Ecology of the core microbiome in natural Lotus corniculatus populations

了解植物微生物组是当前植物科学的主要挑战之一。特别是，我们对自然种群中植物微生物组的动态，以及在生态现实条件下决定微生物组变化的不同生物过程的相对重要性的理解仍然有限。在本提案中，我们概述了一个项目的继续，我们已经开始研究普通豆科植物莲花的天然微生物组，特别关注器官特异性核心微生物组，以及影响天然微生物组变异的不同因素和过程。在项目的第一阶段，我们在多个地点和年份对L. corniculatus的根、茎、花和种子微生物组进行了广泛的采样。首先，分析表明，根微生物组的多样性和稳定性特别高，而且这种多样性会降低，但随着离根距离的增加，植物器官的微生物组变异性会增加。此外，我们还发现了复杂的微生物网络，其中有几个子网络和许多中心物种，这些物种不属于核心群落的一部分，并且在不同的地点有所不同。为了了解这种微生物组变化的可能驱动因素，我们根据生长环分析确定了所有样本植物的年龄，并对它们进行了基因分型。此外，我们还进行了卫星实验，测试了基因型对自发微生物定植的影响，以及微生物通过种子的垂直传播。最后，我们已经开始建立一个以知识为基础的微生物培养物的广泛收集，作为未来实验和更广泛的科学界的资源。在我们项目的下一阶段，我们特别计划(1)完善我们对器官特异性微生物网络的分析，并通过SynCom实验（使用我们在第一阶段的培养物）验证微生物群落的器官特异性，(2)进一步表征垂直传播的微生物，特别是研究它们的功能和传播机制，(3)扩大我们对栖息地因素的分析，(4)构建一个综合多个实验和两个阶段结果的羊角草微生物组动力学预测模型。二期项目完成后，我们将对天然微生物组的变异有一个全面的认识，并为生态植物微生物组研究建立一个具有广泛资源的新模式系统。

Understanding plant microbiomes is one of the key challenges in current plant science. In particular, we still have a limited understanding of the dynamics of plant microbiomes in natural populations, and of the relative importance of different biological processes determining microbiome variation under ecologically realistic conditions. In this proposal, we outline the continuation of a project where we have begun to study the natural microbiome of the common legume Lotus corniculatus, with a particular focus on organ-specific core microbiomes, and on the different factors and processes that influence natural microbiome variation. During the first phase of the project, we have broadly sampled the root, shoot, flower and seed microbiomes of L. corniculatus across multiple sites and years. First analyses show that root microbiomes are particularly diverse and stable, and that diversity decreases, but microbiome variability increases for plant organs, with increasing distance from the root. Moreover, we found complex microbial networks, with several sub-networks and many hub species that are not part of the core community and vary across sites. To understand possible drivers of this microbiome variation, we determined the ages of all sampled plants based on growth ring analysis, and we are also genotyping them. In addition, we have conducted satellite experiments in which we tested genotype effects on spontaneous microbial colonisation, and the vertical transmission of microbes through seeds. Finally, we have begun to establish an extensive knowledge-based collection of microbial cultures, as a resource for future experiments and the broader scientific community. During the next phase of our project, we are planning in particular (1) to refine our analyses of organ-specific microbial networks and verify the organ-specificity of microbial communities through SynCom experiments (using our cultures from phase I), (2) to further characterise vertically transmitted microbes and in particular study their function and mechanisms of transmission, (3) to broaden our analyses of habitat factors, with shallower but geographically broader sampling of plants and microbiomes, and (4) to construct a predictive model of L. corniculatus microbiome dynamics that integrates results from multiple experiments and from both phases. After the second phase of our project, we will have achieved a comprehensive understanding of natural microbiome variation, and we will have established Lotus corniculatus as a new model system with extensive resources for ecological plant microbiome research.