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地提高农业生产的全球挑战。为了养活不断增长的全球人口，需要增加营养密集型作物的产量。然而，必须减少化学投入，必须更好地管理水等宝贵资源，以尽量减少对环境的不利影响，包括气候污染，同时恢复土壤肥力。土壤中的微生物对土壤健康和功能至关重要。植物生长促进根瘤菌（PGPR）生长在根际，为植物提供养分，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，植物通过它们的根分泌分子，这些分子被细菌利用，因此形成了一种互利关系。普遍存在的PGPR，固氮菌，通过从移动的遗传元件（MGE）上的土壤微生物中获得性状来适应植物联合体，MGE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是昂贵的，因此细菌携带防御系统来限制MGE的摄取。固氮菌菌株在防御系统的数量和类型上各不相同，但防御在固氮菌基因组进化中的作用以及关键的是，它们如何影响植物生长促进，尚未研究。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固氮菌基因组进化。由于小麦在英国是一种重要的作物，我将从英国不同土壤中生长的小麦根际分离固氮菌。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固氮菌中存在的MGE的丰度和多样性。为了预测防御系统如何影响MGE摄取，我将量化防御系统的数量和类型，并进行统计建模，以测试防御系统和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系统的突变体进行实验测试，我将使用不同的MGE和一系列传递机制进行感染测定，以了解哪些类型的MGE受到每个系统的限制。目前尚不清楚是否防御，通过限制MGE摄取，限制宿主的进化潜力，或保护基因组免受昂贵的元素。为了深入了解系统在固氮菌中的作用，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测定和植物生长实验。我将比较防御系统敲除突变体，突变体，已获得新的MGE和祖先菌株的性能。从这些实验中，我将有一个更好的了解如何防御形状固氮菌的演变。拟议的项目将在埃克塞特大学，在那里我将与世界领先的专家在微生物进化，生态学和土壤微生物学。优秀的指导，以及科学技能和领导力方面的宝贵培训，将确保我在整个奖学金期间取得成功，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，以确保在这个跨学科项目的各个方面都取得卓越成绩，其中包括小麦根际和土壤微生物组专家莫赫林，在固氮菌操作和基因组学方面拥有丰富经验的Wisniewski-Dyé，以及将对有益菌株进行进一步分析和开发的先正达。利用可持续农业结束全球饥饿是联合国的一个主要目标，拟议中的项目，将阿古拉用于促进小麦生长，将是一个宝贵的贡献。此外，利用土壤微生物组将是提高作物成功率的关键组成部分，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.