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

不同植物种类寄主的根微生物群在细菌种类的流行度和相对丰度上存在差异。在此之前，我在非生菌菌群重建系统中培养了日本莲花（Lotus japonicus）和拟南芥（Arabidopsis thaliana），以研究这些植物物种特异性细菌群落的组装，以及来自特定植物物种的共生菌（非有害细菌）是否继承了对其宿主的偏好。以莲藕和拟南芥根培养物设计的合成菌群（SynComs）作为接种物。我表明，在莲花和拟南芥衍生细菌混合群落的竞争环境中，菌株在其原始宿主（“本地”菌株）的根上积累的相对丰度高于其他植物物种，这表明共生细菌对宿主的偏好模式。进一步的实验表明，寄主偏好需要寄主积极参与，这与入侵已建立的根群落的能力有关。在这个项目中，我的目标是破译共生宿主偏好的机制和时空动态。我的目标是：(i)确定寄主本地细菌群落对植物的影响，（ii）探索细菌群落组装和寄主偏好的定植模式和机制，以及（iii）研究根分泌物在群落建立和细菌性状调节中的作用。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构系统，以及最先进的社区分析方法。对与原生和非原生SynComs共培养的两种宿主进行RNA序列分析，并进行针对性的下游实验，以确定参与细菌宿主偏好的宿主遗传因素。评估植物在生物和非生物胁迫下的表现将揭示寄主特定群落的潜在好处。利用荧光标记共生体单独和在群落背景下对根定殖的时空观察，我将解决本地菌株是否显示宿主特异性定殖模式，以及这些模式是否受到非本地群落的干扰，反之亦然。通过将细菌SynComs在植物物种特异性分泌物中体外培养后的群落分析与分泌物的代谢组学分析相结合，我旨在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，对原生和非原生SynComs在不同根分泌物中孵育后的细菌亚转录组进行表征，将确定两种寄主诱导的共同和特定的共生性状。总的来说，通过这个研究项目，我将推进我们对植物微生物群建立和共生宿主偏好的理解，这对生态友好和可持续的农业实践具有重要意义。

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.