The plant vascular system has remained an underexplored niche despite its potential for hosting beneficial microbes. The aim of this work was to determine the origin of the microbial endophytes inhabiting grapevine. We focused on a single commercial vineyard in California over a two-year period and used an amplicon metagenomics approach to profile the bacterial (16S-V4) and fungal (ITS) communities of the microbiome across a continuum of six grapevine compartments: bulk soil, rhizosphere, root, cordon, cane and sap. Our data supported that roots are a bottleneck to microbial richness and that they are mostly colonized with soilborne microbes, including plant growth-promoting bacteria recruited by the host, but also saprophytic and pathogenic fungal invaders. A core group of taxa was identified throughout the vine; however, there was clear partitioning of the microbiome with niche adaptation of distinct taxonomic groups. Above- and belowground plant tissues displayed distinct microbial fingerprints and were intermixed in a limited capacity mostly by way of the plant sap. We discuss how cultural practices and human contact may shape the endosphere microbiome and identify potential channels for transmission of its residents.

中文翻译：

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葡萄的内生微生物集合体。

尽管植物血管系统具有容纳有益微生物的潜力，但它仍然是一个未开发的领域。这项工作的目的是确定居住在葡萄藤上的微生物内生菌的起源。我们在两年内专注于加利福尼亚州的一家商业葡萄园，并使用扩增子宏基因组学方法对连续六个葡萄树区隔中的微生物组的细菌（16S-V4）和真菌（ITS）群落进行了分析：散装土壤，根际，根部，警戒线，甘蔗和汁液。我们的数据支持根系是微生物丰富性的瓶颈，并且它们大多被土壤微生物定居，包括宿主招募的植物生长促进细菌，以及腐生和病原性真菌入侵者。在整个葡萄藤中都鉴定出一个核心的分类单元。然而，微生物组有明显的划分，并且具有不同分类组的生态位适应性。地上和地下植物组织显示出明显的微生物指纹，并且主要通过植物汁液以有限的能力混合。我们讨论文化习俗和人与人之间的关系如何影响内球微生物组，并确定其居民传播的潜在渠道。