Organic Fertilizer Substitution Modulates Soil Properties and Microbial Communities in a Vegetable–Earthworm Co-Cultivation System

In intensive vegetable production systems, long-term reliance on chemical fertilizers often leads to soil degradation and microbial imbalance, highlighting the need for sustainable biotillage strategies. In this study, a long-term field experiment examined how vegetable-earthworm co-cultivation (VE) combined with different fertilization regimes affects vegetable yield, soil physicochemical properties, and microbial communities. VE significantly improved vegetable yield, with full chemical fertilization (VE_IF100) and a 30% reduction in chemical fertilizer supplemented with organic fertilizer (VE_IF70) increasing yields by 30.86% and 26.02%, respectively, relative to full fertilization without earthworms (CK_IF100). VE also moderated soil pH toward neutrality. VE_IF100 decreased the soil C/N ratio, whereas VE_IF70 increased it and enhanced available hydrolyzable nitrogen, indicating a more balanced nutrient transformation. Microbial analysis revealed that VE_IF100 reduced bacterial abundance while strongly increasing fungal abundance, decreasing the bacteria-to-fungi ratio from 3.51 to 0.53. In contrast, VE_IF70 restored the bacteria-to-fungi ratio to 1.65 and increased fungal diversity, with the Shannon and Chao1 indices exceeding those in VE_IF100. Bacterial genera associated with nutrient cycling and plant growth promotion (e.g., <i>Brevundimonas</i>, <i>Anaeromyxobacter</i>) were enriched under VE_IF70, while fungal taxa with antagonistic and biocontrol potential (e.g., <i>Chaetomium</i>, <i>Arthrobotrys</i>) also increased. Redundancy analysis identified the soil C/N ratio (ranging from 5.94 to 8.60 across treatments) as a key driver of both bacterial and fungal community structures, whereas pH exerted a stronger influence on fungi. Random forest analysis indicated that the annual total vegetable yield was primarily driven by fertilization and available phosphorus in VE systems, whereas pH and bacterial abundance were the main drivers in CK systems. Overall, earthworm inoculation combined with partial organic fertilizer substitution improved soil conditions, reshaped microbial communities, and maintained high yield, demonstrating a practical strategy for sustainable vegetable production.