Effects of different cultivation methods on microbial community structure of lettuce based on metagenomic analysis

Lettuce cultivation primarily involves two methods: traditional soil-based cultivation and modern hydroponic systems. However, research on the microbial community structure of lettuce under these distinct cultivation approache is still limited.

This study employed whole-genome shotgun metagenomic sequencing (metagenomic sequencing) to analyze the impact of soil-based and hydroponic cultivation systems on the microbial community structure and functional profiles of lettuce.

The microbial diversity index of soil samples was significantly higher than that of hydroponic samples, indicating a more diverse and complex microbial community in the soil environment. Key functional phylum, including Acidobacteriota and Actinomycetota, were more abundant in soil samples, supporting nutrient cycling and plant-microbe interactions through pathways involved in carbon metabolism, organic matter decomposition, and antibiotic biosynthesis. In contrast, hydroponic samples were dominated by Cyanobacteriota and Verrucomicrobiota, with enrichment of pathways associated with stress response, including quorum sensing, ABC transporters, and oxidative phosphorylation. Although α-diversity did not differ significantly between cultivation systems, their microbial community composition and functional profiles were markedly distinct: soil-grown lettuce exhibited enrichment in sugar catabolism and synergistic prokaryotic metabolic functions, whereas hydroponic lettuce showed a predominance of energy metabolism and enrichment of viral-related pathways. Furthermore, differential distribution of antibiotic resistance genes underscores the role of environmental selective pressures in shaping microbial functional adaptations.

This study demonstrates that different cultivation methods significantly influence the microbial community structure and function in lettuce. These findings provide a theoretical foundation for optimizing cultivation systems and offer scientific guidance for precisely modulating microbial functions to promote lettuce growth and health.