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”是生物学中最迷人的问题之一。这一基本概念具有广泛的意义：例如在农业中，作物与大量微生物相互作用，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。在过去的十年里，实验和计算方法的进步为植物微生物组如何组装提供了前所未有的见解。土壤是植物微生物组的主要来源，其组成通过植物物种和基因型特异性机制进行微调，还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一系列基于免疫反应的积极相互作用发生的。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，微生物组中的“不需要的”成员可以建立并导致植物疾病，或罕见的人类疾病。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需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。我们的项目将通过表征微生物组，宿主基因型和植物免疫力之间的三方相互作用，为可持续农业和粮食安全做出贡献，以提高作物生产力和健康。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。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以及对植物免疫力的影响，以获得有益的结果。我们将使用园艺物种（例如菠菜和番茄），其中多种基因型可用，并且我们有番茄微生物组的数据，关于两个物种与微生物组中不需要的成员（食源性病原体：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组是什么？在正常的生长周期内，与地方性微生物组相比，合成群落的建立情况如何？免疫反应如何比较？用合成群落接种会影响微生物组中有害病原体的建立吗？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。学生将利用SRUC和UoD提供的最先进的实验和计算设施，并受益于嵌入宿主机构（英国植物微生物组Cryobank BBR和欧盟微生物组食品系统项目CIRCLES）的现有研究网络。

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).