial degradation of organic pollutants – applications

Soil constitutes the major sink of organic pollutants where the end-up intentionally (pesticides) or unintentionally (veterinary medicines and plastics) through unsustainable disposal practices. Microbial degradation of pesticides and veterinary medicines constitutes the main dissipation process driving their persistence in soil, unlike plastics whose microbial degradation becomes important only upon abiotic processes make these recalcitrant materials vulnerable to biotic transformations. We study the degradation of organic pollutants in soil but further isolate and characterize microorganisms able to actively degrade these pollutants. Eventually the transformation pathways of these chemicals in the isolated microorganisms is determined via advanced analytical methods and omic analyses and their further use in bioremediation approaches or in the development of bioprocesses for the depuration of agro-industrial effluents is explored. We have a rich collection of bacterial and fungal isolates (over 50) able to degrade a wide range of pesticides, antibiotics, anthelminthic compounds and other pharmaceuticals. We have used these microbes as inocula for (a) the treatment of wastewaters from fruit-packaging industries carrying high load of toxic ad persistent fungicides (b) as bioaumentation agents in on-farm biodepuration systems like biobeds firstly introduced in Greece by our group.

Personnel

Dimitrios Karpouzas

, Professor in Enviromental Microbiology & Biotechnology

Publications

Michelioudakis, V., Zafranas, A., Myrisiotis, C., Makri, S., Katsoula, A., Campos, M., Vasileiadis, S., & Karpouzas, D. G. (2026). Comparative Genomic and Transcriptomic Analysis Reveals Why Paenarthrobacter Strains Are Specialists in the Degradation of the Fungicide Iprodione. Microbial Biotechnology, 19(2), e70319. https://doi.org/10.1111/1751-7915.70319

Perruchon, C., Tagkalidou, N., Kalogiouri, N., Katsivelou, E., Karas, P. A., Menkissoglu-Spiroudi, U., Vasileiadis, S., & Karpouzas, D. G. (2025). Isolation of a Sphingomonas strain able to degrade the pleuromutilin antibiotic tiamulin: In vitro characterization of the antibiotic transformation capacity and pathway elucidation via comparative genomics, transcriptomics, and metabolomics. Environmental Science and Pollution Research, 32(40), 23081–23096. https://doi.org/10.1007/s11356-025-36996-y

Karas, P. A., Vasileiadis, S., Papazlatani, C., Batsaki, A., Mavriou, Z., Alexandropoulou, I., Melidis, P., Ntougias, S., & Karpouzas, D. G. (2025). Depuration of fungicide-contaminated effluents from fruit-packaging plants in a full-scale modular bioreactor inoculated with tailor-made microbial inocula. Journal of Hazardous Materials, 494, 138535. https://doi.org/10.1016/j.jhazmat.2025.138535

Papazlatani C., Vasileiadis S., Panagopoulou E., Damalas D., Karas P.A., Gerovasileiou E., Thomaidis N., Karpouzas D.G., (2025) Genomic, transcriptomic and suspect/non-target screening analyses reveal the role of CYP450s in the degradation of imazalil and delineate its transformation pathway by Cladosporium herbarum. Microbial Biotechnology 18:e70102 https://doi.org/10.1111/1751-7915.70102

Lamprou E., Liu H., Lagos S., Cooper M., McLean J., Thiour-Mauprivez C., Spor A., Martin-Laurent F., Rillig M., Karpouzas D.G., (2025) Pesticide, veterinary medicines and microplastics: tripartite interactions drive the transformation of albendazole and pyraclostrobin in agricultural soils. Journal of Agricultural & Food Chemistry https://doi.org/10.1021/acs.jafc.5c09441

Katsivelou E., Perruchon C., Lithtourgidis A., Kotsopoulos T., Vasileiadis S., Karpouzas D.G., (2024) Bioaugmentation of manures by a tiamulin-degrading Sphingomonas as a mean to alleviate environmental dispersal of antibiotic residues. Bioremediation Journal https://doi.org/10.1080/10889868.2024.2343863

Elgueta S., Perruchon C., Rutz T., Rillig JI., Diez M.C., Karpouzas D.G., Campos MA., (2024) Bioaugmentation of a biobed packing material with an iprodione-degrading bacterial consortium enhances the dissipation of iprodione and mitigates adverse effect on the microbiota. Journal of Soil Science and Plant Nutrition https://doi.org/10.1007/s42729-024-01840-8

Sakaveli, F., Petala, M., Tsiridis, V., Karas, P. A., Karpouzas, D. G., & Darakas, E. (2023). Effect of attapulgite on anaerobic digestion of primary sludge and downstream valorization of produced biosolids. Renewable Energy, 217, 119211. https://doi.org/10.1016/j.renene.2023.119211

Kalamaras, S. D., Christou, M. L., Tzenos, C. A., Vasileiadis, S., Karpouzas, D. G., & Kotsopoulos, T. A. (2023). Investigation of the Critical Biomass of Acclimated Microbial Communities to High Ammonia Concentrations for a Successful Bioaugmentation of Biogas Anaerobic Reactors with Ammonia Inhibition. Microorganisms, 11(7), 1710. https://doi.org/10.3390/microorganisms11071710

Lagos, S., Koutroutsiou, K., & Karpouzas, D. G. (2023). Isolation of soil bacteria able to degrade the anthelminthic compound albendazole. PeerJ, 11, e16127. https://doi.org/10.7717/peerj.16127

Papazlatani, C. V., Kolovou, M., Gkounou, E. E., Azis, K., Mavriou, Z., Testembasis, S., Karaoglanidis, G. S., Ntougias, S., & Karpouzas, D. G. (2022). Isolation, characterization and industrial application of a Cladosporium herbarum fungal strain able to degrade the fungicide imazalil. Environmental Pollution, 301, 119030. https://doi.org/10.1016/j.envpol.2022.119030

Lagos, S., Moutzoureli, C., Spiropoulou, I., Alexandropoulou, A., Karas, P. A., Saratsis, A., Sotiraki, S., & Karpouzas, D. G. (2022). Biodegradation of anthelmintics in soils: Does prior exposure of soils to anthelmintics accelerate their dissipation? Environmental Science and Pollution Research, 29(41), 62404–62422. https://doi.org/10.1007/s11356-022-19964-8

Papazlatani, C. V., Karas, P. A., Lampronikou, E., & Karpouzas, D. G. (2022). Using biobeds for the treatment of fungicide-contaminated effluents from various agro-food processing industries: Microbiome responses and mobile genetic element dynamics. Science of The Total Environment, 823, 153744. https://doi.org/10.1016/j.scitotenv.2022.153744

Perruchon, C., Katsivelou, E., Karas, P. A., Vassilakis, S., Lithourgidis, A. A., Kotsopoulos, T. A., Sotiraki, S., Vasileiadis, S., & Karpouzas, D. G. (2022). Following the route of veterinary antibiotics tiamulin and tilmicosin from livestock farms to agricultural soils. Journal of Hazardous Materials, 429, 128293. https://doi.org/10.1016/j.jhazmat.2022.128293

Christou ML., Vasileiadis S., Angelidaki I., Karpouzas D.G., Kotsopoulos T., (2021) Effects of organic loading rate and hydraulic retention time on bioaugmentation performance to tackle ammonia inhibition in anaerobic digestion. Bioresource Technology 320: 124323 https://doi.org/10.1016/j.biortech.2021.125246

Lagos S., Perruchon C., Tsikriki, A., Gourombinos E., Vasileiadis S., Sotiraki S., Karpouzas D.G., (2021) Bioaugmentation of animal feces as a mean to mitigate environmental contamination with anthelmintic benzimidazoles. Journal of Hazardous Materials https://doi.org/10.1016/j.jhazmat.2021.126439

Azis K., Mavriou Z., Karpouzas D.G., Ntougias S., Melidis P., (2021) Evaluation of sand filtration and activated carbon adsorption for the post-treatment of a secondary biologically-treated fungicide-containing wastewater from fruit-packaging plants. Processes 9, 1223. https://doi.org/10.3390/pr9071223

Mavriou, Ζ., Alexandropoulou, I., Melidis, P., Karpouzas, D. G., & Ntougias, S. (2022). Bioprocess performance, transformation pathway, and bacterial community dynamics in an immobilized cell bioreactor treating fludioxonil-contaminated wastewater under microaerophilic conditions. Environmental Science and Pollution Research, 29(20), 29597–29612. https://doi.org/10.1007/s11356-021-16452-3

Christou M.L., Vasileiadis S., Kalamaras SD., Karpouzas D.G., Angelidaki I., Kotsopoulos T., (2020) Ammonia-induced inhibition of manure-based continuous biomethanation process under different organic loading rates and associated microbial community dynamics. Bioresource Technology 320: 124323 https://doi.org/10.1016/j.biortech.2020.124323

Perruchon C., Vasileiadis S., Papadopoulou ES., Karpouzas D.G., (2020) Genome-based metabolic reconstruction unravels the key role of B12 in methionine auxotrophy of an ortho-phenylphenol-degrading Sphingomonas haloaromaticamans. Frontiers in Microbiology 10 January 2020 | https://doi.org/10.3389/fmicb.2019.03009

Katsoula A., Vasileiadis S., Sapountzi M., Karpouzas D.G., (2020) The response of soil and phyllosphere microbial communities to repeated application of the fungicide iprodione: Accelerated biodegradation or toxicity? FEMS Microbiology Ecology fiaa056, https://doi.org/10.1093/femsec/fiaa056

Papazlatani CV., Karas P.A., Tucat G., Karpouzas D.G., (2019) Expanding the use of biobeds: Dissipation and adsorption of pesticides contained in effluents from seed-coating, bulb disinfestation and fruit-packaging activities. Journal of Environmental Management 248: 15 October 2019, 109221 https://doi.org/10.1016/j.jenvman.2019.06.122

Navrozidou E., Remmas N., Melidis P., Karpouzas D.G., Tsiamis G., Ntougias S., (2019) Biodegradation potential and diversity of diclofenac-degrading microbiota in an immobilized cell biofilter. Processes 7(9), 554; https://doi.org/10.3390/pr7090554

Lagos E., Perruchon C., Katsoula A., Karpouzas D.G., (2019) The isolation and characterization of soil bacteria able to rapidly degrade the organophosphorus nematicide fosthiazate. Letters in Applied Microbiology 68: 149-155 https://doi.org/10.1111/lam.13098

Papadopoulou E.S., Genitsaris S., Omirou M., Perruchon C., Stamatopoulou A., Ioannides I., Karpouzas D.G., (2018) Bioaugmentation of thiabendazole-contaminated soils from a wastewater disposal site: Factors driving the efficacy of this strategy and the diversity of the indigenous soil bacterial community. Environmental Pollution 233: 16-25 https://doi.org/10.1016/j.envpol.2017.10.021

Papadopoulou E.S, Perruchon C., Vasileiadis S., Rousidou K., Tanou G., Samiotaki M., Molassiotis A., Karpouzas D.G., (2018) Metabolic and evolutionary insights in the transformation of diphenylamine by a Pseudomonas putida strain unravelled by genomic, proteomic and transcription analysis. Frontiers in Microbiology 9: 676, doi: 10.3389/fmicb.2018.00676

Rousidou C, Karaiskos D, Myti D, Karanasios E, Karas P, Tourna M, Tzortzakakis EA, Karpouzas DG (2017) Distribution and function of carbamate hydrolase genes cehA and mcd in soils: the distinct role of soil pH, FEMS Microbiology Ecology, Volume 93, Issue 1, fiw219, https://doi.org/10.1093/femsec/fiw219

Campos M., Perruchon C., Karas P.A.., Karavasilis D., Diez M.C., Karpouzas D.G., (2017) Biodegradation and rhizosphere-assisted bioaugmentation as strategies for optimization of the dissipation capacity of biobeds. Journal of Environmental Management 187(1): 103-110 https://doi.org/10.1016/j.jenvman.2016.11.031

Perruchon, C., Chatzinotas, A., Omirou, M. et al. Isolation of a bacterial consortium able to degrade the fungicide thiabendazole: the key role of a Sphingomonas phylotype. Appl Microbiol Biotechnol 101, 3881–3893 (2017). https://doi.org/10.1007/s00253-017-8128-5

Perruchon, C., Vasileiadis S., Rousidou C., Papadopoulou E.S., Tanou G., Samiotaki M., Garagounis C., Molassiotis A., Papadopoulou K.K., Karpouzas D.G., (2017) Metabolic pathway and cell adaptation mechanisms revealed through genomic, proteomic and transcription analysis of a Sphingomonas haloaromaticamans strain degrading ortho-phenylphenol. Scientific Reports 7: Article 6449, doi:10.1038/s41598-017-06727-6

Perruchon, C., Pantoleon, A., Veroutis, D. et al. Characterization of the biodegradation, bioremediation and detoxification capacity of a bacterial consortium able to degrade the fungicide thiabendazole. Biodegradation 28, 383–394 (2017). https://doi.org/10.1007/s10532-017-9803-z

Elgueta, S., Correa, A., Campo, M., Gallardo, F., Karpouzas, D., & Diez, M. C. (2017). Atrazine, chlorpyrifos, and iprodione effect on the biodiversity of bacteria, actinomycetes, and fungi in a pilot biopurification system with a green cover. Journal of Environmental Science and Health, Part B, 52(9), 651–657. https://doi.org/10.1080/03601234.2017.1330070

Campos, M., Karas, P. S., Perruchon, C., Papadopoulou, E. S., Christou, V., Menkissoglou-Spiroudi, U., Diez, M. C., & Karpouzas, D. G. (2017). Novel insights into the metabolic pathway of iprodione by soil bacteria. Environmental Science and Pollution Research, 24(1), 152–163. https://doi.org/10.1007/s11356-016-7682-1

Papadopoulou, E.S., Lagos, S., Spentza, F., Vidiadakis, E., Karas, P.A., Klitsinaris, T. and Karpouzas, D.G. (2016), The dissipation of fipronil, chlorpyrifos, fosthiazate and ethoprophos in soils from potato monoculture areas: first evidence for the enhanced biodegradation of fosthiazate. Pest. Manag. Sci., 72: 1040-1050. https://doi.org/10.1002/ps.4092

Perruchon C, Patsioura V, Vasiliadis, S. Karpouzas DG (2016) Isolation and characterisation of a Sphingomonas strain able to degrade the fungicide ortho-phenylphenol. Pest Management Science 72(1): 113-124 DOI: 10.1002/ps.3970.

Karas P.A, Makri S, Papadopoulou ES, Ehaliotis C, Menkissoglu-Spiroudi U, Karpouzas DG (2016) The potential of organic substrates based on mushroom substrate and straw to dissipate fungicides contained in effluents from the fruit-packaging industry – Is there a role for Pleurotus ostreatus. Ecotoxicology and Environmental Safety 124: 447-454 DOI: 10.1016/j.ecoenv.2015.11.022

Rousidou C, Chanika E, Georgiadou D, Soueref E, Katsarou D, Kolovos P, Ntougias S, Tourna M, Tzortzakakis E.A, Karpouzas DG (2016) Isolation of oxamyl-degrading bacteria and identification of cehA as a novel oxamyl hydrolase gene. Frontiers in Microbiology 7: 616 (DOI:10.3389/fmicb.2016. 00616) DOI: 10.3389/fmicb.2016.00616

Karas, P. A., Perruchon, C., Karanasios, E., Papadopoulou, E. S., Manthou, E., Sitra, S., Ehaliotis, C., & Karpouzas, D. G. (2016). Integrated biodepuration of pesticide-contaminated wastewaters from the fruit-packaging industry using biobeds: Bioaugmentation, risk assessment and optimized management. Journal of Hazardous Materials, 320, 635–644. https://doi.org/10.1016/j.jhazmat.2016.07.071