Genomics and Applied Biology 2026, Vol.17, No.1, 37-50 http://bioscipublisher.com/index.php/gab 42 Figure 3 Cluster analysis of the top 50 soil bacteria at the genus level (Adopted from Abudurezike et al., 2025) Image caption: CK -no fertilization; CF -only the chemical fertilizer; T1 -25% organic replacement; T2 -50% organic replacement; T3 -75% organic replacement; and T4 -100% organic replacement. The color bar represents the relative abundance of genera across treatments (Adopted from Abudurezike et al., 2025) 4.3 Differences in microbial community structure under different fertilization regimes Distinct fertilization regimes produce markedly different soil microbial community structures. Long-term studies comparing mineral-only, organic-only, and combined fertilization reveal that organic treatments increase total organic carbon (TOC), pH, and nutrient pools more than mineral fertilizers alone, driving shifts toward copiotrophic bacterial groups such as Proteobacteria and Firmicutes (Francioli et al., 2016; Lin et al., 2019). In contrast, mineral-fertilized soils often show enrichment of oligotrophic taxa adapted to low-nutrient environments. Fungal communities also differ; organic amendments favor Zygomycota and Basidiomycota while mineral treatments may support higher chitinase activity but lower overall fungal diversity (Francioli et al., 2016). Network analyses indicate that organic fertilization fosters more complex co-occurrence patterns among microbes compared to chemical fertilization, reflecting stronger synergistic interactions within the community (Lin et al., 2019; Pan et al., 2025). Moreover, aggregate size influences community composition; microaggregates harbor distinct keystone taxa sensitive to fertilization type (Lin et al., 2019). These structural differences translate into functional variations affecting nutrient cycling efficiency and disease suppression capacity. Overall, integrating organic fertilizers into greenhouse tomato cultivation promotes a more diverse, stable, and functionally robust soil microbiome than exclusive reliance on chemical fertilizers. 5 Effects of Organic Fertilizer Application on Soil Microbial Functions 5.1 Effects of organic fertilizers on microbial metabolic functions and enzyme activities Organic fertilizer application significantly enhances soil microbial metabolic functions and enzyme activities, which are critical for nutrient cycling and soil health. Meta-analyses show that organic amendments increase
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