Plant microbiomes have important roles in plant health and productivity. However, despite flowers being directly linked to reproductive outcomes, little is known about the microbiomes of flowers and their potential interaction with pathogen infection. Here, we investigated the temporal spatial dynamics of the apple stigma microbiome when challenged with a phytopathogen Erwinia amylovora, the causal agent of fire blight disease. We profiled the microbiome from the stigmas of individual flowers, greatly increasing the resolution at which we can characterize shifts in the composition of the microbiome. Individual flowers harbored unique microbiomes at the operational taxonomic unit level. However, taxonomic analysis of community succession showed a population gradually dominated by bacteria within the families Enterobacteriaceae and Pseudomonadaceae. Flowers inoculated with E. amylovora established large populations of the phytopathogen, with pathogen-specific gene counts of >3.0 × 10⁷ in 90% of the flowers. Yet, only 42% of inoculated flowers later developed fire blight symptoms. This reveals that pathogen abundance on the stigma is not sufficient to predict disease outcome. Our data demonstrate that apple flowers represent an excellent model in which to characterize how plant microbiomes establish, develop, and correlate with biological processes such as disease progression in an experimentally tractable plant organ.

植物微生物组在植物健康和生产力方面具有重要作用。然而，尽管花与生殖结果直接相关，但人们对花的微生物组及其与病原体感染的潜在相互作用知之甚少。在这里，我们研究了苹果柱头微生物群在受到火疫病病原体欧文氏菌攻击时的时空动态。我们从单朵花的柱头中分析了微生物组，大大提高了我们可以表征微生物组组成变化的分辨率。单个花在操作分类单元级别具有独特的微生物组。然而，群落演替的分类学分析表明，种群逐渐以家族内的细菌为主。肠杆菌科和假单胞菌科。接种了梨火疫病菌的花建立了大量的植物病原体，90% 的花中病原体特异性基因计数>3.0 × 10 ⁷。然而，只有 42% 的接种花后来出现了火疫病症状。这表明柱头上的病原体丰度不足以预测疾病结果。我们的数据表明，苹果花代表了一个极好的模型，在该模型中，可以表征植物微生物组如何建立、发展以及与生物过程（如实验易处理的植物器官中的疾病进展）相关联。