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

IF 2.6 4区生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

3 Biotech Pub Date : 2025-07-01 Epub Date: 2025-06-17 DOI:10.1007/s13205-025-04380-9

Adekunle Raimi, Rasheed Adeleke

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引用次数: 0

Abstract

This study evaluated the diversity and functional structure of endophytic bacterial communities residing within four common leafy vegetables: Brassica oleracea, Lactuca sativa, Allium cepa, and Spinacia oleracea, 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 Serratia and Streptomyces, and module hubs like Solirubrobacter, Corynebacterium, and Mycobacterium. 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.

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食用蔬菜作物内生细菌群落多样性和功能结构的高通量测序分析：对植物微生物品质的潜在意义。

本研究评估了有机（of）和常规（CF）耕作系统下4种常见叶菜：甘蓝、莴苣、葱和甘蓝的内生细菌群落的多样性和功能结构。利用高通量16S rRNA基因测序和PICRUSt2管道，研究了植物种类、器官（叶/根）和肥料类型对这些微生物群落的影响。结果表明，植物种类和器官类型对内生细菌群落组成和多样性有显著影响。洋葱群落特征明显，根系的多样性和丰富度高于叶片。肥料类型对细菌多样性有显著影响，CF农场的细菌多样性高于OF。微生物网络分析确定了关键分类群，包括沙雷氏菌和链霉菌等网络枢纽，以及Solirubrobacter、棒状杆菌和分枝杆菌等模块枢纽。功能预测表明不同的代谢能力，器官类型显著影响途径丰度（叶片富集碳水化合物降解，根系富集养分代谢/降解）。OF农场对某些潜在毒力途径的预测丰度较高，而CF农场对某些生物技术途径的预测丰度较高。蔬菜养分含量与细菌群落组成和预测代谢途径均显著相关。这项研究强调了耕作方式、植物因子、内生微生物群及其功能潜力之间复杂的相互作用，强调了蔬菜微生物质量和潜在的人类健康的意义。补充信息：在线版本包含补充资料，可在10.1007/s13205-025-04380-9获得。

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来源期刊

3 Biotech Agricultural and Biological Sciences-Agricultural and Biological Sciences (miscellaneous)

CiteScore

6.00

自引率

0.00%

发文量

314

期刊介绍： 3 Biotech publishes the results of the latest research related to the study and application of biotechnology to: - Medicine and Biomedical Sciences - Agriculture - The Environment The focus on these three technology sectors recognizes that complete Biotechnology applications often require a combination of techniques. 3 Biotech not only presents the latest developments in biotechnology but also addresses the problems and benefits of integrating a variety of techniques for a particular application. 3 Biotech will appeal to scientists and engineers in both academia and industry focused on the safe and efficient application of Biotechnology to Medicine, Agriculture and the Environment.