Determining the role of defence systems in the evolution of the Azospirillum-wheat mutualism to enhance crop yields for sustainable agriculture

粮食生产者面临着可持续提高农业生产的全球性挑战。需要增加营养密集作物的产量来养活不断增长的全球人口。然而，必须减少化学投入，必须更好地管理诸如水等宝贵资源，以尽量减少不利的环境影响，包括气候污染，同时恢复土壤肥力。土壤中的微生物对土壤的健康和功能至关重要。植物生长促进根瘤菌（PGPR）在根际生长，为植物提供营养，并产生刺激根系发育的分子，以增强生长和恢复力。作为回报，植物通过根部分泌分子供细菌使用，从而形成了一种互惠关系。无所不在的PGPR， Azospirillum，通过在移动遗传元件（MGEs）上获得土壤微生物的特性来适应植物结合，MGEs是在细菌之间水平移动的DNA片段。MGE的获取可以加速细菌的进化，但它们对宿主来说也可能是昂贵的，因此细菌携带防御系统来限制MGE的摄取。氮螺旋藻菌株在防御系统的数量和类型上有所不同，但防御系统在氮螺旋藻基因组进化中的作用，以及它们如何影响植物生长促进，尚未得到研究。我提议的研究将使用生物信息学、分子生物学和植物实验来确定细菌防御系统如何影响氮螺旋藻基因组进化。由于小麦在英国是一种重要的作物，我将从不同英国土壤中种植的小麦根际分离出氮螺旋体。我将对基因组进行测序，并使用生物信息学管道和专用预测工具来评估我的分离株和其他相关偶氮螺旋菌中存在的MGEs的丰度和多样性。为了预测防御系统如何影响MGE的吸收，我将量化现有防御的数量和类型，并执行统计建模，以测试防御系统与MGE丰度之间的关联。与低MGE负荷相关的系统将通过创建缺乏该系统的突变体进行实验测试，我将使用不同的MGE和一系列递送机制进行感染分析，以了解每种系统限制哪些类型的MGE。目前尚不清楚，通过限制MGE的摄取，防御是否限制了宿主的进化潜力，或者保护基因组免受昂贵元素的侵害。为了深入了解系统在氮螺旋体中的作用，以及至关重要的是，防御- mge动力学如何影响植物生长促进，我将进行植物相关性状的体外分析和植物生长实验。我将比较防御系统敲除突变体，获得新MGEs的突变体和祖先菌株的性能。通过这些实验，我将对防御如何影响偶氮螺旋体的进化有更深入的了解。拟议的项目将在埃克塞特大学进行，我将在那里与世界领先的微生物进化、生态学和土壤微生物学专家合作。优秀的导师，在科学技能和领导能力方面的宝贵培训，将确保我在整个奖学金期间的成功，并使我能够开始我的独立研究生涯。我将与三个项目合作伙伴合作，以确保这个跨学科项目在各个方面都取得卓越成就，其中包括小麦根际和土壤微生物组专家Mauchline，在氮螺旋体操纵和基因组学方面拥有丰富经验的wisniewski - dy<s:1>，以及将进行进一步分析和开发有益菌株的先正达。利用可持续农业结束全球饥饿是联合国的一个主要目标，而拟建的项目将对用于促进小麦生长的氮螺旋体进行鉴定，这将是一个有价值的贡献。此外，利用土壤微生物群将是提高作物产量的关键组成部分，同时为子孙后代保护环境。

Food producers face the global challenge of sustainably enhancing agricultural production. Increased production of nutrient dense crops is needed to feed the growing global population. However, chemical inputs must be reduced, and valuable resources, such as water, must be better managed to minimise adverse environmental impacts, including climate pollution, while restoring soil fertility. Microbes in the soil are essential for soil health and function. Plant growth promoting rhizobia (PGPR) grow in the rhizosphere and make nutrients available for plants, and produce molecules that stimulate root development, to enhance growth and resilience. In return, plants secrete molecules through their roots that are used by bacteria, hence forming a mutualistic relationship. The ubiquitous PGPR, Azospirillum, adapted to plant association by acquiring traits from soil microbes on mobile genetic elements (MGEs), which are pieces of DNA that move horizontally between bacteria. MGE acquisition can accelerate bacterial evolution, but they can also be costly to the host, so bacteria carry defence systems to limit MGE uptake. Azospirillum strains vary in the number and type of defence systems, but the role of defences in azospirilla genome evolution and crucially, how they affect plant growth promotion, has not been studied. My proposed research will use bioinformatics, molecular biology and plant experiments to determine how bacterial defence systems affect Azospirillum genome evolution. Since wheat is an important crop in the UK, I will isolate azospirilla from the rhizosphere of wheat grown in diverse UK soils. I will sequence the genomes and use bioinformatics pipelines and dedicated predictor tools to assess the abundance and diversity of MGEs present in my isolates and other related Azospirillum. To predict how defence systems may influence MGE uptake, I will quantify the number and types of defences present and perform statistical modelling to test for associations between defence system and MGE abundance. Systems associated with low MGE loads will be experimentally tested by creating mutants lacking the systems and I will perform infection assays using diverse MGEs and a range of delivery mechanisms to understand which types of MGEs are restricted by each system. It is not clear whether defences, by limiting MGE uptake, constrain the evolutionary potential of the host, or protect the genome against costly elements. To gain insight into the role systems play in azospirilla, and crucially, how the defence-MGE dynamics affect the plant growth promotion, I will perform in vitro assays for plant associated traits and plant growth experiments. I will compare the performance of the defence system knockout mutants, mutants that have acquired new MGEs and the ancestral strain. From these experiments, I will have a greater understanding of how defences shape azospirilla evolution.The proposed project will be carried out at the University of Exeter, where I will work with world-leading experts in microbial evolution, ecology and soil microbiology. Excellent mentorship, and valuable training in scientific skills and leadership, will ensure my success throughout the Fellowship and enable me to launch my independent research career. I will work with three project partners to ensure excellence in all aspects of this interdisciplinary project, including Mauchline, an expert in the wheat rhizosphere and the soil microbiome, Wisniewski-Dyé, who has vast experience in azospirilla manipulation and genomics, and Syngenta, who will perform further analysis and development of beneficial strains. Ending global hunger using sustainable agriculture is a major goal of the UN and the proposed project, to characterise azospirilla to be used for wheat growth promotion, will be a valuable contribution. Further, harnessing the soil microbiome will be a critical component of improving the success of crops, while protecting the environment for future generations.