Université de Lorraine, INRAE, IAM, Nancy, France.
Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Haidian District, Beijing, China.
Appl Environ Microbiol. 2021 Feb 26;87(6). doi: 10.1128/AEM.02541-20.
Through their roots, trees interact with a highly complex community of microorganisms belonging to various trophic guilds and contributing to tree nutrition, development, and protection against stresses. Tree roots select for specific microbial species from the bulk soil communities. The root microbiome formation is a dynamic process, but little is known on how the different microorganisms colonize the roots and how the selection occurs. To decipher whether the final composition of the root microbiome is the product of several waves of colonization by different guilds of microorganisms, we planted sterile rooted cuttings of gray poplar obtained from plantlets propagated in axenic conditions in natural poplar stand soil. We analyzed the root microbiome at different time points between 2 and 50 days of culture by combining high-throughput Illumina MiSeq sequencing of the fungal ribosomal DNA internal transcribed spacer and bacterial 16S rRNA amplicons with confocal laser scanning microscopy observations. The microbial colonization of poplar roots took place in three stages, but bacteria and fungi had different dynamics. Root bacterial communities were clearly different from those in the soil after 2 days of culture. In contrast, if fungi were also already colonizing roots after 2 days, the initial communities were very close to that in the soil and were dominated by saprotrophs. They were slowly replaced by endophytes and ectomycorhizal fungi. The replacement of the most abundant fungal and bacterial community members observed in poplar roots over time suggest potential competition effect between microorganisms and/or a selection by the host. The tree root microbiome is composed of a very diverse set of bacterial and fungal communities. These microorganisms have a profound impact on tree growth, development, and protection against different types of stress. They mainly originate from the bulk soil and colonize the root system, which provides a unique nutrient-rich environment for a diverse assemblage of microbial communities. In order to better understand how the tree root microbiome is shaped over time, we observed the composition of root-associated microbial communities of naive plantlets of poplar transferred in natural soil. The composition of the final root microbiome relies on a series of colonization stages characterized by the dominance of different fungal guilds and bacterial community members over time. Our observations suggest an early stabilization of bacterial communities, whereas fungal communities are established following a more gradual pattern.
通过根系，树木与属于不同营养类群的高度复杂的微生物群落相互作用，这些微生物有助于树木的营养、发育，并保护其免受压力。树木的根系从土壤微生物群落中选择特定的微生物物种。根微生物组的形成是一个动态过程，但对于不同微生物如何定植在根上以及如何进行选择知之甚少。为了解释最终的根微生物组组成是否是不同营养类群的微生物多次定植的产物，我们在无菌条件下从植物工厂繁殖的实生苗中获得的灰色杨树无菌生根插条种植在天然杨树林土壤中，并在 2 至 50 天的培养过程中，通过结合高通量 Illumina MiSeq 测序真菌核糖体 DNA 内转录间隔区和细菌 16S rRNA 扩增子与共聚焦激光扫描显微镜观察，分析了根微生物组。杨树根系的微生物定植分为三个阶段，但细菌和真菌的定植动态不同。培养 2 天后，根细菌群落与土壤中的细菌群落明显不同。相比之下，如果真菌在培养 2 天后也已经定植在根上，那么最初的群落与土壤中的非常相似，主要是腐生菌。它们逐渐被内生菌和外生菌根真菌取代。在一段时间内，杨树根系中最丰富的真菌和细菌群落成员的替代表明微生物之间存在潜在的竞争效应和/或宿主选择。树木的根微生物组由一套非常多样化的细菌和真菌群落组成。这些微生物对树木的生长、发育和对不同类型胁迫的保护有深远的影响。它们主要来源于土壤，并定植在根系中，为各种微生物群落提供了一个独特的富营养环境。为了更好地了解树木根微生物组随时间的变化情况，我们观察了转移到自然土壤中的杨树实生苗根相关微生物群落的组成。最终根微生物组的组成依赖于一系列定植阶段，这些阶段的特征是不同真菌类群和细菌群落成员随时间的优势变化。我们的观察结果表明细菌群落早期稳定，而真菌群落的建立则遵循更为渐进的模式。
