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Uluslararası Fen Araştırmalarında Yenilikçi Yaklaşımlar Dergisi 2026, Cilt 10(1) 1-25

Herbicide Effects on Bacterial Communities and Soil Functions in Rice Agroecosystems: A Critical Narrative Review

Famubo Joseph • Sule Manga • Adamu Almustapha Ali̇ero • Adamu Muhammad • Musa Isah • Peter Olugbemi
Bu makaleye atıf yap
Makale Türü
Derleme Makalesi
Yayın Tarihi
October 24, 2026
Sayfa Sayısı
1-25
DOI
10.29329/ijiasr.2026.1442.4

Öz

Rice fields are complex agroecosystems in which soil bacterial communities play essential roles in nutrient cycling, organic matter decomposition, soil fertility, and plant health. Herbicides are widely used in rice production to control weeds and enhance crop productivity; however, their effects extend beyond target plants and influence non-target soil microorganisms. This narrative review synthesises current knowledge on how herbicides influence bacterial populations in rice ecosystems. Evidence indicates that herbicide application often causes short-term reductions in bacterial abundance, microbial biomass, and soil enzymatic activities, particularly during the first few weeks after application. Nevertheless, many bacterial communities exhibit partial or complete recovery as herbicide residues degrade over time. Herbicides can alter bacterial community composition by suppressing sensitive functional groups, including nitrifying and nitrogen-fixing bacteria, while promoting herbicide-degrading taxa such as certain Bacillus and Actinobacteria species. These shifts may affect critical ecosystem processes, especially nitrogen cycling, nutrient availability, and soil multifunctionality. Long-term or excessive herbicide exposure can reduce microbial diversity, simplify ecological networks, and weaken soil resilience, potentially compromising sustainable rice production. The review also highlights how rice establishment systems, herbicide dosage, and environmental conditions influence bacterial responses. Emerging alternatives, including bioorganic fertilizers, microbial inoculants, integrated weed management, and microbiome-based remediation approaches, show promise for minimizing adverse effects on soil bacteria while maintaining effective weed control.

Anahtar Kelimeler: Herbicides Rice Fields Soil Bacteria Microbial Diversity Sustainable Weed Management
Bu makaleye atıf yap
Joseph, F., Manga, S., Almustapha Ali̇ero, A., Muhammad, A., Isah, M., & Olugbemi, P. (2026). Herbicide Effects on Bacterial Communities and Soil Functions in Rice Agroecosystems: A Critical Narrative Review. Uluslararası Fen Araştırmalarında Yenilikçi Yaklaşımlar Dergisi, 10(1), 1-25. https://doi.org/10.29329/ijiasr.2026.1442.4

  • Baćmaga, M., Wyszkowska, J., & Kucharski, J. (2024). Environmental implications of herbicide use. Molecules, 29. https://doi.org/10.3390/molecules29245965 [Google Scholar] [Crossref] 
  • Bearson, B., Douglass, C., Duke, S., Moorman, T., & Tranel, P. (2024). Effects of glyphosate on antibiotic resistance in soil bacteria and its potential significance: A review. Journal of Environmental Quality, 54, 160–180. https://doi.org/10.1002/jeq2.20655 [Google Scholar] [Crossref] 
  • Bhardwaj, L., Kumar, D., Singh, U., Joshi, C., & Dubey, S. (2024a). Herbicide application impacted soil microbial community composition and biochemical properties in a flooded rice field. The Science of the Total Environment, 169911. https://doi.org/10.1016/j.scitotenv.2024.169911 [Google Scholar] [Crossref] 
  • Bhardwaj, L., Reddy, B., & Dubey, S. (2023). Deciphering insights into rhizospheric microbial community and soil parameters under the influence of herbicides in zero-tillage tropical rice-agroecosystem. Environmental Research, 117033. https://doi.org/10.1016/j.envres.2023.117033 [Google Scholar] [Crossref] 
  • Bhardwaj, L., Reddy, B., Nath, A., & Dubey, S. (2024b). Influence of herbicide on rhizospheric microbial communities and soil properties in irrigated tropical rice field. Ecological Indicators. https://doi.org/10.1016/j.ecolind.2023.111534 [Google Scholar] [Crossref] 
  • Bonnar, D. J., & Tjeerdema, R. S. (2025). Environmental fate and aquatic risk assessment of oxyfluorfen in California rice fields. Integrated Environmental Assessment and Management, 21(1), 172–183. https://doi.org/10.1093/inteam/vjae001 [Google Scholar] [Crossref] 
  • Bourhane, Z., Lanzén, A., Cagnon, C., Said, B. O., Mahmoudi, E., Coulon, F., Atai, E., Borja, Á., Cravo-Laureau, C., & Duran, R. (2021). Microbial diversity alteration reveals biomarkers of contamination in soil-river-lake continuum. Journal of Hazardous Materials, 421, 126789. https://doi.org/10.1016/j.jhazmat.2021.126789 [Google Scholar] [Crossref] 
  • Chaudhary, P., Xu, M., Ahamad, L., Chaudhary, A., Kumar, G., Adeleke, B., Verma, K., Hu, D., Širić, I., Kumar, P., Popescu, S., & Fayssal, A. (2023). Application of synthetic consortia for improvement of soil fertility, pollution remediation, and agricultural productivity: A review. Agronomy. https://doi.org/10.3390/agronomy13030643 [Google Scholar] [Crossref] 
  • Chudzik, G., Arneson, N., DeWerff, R. P., Mobli, A., Mueller, T. C., & Werle, R. (2026). Impact of application time on soil residual herbicide dissipation in early-planted soybean. Weed Technology, 40. https://doi.org/10.1017/wet.2025.10076 [Google Scholar] [Crossref] 
  • Codello, A., Hose, G., & Chariton, A. (2022). Microbial co-occurrence networks as a biomonitoring tool for aquatic environments: A review. Marine and Freshwater Research. https://doi.org/10.1071/MF22045 [Google Scholar] [Crossref] 
  • Daisley, B., Chernyshova, A., Thompson, G., & Allen-Vercoe, E. (2022). Deteriorating microbiomes in agriculture the unintended effects of pesticides on microbial life. Microbiome Research Reports, 1. https://doi.org/10.20517/mrr.2021.08 [Google Scholar] [Crossref] 
  • De Andrade, L., Santos, C., Frezarin, E., Sales, L., & Rigobelo, E. (2023). Plant growth-promoting rhizobacteria for sustainable agricultural production. Microorganisms, 11. https://doi.org/10.3390/microorganisms11041088 [Google Scholar] [Crossref] 
  • De Cássia Araújo De Medeiros, R., Silva, T. S., Teófilo, T., Da Silva, F. D., De Freitas Souza, M., Passos, A. B., Fernandes, B. C., Lins, H., Chagas, P. S. D., Souza, C. S. M., Holanda, I., & Silva, D. V. (2024). Herbicide leaching in soil with different properties: Perspectives from commercial formulations and analytical standards. Toxics, 12. https://doi.org/10.3390/toxics12030199 [Google Scholar] [Crossref] 
  • Debode, F., Caulier, S., Demeter, S., Dubois, B., Gelhay, V., Hulin, J., Muhovski, Y., Ninane, V., Rousseau, G., & Bragard, C. (2024). Roadmap for the integration of environmental microbiomes in risk assessments under EFSA's remit. EFSA Supporting Publications. https://doi.org/10.2903/sp.efsa.2024.en-8602 [Google Scholar] [Crossref] 
  • Deka, N., Kumari, G., & Nath, T. (2025). Microbial dynamics in rice ecosystem under supplementation of organic sources of nitrogen with inorganics and their concomitant impact on yield. Scientific Reports, 15. https://doi.org/10.1038/s41598-025-86461-6 [Google Scholar] [Crossref] 
  • deNux, C., Hou, A., & Fultz, L. (2024). Evaluation of organic and synthetic herbicide applications on weed suppression in a conventional cropping system in Louisiana. Sustainability. https://doi.org/10.3390/su16073019 [Google Scholar] [Crossref] 
  • Dubey, S. K., Kumar, A., Singh, M., Singh, A. K., Tyagi, S., & Kumar, V. (2018). Effect of six herbicides on soil microbial population and yield in direct-seeded rice. Journal of Pharmacognosy and Phytochemistry, 4, 83–87. [Google Scholar]
  • Dubey, S., Kumar, A., Singh, M., Singh, A., & Prakash, V. (2023). Impact of herbicides on yield of direct-seeded rice and microbial population in soil. Current Journal of Applied Science and Technology. https://doi.org/10.9734/cjast/2023/v42i384250 [Google Scholar] [Crossref] 
  • Feng, Y., Tian, L., Zhang, F., Zhang, Y., Hou, H., Wang, M., Yang, Q., Feng, B., & Gao, X. (2025). Modulating effects of herbicide-safener co-application on rhizosphere microbiota and soil function in proso millet (Panicum miliaceum L.). Journal of Hazardous Materials, 499, 140320. https://doi.org/10.1016/j.jhazmat.2025.140320 [Google Scholar] [Crossref] 
  • He, X., Wu, C., Tan, H., Deng, X., & Li, Y. (2023). Impact of combined exposure to glyphosate and diquat on microbial community structure and diversity in lateritic paddy soil. Sustainability. https://doi.org/10.3390/su15118497 [Google Scholar] [Crossref] 
  • Hernandez, D. J., David, A. S., Menges, E., Searcy, C. A., & Afkhami, M. E. (2021). Environmental stress destabilizes microbial networks. The ISME Journal, 15, 1722–1734. https://doi.org/10.1038/s41396-020-00882-x [Google Scholar] [Crossref] 
  • Jeyaseelan, A., Murugesan, K., Thayanithi, S., & Palanisamy, S. (2023). A review of the impact of herbicides and insecticides on the microbial communities. Environmental Research, 118020. https://doi.org/10.1016/j.envres.2023.118020 [Google Scholar] [Crossref] 
  • Johnsen, K., Jacobsen, C., Torsvik, V., & Sørensen, J. (2001). Pesticide effects on bacterial diversity in agricultural soils: A review. Biology and Fertility of Soils, 33, 443–453. https://doi.org/10.1007/s003740100351 [Google Scholar] [Crossref] 
  • Karpouzas, D., Vryzas, Z., & Martin-Laurent, F. (2022). Pesticide soil microbial toxicity: Setting the scene for a new pesticide risk assessment for soil microorganisms (IUPAC Technical Report). Pure and Applied Chemistry, 94, 1161–1194. https://doi.org/10.1515/pac-2022-0201 [Google Scholar] [Crossref] 
  • Karubakee, S., Dash, R., Pradhan, S. K., Patra, A. K., Biswal, S., Panda, N., Sahoo, M. M., Babu, P. M., & Adak, T. (2026). Unveiling rhizobacterial diversity in rice-maize systems in response to penoxsulam-pendimethalin application. BMC Plant Biology, 26. https://doi.org/10.1186/s12870-026-08278-3 [Google Scholar] [Crossref] 
  • Laroche, O., Pochon, X., Tremblay, L., Ellis, J., Lear, G., & Wood, S. (2018). Incorporating molecular-based functional and co-occurrence network properties into benthic marine impact assessments. FEMS Microbiology Ecology, 94. https://doi.org/10.1093/femsec/fiy167 [Google Scholar] [Crossref] 
  • Layeghifard, M., Hwang, D., & Guttman, D. (2016). Disentangling interactions in the microbiome: A network perspective. Trends in Microbiology, 25, 217–228. https://doi.org/10.1016/j.tim.2016.11.008 [Google Scholar] [Crossref] 
  • Li, D., Chen, J., Zhang, X., Shi, W., & Li, J. (2022). Structural and functional characteristics of soil microbial communities in response to different ecological risk levels of heavy metals. Frontiers in Microbiology, 13. https://doi.org/10.3389/fmicb.2022.1072389 [Google Scholar] [Crossref] 
  • Li, Y., He, M., Song, Y., Liu, L., Xiao, J., Wang, J., Yang, B., Ouyang, S., Li, X., Peng, D., & Zhu, Z. (2026). Herbicide application under co-cultivation is associated with early microbiome assembly shifts and later physiological decline in rice. Microorganisms, 14. https://doi.org/10.3390/microorganisms14051137 [Google Scholar] [Crossref] 
  • Li, Z., Han, J., Bai, H., Peng, D., Wang, L., & Bai, L. (2021a). Effects of novel bioorganic fertilizer application on soil enzymes and bacterial community in multi-site rice paddies in China. AMB Express, 11. https://doi.org/10.1186/s13568-021-01241-5 [Google Scholar] [Crossref] 
  • Li, Z., Jian, H., Liu, D., Liu, X., & Bai, L. (2021b). Response of soil bacterial community to bioorganic fertilizer application as a weed management strategy in rice paddy. Research Square. https://doi.org/10.21203/rs.3.rs-392035/v1 [Google Scholar] [Crossref] 
  • Li, Z., Luo, S., Peng, Y., Jin, C., & Liu, D. (2023). Effect of long-term application of bioorganic fertilizer on the soil property and bacteria in rice paddy. AMB Express, 13. https://doi.org/10.1186/s13568-023-01559-2 [Google Scholar] [Crossref] 
  • Magnoli, K., Carranza, C., Aluffi, M., Magnoli, C., & Barberis, C. (2020). Herbicides based on 2,4-D: Its behavior in agricultural environments and microbial biodegradation aspects: A review. Environmental Science and Pollution Research, 27, 38501–38512. https://doi.org/10.1007/s11356-020-10370-6 [Google Scholar] [Crossref] 
  • Marín-Benito, J., Andrades, M., Sánchez-Martín, M., & Rodríguez-Cruz, M. S. (2025). Dissipation of two acidic herbicides in agricultural soil: Impact of green compost application, herbicide rate, and soil moisture. Agriculture. https://doi.org/10.3390/agriculture15050552 [Google Scholar] [Crossref] 
  • Martinez, D., Loening, U., & Graham, M. (2018). Impacts of glyphosate-based herbicides on disease resistance and health of crops: A review. Environmental Sciences Europe, 30. https://doi.org/10.1186/s12302-018-0131-7 [Google Scholar] [Crossref] 
  • Mathew, A., Prabukumar, G., Senthivelu, M., Gnanachitra, M., & Prasad, V. (2023). Impact of pre- and post-emergence herbicide application on soil microbial population assessment in direct wet-seeded rice. International Journal of Environment and Climate Change. https://doi.org/10.9734/ijecc/2023/v13i92405 [Google Scholar] [Crossref] 
  • Meena, R., Kumar, S., Datta, R., Lal, R., Vijayakumar, V., Brtnický, M., Sharma, M., Yadav, G., Jhariya, M., Jangir, C., Pathan, S., Dokulilová, T., Pecina, V., & Marfo, T. (2020). Impact of agrochemicals on soil microbiota and management: A review. Land, 9. https://doi.org/10.3390/land9020034 [Google Scholar] [Crossref] 
  • Michael, I., Abamba, E., Chikukula, A., Dugeri, D., Ibeneme, U., Olukayode, O., Okpro, O., & Akpome, A. (2024). Herbicides' effects on soil functions: A review. Asian Soil Research Journal, 8. https://doi.org/10.9734/asrj/2024/v8i4160 [Google Scholar] [Crossref] 
  • Moccellin, R., Corrêa, B., Castilhos, D., & Moura, A. (2023). Bacterial biocontrol agents of rice diseases: Compatible with pesticides and effects on rhizospheric soil microbiota. Revista Ciência Agronômica. https://doi.org/10.5935/1806-6690.20240015 [Google Scholar] [Crossref] 
  • Némethová, E., Řezáč, M., Gryndler, M., Abeyawardana, O. A. J., & Řezáčová, V. (2026). Soil pH mediates the impact of pesticides on bacterial communities, diversity, and abundance. Frontiers in Microbiology, 16. https://doi.org/10.3389/fmicb.2025.1670425 [Google Scholar] [Crossref] 
  • Onwona-Kwakye, M., Plants-Paris, K., Keita, K., Lee, J., Brink, P., Hogarh, J., & Darkoh, C. (2020). Pesticides decrease bacterial diversity and abundance of irrigated rice fields. Microorganisms, 8. https://doi.org/10.3390/microorganisms8030318 [Google Scholar] [Crossref] 
  • Pan, Z., Wang, W., Xu, W., Yin, Y., Xu, X., Zhu, L., Duan, Y., Lin, J., Ferraro, D., De Paula, R., Torabi, E., & Huang, Q. (2025). Continental-scale characterization of pesticide cocktails in paddy soils: Associations with microbial community structure, function, and extracellular vesicle occurrence. Journal of Hazardous Materials, 498, 139879. https://doi.org/10.1016/j.jhazmat.2025.139879 [Google Scholar] [Crossref] 
  • Pattanayak, S., Jena, S., Das, P., Maitra, S., Shankar, T., Praharaj, S., Mishra, P., Mohanty, S., Pradhan, M., Swain, D., Pramanick, B., Gaber, A., & Hossain, A. (2022). Weed management and crop establishment methods in rice (Oryza sativa L.) influence the soil microbial and enzymatic activity in a sub-tropical environment. Plants, 11. https://doi.org/10.3390/plants11081071 [Google Scholar] [Crossref] 
  • Qian, H., Zhu, Y., Chen, S., Jin, Y., Lavoie, M., Ke, M., & Fu, Z. (2018). Interacting effect of diclofop-methyl on the rice rhizosphere microbiome and denitrification. Pesticide Biochemistry and Physiology, 146, 90–96. https://doi.org/10.1016/j.pestbp.2018.03.002 [Google Scholar] [Crossref] 
  • Ribas, M. P., García-Ulloa, M., Espunyes, J., & Cabezón, Ó. (2023). Improving the assessment of ecosystem and wildlife health: Microbiome as an early indicator. Current Opinion in Biotechnology, 81, 102923. https://doi.org/10.1016/j.copbio.2023.102923 [Google Scholar] [Crossref] 
  • Rodríguez-De-Barbieri, V., González-Barrios, P., Rovira, P., Marchesi, C., Cuadro, R., Zarza, R., & Kaspary, T. (2025). Residual effect of imidazolinone herbicides on emergence and early development of forage species in rice-livestock systems. International Journal of Plant Biology. https://doi.org/10.3390/ijpb16030110 [Google Scholar] [Crossref] 
  • Ruuskanen, S., Fuchs, B., Nissinen, R., Puigbò, P., Rainio, M., Saikkonen, K., & Helander, M. (2022). Ecosystem consequences of herbicides: The role of microbiome. Trends in Ecology & Evolution. https://doi.org/10.1016/j.tree.2022.09.009 [Google Scholar] [Crossref] 
  • Shafiq, M., Okoye, C., Nazar, M., Khattak, W., & Algammal, A. (2024). Ecological consequences of antimicrobial residues and bioactive chemicals on antimicrobial resistance in agroecosystems. Journal of Advanced Research, 74, 99–120. https://doi.org/10.1016/j.jare.2024.10.013 [Google Scholar] [Crossref] 
  • Sibalekile, A., Araya, T., Hernandez, J., & Kotzé, E. (2025). Glyphosate-microbial interactions: Metagenomic insights and future directions. Frontiers in Microbiology, 16. https://doi.org/10.3389/fmicb.2025.1570235 [Google Scholar] [Crossref] 
  • Šunjka, D. B., Pucarević, M., Lazić, S., Stojić, N., Milošević, L., Bilali, E. H., Bošković, D. D., Vuković, S., Mitrić, S., Berjan, S., Šušnjar, A., & Ećimović, J. (2024). Monitoring of herbicide residues in agricultural soils in Vojvodina Province (Northern Serbia). Land. https://doi.org/10.3390/land13091347 [Google Scholar] [Crossref] 
  • Thorpe, A., Busi, S. B., Warren, J., Newbold, L. K., Taylor, J. D., Walsh, K., & Read, D. S. (2026). River microbiomes as sentinels of national-scale freshwater ecosystems. Global Change Biology, 32. https://doi.org/10.1111/gcb.70809 [Google Scholar] [Crossref] 
  • Toju, H., Suzuki, K., Sánchez-Pinillos, M., Shima, G., Kageyama, T., Hayashi, I., Noguchi, M., Fujita, H., Goto, Y., Nakaoka, S., Ushio, M., Ichihashi, Y., Fricke, W., Mizumoto, K., Takayasu, L., Suda, W., Takayasu, M., Yamamichi, M., & Weckwerth, W. (2026). Microbiome assembly statistics toward ecosystem-scale insights, forecasting, and management. The ISME Journal, 20. https://doi.org/10.1093/ismejo/wrag085 [Google Scholar] [Crossref] 
  • van Bruggen, A., He, M., Shin, K., Mai, V., Jeong, K., Finckh, M., & Morris, J. (2018). Environmental and health effects of the herbicide glyphosate. The Science of the Total Environment, 616–617, 255–268. https://doi.org/10.1016/j.scitotenv.2017.10.309 [Google Scholar] [Crossref] 
  • Vischetti, C., Casucci, C., De Bernardi, A., Monaci, E., Tiano, L., Marcheggiani, F., Ciani, M., Comitini, F., Marini, E., Taskin, E., & Puglisi, E. (2020). Sub-lethal effects of pesticides on the DNA of soil organisms as early ecotoxicological biomarkers. Frontiers in Microbiology, 11. https://doi.org/10.3389/fmicb.2020.01892 [Google Scholar] [Crossref] 
  • Vishwakarma, K., Kumar, N., Shandilya, C., Mohapatra, S., Bhayana, S., & Varma, A. (2020). Revisiting plant–microbe interactions and microbial consortia application for enhancing sustainable agriculture: A review. Frontiers in Microbiology, 11. https://doi.org/10.3389/fmicb.2020.560406 [Google Scholar] [Crossref] 
  • Wang, J., Han, C., Wu, D., Zhou, W., Gao, M., & Li, Y.-S. (2025). Microbial composition, assembly, and functional characteristics of generalized and specialized subcommunities under flooded paddy fields: Long-term pesticide versus non-pesticide models. Frontiers in Microbiology, 16. https://doi.org/10.3389/fmicb.2025.1636555 [Google Scholar] [Crossref] 
  • Yadav, S., Srivastava, R., Singh, N., Kanda, T., Verma, E., Choudhary, P., Yadav, S., & Atri, N. (2025). Cyanobacteria-pesticide interactions and their implications for sustainable rice agroecosystems. International Journal of Microbiology, 2025. https://doi.org/10.1155/ijm/7265036 [Google Scholar] [Crossref] 
  • Yasir, M., Hossain, A., & Pratap-Singh, A. (2025). Pesticide degradation: Impacts on soil fertility and nutrient cycling. Environments. https://doi.org/10.3390/environments12080272 [Google Scholar] [Crossref] 
  • Yu, H., Cui, H., Chen, J., & Li, X. (2024). The herbicidal activity of pre-emergence herbicide cinmethylin and its potential risks on soil ecology: pH, enzyme activities and bacterial community. Environmental Microbiome, 19. https://doi.org/10.1186/s40793-024-00608-y [Google Scholar] [Crossref] 
  • Zárate, A., Barrientos, L., Florez, J. Z., Buschmann, A. H., Pérez-Santos, I., Abanto, M., Bruna, P., Leyton, B., Vásquez, C., Inostroza, P., Lundin, D., Borrego, C. M., Balcázar, J. L., & Vila-Costa, M. (2025). Capturing the spatial structure of the benthic microbiome under an intensive aquaculture scenario in Chilean Patagonia. BMC Microbiology, 25. https://doi.org/10.1186/s12866-025-04460-z [Google Scholar] [Crossref]