Genomics and Applied Biology 2026, Vol.17, No.1, 37-50 http://bioscipublisher.com/index.php/gab 39 2.2 Effects of long-term greenhouse cultivation on soil microbial diversity Long-term greenhouse tomato monoculture has been consistently associated with declines in soil microbial diversity and richness, particularly affecting bacterial and fungal communities essential for maintaining soil ecosystem functions. Studies tracking fields with 5 to over 20 years of continuous tomato cropping report significant reductions in both bacterial and fungal diversity indices compared to non-cultivated or rotational cropland soils (Fan et al., 2024; Hu et al., 2025). This loss of microbial diversity is often accompanied by shifts in dominant taxa; for instance, Actinobacteria abundance tends to decrease while certain pathogenic fungi such as Fusarium increase with prolonged monoculture (Chen et al., 2022). Such changes reduce the resilience of the microbial community against environmental stresses and pathogen invasion. Microbial community structure also undergoes notable alterations under long-term greenhouse conditions. Beta diversity analyses reveal distinct clustering patterns corresponding to different durations of monoculture, indicating progressive divergence from healthy baseline communities (Fan et al., 2024). Network complexity within bacterial communities may initially increase but eventually declines after extended cropping periods, reflecting reduced microbial interactions and stability (Dang et al., 2022; Hu et al., 2025). These structural shifts are linked with functional consequences such as impaired nutrient cycling and diminished disease suppression capacity. Maintaining or restoring microbial diversity through management interventions is therefore critical for sustaining productive greenhouse tomato cultivation. 2.3 Microbial mechanisms underlying soil degradation and continuous cropping obstacles Soil degradation under continuous greenhouse tomato cultivation is driven largely by microbial community imbalances that disrupt key ecological processes supporting soil health. One major mechanism involves the accumulation of pathogenic fungi like Fusarium, Alternaria, and Cladosporium that cause diseases such as wilt and leaf mold; their relative abundance increases significantly with longer monoculture duration (He et al., 2025; Hu et al., 2025). Concurrently, beneficial bacteria genera including Bacillus, Paenibacillus, and Streptomyces decline, weakening natural disease suppression mechanisms. This shift from a balanced microbiome toward pathogen dominance contributes directly to continuous cropping obstacles. In addition to pathogen proliferation, long-term monoculture alters microbial functional potential related to carbon and nitrogen cycling. Functional gene predictions indicate decreased expression of genes involved in organic matter decomposition and nutrient transformation after extended cropping periods (Dang et al., 2022; Li et al., 2025). This results in impaired metabolic activity within the microbial community, reducing nutrient availability for plants despite high total nutrient contents in the soil. Furthermore, increased stress resistance genes suggest that microbes experience environmental pressures such as nutrient imbalances or toxic accumulations under continuous cropping (Dang et al., 2022). Understanding these microbial mechanisms provides a foundation for developing strategies-such as organic amendments or crop rotation -to mitigate soil degradation and enhance sustainability in greenhouse tomato production systems. 3 Types of Organic Fertilizers and Their Mechanisms in Soil Improvement 3.1 Common types of organic fertilizers and their nutrient characteristics Organic fertilizers commonly used in agriculture include manure, compost, biochar, and insect-derived fertilizers such as those from black soldier fly larvae. Manure and compost are rich in organic matter and provide a broad spectrum of nutrients including nitrogen (N), phosphorus (P), and potassium (K), which are essential for plant growth. Biochar, a carbon-rich product derived from pyrolyzed biomass, is valued for its ability to improve soil structure and nutrient retention but generally contains lower nutrient concentrations compared to manure or compost (Khan et al., 2024; Wang et al., 2024). Recently, black soldier fly (BSF) organic fertilizer has gained attention due to its high nutrient content and ability to enhance soil fertility through the bioconversion of organic waste into nutrient-rich amendments (Zhao et al., 2025). These diverse organic fertilizers differ not only in nutrient composition but also in their effects on soil microbial communities and nutrient cycling processes. The nutrient release patterns of these organic fertilizers vary significantly. Manure and compost typically release nutrients more slowly than chemical fertilizers, providing a sustained supply that supports long-term soil fertility. Biochar’s primary role is improving soil physical properties such as porosity and water retention rather than
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