Using phages as a precision tool to control pathogen abundance and virulence in the plant rhizosphere microbiome

植物病原菌给食品生产系统造成了巨大的经济损失。其主要原因是几乎没有任何有效的控制方法来减轻这种损害。在这项提案中，我们将开发一个预测框架和全面了解如何控制植物根际微生物组中的植物病原性青枯雷尔氏菌细菌通过使用细菌特异性病毒，细菌。我们将重点关注三个关键方面，这些方面使植物保护特别有用的工具。首先，我们将探索噬菌体特异性的优势，并测试我们是否可以通过选择性地只针对病原体来“精确编辑”微生物组。这不仅对于有效性而且对于安全使用植物的安全性都很重要，因为它们不应该对根际周围的微生物组造成附带损害。其次，我们将确定噬菌体选择病原体的竞争力和毒力的进化后果，使用代谢建模和直接实验。虽然病原体可能会迅速进化出对细菌的耐药性，但这通常对病原体来说是昂贵的。因此，噬菌体可以作为“进化工具”，通过选择产生高代谢负荷或损害毒力基因表达的抗性适应来削弱病原体。第三，我们将探索噬菌体介导的病原体毒力和微生物组组成的变化是否可预测地改变植物免疫应答，对植物健康具有潜在的额外有益影响。在这里，我们将超越以病原体为中心的观点，通过系统地探索在自然根际微生物组存在和不存在的情况下，当受到噬菌体抗性和易感病原体的挑战时，植物基因表达的反应，建立对社区水平反馈的全面理解。最后，将选择最有前途的农杆菌用于工业生产，并在温室马铃薯试验中验证其生物防治功效和安全性。为了实现这些目标，我们将汇集一个跨学科的研究团队，由在生态学和噬菌体-细菌-植物相互作用，基因组学，代谢建模和植物转录组学的进化方面经验丰富的学者和行业合作伙伴组成。这项研究具有创新性，及时性，并将传统作物保护的界限推向了使用植物根际病原菌的精确控制。

Plant pathogenic bacteria cause considerable economic losses to food production systems. The main reason for this is that hardly any effective control methods exist to mitigate this damage. In this proposal, we will develop a predictive framework and holistic understanding of how to control plant pathogenic Ralstonia solanacearum bacterium in the plant rhizosphere microbiomes by using bacteria-specific viruses, phages. We will focus on three key aspects that make phages especially useful tools for crop protection. First, we will explore the advantage of phage specificity and test if we can 'precision edit' microbiomes by selectively targeting only the pathogen. This is important not only for the efficacy but also for the safe use of phages as they should not cause collateral damage to the surrounding microbiome in the rhizosphere. Second, we will determine the evolutionary consequences of phage selection for pathogen competitiveness and virulence using metabolic modelling and direct experimentation. While it is likely that pathogens can rapidly evolve resistance to phages, this is often costly to the pathogen. Phages could thus be used as 'evolutionary tools' to weaken the pathogen by selecting resistance adaptations that incur high metabolic burden or impair virulence gene expression. Third, we will explore if phage-mediated changes in pathogen virulence and microbiome composition predictably alter plant immune responses having potential additional beneficial effects on the plant health. Here, we will move beyond pathogen-centric view to build a holistic understanding of community-level feedbacks by systematically exploring responses in plant gene expression when challenged with phage resistant and susceptible pathogens in the absence and presence of natural rhizosphere microbiome. Finally, the most promising phages will be selected for industrial manufacturing and their biocontrol efficacy and safety validated in greenhouse trials using potato. To achieve these goals, we will bring together an interdisciplinary research team consisting of academics and industry partners experienced in ecology and evolution of phage-bacteria-plant interactions, genomics, metabolic modelling and plant transcriptomics. The proposed research is innovative, timely and pushes the boundaries of traditional crop protection to precision control of plant pathogenic bacteria in the plant rhizosphere using phages.