Genomics and Applied Biology 2026, Vol.17, No.1, 37-50 http://bioscipublisher.com/index.php/gab 41 fly-derived fertilizer or biochar-organic fertilizer mixtures upregulate genes involved in carbon fixation pathways such as the Calvin-Benson-Bassham cycle while suppressing genes related to carbon degradation, promoting net carbon sequestration in soils (Yang et al., 2025; Zhao et al., 2025). In terms of nitrogen cycling, the abundance of functional genes associated with nitrification, denitrification (e.g., nirK, nirS), ammonification, and nitrogen fixation increases significantly after organic fertilizer application, accelerating nitrogen turnover efficiency beyond additive effects seen with chemical fertilization alone (Chu et al., 2025). Furthermore, long-term application of manure-based or integrated chemical-organic fertilization enhances microbial diversity and stability while slowing down rapid nutrient transformation processes typical under exclusive chemical fertilization regimes (Ying et al., 2023; Chen et al., 2025). This balance helps maintain sustained nutrient availability without excessive losses through leaching or gaseous emissions. Structural equation modeling indicates that improved microbial functional potential mediated by enhanced bacterial diversity directly contributes to increased ecosystem multifunctionality under combined fertilization strategies (Ying et al., 2023). Overall, the use of organic fertilizers fosters a more resilient soil microbial ecosystem that supports efficient carbon-nitrogen cycling critical for sustainable greenhouse tomato cultivation. 4 Effects of Organic Fertilizer Application on Soil Microbial Community Structure 4.1 Influence of organic fertilizers on microbial abundance and diversity Organic fertilizer application generally enhances soil microbial abundance and diversity compared to conventional chemical fertilization. Studies have shown that partial substitution of chemical fertilizers with organic ones significantly increases bacterial richness and diversity indices such as ACE and Chao1, alongside improvements in soil pH, organic matter, and nutrient availability (Guo et al., 2025). These changes create a more favorable environment for microbial growth, leading to denser and more complex microbial networks. For example, the abundance of dominant bacterial phyla like Proteobacteria and fungal groups such as Basidiomycota can increase substantially under organic fertilization regimes (Pan et al., 2025). This enhanced microbial diversity is critical for maintaining soil health and resilience in intensive cropping systems. Moreover, the degree of organic fertilizer substitution influences microbial community evenness and richness differently depending on soil cultivation duration. In soils with longer cultivation histories, moderate to high organic substitution ratios (25%-75%) tend to optimize microbial diversity and evenness, while very low or very high substitution rates may be less effective (Guo et al., 2025). Organic amendments stimulate enzyme activities related to nutrient cycling, further supporting microbial proliferation (Lazcano et al., 2013). These findings suggest that tailored organic fertilizer applications can sustainably improve microbial abundance and diversity in greenhouse soils. 4.2 Regulatory effects of organic fertilizers on dominant microbial groups and functional microorganisms Organic fertilizers selectively promote beneficial microbial taxa while suppressing some oligotrophic or pathogenic groups. Long-term manure application has been shown to increase the relative abundance of copiotrophic bacteria such as Bacillales, Gaiellales, and fungal orders like Pezizales, which are associated with efficient organic matter decomposition and nutrient cycling (Lin et al., 2019). Conversely, soils without manure tend to harbor more oligotrophic taxa like Acidobacteria that thrive in nutrient-poor conditions (Francioli et al., 2016). Organic amendments also enhance populations of plant-beneficial microbes including Actinobacteriota and Glomeromycota fungi, which contribute to nutrient uptake and disease resistance (Shu et al., 2022; Abudurezike et al., 2025). Functional microorganisms involved in carbon and nitrogen cycling respond positively to organic fertilizer inputs. For instance, genes linked to urease activity and catalase are stimulated by organic amendments, improving nitrogen mineralization processes (Lazcano et al., 2013; Guo et al., 2025). Additionally, shifts in fungal communities toward Ascomycota and Basidiomycota dominance under organic fertilization enhance decomposition of complex organics (Figure 3) (Abudurezike et al., 2025; Cong et al., 2025). These regulatory effects help restore balanced microbial functions critical for sustaining soil fertility under intensive greenhouse cultivation.
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