Plant-specific microbial diversity facilitates functional redundancy at the soil-root interface

IF 3.9 2区 农林科学 Q1 AGRONOMY
Wisnu Adi Wicaksono, Martina Köberl, Richard Allen White, Janet K. Jansson, Christer Jansson, Tomislav Cernava, Gabriele Berg
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Abstract

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.

植物特有的微生物多样性促进了土壤-根界面的功能冗余
目的反映宿主-微生物协同进化的植物特异性微生物多样性多表现在结构水平上,而在功能水平上表现较少。研究了埃及有机栽培药用植物土壤根界面3个区室(根内圈、根际、块土)的微生物组。本研究旨在探讨根际对荒漠农业土壤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。方法利用16S rRNA基因扩增子和霰弹枪宏基因组测序技术,对微生物群落结构、多样性和微生物功能进行评价。结果发现了典型的根际效应和植物物种特异性的细菌多样性富集。一年生植物金盏菊(Calendula officinalis)和洋甘菊(Matricaria chamomilla)的相似性高于多年生植物龙葵(Solanum distichum)。总的来说,植物物种解释了根际细菌群落结构变化的50.5%。我们的研究结果表明,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植物有益功能的冗余有关,而与氨基酸离子转运代谢、碳水化合物转运代谢、防御机制和次生代谢物生物合成相关的特定基因的富集更为特异性。结论本研究探索了药用植物土壤-根界面的微生物群落连续体,揭示了显著的细菌群落结构变化和植物特异性。该研究提供了对促进根际功能的基本微生物组成分的见解。
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来源期刊
Plant and Soil
Plant and Soil 农林科学-农艺学
CiteScore
8.20
自引率
8.20%
发文量
543
审稿时长
2.5 months
期刊介绍: Plant and Soil publishes original papers and review articles exploring the interface of plant biology and soil sciences, and that enhance our mechanistic understanding of plant-soil interactions. We focus on the interface of plant biology and soil sciences, and seek those manuscripts with a strong mechanistic component which develop and test hypotheses aimed at understanding underlying mechanisms of plant-soil interactions. Manuscripts can include both fundamental and applied aspects of mineral nutrition, plant water relations, symbiotic and pathogenic plant-microbe interactions, root anatomy and morphology, soil biology, ecology, agrochemistry and agrophysics, as long as they are hypothesis-driven and enhance our mechanistic understanding. Articles including a major molecular or modelling component also fall within the scope of the journal. All contributions appear in the English language, with consistent spelling, using either American or British English.
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