High-throughput sequencing analysis of community diversity and functional structure of endophytic bacteria in edible vegetable crops: potential implication on plant microbiological quality.

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This study evaluated the diversity and functional structure of endophytic bacterial communities residing within four common leafy vegetables: and , cultivated under organic (OF) and conventional (CF) farming systems. Utilizing high-throughput 16S rRNA gene sequencing and the PICRUSt2 pipeline, the research assessed the influence of plant species, organ (leaf/root), and fertilizer type on these microbial communities. Findings revealed that plant species and organ type significantly shaped endophytic bacterial community composition and diversity. Onion communities were distinct, and roots exhibited higher diversity and richness compared to leaves. Fertilizer type significantly impacted overall bacterial diversity, with CF farms showing higher diversity than OF. Microbial network analysis identified keystone taxa, including network hubs like and , and module hubs like , , and . Functional predictions indicated diverse metabolic capabilities, with organ type significantly affecting pathway abundance (leaves enriched in carbohydrate degradation, roots in nutrient metabolism/degradation). OF farms showed higher predicted abundance of some potential virulence pathways, while CF farms had higher abundance of certain biotechnological pathways. Vegetable nutrient content significantly correlated with both bacterial community composition and predicted metabolic pathways. This study highlights the complex interplay between farming practices, plant factors, endophytic microbiomes, and their functional potential, underscoring implications for vegetable microbiological quality and potential human health.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-025-04380-9.