Competitiveness prediction for nodule colonization in Sinorhizobium meliloti through combined in vitro tagged strain characterization and genome-wide association analysis

Associations between leguminous plants and symbiotic nitrogen-fixing rhizobia are a classic example of mutualism between a eukaryotic host and a specific group of prokaryotic microbes. Although this symbiosis is in part species-specific, different rhizobial strains may colonise the same nodule. Some rhizobial strains are commonly known as better competitors than others, but detailed analyses that aim to predict rhizobial competitive abilities based on genomes are still scarce. Here, we performed a bacterial genome-wide association (GWAS) analysis to define the genomic determinants related to the competitive capabilities in the model rhizobial species Sinorhizobium meliloti. For this, 13 tester strains were GFP-tagged and assayed vs. 3 RFP-tagged reference competitor strains (Rm1021, AK83, and BL225C) in a Medicago sativa nodule occupancy test. Competition data and strain genomic sequences were employed to build a model for GWAS based on k-mers. Among the k-mers with the highest scores, ...

豆科植物与共生固氮根瘤菌之间的共生关系，是真核宿主与特定原核微生物类群间互利共生的经典范例。尽管该共生关系在一定程度上具有物种特异性，但不同的根瘤菌菌株可定植于同一根瘤中。部分根瘤菌菌株通常被认为比其他菌株具有更强的竞争能力，但目前旨在通过基因组预测根瘤菌竞争能力的详细分析仍较为匮乏。本研究针对模式根瘤菌物种苜蓿中华根瘤菌（Sinorhizobium meliloti），开展细菌全基因组关联分析（Genome-Wide Association Study, GWAS），以明确与其竞争能力相关的基因组决定因子。为此，我们对13株待测菌株进行绿色荧光蛋白（Green Fluorescent Protein, GFP）标记，并与3株红色荧光蛋白（Red Fluorescent Protein, RFP）标记的参比竞争菌株（Rm1021、AK83及BL225C）在紫花苜蓿（Medicago sativa）根瘤定殖试验中开展竞争测定。我们利用竞争试验数据与菌株基因组序列，构建了基于k聚体（k-mers）的全基因组关联分析模型。在得分最高的k聚体中，……