Isolation, identification, and characterization of bacterial strains with potential for degradation of the pesticides chlorothalonil and chlorpyrifos

Keywords: Bacterial bioremediation, chlorpyrifos, chlorothalonil, fungicide, insecticide, soil contamination


Indiscriminate use of highly toxic pesticides in agriculture has produced soil contamination and deterioration of ecosystems. A promising solution to this environmental problem is bioremediation, which includes the use of bacteria to degrade contaminating substances. [Objective] The objective of this work was to isolate, identify, and characterize bacterial strains capable of degrading the pesticides chlorothalonil and chlorpyrifos to determine their potential use in bioremediation of contaminated soils. [Methodology] The strains were isolated from agricultural soils using enrichment cultures containing chlorothalonil or chlorpyrifos (20 mg/L) as the sole carbon source. The isolated strains were characterized by their morphology, by their physiological responses to 48 biochemical tests and sensitivity to 15 antibiotics, by their growth kinetics, and in molecular terms (amplification of the gene rDNA 16S). [Results] In total, three strains were isolated, one capable of using (and degrading) chlorpyrifos, identified as Stenotrophomonas maltophilia, and two bacterial strains with a partial ability to use chlorothalonil as a carbon source, identified as Enterobacter cloacae and Ochrobactrum anthropi. The three bacterial species are Gram-negative bacilli and have diverse physiological characteristics, including variable resistance to certain antibiotics. [Conclusion] It is concluded that the isolated bacteria have biotechnological potential to be incorporated into a bioremediation strategy for contaminated soils, especially for the elimination of chlorpyrifos. Finally, further research perspectives are proposed to determine more efficient processes of chlorothalonil degradation by cometabolism.



Akbar, S. & Sultan, S. (2016). Soil bacteria showing a potential of chlorpyrifos degradation and plant growth enhancement. Brazilian Journal of Microbiology, 47, 563-570.
Aktar, M. D. W.; Sengupta, D. & Chowdhury, A. (2009). Impact of pesticides use in agriculture: their benefits and hazards. Interdisciplinary Toxicology, 2(1): 1–12.
Bass, C. & Field, L. M. (2011). Gene amplification and insecticide resistance. Pest Management Science. 67(8): 886–890.
Betancourt-Portela, J. M., Bautista-Duarte, P. A., Narváez-Flórez, S. & Parra-Lozano, J. P. (2018). Biodegradation of chlorothalonil fungicide in coastal areas of the Colombian Caribbean suitable for banana crops. Tecciencia, 13(25), 19-28.
Bravo, D. V., de la Cruz, M. E., Herrera, L. G., Ramírez, M. F. (2013). Uso de plaguicidas en cultivos agrícolas como herramienta para el monitoreo de peligros en salud. Uniciencia 27(1): 351-376.
Bravo-Durán, V., Berrocal-Montero, S. E., Ramírez-Muñoz, F., de la Cruz-Malavassi, E., Canto-Mai, N., Tatis-Ramírez, A., Mejía-Merino, W. & Rodríguez-Altamirano, T. (2015). Importación de plaguicidas y peligros en salud en América Central durante el periodo 2005 – 2009, Uniciencia, 29(2): 84-106.
Castresana, J. (2000). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular biology and evolution, 17(4), 540-552.
Caux, P. Y., Kent, R. A., Fan, G. T. & Stephenson, G. L. (1996). Environmental fate and effects of chlorothalonil: A Canadian perspective. Critical Reviews in Environmental Science and Technology, 26(1), 45-93.
Chen, Y., Ye, W., Zhang, Y., & Xu, Y. (2015). High speed BLASTN: An accelerated MegaBLAST search tool. Nucleic Acids Research, 43(16), 7762–7768.
Chibueze, A. C.; Blaise C. C.; & Chijioke, O. G. (2016). Bioremediation techniques–classification based on site of application: principles, advantages, limitations and prospects. World Journal of Microbiology and Biotechnology, 32(180), 1-18.
Cox, C. (1997). Chlorothalonil. Journal of Pesticide Reform, 17(4), 14-20.
Cycoń M., Mrozik, A. & Piotrowska-Seget, Z. (2019). Antibiotics in the soil environment—degradation and their impact on microbial activity and diversity. Frontiers in Microbiology, 10:338. https://doi=10.3389/fmicb.2019.00338
Draper, A., Cullinan, P., Campbell, C., Jones, M. & Taylor, A. N. (2003). Case report. Occupational asthma from fungicides fluazinam and chlorothalonil. Occupational Environmental Medicine Journal, 60, 76–77.
Harada, N., Takagi, K., Baba, K., Fujii, K. & Iwasaki A. (2010). Biodegradation of diphenylarsinic acid to arsenic acid by novel soil bacteria isolated from contaminated soil. Biodegradation, 21, 491–499. 10.1007/s10532-009-9318-3
Hussain, S., Siddique, T., Arshad, M. & Saleem, M. (2009). Bioremediation and phytoremediation of pesticides: Recent Advances. Critical Reviews in Environmental Science and Technology, 39(10), 843-907.
Johnsen, K., Jacobsen, C. S., Torsvik, V. & Sørensen, J. (2001). Pesticide effects on bacterial diversity in agricultural soils – a review. Biology and Fertility of Soils, 33, 443–453.
Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K., von Haeseler, A., & Jermiin, L. S. (2017). ModelFinder: fast model selection for accurate phylogenetic estimates. Nature methods, 14(6), 587-589.
Katayama, A., Isemura, H. & Kuwatsuka, S. (1991). Population change and characteristics of chiorothalonil-degrading bacteria in soil. Journal of Pesticide Science, 16, 239-245.
Katoh, K., & Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. 30(4), 772-780.
Lakshmi, C. V., Kumar, M., Khannaa, S. (2008). Biotransformation of chlorpyrifos and bioremediation of contaminated soil. International Biodeterioration & Biodegradation, 62, 204–209.
Lee, W., Bridge, D. R., Lee A. W., Odom, J. V., Elliott, T. & Olson, J. C. (2012). Bacterial biofilm diversity in contact lens-related disease: Emerging Role of Achromobacter, Stenotrophomonas, and Delftia. Investigative Ophthalmology & Visual Science, 53(7), 3896-3905.
Mau, S., Vega, K. & Sánchez, M. (2011). Aislamiento de bacterias del suelo y su potencial utilización en sistemas de tratamiento de aguas residuales. Revista de Ciencias Ambientales. 42(2): 45-52.
Menon, P., Gopal, M. & Prasad, R. (2004). Influence of two insecticides, chlorpyrifos and quinalphos, on arginine ammonification and mineralizable nitrogen in two tropical soil type. Journal of Agricultural and Food Chemistry, 52, 7370−7376.
Motonaga, K., Takagi, K. & Matumoto, S. (1996). Biodegradation of chlorothalonil in soil after suppression of degradation. Biology and Fertility of Soils, 23, 340-345.
Nandhini, A. R., Harshiny, M. & Gummadi, S. N. (2021). Chlorpyrifos in environment and foods: A critical review of detection methods and degradation pathways. Environmental Science: Processes & Impacts, 1-61.
Nguyen, L. T., Schmidt, H. A., Von Haeseler, A., & Minh, B. Q. (2015). IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular biology and evolution, 32(1), 268-274.
PAN [Pesticide Action Network]. (2021). PAN International List of Highly Hazardous Pesticides. Pesticide Action Network. Disponible en:
Rambaut, A. (2009). FigTree 2012-2014 (Versión 1.4).
Ramírez-Muñoz, F., Fournier-Leiva, M. L., Ruepert, C. & Hidalgo-Ardón, C. (2014). Uso de agroquímicos en el cultivo de papa en Pacayas, Cartago, Costa Rica. Agronomía Mesoamericana 25(2): 337-345.
Ryan, R. P., Monchy, S., Cardinale, M., Taghavi, S., Crossman, L. Avison, M. V., Berg, G., van der Lelie, D. & Dow. J. M. (2009). The versatility and adaptation of bacteria from the genus Stenotrophomonas. Nature Reviews Microbiology 7:514-525. https://doi:10.1038/nrmicro2163
Sun, D., Jeannot, K., Yonghong, X. & Charles W. K. (2019). Horizontal gene transfer mediated bacterial antibiotic resistance. Frontiers in Microbiology 10:1933. http://doi=10.3389/fmicb.2019.01933
Shi, X., Guo R., Takagi, K., Miao, Z. & Li, S. (2011). Chlorothalonil degradation by Ochrobactrum lupini strain TP-D1 and identification of its metabolites. World Journal of Microbiology and Biotechnology, 27, 1755–1764.
Sigler, W. V. & Turco, R. F. (2002). The impact of chlorothalonil application on soil bacterial and fungal populations as assessed by denaturing gradient gel electrophoresis. Applied Soil Ecology, 21, 107–118.
Singh, B. K., Walker, A. & Wright D. J. (2002). Persistence of chlorpyrifos, fenamiphos, chlorothalonil, and pendimethalin in soil and their effects on soil microbial characteristics. Bulletin of Environmental Contamination and Toxicology, 69, 181–188. 10.1007/s00128-002-0045-2
Spierer, O., Miller, D. & O’Brien, T. (2018). Comparative activity of antimicrobials against Pseudomonas aeruginosa, Achromobacter xylosoxidans and Stenotrophomonas maltophilia keratitis isolates. Journal of Ophthalmology, 1–5. http://10.1136/bjophthalmol-2017-311751
Tang, L., Dong, J., Ren, L., Zhu, Q., Huang W., Liu, Y. & Lu D. (2017). Biodegradation of chlorothalonil by Enterobacter cloacae TUAH-1. International Biodeterioration & Biodegradation, 121, 122-130.
Tang, W.; Ji, H. & Xinyun Hou, X. (2017). Research progress of microbial degradation of organophosphorus pesticide. Progress in Applied Microbiology, 29-35.
Trifinopoulos, J., Nguyen, L. T., von Haeseler, A., & Minh, B. Q. (2016). W-IQ-TREE: a fast-online phylogenetic tool for maximum likelihood analysis. Nucleic acids research, 44(1), 232-235.´
Trigo, A., Valencia, A. & Cases, I. (2009). Systemic approaches to biodegradation. FEMS Microbiology Reviews, 33: 98-108.
Tudi, M., Ruan, H. D., Wang, L., Lyu J., Sadler, R., Connell, D., Chu, C. & Phung, D. T. (2021). Agriculture development, pesticide application and its impact on the environment. International Journal of Environmental Research and Public Health, 18(1112), 1-23.
Verma, A. (2021). Bioremediation techniques for soil pollution: An Introduction. In: Ferreira, M. K.; Nogueira de S. R. & Cabral, M. K. Biodegradation technology of organic and inorganic pollutants. IntechOpen. Pp. 289-302.
Vidali, M. (2001). Bioremediation. An overview. Pure Applied Chemistry, 73(7), 163–1172.
Wang, G., Liang, B., Li, F. & Li, S. (2011). Recent advances in the biodegradation of chlorothalonil. Current Microbiology, 63, 450–457.
Wang, X., Sun, S. Y., Lu, J. L. & Bao, J. (2019). Remediating chlorpyrifos-contaminated soil using immobilized microorganism technology. Polish Journal of Environmental Stududies, (28)1, 349-357.
WHO [World Health Organization] & United Nations Environment Programme. (‎1990)‎. Public health impact of pesticides used in agriculture. World Health Organization.
Yang, L.; Zhao, Y., Zhang, B., Yang, C., Zhang, X. (2005). Isolation and characterization of a chlorpyrifos and 3,5,6-trichloro-2-pyridinol degrading bacterium. FEMS Microbiology Letters, 251, 67–73.
Zhang, M. Y., Teng, Y., Zhu, Y., Wang, J., Luo, Y. M., Christie, P., Li, Z. G. & Udeigwe, T. K. (2014). Isolation and characterization of chlorothalonil-degrading bacterial strain H4 and its potential for remediation of contaminated soil. Pedosphere, 24(6): 799–807.
Zhang, Q., Liu, H., Saleem, M. & Wang, C. (2019). Biotransformation of chlorothalonil by strain Stenotrophomonas acidaminiphila BJ1 isolated from farmland soil. Royal Society Open Science, 6(190562), 1-9.
How to Cite
Estrada-Gamboa, J., Umaña-Castro, R., Sancho-Blanco, C., & Orozco-Aceves, M. (2023). Isolation, identification, and characterization of bacterial strains with potential for degradation of the pesticides chlorothalonil and chlorpyrifos. Uniciencia, 37(1), 1-16.
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