Biocompounds in Soil Health and Sustainable Agriculture: Molecular Interactions, Microbial Processes, and Environmental Implications

Authors

  • Zakiyeh Safa * Department of Agricultural Engineering, Islamic Azad University, Rasht Branch, Rasht, Iran.

https://doi.org/10.48313/bic.vi.83

Abstract

Biocompounds are important chemical mediators within soil-plant-microbe systems and play diverse roles in soil biological processes, nutrient cycling, and plant adaptation to environmental stress. Their presence in soil originates from multiple sources, including plant roots, plant residues, and microbial metabolism, resulting in a chemically diverse mixture of phenolics, flavonoids, organic acids, amino acids, peptides, polysaccharides, terpenoids, siderophores, phytohormones, and microbial secondary metabolites. This review examines the roles of biocompounds in soil health and sustainable agriculture, with particular emphasis on their molecular interactions, microbial processes, environmental fate, and ecological implications. The discussion highlights interactions of biocompounds with plant roots, soil minerals, organic matter, and metals, as well as their effects on microbial community structure, metabolic activity, nutrient transformation, and soil organic matter dynamics. Their potential contribution to plant adaptation under drought, salinity, temperature, oxidative, and nutrient stresses is also considered. Particular attention is given to adsorption, degradation, transformation, persistence, bioavailability, and potential effects on non-target organisms, which collectively determine the environmental behavior of biocompounds. Emerging approaches based on metabolomics, multi-omics, spatial analysis, microbiome engineering, Artificial Intelligence (AI), and precision agriculture offer new opportunities to investigate these complex interactions and develop more predictive approaches to soil management. Nevertheless, challenges remain in understanding compound mixtures, transformation products, field-scale variability, and long-term ecological effects. Integrating molecular, microbial, physicochemical, and field-scale approaches will be essential for translating knowledge of biocompounds into environmentally responsible strategies for maintaining soil health and supporting sustainable agricultural systems. 

Keywords:

Soil health, Sustainable agriculture, Rhizosphere, Soil microbiome, Bioavailability, Multi-omics

References

  1. [1] Gallego, I. (2025). Biocompounds of commercial interest from freshwater and marine phytoplankton. In The role of plankton in freshwater and marine ecology. IntechOpen. https://doi.org/10.5772/intechopen.1008500
  2. [2] Alviz-Meza, A., Rojas-Flores, S. J., & Gonzalez-Delgado, A. D. (2026). Research trend in the valorization of Persea Americana: A bibliometric analysis of bioactive compounds, extraction technologies, and applications (2005-2024). Environmental research, engineering and management, 82(1), 65–87. https://doi.org/10.5755/j01.erem.82.1.42769
  3. [3] Gavrilaș, S. (2026). Valorization of sustainable antioxidant sources and new perspectives for utilization. Processes, 14(3), 578. https://doi.org/10.3390/pr14030578
  4. [4] Quintin, D., Garcia-Gomez, P., Ayuso, M., & Sanmartin, A. M. (2019). Active biocompounds to improve food nutritional value. Trends in food science & technology, 84, 19–21. https://doi.org/10.1016/j.tifs.2018.03.024
  5. [5] Sheikh, Z. U. D., Bharti, A., Kotwal, N., Devi, A., Kothari, R., Pathania, D., & Singh, A. (2026). High-valued biomolecules from algal biomass: Research Gaps, innovative roadmaps for safety and quality assurance. In Algae: A promising source of food, feed and bioproducts (pp. 621–655). Springer. https://doi.org/10.1007/978-3-032-22521-4_20
  6. [6] Bayraktar Ekmekcigil, O., Eroglu, S., Bharadwaj, S., Farooqi, A. A., Gozuacik, D., & Kutlu, O. (2026). Targeting the Autophagy-Apoptosis axis in Osteosarcoma: Therapeutic potential of biocompounds: A review. Chemical biology & drug design, 107(2), e70257. https://doi.org/10.1111/cbdd.70257
  7. [7] Ceravolo, G., Ferrandis Rosell, A., Blesa, J., Lopez Malo, D., Scarafoni, A., & Esteve, M. J. (2025). Use of biphasic NADES to evaluate the extraction of biocompounds in hydrophilic phase from Okara. FEBS OPEN BIO, 15(Suppl. 2), 201-201. https://hdl.handle.net/2434/1173873
  8. [8] Berradre, M. N., Arroqui, C., Fernández-Pan, I., Beriain, M. J., Ibañez, F. C., & Vírseda, P. (2026). Eco-friendly recovery of biocompounds from agro-industrial by-products using non-thermal processing. Clean technologies, 8(3), 64. https://doi.org/10.3390/cleantechnol8030064
  9. [9] Styc, Q., Borrelli, P., Evangelista, S. J., Field, D., Francos, N., Heuser, I., ... & McBratney, A. (2026). Soil health within soil security. European journal of soil science, 77(3), e70340. https://doi.org/10.1111/ejss.70340
  10. [10] Joshi, N., Jinger, D., Joshi, S., Joshi, E., Sharma, J. K., Paramesha, V., ... & Madhu, M. (2026). Soil health management strategies for climate-resilient agriculture. Discover soil, 3(1), 39. https://doi.org/10.1007/s44378-026-00194-0
  11. [11] Singh, M., & Singh, K. (2026). Enhancing crop productivity and soil health through precision fertigation: Advancements, challenges and future prospects. Applied water science, 16(4), 130. https://doi.org/10.1007/s13201-026-02767-4
  12. [12] Kumar, S., Dhyani, B. P., Shahi, U. P., Kumar, S., Singh, S. P., Kumar, Y., ... & Pal, R. (2026). Organic waste recycling for soil amendments: Advancing circular bioeconomy and soil health restoration. AgriSustain: An international journal, 4(2), 17-25. https://doi.org/10.5281/zenodo.21767851
  13. [13] Hu, Y., Cross, A., Shen, Z., Bouma, J., & Viscarra Rossel, R. A. (2026). On soil health and the pivotal role of sensing. Soil, 12(1), 227–252. https://doi.org/10.5194/soil-12-227-2026
  14. [14] Allam, A. N., El Gamal, S., & Naggar, V. (2011). Bioavailability: A pharmaceutical review. International journal of novel drug delivery technology, 1(1), 77–93. https://www.researchgate.net/publication/271832890_Bioavailability_A_Pharmaceutical_Review
  15. [15] Joshi, N., Kaur, R., & Nawaz, T. (2026). The soil-root nexus: How soil health shapes plant nutrient uptake and food nutritional security. Plant and soil, 521, 1145–1173. https://doi.org/10.1007/s11104-026-08489-5
  16. [16] Alewell, C., Gupta, S., Poulenard, J., Niquille, N., Kaiser, A., Shokri, N., ... & Borrelli, P. (2026). A first quantitative assessment of soil health at European scale considering soil genesis. Journal of plant nutrition and soil science, 189(1), 6-16. https://doi.org/10.1002/jpln.70034
  17. [17] de Waterbeemd, H., Lennernäs, H., & Artursson, P. (2004). Drug bioavailability. Methods and principles in medicinal chemistry, 18. https://pdfs.semanticscholar.org/97bd/ad11368e3b0609a29cefc55c8f4075475eea.pdf
  18. [18] Caldara, M., Di Gregorio, L., Sarvi, M., Graziano, S., Bindo, A., Salo, T., ... & 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(1), 2858-2883. https://doi.org/10.1007/s42729-026-03037-7
  19. [19] Pradhan, N. C., Gavhane, K. P., Bhalekar, D. G., & Kiran, P. R. (2026). Sustainable agriculture fundamentals. In Health, nutrition and sustainability (pp. 609-626). Academic Press. https://doi.org/10.1016/B978-0-443-32920-3.00026-4
  20. [20] Joshi-Saha, A., & Misra, G. (2026). Legume crops and their role in achieving sustainable agriculture. In Legumes: Genetics and genomics (pp. 1–17). Springer. https://doi.org/10.1007/978-981-97-7538-5_2-1
  21. [21] Jia, X., Zhang, W., & Zhu, T. (2026). Agricultural new productive forces driving sustainable agricultural development: Evidence from Anhui province, China. Sustainability, 18(2), 792. https://doi.org/10.3390/su18020792
  22. [22] Gokul, S., Mohan, V. A., Sabarivasan, R., Adhisankaran, K., Rao, P. T., Harish, M., & De, S. (2026). Sustainable agriculture toward carbon neutrality: A quantitative and qualitative assessment. Environmental and sustainability indicators, 30, 101219. https://doi.org/10.1016/j.indic.2026.101219
  23. [23] Purohit, A., Kounain, S., Madala, C., Chavan, S., Guguloth, N., Kethavathu, S., ... & Thakur, N. R. (2026). Sustainable crops for future food security: Challenges, innovations, and solutions. In Improving crops for future sustainability and climate resilience (pp. 1-40). Singapore: Springer Nature Singapore. https://doi.org/10.1007/978-981-95-2754-0_1
  24. [24] Subramanian, I., Verma, S., Kumar, S., Jere, A., & Anamika, K. (2020). Multi-omics data integration, interpretation, and its application. Bioinformatics and biology insights, 14. https://doi.org/10.1177/1177932219899051
  25. [25] Toutain, P.-L., & Bousquet-mélou, A. (2004). Bioavailability and its assessment. Journal of veterinary pharmacology and therapeutics, 27(6), 455–466. https://doi.org/10.1111/j.1365-2885.2004.00604.x
  26. [26] Danish, K. A., & Lubhan, S. (2016). Various techniques of bioavailability enhancement: A review. Journal of drug delivery and therapeutics (JDDT), 6(3), 34–41. https://jddtonline.info/index.php/jddt/article/view/1228
  27. [27] Hasin, Y., Seldin, M., & Lusis, A. (2017). Multi-omics approaches to disease. Genome biology, 18(1), 83. https://doi.org/10.1186/s13059-017-1215-1
  28. [28] Ongachi, W., Belinder, I., Bhat, B., Hussain, S., & Dub, R. (2026). Strengthening agricultural extension services to enhance farmers’ capacity and resilience for sustainable development; a systematic review. BMC agriculture, 2(1), 17. https://doi.org/10.1186/s44399-026-00039-9
  29. [29] Qiu, W., Tang, X., Shen, Q., & Yuan, J. (2026). Plant-microbiome interactions for rhizosphere health: A three-step framework for crop resilience. Plant, cell & environment. https://doi.org/10.1111/pce.70837
  30. [30] Hartmann, A. (2026). The rhizosphere-A one health concept for co-evolution of beneficial microbes and plants towards sustainable agriculture. Plant and soil, 523(2), 763–773. https://doi.org/10.1007/s11104-025-08056-4
  31. [31] Salata, A., Borisova, G., & Maleva, M. (2026). Microbial allies in stress resilience: The role of plant growth-promoting bacteria in crop rhizosphere, endosphere, and phyllosphere. Journal of agricultural sciences, 32(2), 202–221. https://doi.org/10.15832/ankutbd.1770195
  32. [32] Adebayo, A. A., & Babalola, O. O. (2026). Rhizosphere microbiome as an underexplored resource for agroecosystem sustainability: Insights from the carrot root zone. Environmental microbiology reports, 18(2), e70325. https://doi.org/10.1111/1758-2229.70325
  33. [33] Chen, C., Wang, J., Pan, D., Wang, X., Xu, Y., Yan, J., ... & Liu, G. P. (2023). Applications of multi‐omics analysis in human diseases. MedComm, 4(4), e315. https://doi.org/10.1002/mco2.315
  34. [34] Adhikary, K., Selim, S., Sarkar, R., Ganguly, K., Das, J., Almuhayawi, M. S., ... & Karak, P. (2026). Synthetic microbiomes in bioengineered rhizospheres: New frontiers for climate-resilient agriculture. Frontiers in microbiology, 17, 1780132. https://doi.org/10.3389/fmicb.2026.1780132
  35. [35] Etesami, H. (2026). Grand challenges in rhizosphere research for the next decade. Rhizosphere, 38, 101337. https://doi.org/10.1016/j.rhisph.2026.101337
  36. [36] Umutoni, S., Zhang, H., Guo, J., Yu, Z., Shao, H., Yi, X., ... & Yu, Y. (2026). Oral anticancer drug delivery: Strategies for improving bioavailability. Chinese chemical letters, 112362. https://doi.org/10.1016/j.cclet.2026.112362
  37. [37] Shahrajabian, M. H., & Sun, W. (2023). Survey on multi-omics, and multi-omics data analysis, integration and application. Current pharmaceutical analysis, 19(4), 267–281. https://doi.org/10.2174/1573412919666230406100948
  38. [38] Khalid, N. U. A., Rivera-Delgado, E., & von Erlach, T. (2026). Navigating the complexity of oral peptide delivery: Challenges and strategies to enhance oral bioavailability. Frontiers in drug delivery, 6, 1809842. https://doi.org/10.3389/fddev.2026.1809842
  39. [39] Hosszú, Z., Pártos, P., Mahdavi, M., Ujhelyi, Z., Fehér, P., Haimhoffer, Á., ... & Pető, Á. (2026). The role and potential of nanotechnology in improving solubility and enhancing bioavailability. Pharmaceutics, 18(4), 478. https://doi.org/10.3390/pharmaceutics18040478
  40. [40] Vandereyken, K., Sifrim, A., Thienpont, B., & Voet, T. (2023). Methods and applications for single-cell and spatial multi-omics. Nature reviews genetics, 24(8), 494–515. https://doi.org/10.1038/s41576-023-00580-2
  41. [41] Tiwari, P., Pandey, R., & Chadha, S. (2026). Integrative multi-omics approaches for personalized medicine and health. Current bioinformatics, 21(2), 109–121. https://doi.org/10.2174/0115748936360644250127095005
  42. [42] Moar, K., Pant, A., & Maurya, P. K. (2026). Artificial intelligence, machine learning, and multi-omics: The future of cancer and precision oncology. Indian journal of clinical biochemistry, 1–18. https://doi.org/10.1007/s12291-026-01425-5

Published

2026-08-06

Issue

Vol. 3 No. 4 (2026): Biocompounds (BIC)

Section

Articles

How to Cite

Safa, Z. (2026). Biocompounds in Soil Health and Sustainable Agriculture: Molecular Interactions, Microbial Processes, and Environmental Implications. Biocompounds, 3(4), 284-313. https://doi.org/10.48313/bic.vi.83

Similar Articles

1-10 of 22

You may also start an advanced similarity search for this article.