Organic Fertilization and Crop Type Shape Soil Microbial Functions and Health in Greenhouse Vegetable Systems

Greenhouse vegetable production is expanding in arid regions, but information on microbial responses to contrasting management systems remains limited. This study investigated chemical properties, microbial abundance, activity, taxonomic diversity, and function potential based on 16S rRNA gene and ITS sequencing of soil samples collected from organically and conventionally managed cucumber, tomato, and eggplant crops in irrigated greenhouses in Oman. Organic management increased mean soil organic matter from 3.9% to 7.3%, representing an 87% increase, and bacterial abundance from 20.2 to 95.7 × 104 CFU g−1, representing a 4.7-fold increase compared with conventional management (p < 0.05). Organic management increased pooled bacterial functional diversity, including the Shannon index from 2.73 to 2.96 and the Simpson index from 0.89 to 0.92, whereas the fungal Shannon diversity index decreased from 2.90 to 2.34 and evenness from 0.40 to 0.29 (p < 0.05). Taxonomy-based functional inference indicated shifts in carbon- and nitrogen-cycling potential and reduced representation of methanogenesis-associated functions under organic management. PERMANOVA showed that crop type explained the largest proportion of multivariate variation (R2 = 0.350), followed by the management × crop interaction (R2 = 0.236) and management system (R2 = 0.134; all p = 0.001). These results indicate that crop species is a major driver of soil microbial characteristics in arid-climate greenhouses, while organic management modified microbial abundance, diversity, and function in a crop-dependent manner.