The plant growth-promoting rhizobacterium Delftia acidovorans RAY209 is capable of establishing strong root attachment during early plant development at 7 days post-inoculation. The transcriptional response of RAY209 was measured using RNA-seq during early (day 2) and sustained (day 7) root colonization of canola plants, capturing RAY209 differentiation from a medium-suspended cell state to a strongly root-attached cell state. Transcriptomic data was collected in an identical manner during RAY209 interaction with soybean roots to explore the putative root colonization response to this globally relevant crop. Analysis indicated there is an increased number of significantly differentially expressed genes between medium-suspended and root-attached cells during early soybean root colonization relative to sustained colonization, while the opposite temporal pattern was observed for canola root colonization. Regardless of the plant host, root-attached RAY209 cells exhibited the least amount of differential gene expression between early and sustained root colonization. Root-attached cells of either canola or soybean roots expressed high levels of a fasciclin gene homolog encoding an adhesion protein, as well as genes encoding hydrolases, multiple biosynthetic processes, and membrane transport. Notably, while RAY209 ABC transporter genes of similar function were transcribed during attachment to either canola or soybean roots, several transporter genes were uniquely differentially expressed during colonization of the respective plant hosts. In turn, both canola and soybean plants expressed genes encoding pectin lyase and hydrolases – enzymes with purported function in remodelling extracellular matrices in response to RAY209 colonization. RAY209 exhibited both a core regulatory response and a planthost-specific regulatory response to root colonization, indicating that RAY209 specifically adjusts its cellular activities to adapt to the canola and soybean root environments. This transcriptomic data defines the basic RAY209 response as both a canola and soybean commercial crop and seed inoculant.

中文翻译：

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转录组学揭示植物生长促进细菌 Delftia acidovorans RAY209 在与油菜和大豆根相互作用期间的核心活性

促进植物生长的根瘤菌Delftia acidovorans RAY209 能够在接种后 7 天的早期植物发育过程中建立牢固的根系附着力。在油菜植物的早期（第 2 天）和持续（第 7 天）根定植期间，使用 RNA-seq 测量 RAY209 的转录反应，捕获 RAY209 从中等悬浮细胞状态到强根附着细胞状态的分化。在 RAY209 与大豆根相互作用期间以相同的方式收集转录组数据，以探索对这种全球相关作物的假定根定植反应。分析表明，相对于持续定植，在早期大豆根定植期间，培养基悬浮细胞和根附着细胞之间显着差异表达的基因数量增加，而双低油菜籽根定植则观察到相反的时间模式。无论植物宿主如何，附着根的 RAY209 细胞在早期和持续根定植之间表现出最少的差异基因表达。双低油菜或大豆根的根附着细胞表达高水平的成束蛋白基因同系物编码粘附蛋白，以及编码水解酶、多种生物合成过程和膜转运的基因。值得注意的是，虽然功能相似的 RAY209 ABC 转运蛋白基因在附着于油菜或大豆根的过程中被转录，但几个转运蛋白基因在各自植物宿主的定殖过程中具有独特的差异表达。反过来，双低油菜籽和大豆植物都表达了编码果胶裂解酶和水解酶的基因——据称这些酶在响应 RAY209 定植时具有重塑细胞外基质的功能。RAY209 对根部定植表现出核心调节反应和植物宿主特异性调节反应，表明 RAY209 专门调整其细胞活动以适应油菜和大豆根部环境。该转录组数据将基本 RAY209 响应定义为双低油菜籽和大豆商业作物和种子接种剂。