Aims

Plant-specific microbial diversity reflecting host-microbe coevolution was frequently shown at the structural level but less on the functional scale. We studied the microbiome of three compartments at the soil root interface (root endosphere, rhizosphere, bulk soil) of medicinal plants cultivated under organic management in Egypt. The study aimed to examine the impact of the rhizosphere on microbial community composition and diversity in desert agricultural soil, as well as to identify specific functions associated with the rhizosphere.

Methods

The microbiome community structure, diversity, and microbial functioning were evaluated through the utilization of 16S rRNA gene amplicon and shotgun metagenome sequencing.

Results

We found the typical rhizosphere effect and plant-species-specific enrichment of bacterial diversity. The annual plants Calendula officinalis and Matricaria chamomilla (Asteraceae) were more similar than the perennial Solanum distichum (Solanaceae). Altogether, plant species explained 50.5% of the variation in bacterial community structures in the rhizosphere. Our results indicate a stronger effect of the plant species in terms of modulating bacterial community structures in the rhizosphere than in root endosphere samples. The plant-driven rhizosphere effect could be linked to redundant plant beneficial functions in the microbiome, while enrichment of specific genes related to amino acid ion transport and metabolism, carbohydrate transport and metabolism, defense mechanisms, and secondary metabolites biosynthesis were more specific.

Conclusions

The study explores the microbiome continuum at the soil-root interface of medicinal plant species, revealing significant bacterial community structure shifts and plant specificity. The study provides insights into the essential microbiome components contributing to rhizosphere functionality.

中文翻译：

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植物特有的微生物多样性促进了土壤-根界面的功能冗余

 目标

反映宿主-微生物协同进化的植物特异性微生物多样性经常显示在结构水平上，但在功能尺度上较少。我们研究了埃及有机管理下种植的药用植物的土壤根界面（根内圈、根际、块状土壤）的三个隔室的微生物组。该研究旨在检查根际对沙漠农业土壤中微生物群落组成和多样性的影响，并确定与根际相关的特定功能。

 方法

通过使用 16S rRNA 基因扩增子和鸟枪法宏基因组测序评估微生物组群落结构、多样性和微生物功能。

 结果

我们发现了典型的根际效应和细菌多样性的植物物种特异性富集。一年生植物 Calendula officinalis 和 Matricaria chamomilla （菊科） 比多年生 Solanum distichum （Solanaceae） 更相似。总的来说，植物物种解释了根际细菌群落结构变化的 50.5%。我们的结果表明，植物物种在调节根际细菌群落结构方面的作用比根内圈样品更强。植物驱动的根际效应可能与微生物组中多余的植物有益功能有关，而与氨基酸离子转运和代谢、碳水化合物转运和代谢、防御机制和次生代谢产物生物合成相关的特定基因的富集则更具特异性。

 结论

该研究探索了药用植物物种土壤-根界面的微生物组连续体，揭示了显着的细菌群落结构变化和植物特异性。该研究提供了对有助于根际功能的基本微生物组成分的见解。