Ecology of the core microbiome in natural Lotus corniculatus populations

点击翻译按钮获取中文摘要

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.