The Impact of Bio Compost Use on the Agricultural Soil Microbiome: Evidence from a Laboratory-Scale Study

Authors

  • Angelantonio Calabrese

    Water Research Institute, National Research Council, Bari 70132, Italy
  • Fabiola Turchese Liuzzi

    Water Research Institute, National Research Council, Bari 70132, Italy
  • Mariavirginia Campanale

    Istituto di Ricerca Minds Srl, Bari 70124, Italy

DOI:

https://doi.org/10.30564/jees.v8i6.13183
Received: 17 February 2026 | Revised: 20 March 2026 | Accepted: 27 March 2026 | Published Online: 5 June 2026

Abstract

Composted organic amendments are increasingly recognized as viable alternatives to synthetic fertilizers, driven by the rising interest in organic waste recycling and sustainable soil management. This study aims to evaluate the long-term effects of bio compost, derived from organic waste, on the chemical and microbiological properties of agricultural soils. A one-year laboratory-scale experiment was conducted using nine microcosm replicates with increasing doses of compost (ratios 1:1, 1:2, 1:4), applied in both powder and granular forms, with and without the addition of water. Microbiological analysis based on 16S rRNA gene sequencing revealed significant shifts in microbial composition. The results demonstrated a consistent increase in microbiological DNA concentration in samples amended with bio-compost, showing a 50% increase from the initial concentration. Furthermore, regarding species composition, bio-compost altered the bacterial population in favor of the predominant species introduced into the soil, indicating a selective enhancement of the bacterial community. Additionally, the addition of water did not affect either the quantity or quality of the bacterial composition. Microbial biomass significantly improved following compost application, with powdered formulations proving more effective than granular ones, and drought conditions often eliciting more pronounced responses. These findings demonstrate that the amendment can improve soil quality by minimizing disruption to microbial communities and promoting long-term soil fertility. Adopting this approach appears beneficial for circular, bio-based agricultural systems.

 

Keywords:

Microbial Consortium; Bio Compost Impact; Metagenomics Analysis; Bacterial Community; Microbiome Evolution

References

[1] Bustamante, M.A., Gomis, M.P., Pérez-Murcia, M.D., et al., 2021. Use of Livestock Waste Composts as Nursery Growing Media: Effect of a Washing Pre-Treatment. Scientia Horticulturae. 281, 109954. DOI: https://doi.org/10.1016/j.scienta.2021.109954

[2] Sánchez-Monedero, M.A., Cayuela, M.L., Sánchez-García, M., et al., 2019. Agronomic Evaluation of Biochar, Compost and Biochar-Blended Compost across Different Cropping Systems: Perspective from the European Project FERTIPLUS. Agronomy. 9(5), 225. DOI: https://doi.org/10.3390/agronomy9050225

[3] Bisht, N., Chauhan, P.S., 2021. Excessive and Disproportionate Use of Chemicals Cause Soil Contamination and Nutritional Stress. In: Larramendy, M.L., Soloneski, S. (Eds.). Soil Contamination—Threats and Sustainable Solutions. IntechOpen: London, UK. DOI: https://doi.org/10.5772/intechopen.94593

[4] Zhang, L., Yan, C., Guo, Q., et al., 2018. The Impact of Agricultural Chemical Inputs on the Environment: Global Evidence from Informetrics Analysis and Visualization. International Journal of Low-Carbon Technologies. 13(4), 338–352. DOI: https://doi.org/10.1093/ijlct/cty039

[5] Ravindran, B., Awasthi, K.M., Karmegam, N.G., et al., 2022. Co-Composting of Food Waste and Swine Manure Augmenting Biochar and Salts: Nutrient Dynamics, Gaseous Emissions, and Microbial Activity. Bioresource Technology. 344, 126300. DOI: https://doi.org/10.1016/j.biortech.2021.126300

[6] Eifediyi, E., Ahamefule, H., Remison, S., et al., 2015. Effects of Neem Seed Cake on the Growth and Yield of Okra (Abelmoschus esculentus (L.) Moench) in Ilorin, North-Central Nigeria. Agro-Science. 12(2), 20–27. DOI: https://doi.org/10.4314/as.v12i2.3

[7] Machado, R.M.A., Alves-Pereira, I., Robalo, M., et al., 2021. Effects of Municipal Solid Waste Compost Supplemented with Inorganic Nitrogen on Physicochemical Soil Characteristics, Plant Growth, Nitrate Content, and Antioxidant Activity in Spinach. Horticulturae. 7(3), 53. DOI: https://doi.org/10.3390/horticulturae7030053

[8] Pathak, P., Singh, C., Chaudhary, N., et al., 2020. Application of Biochar, Leaf Compost, and Spent Mushroom Compost for Tomato Growth in Alternative to Chemical Fertilizer. Research Journal of Agricultural Sciences. 11(6), 1362–1366.

[9] Bouajila, K., Sanaa, M., 2011. Effects of Organic Amendment on Soil Physico-Chemical and Biological Properties. Journal of Materials and Environmental Science. 2(S1), 485–490.

[10] Daniel, F., Bruno, G., 2012. Synergisms between Compost and Biochar for Sustainable Soil Amelioration. In: Kumar, S. (Ed.). Management of Organic Waste. IntechOpen: London, UK. DOI: https://doi.org/10.5772/31200

[11] Roghanian, S., Hosseini, H.M., Savaghebi, G., et al., 2012. Effects of Composted Municipal Waste and Its Leachate on Some Soil Chemical Properties and Corn Plant Responses. International Journal of Agriculture: Research and Review. 2(6), 801–814.

[12] Amlinger, F., Peyr, S., Geszti, J., et al., 2007. Beneficial Effects of Compost Application on Fertility and Productivity of Soils. Available from: https://www.bmluk.gv.at/dam/jcr:fe3ea151-bcb8-4631-be16-64af4cc3e120/Studie_CompBenefits.pdf (cited 16 February 2026).

[13] Brown, S., Cotton, M., 2011. Changes in Soil Properties and Carbon Content Following Compost Application: Results of On-Farm Sampling. Compost Science and Utilization. 19(2), 87–96. DOI: https://doi.org/10.1080/1065657X.2011.10736983

[14] Siles, J.A., García-Sánchez, M., Gómez-Brandón, M., et al., 2021. Studying Microbial Communities Through Co-Occurrence Network Analyses during Processes of Waste Treatment and in Organically Amended Soils: A Review. Microorganisms. 9(6), 1165. DOI: https://doi.org/10.3390/microorganisms9061165

[15] Vishan, I., Kanekar, H., Kalamdhad, A., et al., 2014. Microbial Population, Stability, and Maturity Analysis of Rotary Drum Composting of Water Hyacinth. Biologia. 69(10), 1303–1313. DOI: https://doi.org/10.2478/s11756-014-0450-0

[16] Aguilar-Paredes, A., Valdés, G., Araneda, N., et al., 2023. Microbial Community in the Composting Process and Its Positive Impact on the Soil Biota in Sustainable Agriculture. Agronomy. 13(2), 542. DOI: https://doi.org/10.3390/agronomy13020542

[17] Wang, X., He, X., Liang, J., et al., 2022. Succession of Microbial Community during the Co-Composting of Food Waste Digestate and Garden Waste. International Journal of Environmental Research and Public Health. 19(16), 9945. DOI: https://doi.org/10.3390/ijerph19169945

[18] Liu, X., Shi, Y., Kong, L., et al., 2022. Long-Term Application of Bio-Compost Increased Soil Microbial Community Diversity and Altered Its Composition and Network. Microorganisms. 10(2), 462. DOI: https://doi.org/10.3390/microorganisms10020462

[19] Zhang, X., Li, L., Butcher, J., et al., 2019. Advancing Functional and Translational Microbiome Research Using Meta-Omics Approaches. Microbiome. 7, 154. DOI: https://doi.org/10.1186/s40168-019-0767-6

[20] Werner, D., Acharya, K., Blackburn, A., et al., 2022. MinION Nanopore Sequencing Accelerates Progress towards Ubiquitous Genetics in Water Research. Water. 14(16), 2491. DOI: https://doi.org/10.3390/w14162491

[21] Santos, A., van Aerle, R., Barrientos, L., et al., 2020. Computational Methods for 16S Metabarcoding Studies Using Nanopore Sequencing Data. Computational and Structural Biotechnology Journal. 18, 296–305. DOI: https://doi.org/10.1016/j.csbj.2020.01.005

[22] Kumar, P., Aeron, A., Shaw, N., et al., 2020. Seed Bio-Priming with Tri-Species Consortia of Phosphate Solubilizing Rhizobacteria (PSR) and Its Effect on Plant Growth Promotion. Heliyon. 6(12), e05701. DOI: https://doi.org/10.1016/j.heliyon.2020.e05701

[23] Zhao, Q., Thompson, A.M., Callister, S.J., et al., 2022. Dynamics of Organic Matter Molecular Composition under Aerobic Decomposition and Their Response to the Nitrogen Addition in Grassland Soils. Science of The Total Environment. 806, 150514. DOI: https://doi.org/10.1016/j.scitotenv.2021.150514

[24] Köberl, M., Kusstatscher, P., Wicaksono, W.A., et al., 2022. Increased Yield and High Resilience of Microbiota Representatives with Organic Soil Amendments in Smallholder Farms of Uganda. Frontiers in Plant Science. 12, 815377. DOI: https://doi.org/10.3389/fpls.2021.815377

[25] Reeve, J.R., Endelman, J.B., Miller, B.E., et al., 2012. Residual Effects of Compost on Soil Quality and Dryland Wheat Yield Sixteen Years after Compost Application. Soil Science Society of America Journal. 76(1), 278–285. DOI: https://doi.org/10.2136/sssaj2011.0123

[26] Meisner, A., Snoek, B.L., Nesme, J., et al., 2021. Soil Microbial Legacies Differ Following Drying-Rewetting and Freezing-Thawing Cycles. The ISME Journal. 15(4), 1207–1221. DOI: https://doi.org/10.1038/s41396-020-00844-3

[27] Schloter, M., Nannipieri, P., Sørensen, S.J., et al., 2018. Microbial Indicators for Soil Quality. Biology and Fertility of Soils. 54(1), 1–10. DOI: https://doi.org/10.1007/s00374-017-1248-3

Downloads

How to Cite

Calabrese, A., Liuzzi, F. T., & Campanale, M. (2026). The Impact of Bio Compost Use on the Agricultural Soil Microbiome: Evidence from a Laboratory-Scale Study. Journal of Environmental & Earth Sciences, 8(6), 35–49. https://doi.org/10.30564/jees.v8i6.13183

Issue

Vol. 8 , Iss. 6 (June 2026): In Progress

Article Type

Article

License

Copyright © 2026 Angelantonio Calabrese, Fabiola Turchese Liuzzi, Mariavirginia Campanale

Creative Commons License

This is an open access article under the Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) License.

Crossref
Scopus
Google Scholar
Europe PMC