Understanding the genetic and environmental factors that structure plant microbiomes is necessary for leveraging these interactions to address critical needs in agriculture, conservation, and sustainability. Legumes, which form root nodule symbioses with nitrogen-fixing rhizobia, have served as model plants for understanding the genetics and evolution of beneficial plant-microbe interactions for decades, and thus have added value as models of plant-microbiome interactions. Here we use a common garden experiment with 16S rRNA gene amplicon and shotgun metagenomic sequencing to study the drivers of microbiome diversity and composition in three genotypes of the model legume Medicago truncatula grown in two native soil communities. Bacterial diversity decreased between external (rhizosphere) and internal plant compartments (root endosphere, nodule endosphere, and leaf endosphere). Community composition was shaped by strong compartment × soil origin and compartment × plant genotype interactions, driven by significant soil origin effects in the rhizosphere and significant plant genotype effects in the root endosphere. Nevertheless, all compartments were dominated by Ensifer, the genus of rhizobia that forms root nodule symbiosis with M. truncatula, and additional shotgun metagenomic sequencing suggests that the nodulating Ensifer were not genetically distinguishable from those elsewhere in the plant. We also identify a handful of OTUs that are common in nodule tissues, which are likely colonized from the root endosphere. Our results demonstrate strong host filtering effects, with rhizospheres driven by soil origin and internal plant compartments driven by host genetics, and identify several key nodule-inhabiting taxa that coexist with rhizobia in the native range. Our results set the stage for future functional genetic experiments aimed at expanding our pairwise understanding of legume-rhizobium symbiosis toward a more mechanistic understanding of plant microbiomes.

中文翻译：

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模型豆科植物苜蓿中的土壤来源和植物基因型结构不同的微生物组室

了解构成植物微生物组的遗传和环境因素对于利用这些相互作用来满足农业、保护和可持续性方面的关键需求是必要的。豆科植物与固氮根瘤菌形成根瘤共生体，几十年来一直是了解有益植物-微生物相互作用的遗传学和进化的模式植物，因此作为植物-微生物组相互作用的模型具有附加值。在这里，我们使用带有 16S rRNA 基因扩增子和鸟枪法宏基因组测序的普通花园实验来研究在两个原生土壤群落中生长的模型豆科植物蒺藜苜蓿的三种基因型中微生物组多样性和组成的驱动因素。外部（根际）和内部植物区室（根内圈、根瘤内圈和叶内圈）。群落组成由强烈的区室×土壤起源和区室×植物基因型相互作用形成，受根际显着土壤起源效应和根内圈显着植物基因型效应驱动。尽管如此，所有隔间都由 Ensifer 主导，Ensifer 是与 M. truncatula 形成根瘤共生的根瘤菌属，额外的鸟枪宏基因组测序表明，根瘤 Ensifer 在遗传上与植物中的其他部分没有区别。我们还确定了一些在根瘤组织中常见的 OTU，它们很可能从根内圈定植。我们的结果证明了强大的寄主过滤效应，根际由土壤来源驱动，内部植物区室由寄主遗传驱动，并确定与原生范围内的根瘤菌共存的几个关键的根瘤栖息分类群。我们的结果为未来的功能遗传实验奠定了基础，旨在扩大我们对豆科植物 - 根瘤菌共生的成对理解，以更深入地了解植物微生物组。