我国蚕豆根瘤菌生物地理分布形成机制的泛基因组学研究

Rhizobia can establish the most efficient natural biological nitrogen-fixing system with legumes, hence playing important roles in the global nitrogen cycle and sustainable agriculture. In agricultural practice, high-efficiency nitrogen-fixing rhizobia strains are inoculated for legume crops to increase the yields, however these strains often can not compete with the indigenous ones in soil survival and competitive nodulation, resulting in poor inoculation effect. An in-depth understanding on the adaptation mechanism of rhizobia to the soil environment is the key to solving the above problems. A large number of studies have found that, rhizobia associated with any legume host usually exhibit significant biogeographical distribution at genus or species level, which strongly correlated to soil factors such as pH and salinity. So, how do rhizobia populations adapt to different soil environments through genetic variation? This has been untestable because of the lack of population genomic data with high resolution. In this proposal, by using large-scale genome sequencing and genome-wide association studys, genes involved in adaptations to different pH/salinity conditions in different populations of faba bean rhizobia, isolated from different ecoregions in China, will be identified. Further population genetics analysis will be performed for these genes to investigate the role of lateral gene transfer, recombination and natural selection in the adaptive evolution of faba bean rhizobia.

根瘤菌可以与豆科植物共生形成自然界中最高效的生物固氮体系，在全球氮循环和可持续发展农业中有重要作用。在农业实践中，人们希望通过接种高效固氮菌株来提高豆科作物的产量，但这些高效菌往往土壤存活能力和竞争结瘤能力不及土著菌，导致接种效果不佳。深入理解根瘤菌对土壤环境的适应机制是破解上述应用难题的关键。大量研究发现，与各种宿主结瘤的根瘤菌都在属种等分类水平上具有显著的生物地理分布特征，并且通常与土壤pH、含盐量等因素相关。那么，不同根瘤菌种群是如何通过遗传变异适应不同土壤环境的呢？受限于种群基因组数据的缺乏，围绕这一重要问题的深入研究一直未能展开。本项目拟利用我们前期积累的我国不同生态区蚕豆根瘤菌种质资源，通过大规模基因组测序和全基因组关联分析找出不同种群适应不同pH/含盐量条件的相关基因，并利用种群遗传学分析阐明水平转移、遗传重组和自然选择在蚕豆根瘤菌适应性进化中的作用机制。

根瘤菌-豆科植物共生体系是自然界中最高效的生物固氮系统，而农业生产中人工接种的高效固氮菌通常因为不能适应当地土壤而导致接种效果不佳。已有研究表明，土壤pH是造成根瘤菌适应性种群分化并造成其在属种水平上呈现生物地理分布特征的最关键因素之一。本项目通过基因组测序获得了120株蚕豆根瘤菌的基因组序列，通过泛基因组学分析挖掘获得了一个帮助Rhizobium anhuiense适应酸性土壤的种群特异酸适应基因岛（AFI, acid fitness island），该基因岛由19个基因组成，包含了编码精氨酸-鸟氨酸偶联脱氨降解途径跨膜转运蛋白和酶类、K+通道蛋白、H+/Ca2+通道蛋白、重金属外排蛋白和FixLK家族双组分调控蛋白等基因，遗传学实验结果表明代表菌株Ran651241缺失AFI会导致脱氨产碱能力的丧失，泛基因组水平基因gain/loss分析和基因组共线性分析表明AFI中不同基因在Rhizobium属起源之后通过多次水平基因转移事件获得并经过基因组重组而整合为功能岛，部分种群可能在后期因向偏碱性生态位迁移时丧失选择压力而发生丢失。本项目的研究工作不仅揭示了蚕豆根瘤菌适应不同pH土壤分化的遗传机制，也为通过合成生物学手段构建高抗逆、广适应工程根瘤菌提供了优秀的基因资源。