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International Journal of Innovative Approaches in Agricultural Research 2026, Vol 10(1) 1-20

Effects of Some Organic Fertilizer Sources on the Biological Health of Agricultural Soils

Tülay Dizikisa • Nesrin Yıldız
Cite this article
Article Type
Review article
Publication Date
September 30, 2026
Pages
1-20
DOI
10.29329/ijiaar.2026.1423.26

Abstract

Organic fertilizers directly shape microbial activity and biological cycles, which form the heart of the soil ecosystem. The effects of organic fertilizer sources of animal and plant origin on soil biological health vary depending on the form of the nutrients they contain and the quality of their carbon. In this review, the effects of certain animal- and plant-based fertilizers, compost, vermicompost, biochar-enriched organic materials, and waste-based organic sources on soil biological health were examined comparatively based on microbial biomass, enzyme activities, microbial diversity, carbon dynamics, and nutrient element transformations. The results of the study indicate that the biological effects of animal- and plant-based organic materials added to agricultural soils are determined by carbon quality, the carbon-to-nitrogen ratio, decomposition rate, nutrient composition, biologically active components, and application conditions. While animal-based manures support microbial activity and nutrient transformations in the short term due to their easily degradable organic compounds and high nutrient content, compost, vermicompost, biochar, and other carbon-stable organic materials play significant roles in maintaining the continuity of microbial habitats, conserving organic carbon, and supporting long-term biological functions. Furthermore, the effects of organic inputs cannot be explained solely by an increase in microbial biomass; they must also be evaluated in conjunction with changes in carbon use efficiency, enzyme activities, functional microbial capacity, and nutrient cycles. However, it is essential to acknowledge that organic amendments may contain hazardous residues and could pose potential risks to agricultural product safety and agroecosystems. Current findings indicate that, in sustainable soil management, integrated application strategies that leverage the complementary properties of diverse organic sources are more effective than relying on the superiority of a single organic material. It has been emphasized that, in the future evaluation of organic fertilizers, the use of next-generation molecular analyses which reveal the structure and function of microbial communities in conjunction with traditional biological indicators will contribute to a more comprehensive understanding of soil biological processes.

Keywords: Soil Biological Health Organic Fertilizers Soil Microbiome Microbial Activity Soil Enzyme Activities Carbon-to-Nitrogen Ratio (C/N Ratio) Soil Organic Carbon Soil Biota
Cite this article
Dizikisa, T. & Yıldız, N. (2026). Effects of Some Organic Fertilizer Sources on the Biological Health of Agricultural Soils. International Journal of Innovative Approaches in Agricultural Research, 10(1), 1-20. https://doi.org/10.29329/ijiaar.2026.1423.26

  • Agegnehu, G., Srivastava, A. K., & Bird, M. I. (2017). The role of biochar and biochar-compost in improving soil quality and crop performance: A review. Applied Soil Ecology, 119, 156-170. [Google Scholar]
  • Angelova, V. R., Akova, V. I., Artinova, N. S., & Ivanov, K. I. (2013). The effects of organic amendments on soil chemical characteristics. Bulgarian Journal of Agricultural Science, 19(5), 958-971. [Google Scholar]
  • Arancon, N. Q., Edwards, C. A., Bierman, P., Metzger, J. D., & Lucht, C. (2005). Effects of vermicomposts produced from cattle manure, food waste and paper waste on the growth and yield of peppers in the field. Pedobiologia, 49(4), 297-306. [Google Scholar]
  • Aytenew, M., & Bore, G. (2020). Effects of organic amendments on soil fertility and environmental quality: A review. Plant Science, 8(5), 112-119. [Google Scholar]
  • Bernal, M. P., Alburquerque, J. A., & Moral, R. (2009). Composting of animal manures and chemical criteria for compost maturity assessment: A review. Bioresource Technology, 100(22), 5444-5453. [Google Scholar]
  • Blanco-Canqui, H. (2021). Does biochar improve all soil ecosystem services? GCB Bioenergy, 13(2), 291-304. [Google Scholar]
  • Bonanomi, G., Lorito, M., Vinale, F., & Woo, S. L. (2018). Organic amendments, beneficial microbes, and soil microbiota: Toward a unified framework for disease suppression. Annual Review of Phytopathology, 56, 1-20. [Google Scholar]
  • Bünemann, E. K., Bongiorno, G., Bai, Z., Creamer, R. E., De Deyn, G., de Goede, R., Fleskens, L., Geissen, V., Kuyper, T. W., Mäder, P., Pulleman, M., Sukkel, W., van Groenigen, J. W., & Brussaard, L. (2018). Soil quality A critical review. Soil Biology and Biochemistry, 120, 105-125. [Google Scholar]
  • Burns, R. G., DeForest, J. L., Marx, M. C., Stott, D. E., Smalla, K., Tebbe, C. C., Freeman, C., Mitchell, R. J., & Whiteley, A. S. (2013). Soil enzymes in a changing environment: Current knowledge and future directions. Soil Biology and Biochemistry, 58, 216-234. [Google Scholar]
  • Caldara, M., Di Gregorio, L., Sarvi, M., Graziano, S., Bindo, A., Salo, T., Nolfi, L., Costanzo, M., Lamanna, G., Scanferla, V., Varese, G. C., Bernini, R., Palojärvi, A., Marmiroli, N., & Bevivino, A. (2026). Impacts on soil health of soil improvers derived from agri-food processing residues: A systematic review with a focus on European field studies. Journal of Soil Science and Plant Nutrition, 26, 2858-2883. [Google Scholar]
  • Çengel, M., Okur, N., & Yılmaz, F. İ. (2009). Organik bağ topraklarında yeşil gübre bitkileri ve çiftlik gübresi uygulamalarının topraktaki mikrobiyal aktiviteye etkileri. Journal of Agriculture Faculty of Ege University, 46(1), 25-31. [Google Scholar]
  • Chen, X., Ma, X., Liu, Z., Gu, H., Fang, H., Shen, Z., Zhang, H., Wan, S., Li, W., Hao, X., Clarke, N. J., & Liu, J. (2025). Organic fertilizers increase microbial community diversity and stability slowing down the transformation process of nutrient cycling. Environmental Microbiome, 20, Article 91. [Google Scholar]
  • Chung, W. J., Chang, S. W., Chaudhary, D. K., Shin, J., Kim, H., Karmegam, N., Govrathanan, M., & Ravindran, B. (2021). Effect of biochar amendment on compost quality gaseous emissions and pathogen reduction during in-vesel composting of chicken manure. Chemosphere, 289, 131129. [Google Scholar]
  • Cui, J., Yang, B., Zhang, M., Song, D., Xu, X., Ai, C., Liang, G., & Zhou, W. (2023). Investigating the effects of organic amendments on soil microbial composition and its linkage to soil organic carbon: A global meta-analysis. Science of the Total Environment, 894, 164899. [Google Scholar]
  • Delgado-Baquerizo, M., Eldridge, D. J., Liu, Y.-R., Sokoya, B., Wang, J.-T., Hu, H.-W., He, J.-Z., Bastida, F., Moreno, J. L., Bamigboye, A. R., Blanco-Pastor, J. L., Cano-Díaz, C., Illán, J. G., Makhalanyane, T. P., Siebe, C., Trivedi, P., Zaady, E., Verma, J. P., Wang, L., . . . Fierer, N. (2021). Global homogenization of the structure and function in the soil microbiome of urban greenspaces. Science Advances, 7(28), 1-14. [Google Scholar]
  • Diacono, M., & Montemurro, F. (2010). Long-term effects of organic amendments on soil fertility: A review. Agronomy for Sustainable Development, 30, 401-422. [Google Scholar]
  • Dick, R. P. (1994). Soil enzyme activities as indicators of soil quality. In J. W. Doran, D. C. Coleman, D. F. Bezdicek, & B. A. Stewart (Eds.), Defining soil quality for a sustainable environment (pp. 107-124). Soil Science Society of America. https://doi.org/10.2136/sssaspecpub35.c7 [Google Scholar] [Crossref] 
  • Dikici, H., Qader, R. K., & Demir, Ö. F. (2017). Karbon/Azot oranının organik toprakların bazı özellikleri üzerine etkisi. Toprak Su Dergisi, Özel Sayı, 66-70. [Google Scholar]
  • Edwards, J. H., & Someshwar, A. V. (2000). Chemical, physical, and biological characteristics of agricultural and forest by-products for land application. In J. F. Power, W. A. Dick, R. M. Kashmanian, J. T. Sims, R. J. Wright, M. D. Dawson, & D. Bezdicek (Eds.), Land application of agricultural, industrial, and municipal by-products (pp. 1-62). Soil Science Society of America. [Google Scholar]
  • Epstein, E. (2003). Land application of sewage sludge and biosolids. CRC Press. [Google Scholar]
  • Fierer, N. (2017). Embracing the unknown: Disentangling the complexities of the soil microbiome. Nature Reviews Microbiology, 15, 579-590. [Google Scholar]
  • Fontaine, S., Barot, S., Barré, P., Bdioui, N., Mary, B., & Rumpel, C. (2007). Stability of organic carbon in deep soil layers controlled by fresh carbon supply. Nature, 450(7167), 277-280. [Google Scholar]
  • Geisseler, D., & Scow, K. M. (2014). Long-term effects of mineral fertilizers on soil microorganisms-A review. Soil Biology and Biochemistry, 75, 54-63. [Google Scholar]
  • Gil-Martínez, M., Madejón, P., Madejón, E., & de Sosa, L. L. (2025). Compost and vegetation cover drive soil fertility, microbial activity, and community in organic farming soils. Plant and Soil, 516(1-2), 299-321. [Google Scholar]
  • Hartmann, M., & Six, J. (2023). Soil structure and microbiome functions in agroecosystems. Nat Rev Earth Environ, 4, 4-18. [Google Scholar]
  • He, Z., Ding, B., Pei, S., Cao, H., Liang, J., & Li, Z. (2023). The impact of organic fertilizer replacement on greenhouse gas emissions and its influencing factors. Science of the Total Environment, 905, 166917. [Google Scholar]
  • Howe, J. A., McDonald, M. D., Burke, J., Robertson, I., Coker, H., Gentry, T. J., & Lewis, K. L. (2024). Influence of fertilizer and manure inputs on soil health: A review. Soil Security, 16, 100155. [Google Scholar]
  • İlay, R., Aktaş, M., Aslantekin, N. B., & Özcan, H. (2021). Farklı kaynaklardan elde edilen organik materyalin kumlu tın bünyeli toprağın bazı özellikleri üzerine etkileri. Toprak Bilimi ve Bitki Besleme Dergisi, 9(1), 30-38. [Google Scholar]
  • Irmak Yılmaz, F., & Kurt, S. (2018). Biyokömür ve vermikompost uygulamalarının toprağın bazı biyolojik özellikleri üzerine etkisi. Toprak Bilimi ve Bitki Besleme Dergisi, 6(2), 143-150. [Google Scholar]
  • Jansson, J. K., & Hofmockel, K. S. (2020). Soil microbiomes and climate change. Nature Reviews Microbiology, 18(1), 35-46. [Google Scholar]
  • Jeffery, S., Abalos, D., Prodana, M., Bastos, A. C., van Groenigen, J. W., Hungate, B. A., & Verheijen, F. (2017). Biochar boosts tropical but not temperate crop yields. Environmental Research Letters, 12(5), 053001. [Google Scholar]
  • Joshi, R., Singh, J., & Vig, A. P. (2015). Vermicompost as an effective organic fertilizer and biocontrol agent: Effect on growth, yield and quality of plants. Reviews in Environmental Science and Bio/Technology, 14, 137-159. [Google Scholar]
  • Karlen, D. L., Ditzler, C. A., & Andrews, S. S. (2003). Soil quality: Why and how? Geoderma, 114(3-4), 145-156. [Google Scholar]
  • Kätterer, T., Bolinder, M. A., Berglund, K., & Kirchmann, H. (2012). Strategies for carbon sequestration in agricultural soils in northern Europe. Acta Agriculturae Scandinavica, Section A-Animal Science, 62(4), 181-198. [Google Scholar]
  • Kraut-Cohen, J., Zolti, A., Rotbart, N., Bar-Tal, A., Laor, Y., Medina, S., Shawahna, R., Saadi, I., Raviv, M., Green, S. J., Yermiyahu, U., & Minz, D. (2023). Short- and long-term effects of continuous compost amendment on soil microbiome community. Computational and Structural Biotechnology Journal, 21, 3280-3292. [Google Scholar]
  • Kumar, Y., Ren, W., Tao, H., Tao, B., & Lindsey, L. E. (2025). Impact of biochar amendment on soil microbial biomass carbon enhancement under field experiments: A meta-analysis. Biochar, 7, Article 2. [Google Scholar]
  • Lal, R. (2020). Soil organic matter and water retention. Agronomy Journal, 112(5), 3265-3277. [Google Scholar]
  • Larney, F. J., & Angers, D. A. (2012). The role of organic amendments in soil reclamation: A review. Canadian Journal of Soil Science, 92(1), 19-38. [Google Scholar]
  • Lavallee, J. M., Soong, J. L., & Cotrufo, M. F. (2020). Conceptualizing soil organic matter into particulate and mineral-associated forms to address global change. Global Change Biology, 26(1), 261-273. [Google Scholar]
  • Lazcano, C., & Domínguez, J. (2011). The use of vermicompost in sustainable agriculture: Impact on plant growth and soil fertility. In M. Miransari (Ed.), Soil nutrients. Nova Science Publishers. [Google Scholar]
  • Lehmann, J., Bossio, D. A., Kögel-Knabner, I., & Rillig, M. C. (2020). The concept and future prospects of soil health. Nature Reviews Earth & Environment, 1, 544-553. [Google Scholar]
  • Liu, S., Wang, J., Pu, S., Blagodatskaya, E., Kuzyakov, Y., & Razavi, B. S. (2020). Impact of manure on soil biochemical properties: A global synthesis. Science of the Total Environment, 745, 141003. [Google Scholar]
  • Liu, W., Yang, Z., Ye, Q., Peng, Z., Zhu, S., Chen, H., Liu, D., Li, Y., Deng, L., Shu, X., & Huang, H. (2023). Positive effects of organic amendments on soil microbes and their functionality in agro-ecosystems. Plants, 12(22), 3790. [Google Scholar]
  • Lori, M., Symnaczik, S., Mäder, P., De Deyn, G., & Gattinger, A. (2017). Organic farming enhances soil microbial abundance and activity-A meta-analysis and meta-regression. PLOS ONE, 12(7), e0180442. [Google Scholar]
  • Ma, Q., Wen, Y., Wang, D., Sun, X., Hill, P. W., Macdonald, A., Chadwick, D. R., Wu, L., & Jones, D. L. (2020). Farmyard manure applications stimulate soil carbon and nitrogen cycling by boosting microbial biomass rather than changing its community composition. Soil Biology and Biochemistry, 144, Article 107760. [Google Scholar]
  • Mäder, P., Fließbach, A., Dubois, D., Gunst, L., Fried, P., & Niggli, U. (2002). Soil fertility and biodiversity in organic farming. Science, 296(5573), 1694-1697. [Google Scholar]
  • Moorhead, D. L., Rinkes, Z. L., Sinsabaugh, R. L., & Weintraub, M. N. (2013). Dynamic relationships between microbial biomass, respiration, inorganic nutrients and enzyme activities: Informing enzyme-based decomposition models. Frontiers in Microbiology, 4, Article 223. [Google Scholar]
  • Nannipieri, P., Trasar-Cepeda, C., & Dick, R. P. (2018). Soil enzyme activity: A brief history and biochemistry as a basis for appropriate interpretations and meta-analysis. Biology and Fertility of Soils, 54, 11-19. [Google Scholar]
  • Okur, N., Kayıkçıoğlu, H. H., Okur, B., & Delibacak, S. (2008). Organic amendment based on tobacco waste compost and farmyard manure: Influence on soil biological properties and butter-head lettuce yield. Turkish Journal of Agriculture and Forestry, 32(2), 91-99. [Google Scholar]
  • Ouyang, Y., Reeve, J. R., & Norton, J. M. (2022). The quality of organic amendments affects soil microbiome and nitrogen-cycling bacteria in an organic farming system. Frontiers in Soil Science, 2, Article 869136. [Google Scholar]
  • Pan, C.-C., & Huang, C.-H. (2024). Cow dung compost and vermicompost amendments promote soil carbon stock by enhancing labile organic carbon and residual oxidizable carbon fractions in maize field soil. Soil Use and Management, 40(4), e13122. [Google Scholar]
  • Rayne, N., & Aula, L. (2020). Livestock manure and the impacts on soil health: A review. Soil Systems, 4(4), Article 64. [Google Scholar]
  • Ross, A. T., & Emery, S. M. (2025). Microbial inocula enhance effects of biochar amendments on crop productivity, soil health, and microbial communities: A meta-analysis. Soil Science Society of America Journal, 89(1), e20792. [Google Scholar]
  • Semenov, M. V., Zhelezova, A. D., Ksenofontova, N. A., Ivanova, E. A., Nikitin, D. A., & Semenov, V. M. (2025). Microbiological indicators for assessing the effects of agricultural practices on soil health: A review. Agronomy, 15(2), 335. [Google Scholar]
  • Shober, A. L., Stehouwer, R. C., Macneal, K. E., & McNitt, A. S. (2003). On-farm assessment of biosolids effects on soil and crop tissue quality. Journal of Environmental Quality, 32(5), 1873-1880. [Google Scholar]
  • Shu, X., He, J., Zhou, Z., Xia, L., Hu, Y., Zhang, Y., Zhang, Y., Luo, Y., Chu, H., Liu, W., Yuan, S., Gao, X., & Wang, C. (2022). Organic amendments enhance soil microbial diversity, microbial functionality and crop yields: A meta-analysis. Science of the Total Environment, 829, 154627. [Google Scholar]
  • Siedt, M., Schäffer, A., Smith, K. E. C., Nabel, M., Roß-Nickoll, M., & van Dongen, J. T. (2021). Comparing straw, compost, and biochar regarding their suitability as agricultural soil amendments to affect soil structure, nutrient leaching, microbial communities, and the fate of pesticides. Science of the Total Environment, 751, 141607. [Google Scholar]
  • Singh, N. K., Sachan, K., Bp, M., Panotra, N., & Katiyar, D. J. A. J. O. S. S. (2024). Building soil health and fertility through organic amendments and practices: A review. Asian Journal of Soil Scienceand Plant Nutrition, 10(1), 175-197. [Google Scholar]
  • Sokol, N. W., Slessarev, E., Marschmann, G. L., Nicolas, A., Blazewicz, S. J., Brodie, E. L., Firestone, M. K., Foley, M. M., Hestrin, R., Hungate, B. A., Koch, B. J., Stone, B. W., Sullivan, M. B., Zablocki, O., LLNL Soil Microbiome Consortium, & Pett-Ridge, J. (2022). Life and death in the soil microbiome: How ecological processes influence biogeochemistry. Nature Reviews Microbiology, 20(7), 415-430. [Google Scholar]
  • Thapa, B., Awal, R., Fares, A., Rahman, A., Veettil, A., Elhassan, M., & Niraj, K. C. (2025). Improving soil health through manure and biochar amendments under climate-smart agriculture. Soil Science Society of America Journal, 89(5), e70129. [Google Scholar]
  • Toprak, T., & Kızılkaya, R. (2026). Effect of vermicomposts obtained from hazelnut husuk-farmyard manure mixtures on their chemical properties, wheat yield, and soil microbial biomass carbon. Toprak Bilimi ve Bitki Besleme Dergisi, 14(1), 25-34. [Google Scholar]
  • Trivedi, P., Leach, J. E., Tringe, S. G., Sa, T., & Singh, B. K. (2020). Plant-microbiome interactions: From community assembly to plant health. Nature Reviews Microbiology, 18, 607-621. [Google Scholar]
  • Xing, Y., Xie, Y., & Wang, X. (2025). Enhancing soil health through balanced fertilization: A pathway to sustainable agriculture and food security. Frontiers in Microbiology, 16, 1536524. [Google Scholar]
  • Xu, J., Li, Y., & Li, L. (2025). A comprehensive review of the effects of organic amendments on soil health and fertility: Mechanisms, greenhouse gas emissions, and implications for sustainable agriculture. Agronomy, 15(12), 2705. [Google Scholar]