Mechanisms and dynamics underlying host preference of commensal root-associated bacteria

不同的植物物种宿主根微生物群在细菌物种的流行和相对丰度方面不同。在此之前，我在gnotobiotic微生物群重建系统中种植了莲花和拟南芥，以研究这种植物物种特异性细菌群落的组装，以及来自给定植物物种的细菌（非有害细菌）是否继承了对宿主的偏好。使用从莲花和拟南芥根培养物收集物设计的合成细菌群落（SynComs）作为接种物。我表明，在竞争的背景下，在一个混合的社区莲花和紫茎泽兰衍生的细菌，菌株积累到更高的相对丰度的根上的原始主机（“本地”菌株）比其他植物物种，指示模式的主机之间的偏好紫茎泽兰细菌。进一步的实验表明，主机偏好需要积极的主机参与，它是与入侵到建立根社区的能力。在这个项目中，我的目标是破译的机制和时空动态的昆虫寄主偏好。我的目标是（一）确定对植物的影响，主机本地细菌群落，（二）探讨殖民模式和机制的细菌群落组装和主机的偏好，和（三）调查的作用，根分泌物在社区建立和调节细菌性状。为了实现这一目标，我将应用转录组学，代谢，遗传和显微镜技术与比较重建系统，除了国家的最先进的社区分析方法。与天然和非天然SynComs共培养的两种宿主的RNA测序分析和靶向下游实验将鉴定涉及细菌宿主偏好的宿主遗传因子。在SynComs的存在下，评估植物在生物和非生物胁迫下的表现将揭示托管特定社区的潜在好处。使用时空观察的根殖民荧光标记的arthrosals单独和在社会背景下，我将解决如果本地菌株显示主机特定的殖民模式，如果这些被干扰的非本地社区，反之亦然。通过将在植物物种特异性分泌物中体外孵育后的细菌SynComs的群落分析与分泌物的代谢组学分析相结合，我的目标是确定触发宿主特异性微生物群组装和宿主偏好的化合物。此外，在不同根分泌物中孵育天然和非天然SynComs后的细菌元转录组的表征将识别由两种宿主诱导的共同和特定的植物性状。总的来说，通过这项研究计划，我将推进我们对植物微生物群建立和植物宿主偏好的理解，这对生态友好和可持续的农业实践具有影响。

Different plant species host root microbiota that differ in prevalence and relative abundance of bacterial species. Previously, I grew Lotus japonicus and Arabidopsis thaliana in gnotobiotic microbiota reconstitution systems to investigate the assembly of such plant species-specific bacterial communities, and whether commensals (not harmful bacteria) derived from a given plant species inherit a preference for their host. Synthetic bacterial communities (SynComs) designed from Lotus and Arabidopsis root culture collections were used as inoculum. I showed that, in a competition context within a mixed community of Lotus- and Arabidopsis-derived bacteria, strains accumulated to higher relative abundances on roots of their original host (“native” strains) than on the other plant species, indicating patterns of host preference among commensal bacteria. Further experiments revealed that host preference requires active host participation, and that it is linked to the ability to invade into established root communities. In this project, I aim to decipher the mechanisms and spatiotemporal dynamics of commensal host preference. My objectives are to (i) identify the impact on the plant of hosting native bacterial communities, (ii) explore colonization patterns and mechanisms of bacterial community assembly and host preference, and (iii) investigate the role of root exudates in community establishment and regulation of bacterial traits. To achieve this, I will apply transcriptomic, metabolic, genetic, and microscopy techniques with the comparative reconstitution system, in addition to state-of-the-art community profiling methods. RNA seq analysis of the two hosts co-cultivated with native and non-native SynComs and targeted downstream experiments will identify host genetic factors involved in bacterial host preference. Evaluating plant performance under biotic and abiotic stresses in the presence of SynComs will reveal potential benefits of hosting specific communities. Using spatiotemporal observation of root colonization by fluorescently tagged commensals alone and in a community context, I will address if native strains display host-specific colonization patterns, and if these are disturbed by non-native communities and vice versa. By coupling community profiling of bacterial SynComs after in vitro incubation in plant species-specific exudates with the exudates’ metabolomic profiling, I aim to identify compounds triggering host-specific microbiota assembly and host preference. Furthermore, the characterization of bacterial metatranscriptomes after incubation of native and non-native SynComs in different root exudates will identify both common and specific commensal traits induced by the two hosts. Overall, with this research programme, I will advance our understanding of plant microbiota establishment and commensal host preference, which has implications for eco-friendly and sustainable agricultural practices.