Plant Microbiome Engineering

最近组学技术的飞跃使我们对人类和人类微生物组之间相互作用的许多健康影响有了前所未有的了解。现在，全面描述生物圈的另一个关键组成部分的大门已经打开：植物微生物组。植物负责陆地环境中的大多数初级生产，是粮食生产系统的重要组成部分。植物微生物群既有益于植物健康，也会破坏植物健康，改变这种组合的平衡对粮食生产具有巨大影响。有益微生物可以增加养分利用率，促进植物生长，抑制病原体，并可能帮助植物抵御高温和干旱。尽管几十年来人们都知道植物微生物群是植物健康的关键组成部分，但我们才刚刚开始对它产生系统级的理解。由于土壤微生物组合是具有可塑性的功能多样性的丰富来源，因此更好地了解植物微生物组将使其能够被设计为促进特定的有益微生物分类群，功能和活动。因此，我的研究项目的目标是双重的：1)使用组学技术和大规模数据分析来了解植物和它们的微生物组之间的相互作用，从长远来看，2)利用这种独特的关系来设计植物微生物组，并为诸如粮食生产、土壤污染和全球变暖等问题提供现实世界的解决方案。在接下来的五到十年里，我的研究计划将集中在三个主要目标上，使用加拿大最重要的作物之一小麦（Triticum aestivum）作为模式作物植物。总体目标是设计一种小麦微生物群，使其能够更好地适应加拿大南部未来的气候情景，并允许在次优条件下生长，促进更可持续的农业。拟议的计划将受益于加拿大国家研究委员会（NRC）小麦改良旗舰计划提供的协同作用，我参与了有益生物相互作用主题。这三个目标是：

Recent leaps in ‘omics technologies have provided us with an unprecedented understanding of the numerous health implications of interactions between humans and the human microbiome. The door is now open to comprehensively characterize another crucial component of the biosphere: the plant microbiome. Plants are responsible for most primary production in terrestrial environments, and are vital components of food production systems. The plant microbiome can both benefit and undermine plant health, and shifting the balance of this assemblage has huge implications for food production. Beneficial microbes can increase nutrient availability, promote plant growth, suppress pathogens, and may help plants to withstand heat and drought. Even though it has been known for decades that the plant microbiome is a key component of plant health, we are only beginning to produce a system-level understanding of it. As soil microbial assemblages are a rich source of functional diversity with demonstrated plasticity, a better understanding of the plant microbiome will allow it to be engineered to promote specific beneficial microbial taxa, functions and activities. Therefore, the goals of my research program are twofold: 1) use ‘omics technologies and large-scale data analysis to understand the interactions between plants and their microbiome and, in the longer-term, 2) harness this unique relationship to engineer the plant microbiome and generate real-world solutions to problems such as food production, soil pollution, and global warming. For the next five to ten years, my research program will be focused on three main aims, using one of the most important Canadian crops, wheat (Triticum aestivum), as a model crop plant. The overarching goal is to engineer a wheat microbiome that would be better adapted to future climate scenarios for southern Canada, and that allows growth in sub-optimal conditions, promoting more sustainable agriculture. The proposed program will benefit from the synergy offered by the National Research Council Canada (NRC) Wheat Improvement Flagship Program for which I am involved within the Beneficial Biotic Interaction theme. The three aims are: 1) The Canadian wheat microbiome. The goal of this aim is to find microbial genes and organisms that would promote plant adaptation to limiting conditions. 2) The plant-microbe meta-organism. The goal of this aim is to identify how the plant and its microbiome interact and if this interaction can be recreated in sterile plants using microbial isolates. 3) New approaches for plant microbiome engineering. This aim will focus on generating a proof of concept for plant microbiome engineering. This research program will innovate by generating a new understanding of the plant microbiome at an unprecedented level of detail, and will lay the ground for targeted rhizosphere engineering. In agro-ecosystems, I expect that a full understanding of the plant microbiome will enable an optimization of plant health, nutrition, and yields, toward a more sustainable agriculture.