Genomics and Applied Biology 2026, Vol.17, No.1, 37-50 http://bioscipublisher.com/index.php/gab 43 microbial diversity and functionality more than mineral-only fertilization, with positive effects on enzymes involved in carbon, nitrogen, and phosphorus cycling (Shu et al., 2022; Liu et al., 2023). For example, β-glucosidase, urease, and phosphatase activities often increase following organic fertilizer application, reflecting enhanced microbial capacity to decompose organic matter and mineralize nutrients (Lazcano et al., 2013; Ren et al., 2021). These enzymatic changes improve soil biochemical processes that support plant growth. Furthermore, combined applications of biochar and organic fertilizers have been found to boost the abundance of functional microbial taxa related to carbon degradation, nitrification, and phosphorus mineralization more effectively than either amendment alone (Hu et al., 2024). This synergy leads to increased ecosystem multifunctionality by enhancing multiple soil functions simultaneously. The improvements in enzyme activities are closely linked to shifts in microbial community structure and increased nutrient availability, highlighting the integral role of organic fertilizers in stimulating microbial metabolism (Ren et al., 2021). 5.2 Influence of organic fertilizers on microorganisms involved in soil nutrient cycling Organic fertilizers promote the proliferation of microorganisms that drive key nutrient cycling processes such as carbon fixation, nitrogen transformation, phosphorus solubilization, and sulfur cycling. Studies report increased abundances of functional genes related to these cycles under organic amendment treatments compared to chemical fertilization (Cui et al., 2023; Hu et al., 2024). For instance, copiotrophic bacterial groups like Proteobacteria and Bacteroidetes -known for their roles in nutrient turnover -are enriched by organic inputs (Tang et al., 2022). Similarly, fungal phyla such as Basidiomycota contribute to complex organic matter decomposition under these regimes. The enhanced presence of microbes involved in nitrogen cycling -including nitrifiers, denitrifiers, and nitrogen fixers -improves nitrogen availability while potentially reducing losses through leaching or gaseous emissions (Hu et al., 2024; Guo et al., 2025). Organic amendments also stimulate phosphorus-mineralizing microbes that increase phosphorus bioavailability critical for tomato growth (Ren et al., 2021; Cui et al., 2023). These functional shifts collectively optimize nutrient transformations in greenhouse soils, supporting sustainable crop production. 5.3 Impacts of microbial functional changes on tomato growth and yield Improvements in soil microbial functions driven by organic fertilizer application translate into enhanced tomato growth and yield outcomes. Increased microbial diversity and enzyme activities correlate positively with higher photosynthetic efficiency and fruit production under greenhouse conditions (Shu et al., 2022). For example, bio-organic fertilizer applied at optimal rates significantly raised net photosynthesis by nearly 30% and fruit yield by over 40%, linked to improved soil organic matter content and total nitrogen levels mediated by beneficial microbes (Lu et al., 2025). Moreover, partial substitution of chemical fertilizers with organic manure enhances soil multifunctionality through increased bacterial-fungal network complexity and keystone taxa abundance, which supports nutrient availability and plant health (Ren et al., 2021; Tang et al., 2022). These microbiome-mediated pathways contribute to more resilient agroecosystems capable of sustaining high yields while reducing reliance on synthetic inputs. Overall, the positive feedback between microbial functional enhancement and tomato productivity underscores the value of integrating organic fertilizers into greenhouse cultivation systems. 6 Case Study: Application Effects of Organic Fertilizer Substitution for Chemical Fertilizer in Greenhouse Tomato Soil 6.1 Experimental design and research methods Several studies have investigated the effects of substituting chemical fertilizers with organic fertilizers in greenhouse tomato cultivation using controlled field and pot experiments. One common approach involves setting up multiple treatments with varying substitution ratios, such as 25%, 50%, and 75% replacement of chemical fertilizer by microbial or bio-organic fertilizers, alongside a full chemical fertilizer control (Tran et al., 2025). These experiments typically measure soil chemical properties, microbial community changes, tomato growth parameters, yield, and fruit quality over one or more growing seasons. Some studies also incorporate microbial
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