Isolation of indigenous soil bacteria with potential application for diuron removal

Berk Emre Engin; Hilal Yılmaz; Esra Meşe Erdoğan; Melek Özkan

doi:10.18393/ejss.2005110

Isolation of indigenous soil bacteria with potential application for diuron removal

Abstract

Diuron is a widely used herbicide in sugarcane, cotton, coffee, and citrus production and is classified as a priority pollutant. Physical and chemical remediation of pesticide-contaminated sites is often technically complex and costly. Microorganism-mediated bioremediation offers an environmentally compatible and cost-effective alternative, particularly when pollutant-specific indigenous microorganisms are used. In this study, microorganisms were isolated from diuron-amended soil microcosms, and their diuron removal capacities were evaluated under different pH and temperature conditions. Fourteen bacterial isolates were initially screened, of which six capable of growing in diuron-supplemented medium were selected. Isolates 2 and 6 achieved the highest removal efficiencies, reaching 53% and 51%, respectively, within 3 days. A mixed microbial culture achieved 60% removal, suggesting potential complementary interactions among the isolates. Based on 16S rRNA gene sequencing, isolate 2 showed 97–99% sequence identity to Bacillus sp., whereas isolate 6 showed 97–99% identity to Cellulomonas sp. The study aimed to identify bacterial strains with potential application in future pesticide bioremediation. Indigenous isolates with high pollutant-removal capacity may improve bioremediation performance in their native environments because they are adapted to prevailing local conditions.

Keywords

Supporting Institution

Scientific and Technological Research Council of Türkiye (TÜBİTAK)

Project Number

1919B012303838

Thanks

This study was supported by the Scientific and Technological Research Council of Türkiye (TÜBİTAK) through the 2209-A University Student Research Projects Support Program (Grant No. 1919B012303838). The authors thank Assist. Prof. Dr. Ümit Barış Kutman for his valuable suggestions.

References

Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J., 1990. Basic local alignment search tool. Journal of Molecular Biology 215(3): 403–410.
Alva, A.K., Singh, M., 1990. Sorption of bromacil, diuron, norflurazon, and simazine at various horizons in two soils. Bulletin of Environmental Contamination and Toxicology 45: 365–374.
Arshad, M., Hussain, S., Saleem, M., 2008. Optimization of environmental parameters for biodegradation of alpha and beta endosulfan in soil slurry by Pseudomonas aeruginosa. Journal of Applied Microbiology 104: 364–370.
Asim, N., Hassan, M., Shafique, F., Ali, M., Nayab, H., Shafi, N., Khawaja, S., Manzoor, S., 2021. Characterizations of novel pesticide-degrading bacterial strains from industrial wastes found in the industrial cities of Pakistan and their biodegradation potential. PeerJ 9: e12211.
ASTM, 2009. ASTM D6913: Standard test methods for particle-size distribution (gradation) of soils using sieve analysis. ASTM International, West Conshohocken, PA, USA. Available at [Access date: 16.02.2026]: https://store.astm.org/d6913-04.html
Ayilara, M.S., Babalola, O.O., 2023. Bioremediation of environmental wastes: The role of microorganisms. Frontiers in Agronomy 5: 1183691.
Bagheri, A., Emami, N., Damalas, C.A., 2021. Farmers’ behavior towards safe pesticide handling: An analysis with the theory of planned behavior. Science of the Total Environment 751: 141709.
Barathidasan, K., Reetha, D., Milton, D.J., Sriram, N., Govindammal, M., 2014. Biodegradation of chlorpyrifos by co-culture of Cellulomonas fimi and Phanerochaete chrysosporium. African Journal of Microbiology Research 8(9): 961–966.

Belz, R.G., Carbonari, C.A., Duke, S.O., 2022. The potential influence of hormesis on evolution of resistance to herbicides. Current Opinion in Environmental Science & Health 27: 100360.
Bhati, T., Gupta, R., Yadav, N., Singh, R., Fuloria, A., Waziri, A., Chatterjee, S., Purty, R., 2019. Assessment of bioremediation potential of Cellulosimicrobium sp. for treatment of multiple heavy metals. Microbiology and Biotechnology Letters 47(2): 269–277.
Bokade, P., Gaur, V.K., Tripathi, V., Bobate, S., Manickam, N., Bajaj, A., 2023. Bacterial remediation of pesticide-polluted soils: Exploring the feasibility of site restoration. Journal of Hazardous Materials 441: 129906.
Borowik, A., Wyszkowska, J., Zaborowska, M., Kucharski, J., 2023. Microbial diversity and enzyme activity as indicators of permethrin-exposed soil health. Molecules 28(12): 4756.
Catalá-Icardo, M., López-Paz, J.L., Peña-Bádena, A., 2011. FI-photoinduced chemiluminescence method for diuron determination in water samples. Analytical Sciences 27(3): 291–296.
Chapman, H.D., 1965. Cation-Exchange Capacity. In: Methods of soil analysis. Part 2. Chemical and microbiological properties. Black, C.A., Evans, D.D., White, J.L., Ensminger, L.E., Clark F.E. (Eds.), Soil Science Society of America. Madison, Wisconsin, USA. pp. 891-901.
Coelho-Moreira, J. da S., Brugnari, T., Sá-Nakanishi, A.B., Castoldi, R., de Souza, C.G.M., Bracht, A., Peralta, R.M., 2018. Evaluation of diuron tolerance and biotransformation by the white-rot fungus Ganoderma lucidum. Fungal Biology 122(6): 471–478.
Cristina dos Reis, F., Mielke, K.C., Mendes, K.F., Nogueira de Sousa, R., Heluany, M.H., Tornisielo, V.L., Filho, R.V., 2023. Diuron, hexazinone, and sulfometuron-methyl applied alone and in mixture in soils: Distribution of extractable residue, bound residue, biodegradation, and mineralization. Heliyon 9(7): e17817.
Cullington, J.E., Walker, A., 1999. Rapid biodegradation of diuron and other phenylurea herbicides by a soil bacterium. Soil Biology and Biochemistry 31(5): 677–686.
Dahal, R.H., Kim, J., Kim, D.U., Dong, K., Hong, Y., Chaudhary, D.K., 2022. Cellulomonas fulva sp. nov., isolated from oil-contaminated soil. International Journal of Systematic and Evolutionary Microbiology 72: 005209.
Ditzler, C., Scheffe, K., Monger, H.C., 2017. Soil survey manual. USDA Agriculture Handbook No: 18. Available at [Access date: 16.02.2026]: https://www.nrcs.usda.gov/sites/default/files/2022-09/The-Soil-Survey-Manual.pdf
Domingues, S.Z., Timmers, L.F.S.M., Granada, C.E., 2022. Cellulase production by bacteria is a strain-specific characteristic with high biotechnological potential: A review of the cellulosome of highly studied strains. Cellulose 29(15): 8065–8083.
Duc, H.D., Thuy, N.T.D., Thanh, L.U., Tuong, T.D., Oanh, N.T., 2022. Degradation of diuron by a bacterial mixture and shifts in the bacterial community during bioremediation of contaminated soil. Current Microbiology 79(1): 11.
Egea, T.C., da Silva, R., Boscolo, M., Rigonato, J., Monteiro, D.A., Grünig, D., da Silva, H., van der Wielen, F., Helmus, R., Parsons, J.R., Gomes, E., 2017. Diuron degradation by bacteria from soil of sugarcane crops. Heliyon 3(12): e00471.
Fucic, A., Duca, R.C., Galea, K.S., Maric, T., Garcia, K., Bloom, M.S., Andersen, H.R., Vena, J.E., 2021. Reproductive health risks associated with occupational and environmental exposure to pesticides. International Journal of Environmental Research and Public Health 18(12): 6576.
Giacomazzi, S., Cochet, N., 2004. Environmental impact of diuron transformation: A review. Chemosphere 56(11): 1021–1032.
Góngora-Echeverría, V.R., García-Escalante, R., Rojas-Herrera, R., Giácoman-Vallejos, G., Ponce-Caballero, C., 2020. Pesticide bioremediation in liquid media using a microbial consortium and bacteria-pure strains isolated from a biomixture used in agricultural areas. Ecotoxicology and Environmental Safety 200: 110734.
Guimarães, A.C.D., Mendes, K.F., dos Reis, F.C., Campion, T.F., Christoffoleti, P.J., Tornisielo, V.L., 2018. Role of soil physicochemical properties in quantifying the fate of diuron, hexazinone, and metribuzin. Environmental Science and Pollution Research 25(13): 12419–12433.
Hao, B., Wu, H., Zhang, S., He, B., 2022. Individual and combined toxicity of microplastics and diuron differs between freshwater and marine diatoms. Science of the Total Environment 853: 158334.
Henn, C., Arakaki, R.M., Monteiro, D.A., Boscolo, M., da Silva, R., Gomes, E., 2020. Degradation of the organochlorinated herbicide diuron by rainforest basidiomycetes. BioMed Research International Article ID 5324391.
Holmes, G., 2014. Australia’s pesticide environmental risk assessment failure: The case of diuron and sugarcane. Marine Pollution Bulletin 88(1–2): 7–13.
Hu, K., Torán, J., López-García, E., Barbieri, M.V., Postigo, C., de Alda, M.L., Caminal, G., Sarrà, M., Blánquez, P., 2020. Fungal bioremediation of diuron-contaminated waters: Evaluation of its degradation and the effect of amendable factors on its removal in a trickle-bed reactor under non-sterile conditions. Science of the Total Environment 743: 140628.
Hultberg, M., Bodin, H., Ardal, E., Asp, H., 2016. Effect of microalgal treatments on pesticides in water. Environmental Technology 37(7): 893–898.
Kaymak, S., Özdem, A., Karahan, A., Özercan, B., Aksu, P., Aydar, A., Kodan, M., Yılmaz, A., Başaran, M.S., Asav, Ü., Erdoğan, P., Güler, Y., 2015. Ülkemizde zirai mücadele girdilerinin değerlendirilmesi. T.C. Gıda, Tarım ve Hayvancılık Bakanlığı, Tarımsal Araştırmalar ve Politikalar Genel Müdürlüğü, Zirai Mücadele Merkez Araştırma Enstitüsü Müdürlüğü, Ankara, Türkiye, 86 p.
Konare, H., Yost, R.S., Doumbia, M., McCarty, G.W., Jarju, A., Kablan, R., 2010. Loss on ignition: Measuring soil organic carbon in soils of the Sahel, West Africa. African Journal of Agricultural Research 5(22): 3088–3095.
Kour, D., Kaur, T., Devi, R., Yadav, A., Singh, M., Joshi, D., Singh, J., Suyal, D.C., Kumar, A., Rajput, V.D., Yadav, A.N., Singh, K., Singh, J., Sayyed, R.Z., Arora, N.K., Saxena, A.K., 2021. Beneficial microbiomes for bioremediation of diverse contaminated environments for environmental sustainability: Present status and future challenges. Environmental Science and Pollution Research 28(20): 24917–24939.
Lee, H., Depuydt, S., Shin, K., Choi, S., Kim, G., Lee, Y.H., Park, J.T., Han, T., Park, J., 2021. Assessment of various toxicity endpoints in duckweed (Lemna minor) at the physiological, biochemical, and molecular levels as a measure of diuron stress. Biology 10(7): 684.
Li, L., Zhao, X., Liu, D., Song, K., Liu, Q., He, Y., 2021. Occurrence and ecological risk assessment of PPCPs in typical inflow rivers of Taihu Lake, China. Journal of Environmental Management 285: 112176.
Lo, C.C., 2010. Effect of pesticides on soil microbial community. Journal of Environmental Science and Health, Part B 45(5): 348–359.
Mahmood, I., Imadi, S.R., Shazadi, K., Gul, A., Hakeem, K.R., 2016. Effects of pesticides on environment. In: Plant, Soil and Microbes. Hakeem, K.R., Akhtar, M.S., Abdullah, S.N.A. (Eds.), Springer International Publishing, Cham, Switzerland, pp. 253–269.
Mori, T., Sudo, S., Kawagishi, H., Hirai, H., 2018. Biodegradation of diuron in artificially contaminated water and seawater by wood colonized with the white-rot fungus Trametes versicolor. Journal of Wood Science 64(5): 690–696.
Odukkathil, G., Vasudevan, N., 2013. Toxicity and bioremediation of pesticides in agricultural soil. Reviews in Environmental Science and Bio/Technology 12: 421–444.
Öğün, E., Atalan, E., Özdemir, K., Yildiz, M., 2013. Determination of antimicrobial activity of Streptomyces strains isolated from around and root soil of some agricultural plants. Yüzüncü Yıl Üniversitesi Fen Bilimleri Enstitüsü Dergisi 18(1–2): 39–47.
Özercan, B., Taşçı, R., 2022. Investigation of pesticide use in Türkiye in terms of provinces, regions and pesticide groups. Ziraat Mühendisliği 375: 75–88.
Raffa, C.M., Chiampo, F., 2021. Bioremediation of agricultural soils polluted with pesticides: A review. Bioengineering 8(7): 92.
Resmi Tarımsal İlaç İstatistikleri, 2022. Resmi tarımsal ilaç istatistikleri. T.C. Tarım ve Orman Bakanlığı. Available at [Access date: 16.02.2026]: https://www.tarimorman.gov.tr/GKGM/Menu/115/Resmi-Tarimsal-Ilac-Istatistikleri
Riah, W., Laval, K., Laroche-Ajzenberg, E., Mougin, C., Latour, X., Trinsoutrot-Gattin, I., 2014. Effects of pesticides on soil enzymes: A review. Environmental Chemistry Letters 12(2): 257–273.
Ross, D.S., Ketterings, Q., 2018. Recommended methods for determining soil cation exchange capacity. In: Recommended Soil Testing Procedures for the Northeastern United States. Available at [Access date: 16.02.2026]: https://www.udel.edu/content/dam/udelImages/canr/pdfs/extension/factsheets/soiltest-recs/CHAP9-2009-2018.pdf
Rouchaud, J., Neus, O., Bulcke, R., Cools, K., Eelen, H., Dekkers, T., 2000. Soil dissipation of diuron, chlorotoluron, simazine, propyzamide, and diflufenican herbicides after repeated applications in fruit tree orchards. Archives of Environmental Contamination and Toxicology 39(1): 60–65.
Sanger, F., Nicklen, S., Coulson, A.R., 1977. DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences of the United States of America 74(12): 5463–5467.
Sessitsch, A., Weilharter, A., Gerzabek, M.H., Kirchmann, H., Kandeler, E., 2001. Microbial population structures in soil particle-size fractions of a long-term fertilizer field experiment. Applied and Environmental Microbiology 67(9): 4215–4224.
Silva Moretto, J.A., Rueda Furlan, J.P., Tonelli Fernandes, A.F., Bauermeister, A., Lopes, N.P., Stehling, E.G., 2019. Alternative biodegradation pathway of the herbicide diuron. International Biodeterioration & Biodegradation 143: 104716.
Singh, D.V., Ali, R., Anita, A., Kulsum, M., Bhat, R.A., 2020. Ecofriendly approaches for remediation of pesticides in contaminated environs. In: Bioremediation and Biotechnology: Persistent and Recalcitrant Toxic Substances. Bhat, R.A., Hakeem, K.R., Saud Al-Saud, N. (Eds.), Vol. 3. Springer, Cham, Switzerland, pp. 173–194.
Sun, H., Li, Y., Gao, S., Shi, G., Cao, L., Li, X., Li, T., Li, T., Wang, M., Li, E., Liu, J., Ni, H., Chen, Y., Liu, Y., 2025. Identification of key chromium resistance genes in Cellulomonas using transcriptomics. Ecotoxicology and Environmental Safety 291: 117843.
Şenay, M.G., 2000. Çayırova (Gebze-Kocaeli) civarında kullanılan pestisitlerin toprak ve yeraltı suyunda dağılımı ve çevre üzerindeki etkileri. Master’s thesis, Gebze Technical University, Department of Environmental Engineering, Kocaeli, Türkiye, 88 p.
Takeshita, V., Mendes, K.F., Christoffoleti, P.J., Tornisielo, V.L., Guimaraes, A.C.D., 2019. Sorption-desorption isotherms of diuron alone and in a mixture in soils with different physicochemical properties. African Journal of Agricultural Research 14(13): 672–679.
Travkin, V., Baskunov, B.P., Golovlev, E.L., Boersma, M.G., Boeren, S., Vervoort, J., van Berkel, W.J.H., Rietjens, I.M.C.M., Golovleva, L.A., 2002. Reductive deamination as a new step in the anaerobic microbial degradation of halogenated anilines. FEMS Microbiology Letters 209(2): 307–312.
Turnbull, G.A., Ousley, M., Walker, A., Shaw, E., Morgan, J.A.W., 2001. Degradation of substituted phenylurea herbicides by Arthrobacter globiformis strain D47 and characterization of a plasmid-associated hydrolase gene, puhA. Applied and Environmental Microbiology 67(5): 2270–2275.
U.S. EPA, 1986. Method 9080: Cation-exchange capacity of soils, ammonium acetate. In: Test Methods for Evaluating Solid Waste, Physical/Chemical Methods. United States Environmental Protection Agency, Washington, DC, USA. Available at [Access date: 16.02.2026]: https://www.epa.gov/sites/default/files/2015-12/documents/9080.pdf
Yadav, M., Yadav, H.S., 2015. Applications of ligninolytic enzymes to pollutants, wastewater, dyes, soil, coal, paper, and polymers. Environmental Chemistry Letters 13(3): 309–318.
Yadav, P., Chivate, M.S., Yadav, V.K., Mishra, V., 2025. Pesticide pollution and mycoremediation: A review of classification, ecotoxicity, health impacts, and multi-omics approaches. Bioresource Technology Reports 31: 102295.
Yilmaz, H., 2021. Aquaporin içeren biomimetik membranlar kullanılarak iz organik kirleticilerin giderimi. PhD thesis, Gebze Technical University, Department of Environmental Engineering, Kocaeli, Türkiye, 156 p.

Details

Primary Language

English

Subjects

Soil Sciences and Plant Nutrition (Other)

Journal Section

Research Article

Authors

Berk Emre Engin This is me
0009-0000-3266-6120
Türkiye

Hilal Yılmaz
0000-0002-5782-0283
Türkiye

Esra Meşe Erdoğan
0000-0001-7425-2399
Türkiye

Melek Özkan ^*
0000-0001-9017-5389
Türkiye

Publication Date

October 5, 2026

Submission Date

February 16, 2026

Acceptance Date

July 16, 2026

Published in Issue

Year 2026 Volume: 15 Number: 4

DOI

https://doi.org/10.18393/ejss.2005110

IZ

https://izlik.org/JA33HU95JA

Cite

RIS / Bibtex

APA

Engin, B. E., Yılmaz, H., Meşe Erdoğan, E., & Özkan, M. (2026). Isolation of indigenous soil bacteria with potential application for diuron removal. Eurasian Journal of Soil Science, 15(4), 538-552. https://doi.org/10.18393/ejss.2005110

AMA

1.Engin BE, Yılmaz H, Meşe Erdoğan E, Özkan M. Isolation of indigenous soil bacteria with potential application for diuron removal. EJSS. 2026;15(4):538-552. doi:10.18393/ejss.2005110

Chicago

Engin, Berk Emre, Hilal Yılmaz, Esra Meşe Erdoğan, and Melek Özkan. 2026. “Isolation of Indigenous Soil Bacteria With Potential Application for Diuron Removal”. Eurasian Journal of Soil Science 15 (4): 538-52. https://doi.org/10.18393/ejss.2005110.

EndNote

Engin BE, Yılmaz H, Meşe Erdoğan E, Özkan M (October 1, 2026) Isolation of indigenous soil bacteria with potential application for diuron removal. Eurasian Journal of Soil Science 15 4 538–552.

IEEE

[1]B. E. Engin, H. Yılmaz, E. Meşe Erdoğan, and M. Özkan, “Isolation of indigenous soil bacteria with potential application for diuron removal”, EJSS, vol. 15, no. 4, pp. 538–552, Oct. 2026, doi: 10.18393/ejss.2005110.

ISNAD

Engin, Berk Emre - Yılmaz, Hilal - Meşe Erdoğan, Esra - Özkan, Melek. “Isolation of Indigenous Soil Bacteria With Potential Application for Diuron Removal”. Eurasian Journal of Soil Science 15/4 (October 1, 2026): 538-552. https://doi.org/10.18393/ejss.2005110.

JAMA

1.Engin BE, Yılmaz H, Meşe Erdoğan E, Özkan M. Isolation of indigenous soil bacteria with potential application for diuron removal. EJSS. 2026;15:538–552.

MLA

Engin, Berk Emre, et al. “Isolation of Indigenous Soil Bacteria With Potential Application for Diuron Removal”. Eurasian Journal of Soil Science, vol. 15, no. 4, Oct. 2026, pp. 538-52, doi:10.18393/ejss.2005110.

Vancouver

1.Berk Emre Engin, Hilal Yılmaz, Esra Meşe Erdoğan, Melek Özkan. Isolation of indigenous soil bacteria with potential application for diuron removal. EJSS. 2026 Oct. 1;15(4):538-52. doi:10.18393/ejss.2005110