Changes in Soil Microbial Community Structure and Function Across Cultivation Durations Under Cucumber–Bitter Melon Rotation for Sustainable Greenhouse Production

Abstract

Greenhouse vegetable production is important for food security, but intensive long-term cultivation can threaten soil sustainability. Although previous studies have reported that cultivation duration alters microbial community structure, research on greenhouse soils with crop rotation involving cucumbers and bitter melons remains rare, especially lacking in predicted microbial functional profiles. Therefore, this study performed 16S rRNA amplicon sequencing on greenhouse soils from four different cultivation years, aiming to evaluate the changes in soil microbial community structure and function due to long-term greenhouse cultivation. Over the first three years of cultivation, both alpha diversity and enzyme activity in the soil increased. Continuous cultivation and routine management were accompanied by marked shifts in the soil microbiota. Specifically, after 9 years, bacterial communities in surface and subsurface soils became highly imbalanced, with the Chao1 index decreasing by 65.64% and 82.46% compared to 3-year soils. Soils with shorter cultivation periods (1 and 3 years) had three times as many biomarkers as those with longer periods (6 and 9 years), and surface soils had nine times more biomarkers than subsurface soils. NH4+-N and urease were significantly associated with bacterial and archaeal communities. PICRUSt2-based predictions suggested that the 9-year greenhouse soils had a higher inferred abundance of genes associated with certain metabolic processes compared to other cultivation durations, indicating potential functional shifts in the microbial community across the cultivation-duration gradient. These findings provide insights into soil microbial responses to cultivation duration and support sustainable management of greenhouse soils under cucumber–bitter melon rotation.