Genomics and Applied Biology 2026, Vol.17, No.1, 37-50 http://bioscipublisher.com/index.php/gab 47 impacts on soil carbon sequestration, greenhouse gas emissions, and microbiome resilience under varying climate scenarios are essential for sustainable intensification goals. Advances in multi-omics technologies (metagenomics, metatranscriptomics) integrated with machine learning will improve functional predictions of microbial communities driving ecosystem services in protected agriculture. Finally, expanding research on interactions between water management practices and fertilization will refine holistic approaches to optimize resource use efficiency while safeguarding soil health in intensive tomato production systems. These directions collectively support the transition toward environmentally sound and productive greenhouse horticulture. Acknowledgments I extends my sincere gratitude to the anonymous reviewers for their valuable and insightful comments, which have greatly strengthened this paper. Conflict of Interest Disclosure The author affirms that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest. References Abudurezike A., Fan L., Yan Z., and Yibati H., 2025, Impact of organic fertilizer substitution on soil microbial communities and cotton yield in Xinjiang, Agronomy, 15(7): 1540. https://doi.org/10.3390/agronomy15071540 Cao J., Qu H., Li R., Wang P., and Chen M., 2025, Effects of returning organic fertilizer and biochar to soil on surface electrochemical properties and nutrients, BioResources, 21(1): 67-80. https://doi.org/10.15376/biores.21.1.67-80 Chen D., Sun W., Xiang S., and Zou S., 2021, High-throughput sequencing analysis of the composition and diversity of the bacterial community in Cinnamomum camphora soil, Microorganisms, 10(1): 72. https://doi.org/10.3390/microorganisms10010072 Chen J., Du Y., Zhu W., Pang X., and Wang Z., 2022, Effects of organic materials on soil bacterial community structure in long-term continuous cropping of tomato in greenhouse, Open Life Sciences, 17: 381-392. https://doi.org/10.1515/biol-2022-0048 Chen Q., Xie J., Li L., Khan K., Wang L., Chang L., and Du C., 2025, Partial substitution of chemical fertilizer with organic fertilizer: a promising circular economy approach for improving soil physical and chemical properties and sustainable crop yields, Frontiers in Plant Science, 16: 1565081. https://doi.org/10.3389/fpls.2025.1565081 Chen X., Liu Z., Gu H., Fang H., Shen Z., Zhang H., Wan S., Li W., Hao X., Clarke N., and Liu J., 2025, Organic fertilizers increase microbial community diversity and stability slowing down the transformation process of nutrient cycling, Environmental Microbiome, 20: 91. https://doi.org/10.1186/s40793-025-00791-6 Chu M., Jiang Y., Gao Y., Jiang Y., Zhang J., Wang W., Liu X., Li S., and Qu J., 2025, Combined application of organic materials improves soil properties and promotes soil nitrogen cycling, Land Degradation & Development, 36(18): 5711-5722. https://doi.org/10.1002/ldr.70032 Cong P., Huang P., and Huang Z., 2025, The response of soil microbial community to application of organic amendment to saline land, Frontiers in Microbiology, 15: 1481156. https://doi.org/10.3389/fmicb.2024.1481156 Cui J., Yang B., Zhang M., Song D., Xu X., Ai C., Liang G., and 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, 893: 164899. https://doi.org/10.1016/j.scitotenv.2023.164899 Dang K., Ji L., Slaughter L., Hou J., Shen M., Li J., and Dong Y., 2022, Synergistic changes of rhizosphere bacterial community and soil properties in greenhouse soils under long-term tomato monoculture, Applied Soil Ecology, 175: 104738. https://doi.org/10.1016/j.apsoil.2022.104738 Edwin N., Duff A., Deveautour C., Brennan F., Abram F., and O’Sullivan O., 2025, Consistent microbial insights across sequencing methods in soil studies: the role of reference taxonomies, mSystems, 10(1): e01059-24. https://doi.org/10.1128/msystems.01059-24 Fan H., Zhang Y., Li J., Jiang J., Waheed A., Wang S., Rasheed S., Zhang L., and Zhang R., 2023, Effects of organic fertilizer supply on soil properties, tomato yield, and fruit quality: a global meta-analysis, Sustainability, 15(3): 2556. https://doi.org/10.3390/su15032556 Fan Y., Jia Y., Zhang X., Geng G., Liu R., Shen L., Hu J., and Hao X., 2024, Conversion to greenhouse cultivation from continuous corn production decreases soil bacterial diversity and alters community structure, Agronomy, 14(9): 2144. https://doi.org/10.3390/agronomy14092144
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