However, mechanistic insights into microbiome-orchestrated grapevine biology remain limited.

Grapevine phyllosphere pan-metagenomics reveals pan-microbiome structure, diversity, and functional roles in downy mildew resistance

（1）Grapevines are among the most economically important fruit crops, and the microbiome profoundly influences their health, yield, and quality.葡萄是经济上最重要的水果作物之一，而微生物组深刻影响着其健康、产量和品质。

（2）However, mechanistic insights into microbiome-orchestrated grapevine biology remain limited.然而，关于微生物组调控葡萄生物学机制的见解仍然有限。

（3） Here, we conduct large-scale pan-metagenomic and pan-metatranscriptomic analyses of the phyllosphere microbiome from 107 grapevine accessions spanning 34 Vitis species.在此，我们对来自107份葡萄种质（涵盖34个葡萄属物种）的叶际微生物组进行了大规模的泛宏基因组和泛宏转录组分析。

（4）We show that the grapevine core microbiome is dominated by phyla Bacillota and Pseudomonadota.我们发现，葡萄核心微生物组以芽孢杆菌门（Bacillota）和假单胞菌门（Pseudomonadota）为主导。

（5） Leveraging PacBio sequencing, we assembled 19 high-quality metagenome-assembled genomes (MAGs) from the grapevine pan-microbiome, representing the first MAG reconstruction in plant-associated microbial communities using PacBio reads.利用PacBio测序技术，我们从葡萄泛微生物组中组装了19个高质量的宏基因组组装基因组（MAGs），这是首次在植物相关微生物群落中使用PacBio读长进行MAG重建。

（6） These MAGs encode genes associated with antibiotic resistance, secondary metabolism, and carbohydrate-active enzymes (CAZymes), which could potentially influence grapevine biology.这些MAGs编码与抗生素抗性、次级代谢和碳水化合物活性酶（CAZymes）相关的基因，这些基因可能潜在影响葡萄的生物学特性。

（7）During downy mildew (DM) infection, DM-resistant grapevines exhibit significantly higher microbial network complexity than susceptible counterparts.在霜霉病感染期间，抗霜霉病的葡萄比感病葡萄表现出显著更高的微生物网络复杂性。

（8） Among the key taxa contributing to this complexity, Bacillota emerged as the dominant phylum, displaying strong abundance correlations with phylum Euglenozoa and Cyanobacteriota, and an isolated Bacillota species from the grapevine leaves, Bacillus cereus, demonstrated potent biocontrol activity against DM infection.在促成这种复杂性的关键类群中，芽孢杆菌门成为优势菌门，与眼虫门和蓝藻菌门表现出强烈的丰度相关性；从葡萄叶片中分离到的一株芽孢杆菌门物种——蜡样芽孢杆菌，展现出对霜霉病感染的强效生物防治活性。

（9） Pan-metatranscriptomic analysis further revealed significant upregulation of eukaryotic microbial genes involved in primary and secondary metabolism.泛宏转录组分析进一步揭示，参与初级代谢和次级代谢的真核微生物基因显著上调。

（10）  Conclusions: This pan-metagenomic study offers unprecedented insights into the complex structure, diversity, and functional roles of the grapevine phyllosphere microbiome and presents valuable genomic and microbial resources for microbiome research and engineering to enhance viticulture productivity and quality.这项泛宏基因组学研究为葡萄叶际微生物组的复杂结构、多样性和功能角色提供了前所未有的见解，并为微生物组研究和工程改造提供了宝贵的基因组和微生物资源，以提高葡萄栽培的生产力和品质。

（11） Result

（12） Grapevine core microbiome is dominated by Bacillota and Pseudomonadota 葡萄藤核心微生物群以芽孢杆菌属和假单胞菌属为主

葡萄叶际泛宏基因组和泛宏转录组学的研究设计

（13） Assembly of grapevine phyllospheric metagenome-assembled genomes (GPMAGs) 葡萄叶际宏基因组的组装

葡萄叶际微生物组的泛宏基因组景观

葡萄叶际宏基因组组装基因组（GPMAGs）的组装与基因组特征

（14）Annotation of grapevine MAGs reveals genes encoding key biological processes 葡萄MAGs注释揭示编码关键生物过程的基因 

（15） Downy mildew resistance relates to complexity of microbial interaction network with presence of key genera 霜霉病抗性与存在关键属的微生物相互作用网络的复杂性有关

霜霉病抗性塑造了具有关键属的复杂微生物互作网络

（16） Downy mildew triggers eukaryotic primary and secondary metabolism of the grapevine microbiome 霜霉病引发葡萄微生物群的真核初级和次级代谢

葡萄叶际真核微生物组对霜霉病菌感染的转录响应

 葡萄藤核心微生物群以芽孢杆菌属和假单胞菌属为主