Microorganisms from all domains of life establish associations with plants. Although some harm the plant, others antagonize pathogens or prime the plant immune system, support the acquisition of nutrients, tune plant hormone levels, or perform additional services. Most culture-independent plant microbiome research has focused on amplicon sequencing of the 16S rRNA gene and/or the internal transcribed spacer (ITS) of rRNA genomic loci, which show the relative abundance of the microbes to each other. Here, we describe shotgun sequencing of 275 wild Arabidopsis thaliana leaf microbiomes from southwest Germany, with additional bacterial 16S and eukaryotic ITS1 rRNA amplicon data from 176 of these samples. Shotgun data, which unlike the amplicon data capture the ratio of microbe to plant DNA, enable scaling of microbial read abundances to reflect the microbial load on the host. In a more cost-effective hybrid strategy, we show they also allow a similar scaling of amplicon data to overcome compositionality problems. Our wild plants were dominated by bacterial sequences, with eukaryotes contributing only a minority of reads. Microbial membership showed weak associations with both site of origin and plant genotype, both of which were highly confounded in this dataset. There was large variation among microbiomes, with one extreme comprising samples of low complexity and a high load of microorganisms typical of infected plants, and the other extreme being samples of high complexity and a low microbial load. Critically, considering absolute microbial load led to fundamentally different conclusions about microbiome assembly and the interaction networks among major taxa.

中文翻译：

---

结合全基因组鸟枪法测序和 rRNA 基因扩增子分析，改进植物叶片中微生物-微生物相互作用网络的检测。


来自生命各个领域的微生物与植物建立了联系。虽然有些会伤害植物，但其他的会对抗病原体或启动植物免疫系统，支持营养物质的获取，调整植物激素水平，或提供额外的服务。大多数不依赖于培养物的植物微生物组研究都集中在 16S rRNA 基因和/或 rRNA 基因组位点的内转录间隔区 (ITS) 的扩增子测序上，这显示了微生物彼此之间的相对丰度。在这里，我们描述了来自德国西南部的 275 个野生拟南芥叶子微生物组的鸟枪法测序，以及来自其中 176 个样本的额外细菌 16S 和真核 ITS1 rRNA 扩增子数据。与扩增子数据捕获微生物与植物 DNA 的比率不同，鸟枪数据能够缩放微生物读数丰度以反映宿主上的微生物负载。在更具成本效益的混合策略中，我们表明它们还允许对扩增子数据进行类似的缩放以克服组合性问题。我们的野生植物以细菌序列为主，真核生物只贡献了一小部分读数。微生物成员资格显示出与起源位点和植物基因型的弱关联，这两者在该数据集中都高度混杂。微生物组之间存在很大差异，一个极端包括受感染植物典型的低复杂性和高微生物负荷的样品，另一种极端是高复杂性和低微生物负荷的样品。至关重要的是，考虑绝对微生物负荷导致了关于微生物组组装和主要分类单元之间的相互作用网络的根本不同的结论。