Genomics and Applied Biology 2026, Vol.17, No.1, 37-50 http://bioscipublisher.com/index.php/gab 44 inoculants like Trichoderma to enhance the bio-organic fertilizer effect (Figure 4) (Ye et al., 2020). Soil enzyme activities and microbial biomass are frequently assessed to understand functional changes induced by fertilization regimes (Rong et al., 2018; Li et al., 2023). Experimental designs often use randomized complete block designs (RCBD) or similar statistical frameworks to ensure reliable comparisons among treatments (Liu et al., 2025; Tran et al., 2025). Measurements include soil nutrient contents (N, P, K), pH, organic matter, microbial diversity via sequencing or phospholipid fatty acid analysis, and enzyme activities such as urease and catalase (Rong et al., 2018; Fan et al., 2023). Tomato agronomic traits like plant height, leaf number, photosynthetic rate, fruit number, weight, and quality indicators (soluble sugars, vitamin C, nitrate content) are recorded to link soil changes with crop performance (Stoleru et al., 2020; Li et al., 2023). These comprehensive methods enable evaluation of how partial organic substitution affects both soil health and tomato productivity. Figure 4 Experimental treatment structure illustrating different substitution ratios of chemical fertilizer with organic or bio-organic fertilizers in greenhouse tomato cultivation experiments (Adopted from Ye et al., 2020) 6.2 Analysis of changes in soil microbial community structure after organic fertilizer application Partial substitution of chemical fertilizers with organic amendments consistently alters soil microbial community structure by increasing microbial abundance and shifting dominant taxa. Studies report that moderate substitution rates (around 25%-30%) enhance bacterial richness and promote copiotrophic groups such as Proteobacteria and Actinobacteria while reducing oligotrophic taxa like Acidobacteria commonly found under pure chemical fertilization (Liu et al., 2025; Tran et al., 2025). Fungal communities also shift toward beneficial groups including Basidiomycota and Glomeromycota that support nutrient cycling and plant health (Ye et al., 2020; Fan et al., 2023). These changes are often accompanied by increased microbial biomass carbon and nitrogen as well as elevated enzyme activities related to nutrient mineralization (Rong et al., 2018; Liu et al., 2025). Metagenomic analyses reveal that organic substitution enriches genes involved in nitrogen cycling processes such as denitrification (nirK, nirS) and nitrogen fixation, indicating enhanced functional potential of the microbiome (Liu et al., 2025). Network complexity within the microbial community increases under organic amendments due to improved soil pH and organic matter content, fostering stronger interactions among microbes (Han et al., 2025). This restructuring supports a more resilient soil ecosystem capable of sustaining nutrient availability for tomatoes. However, excessive substitution beyond moderate levels may reduce yield despite further microbiome shifts, highlighting the importance of balanced fertilization strategies. 6.3 Comprehensive effects on tomato yield, quality, and soil health The integration of organic fertilizers partially replacing chemical inputs generally improves tomato yield stability while enhancing fruit quality attributes such as soluble sugars and vitamin C content. For example, combining
RkJQdWJsaXNoZXIy MjQ4ODYzNA==