The role of evolutionary refinement in horizontal gene transfer of rhizobial symbiosis genes

根瘤菌是固氮细菌，与豆科植物形成密切的细胞内共生关系。根瘤菌将植物无法获得的大气氮转化为植物可以利用的氨。这种关系对全球氮循环至关重要，并将在向可持续粮食生产的转变中发挥关键作用，因为它消除了对污染工业肥料的需求。虽然人们对根瘤菌-豆类相互作用的关注主要集中在单一菌株的功效上，但实际上，天然豆类与多种根瘤菌菌株存在共生关系。人们对根瘤菌种群多样性背后的过程了解甚少，但对共生的功能和根瘤菌种群适应不断变化的环境或新的农业实践的能力至关重要。个体之间的DNA转移——被称为水平基因转移（HGT）——是细菌进化中促进基因组多样化的一个关键过程。有证据表明，HGT是根瘤菌-豆科植物共生的基础；核心共生基因编码在可移动的遗传元件上，通常是质粒（称为对称质粒），并显示出在种群内有规律转移的分布模式。同源质粒重组到不同的细菌宿主中会在根瘤菌群体中产生基因组多样性，因为不同的质粒携带同源基因。虽然这在人口规模上可能是有益的，但在个人层面上解释它是具有挑战性的；质粒的获取对细菌来说通常是昂贵的，因为现有和进入的DNA之间存在冲突，而HGT可能会破坏移动共生基因和染色体中已知参与共生的其他（非移动）基因之间的有益联系。这些挑战可以通过适应来改善冲突或将新基因嵌入现有基因网络来克服。因此，理解对称质粒HGT的动力学首先需要我们了解对称质粒转移的成本（如果有的话），以及如何通过进化解决这些问题。这个项目的目的是为这个过程的基本方面提供关键的见解。我们将开发一个易于处理的模型系统，用于测试a.新的同质粒获取如何影响根瘤菌的适合度和共生性能；b.需要什么样的进化过程来改善和/或优化这种关系。这些关键的见解将使我们能够将这些想法发展成更大的研究途径。这一研究的核心将是多同质粒/细菌模型系统的发展，这对扩大这一研究领域的未来工作至关重要。未来的工作将包括，例如，对限制同质粒转移的机制的详细分析。这个项目的产出将直接通过确定选择目标来解决同质粒转移的障碍。基因敲除/敲低实验可用于研究这些靶标，探索这些屏障的机制基础。其他主要的研究途径将探讨同质粒迁移的生态驱动因素。例如，维持同质粒HGT的一个关键假设是，根瘤菌多样性是有益的，例如在寄主环境不可预测的豆科植物种群中。未来的资助将利用这项研究的结果来调查什么条件有利于sym基因HGT的持续存在。了解多样性的作用、它的障碍和克服这些障碍的过程对于制定豆类作物生产战略将是重要的。在其本地范围之外生长的豆类（例如大豆）接种了1-2株根瘤菌，但是其他策略——例如增加接种剂多样性，甚至通过sym基因HGT对当地根瘤菌种群进行“选择性育种”可能更有效。

Rhizobia are nitrogen-fixing bacteria that form intimate, intracellular symbioses with legume plants. Rhizobia convert atmospheric nitrogen, which is inaccessible to plants, to ammonia which can be used by the plant. This relationship is vital for global nitrogen cycling and will play a key role in the move to sustainable food production as it negates the need for polluting industrial fertilisers. While much attention on rhizobia-legume interactions focuses on the efficacy of single bacterial strains, in reality, natural legumes engage in symbiosis with a large diversity of rhizobia strains. Processes that underlie the diversity within rhizobia populations are poorly understood but will be critical to the functioning of the symbiosis and the capacity for rhizobial populations to adapt to changing environments or new agricultural practices. The transfer of DNA between individuals - known as horizontal gene transfer (HGT) - is a crucial process in bacterial evolution contributing to genome diversification. Evidence suggests that HGT is fundamental to the rhizobia-legume symbiosis; core symbiosis genes are encoded on mobile genetic elements, often plasmids (known as sym-plasmids), and show patterns of distribution indicative of regular transfer within populations. Reshuffling of sym-plasmids into different bacterial hosts generates genomic diversity within rhizobia populations as different plasmids carry sym genes. While this is likely to be beneficial at a population scale, it is challenging to explain at the individual level; Acquisition of plasmids is often costly for bacteria due to conflicts between existing and incoming DNA and HGT could disrupt beneficial associations between mobile symbiosis genes and other (non-mobile) genes in the chromosome known to be involved in the symbiosis. Such challenges can be overcome by adaptation to ameliorate conflicts or embed new genes into existing gene networks. Understanding the dynamics of sym-plasmid HGT therefore first requires us to have an understanding of what - if any - costs there are to sym-plasmid transfer, and how these can be resolved through evolution. The aim of this project is to provide key insights into fundamental aspects of this process. We will develop a tractable model system with which to test a. How novel sym-plasmid acquisition impacts the fitness and symbiotic performance of rhizobia and b. What evolutionary processes are required to ameliorate and/or optimise this relationship. These key insights will allow us to develop these ideas into larger research avenues. Central to this will be the development of a multi sym-plasmid/bacteria model system which will be vital to future work expanding this research field. Future work will include, for example, a detailed analysis of the mechanisms limiting sym-plasmid transfer. The outputs from this project will feed directly into this by identifying targets of selection in resolving barriers to sym-plasmid transfer. Gene knockout/knockdown experiments can then be used to investigate these targets, exploring the mechanistic basis for these barriers. Other major avenues of research will investigate the ecological drivers of sym-plasmid mobility. For example, a key hypothesis for the maintenance of sym-plasmid HGT is that rhizobial diversity is beneficial e.g. in diverse legume populations where the host environment is unpredictable. Future grants would draw on findings from this study to investigate what conditions favour the persistence of sym gene HGT. Understanding the role of diversity, its barriers and the processes that overcome them will be important for developing strategies for legume crop production. Legumes (e.g. soya) grown outside their native ranges are inoculated with 1-2 strains of rhizobia but alternative strategies - such as increasing inoculant diversity or even 'selective breeding' of local rhizobia populations through sym gene HGT could be more effective.