The plant phyllosphere is a well-studied habitat characterized by low nutrient availability and high community dynamics. In contrast, plant trichomes, known for their production of a large number of metabolites, are a yet unexplored habitat for microbes. We analyzed the phyllosphere as well as trichomes of two tomato genotypes (Solanum lycopersicum LA4024, S. habrochaites LA1777) by targeting bacterial 16S rRNA gene fragments. Leaves, leaves without trichomes, and trichomes alone harbored similar abundances of bacteria (108–109 16S rRNA gene copy numbers per gram of sample). In contrast, bacterial diversity was found significantly increased in trichome samples (Shannon index: 4.4 vs. 2.5). Moreover, the community composition was significantly different when assessed with beta diversity analysis and corresponding statistical tests. At the bacterial class level, Alphaproteobacteria (23.6%) were significantly increased, whereas Bacilli (8.6%) were decreased in trichomes. The bacterial family Sphingomonadacea (8.4%) was identified as the most prominent, trichome-specific feature; Burkholderiaceae and Actinobacteriaceae showed similar patterns. Moreover, Sphingomonas was identified as a central element in the core microbiome of trichome samples, while distinct low-abundant bacterial families including Hymenobacteraceae and Alicyclobacillaceae were exclusively found in trichome samples. Niche preferences were statistically significant for both genotypes and genotype-specific enrichments were further observed. Our results provide first evidence of a highly specific trichome microbiome in tomato and show the importance of micro-niches for the structure of bacterial communities on leaves. These findings provide further clues for breeding, plant pathology and protection as well as so far unexplored natural pathogen defense strategies.

中文翻译：

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毛滴虫在番茄的根际形成了特定基因型的微生物热点

植物的叶圈是经过充分研究的生境，其特征在于养分利用率低和群落动态高。相比之下，植物毛状体以产生大量代谢产物而著称，是微生物尚未开发的栖息地。我们通过靶向细菌16S rRNA基因片段，分析了两种番茄基因型（茄属番茄Solanum lycopersicum LA4024，茄子沙门氏菌LA1777）的叶圈和毛状体。叶片，没有毛状体的叶片和仅毛状体具有相似的细菌丰度（每克样品108-109 16S rRNA基因拷贝数）。相反，在毛状体样品中发现细菌多样性显着增加（香农指数：4.4对2.5）。此外，当使用β多样性分析和相应的统计测试进行评估时，社区组成显着不同。在细菌级别上，毛状体中的变形杆菌（23.6％）显着增加，而杆菌（8.6％）则降低了。细菌家族Sphingomonadacea（8.4％）被确定为最突出的毛状体特有特征。Burkholderiaceae和放线菌科显示相似的模式。此外，鞘氨醇单胞菌被认为是毛状体样品核心微生物组中的中心元素，而独特的低丰度细菌家族，包括处女膜菌科和脂环菌科则仅存在于毛状体样品中。生态位偏好对于基因型均具有统计学意义，并且进一步观察到基因型特异性富集。我们的结果提供了番茄中特异的毛状体微生物组的第一个证据，并显示了微生态位对于叶片上细菌群落结构的重要性。这些发现为育种，植物病理学和保护以及迄今为止尚未探索的天然病原体防御策略提供了进一步的线索。