Long-Term Organic Cultivation in Greenhouses Enhances Vegetable Yield and Soil Carbon Accumulation through the Promotion of Soil Aggregation

The long-term use of fertilizers and pesticides in conventional cultivation has resulted in a decrease in soil productivity and vegetable yields in greenhouses. However, there is little research exploring the changes in soil organic carbon and the microbial community mediated by soil aggregates, or their impacts on soil productivity. This study investigated the properties of soil aggregates, including the levels of organic carbon fractions, microbial community, and enzyme activity with the three aggregate classes: microaggregates (<0.25 mm), small macroaggregates (2–0.25 mm) and large macroaggregates (>2 mm) under conventional cultivation (CC), integrated cultivation (IC), and organic cultivation (OC) in greenhouses. The results showed that (1) OC and IC promoted the formation of small macroaggregates and enhanced aggregate stability compared to CC; (2) SOC in the three size fractions of OC increased by 92.06–98.99% compared to CC; EOC increased by 98.47–117.59%; POC increased by 138.59–208.70%; MBC increased by 104.71–230.61%; and DOC increased by 21.93–40.90%, respectively; (3) organic cultivation significantly increased enzyme activity in all three particle-size aggregates and increased the relative abundance of bacteria in microaggregates as well as the relative abundance of fungi in small macroaggregates. Structural equation model (SEM) analysis revealed that organic farming practices fostered the development of smaller macroaggregates, elevated microbial and enzyme activities within soil aggregates, and facilitated the conversion of soil nutrients and carbon sequestration. Therefore, long-term organic cultivation increases soil carbon content and vegetable yield in greenhouses by increasing the proportion of small aggregates. In conclusion, long-term organic cultivation in greenhouses improves soil structure, increase soil fertility and vegetable yield, and has a positive impact on the environment. Organic cultivation increases soil fertility and contributes to maintaining ecological balance and protecting the environment in greenhouses.