Exploring host-microbiota interactions for improved crop health and food safety

了解多细胞生物如何感知微生物的“朋友”或“敌人”是生物学中最令人着迷的问题之一。这一基本概念具有广泛的含义：例如，在农业中，作物植物与众多微生物相互作用，形成一个独特的群落，即“植物微生物组”，它可以调节植物的生长、健康和发育。在过去的十年中，实验和计算方法的进步为植物微生物群的组装提供了前所未有的见解。土壤是植物微生物群的主要来源，其组成受到植物物种和基因型特异性机制的微调，也受到植物发育年龄和作物管理等外部因素的影响。植物对微生物的感知是通过基于免疫反应的一系列积极的相互作用发生的。相互作用的结果可以从症状性疾病到共生和植物生长。偶尔，“不需要的”微生物组成员会形成并引起植物疾病，或者很少引起人类疾病。提高我们对微生物组的理解提高了通过添加微生物组的特定成员来生物控制不想要的病原体的可能性。农业正在经历重大变革，以提高可持续性，例如通过改善土壤健康和减少投入的战略。我们的项目将通过描述微生物组、宿主基因型和植物免疫之间的三方相互作用，为提高作物生产力和健康做出贡献，从而促进可持续农业和粮食安全。这将在微生物学、植物生物学、生物信息学和生物技术的跨学科方法中完成。该项目的主要目的是确定植物微生物组与植物基因型的相互作用及其对植物免疫的影响，以获得有益的结果。我们将使用园艺物种（例如菠菜和番茄），因为它们有多种基因型，并且我们有番茄微生物组的数据，以及这两个物种与微生物组不需要的成员（食源性病原体：肠沙门氏菌和大肠杆菌O157:H7）相互作用的数据。要解决的具体问题是：健康菠菜和番茄植物的内源性微生物群是由什么组成的？在正常的生长周期中，与地方性微生物组相比，合成菌群的建立效果如何？免疫反应如何比较？用合成菌群接种能影响微生物群中不想要的病原体的建立吗？为了解决这些问题，学生将着手进行植物接种、微生物群分析、植物防御反应和特定微生物定量的温室和实验室工作。该学生将利用SRUC和UoD提供的最先进的实验和计算设施，并受益于东道国机构现有的研究网络（英国植物微生物组冷冻银行BBR和欧盟微生物组食品系统项目CIRCLES）。

Understanding how multicellular organisms perceive microbial 'friend' or 'foe' is one of the most fascinating questions in biology. This basic concept has widespread implications: for example in agriculture, crop plants interact with a multitude of microorganisms forming a distinct community, the 'plant microbiome', which can modulate plant growth, health and development. In the last decade, advances in experimental and computational approaches have provided unprecedented insights into how plant microbiomes are assembled. Soil is the principle source of the plant microbiome and its composition is fine-tuned by plant species- and genotype-specific mechanisms, and also impacted by plant developmental age and external factors such as crop management. Plant perception of the microbes occurs via an active series of interactions that are based on immune responses. The outcomes of the interactions can range from symptomatic disease to symbiosis and plant growth. Occasionally 'unwanted' members of the microbiome can become established and cause plant disease, or rarely, human illness. Improving our understanding of the microbiome raises the possibility of biocontrol of unwanted pathogens by the addition of specific members of the microbiome. Agriculture is undergoing major changes to become more sustainable, for example through strategies to improve soil health and reduce inputs. Our project will contribute to sustainable agriculture and food security by characterising the three-way interaction between the microbiome, host genotype and plant immunity, for improved crop productivity & health. This will be done in a cross-disciplinary approach of microbiology, plant biology, bioinformatics and biotechnology. The main aim of the project is to determine the interaction of the plant microbiome with plant genotype and the resulting impact on plant immunity, for beneficial outcomes. We will use horticultural species (e.g. spinach and tomato) for which multiple genotypes are available, and for which we have data on the microbiome for tomato, data on the interactions of both species with unwanted members of the microbiome (foodborne pathogens: Salmonella enterica and Escherichia coli O157:H7).The specific questions to be addressed are:What constitute the endogenous microbiome of healthy spinach and tomato plants?How well does a synthetic community establish compared to the endemic microbiome over a normal growth cycle and how does the immune responses compare?Can inoculation with a synthetic community affect establishment of unwanted pathogens in the microbiome? To address these questions the student will embark on glasshouse and laboratory work for plant inoculations, microbiota analysis, plant defence responses, and specific microbe quantification. The student will capitalise on state of the art experimental and computational facilities available at SRUC and UoD and benefit from being embedded on existing research networks at the host institutions (UK Plant Microbiome Cryobank BBR and EU microbiome food system project CIRCLES).