Microbial Contributions to Soil Health and Crop Yield in Organic Farming Systems
Abstract
Soil health is a critical component of sustainable agriculture, particularly in organic farming systems. Microbial communities play a vital role in maintaining soil quality and enhancing crop productivity. Understanding these contributions is essential for optimizing organic farming practices. This study aims to investigate the specific roles of microbial communities in promoting soil health and improving crop yield in organic farming systems. By examining various microbial interactions and their effects on nutrient cycling, the research seeks to identify key factors influencing agricultural productivity. A field study was conducted on several organic farms, where soil samples were collected and analyzed for microbial diversity and activity. Crop yield data were obtained from participating farmers, and statistical analyses were performed to assess the relationships between microbial metrics and crop productivity. Findings indicate that higher microbial diversity and activity correlate positively with improved soil health indicators, such as organic matter content and nutrient availability. Additionally, crops grown in soils with robust microbial communities demonstrated significantly higher yields compared to those from less diverse microbial environments. This research underscores the importance of microbial contributions to soil health in organic farming systems.
Full text article
References
Álvarez-Martínez, F. J., Barrajón-Catalán, E., Herranz-López, M., & Micol, V. (2021). Antibacterial plant compounds, extracts and essential oils: An updated review on their effects and putative mechanisms of action. Phytomedicine, 90, 153626. https://doi.org/10.1016/j.phymed.2021.153626
Bhat, A. R., Dongre, R. S., Almalki, F. A., Berredjem, M., Aissaoui, M., Touzani, R., Hadda, T. B., & Akhter, M. S. (2021). Synthesis, biological activity and POM/DFT/docking analyses of annulated pyrano[2,3-d]pyrimidine derivatives: Identification of antibacterial and antitumor pharmacophore sites. Bioorganic Chemistry, 106, 104480. https://doi.org/10.1016/j.bioorg.2020.104480
Cortes-Macías, E., Selma-Royo, M., García-Mantrana, I., Calatayud, M., González, S., Martínez-Costa, C., & Collado, M. C. (2021). Maternal Diet Shapes the Breast Milk Microbiota Composition and Diversity: Impact of Mode of Delivery and Antibiotic Exposure. The Journal of Nutrition, 151(2), 330–340. https://doi.org/10.1093/jn/nxaa310
Elhalis, H., Cox, J., Frank, D., & Zhao, J. (2020). The crucial role of yeasts in the wet fermentation of coffee beans and quality. International Journal of Food Microbiology, 333, 108796. https://doi.org/10.1016/j.ijfoodmicro.2020.108796
Fadiji, A. E., & Babalola, O. O. (2020). Metagenomics methods for the study of plant-associated microbial communities: A review. Journal of Microbiological Methods, 170, 105860. https://doi.org/10.1016/j.mimet.2020.105860
Fan, P., Bian, B., Teng, L., Nelson, C. D., Driver, J., Elzo, M. A., & Jeong, K. C. (2020). Host genetic effects upon the early gut microbiota in a bovine model with graduated spectrum of genetic variation. The ISME Journal, 14(1), 302–317. https://doi.org/10.1038/s41396-019-0529-2
Fang, Y., Yan, C., Zhao, Q., Xu, J., Liu, Z., Gao, J., Zhu, H., Dai, Z., Wang, D., & Tang, D. (2021). The roles of microbial products in the development of colorectal cancer: A review. Bioengineered, 12(1), 720–735. https://doi.org/10.1080/21655979.2021.1889109
Fragiadakis, G. K., Wastyk, H. C., Robinson, J. L., Sonnenburg, E. D., Sonnenburg, J. L., & Gardner, C. D. (2020). Long-term dietary intervention reveals resilience of the gut microbiota despite changes in diet and weight. The American Journal of Clinical Nutrition, 111(6), 1127–1136. https://doi.org/10.1093/ajcn/nqaa046
Grant, C. V., Loman, B. R., Bailey, M. T., & Pyter, L. M. (2021). Manipulations of the gut microbiome alter chemotherapy-induced inflammation and behavioral side effects in female mice. Brain, Behavior, and Immunity, 95, 401–412. https://doi.org/10.1016/j.bbi.2021.04.014
Hosseinkhani, F., Heinken, A., Thiele, I., Lindenburg, P. W., Harms, A. C., & Hankemeier, T. (2021). The contribution of gut bacterial metabolites in the human immune signaling pathway of non-communicable diseases. Gut Microbes, 13(1), 1882927. https://doi.org/10.1080/19490976.2021.1882927
Hou, L., Kumar, D., Yoo, C. G., Gitsov, I., & Majumder, E. L.-W. (2021). Conversion and removal strategies for microplastics in wastewater treatment plants and landfills. Chemical Engineering Journal, 406, 126715. https://doi.org/10.1016/j.cej.2020.126715
Hughes, D. A., Bacigalupe, R., Wang, J., Rühlemann, M. C., Tito, R. Y., Falony, G., Joossens, M., Vieira-Silva, S., Henckaerts, L., Rymenans, L., Verspecht, C., Ring, S., Franke, A., Wade, K. H., Timpson, N. J., & Raes, J. (2020). Genome-wide associations of human gut microbiome variation and implications for causal inference analyses. Nature Microbiology, 5(9), 1079–1087. https://doi.org/10.1038/s41564-020-0743-8
Jing, C., Chen, H., Liang, Y., Zhong, Y., Wang, Q., Li, L., Sun, S., Guo, Y., Wang, R., Jiang, Z., & Wang, H. (2021). Clinical Evaluation of an Improved Metagenomic Next-Generation Sequencing Test for the Diagnosis of Bloodstream Infections. Clinical Chemistry, 67(8), 1133–1143. https://doi.org/10.1093/clinchem/hvab061
Koutzoumis, D. N., Vergara, M., Pino, J., Buddendorff, J., Khoshbouei, H., Mandel, R. J., & Torres, G. E. (2020). Alterations of the gut microbiota with antibiotics protects dopamine neuron loss and improve motor deficits in a pharmacological rodent model of Parkinson’s disease. Experimental Neurology, 325, 113159. https://doi.org/10.1016/j.expneurol.2019.113159
Li, Y., Liu, L., & Wang, H. (2022). Mixotrophic denitrification for enhancing nitrogen removal of municipal tailwater: Contribution of heterotrophic/sulfur autotrophic denitrification and bacterial community. Science of The Total Environment, 814, 151940. https://doi.org/10.1016/j.scitotenv.2021.151940
Lim, S. S., Fontmorin, J.-M., Izadi, P., Wan Daud, W. R., Scott, K., & Yu, E. H. (2020). Impact of applied cell voltage on the performance of a microbial electrolysis cell fully catalysed by microorganisms. International Journal of Hydrogen Energy, 45(4), 2557–2568. https://doi.org/10.1016/j.ijhydene.2019.11.142
Liston, A., Humblet-Baron, S., Duffy, D., & Goris, A. (2021). Human immune diversity: From evolution to modernity. Nature Immunology, 22(12), 1479–1489. https://doi.org/10.1038/s41590-021-01058-1
Marchesan, J. T., Girnary, M. S., Moss, K., Monaghan, E. T., Egnatz, G. J., Jiao, Y., Zhang, S., Beck, J., & Swanson, K. V. (2020). Role of inflammasomes in the pathogenesis of periodontal disease and therapeutics. Periodontology 2000, 82(1), 93–114. https://doi.org/10.1111/prd.12269
Nadimpalli, M. L., Marks, S. J., Montealegre, M. C., Gilman, R. H., Pajuelo, M. J., Saito, M., Tsukayama, P., Njenga, S. M., Kiiru, J., Swarthout, J., Islam, M. A., Julian, T. R., & Pickering, A. J. (2020). Urban informal settlements as hotspots of antimicrobial resistance and the need to curb environmental transmission. Nature Microbiology, 5(6), 787–795. https://doi.org/10.1038/s41564-020-0722-0
Shen, Y., Wu, Y., Wang, Y., Li, L., Li, C., Zhao, Y., & Yang, S. (2021). Contribution of autochthonous microbiota succession to flavor formation during Chinese fermented mandarin fish (Siniperca chuatsi). Food Chemistry, 348, 129107. https://doi.org/10.1016/j.foodchem.2021.129107
Sikora, M., Stec, A., Chrabaszcz, M., Knot, A., Waskiel-Burnat, A., Rakowska, A., Olszewska, M., & Rudnicka, L. (2020). Gut Microbiome in Psoriasis: An Updated Review. Pathogens, 9(6), 463. https://doi.org/10.3390/pathogens9060463
Storey, D., McNally, A., Åstrand, M., sa-Pessoa Graca Santos, J., Rodriguez-Escudero, I., Elmore, B., Palacios, L., Marshall, H., Hobley, L., Molina, M., Cid, V. J., Salminen, T. A., & Bengoechea, J. A. (2020). Klebsiella pneumoniae type VI secretion system-mediated microbial competition is PhoPQ controlled and reactive oxygen species dependent. PLOS Pathogens, 16(3), e1007969. https://doi.org/10.1371/journal.ppat.1007969
Sulyok, M., Stadler, D., Steiner, D., & Krska, R. (2020). Validation of an LC-MS/MS-based dilute-and-shoot approach for the quantification of > 500 mycotoxins and other secondary metabolites in food crops: Challenges and solutions. Analytical and Bioanalytical Chemistry, 412(11), 2607–2620. https://doi.org/10.1007/s00216-020-02489-9
Sun, S., Wang, K., Sun, L., Cheng, B., Qiao, S., Dai, H., Shi, W., Ma, J., & Liu, H. (2020). Therapeutic manipulation of gut microbiota by polysaccharides of Wolfiporia cocos reveals the contribution of the gut fungi-induced PGE2 to alcoholic hepatic steatosis. Gut Microbes, 12(1), 1830693. https://doi.org/10.1080/19490976.2020.1830693
Sun, Y., Qi, X., Li, R., Xie, Y., Tang, Q., & Ren, B. (2020). Hydrothermal synthesis of 2D/2D BiOCl/g-C3N4 Z-scheme: For TC degradation and antimicrobial activity evaluation. Optical Materials, 108, 110170. https://doi.org/10.1016/j.optmat.2020.110170
Thiergart, T., Durán, P., Ellis, T., Vannier, N., Garrido-Oter, R., Kemen, E., Roux, F., Alonso-Blanco, C., Ågren, J., Schulze-Lefert, P., & Hacquard, S. (2019). Root microbiota assembly and adaptive differentiation among European Arabidopsis populations. Nature Ecology & Evolution, 4(1), 122–131. https://doi.org/10.1038/s41559-019-1063-3
Versey, Z., Da Cruz Nizer, W. S., Russell, E., Zigic, S., DeZeeuw, K. G., Marek, J. E., Overhage, J., & Cassol, E. (2021). Biofilm-Innate Immune Interface: Contribution to Chronic Wound Formation. Frontiers in Immunology, 12, 648554. https://doi.org/10.3389/fimmu.2021.648554
Wang, L., Luo, Z., Zhen, Z., Yan, Y., Yan, C., Ma, X., Sun, L., Wang, M., Zhou, X., & Hu, A. (2020). Bacterial community colonization on tire microplastics in typical urban water environments and associated impacting factors. Environmental Pollution, 265, 114922. https://doi.org/10.1016/j.envpol.2020.114922
Wang, S., Liu, C., Wang, X., Yuan, D., & Zhu, G. (2020). Dissimilatory nitrate reduction to ammonium (DNRA) in traditional municipal wastewater treatment plants in China: Widespread but low contribution. Water Research, 179, 115877. https://doi.org/10.1016/j.watres.2020.115877
Xu, M., Huang, Q., Xiong, Z., Liao, H., Lv, Z., Chen, W., Luo, X., & Hao, X. (2021). Distinct Responses of Rare and Abundant Microbial Taxa to In Situ Chemical Stabilization of Cadmium-Contaminated Soil. mSystems, 6(5), 10.1128/msystems.01040-21. https://doi.org/10.1128/msystems.01040-21
Yang, J., Zhou, X., Liu, X., Ling, Z., & Ji, F. (2021). Role of the Gastric Microbiome in Gastric Cancer: From Carcinogenesis to Treatment. Frontiers in Microbiology, 12, 641322. https://doi.org/10.3389/fmicb.2021.641322
Zhang, L., Zhang, M., You, S., Ma, D., Zhao, J., & Chen, Z. (2021). Effect of Fe3+ on the sludge properties and microbial community structure in a lab-scale A2O process. Science of The Total Environment, 780, 146505. https://doi.org/10.1016/j.scitotenv.2021.146505
Zhou, Z., Tran, P. Q., Breister, A. M., Liu, Y., Kieft, K., Cowley, E. S., Karaoz, U., & Anantharaman, K. (2022). METABOLIC: High-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks. Microbiome, 10(1), 33. https://doi.org/10.1186/s40168-021-01213-8
Authors
Copyright (c) 2025 Yovita Yovita, Siri Lek, Ton Kiat

This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.