Metapopulation dominance and genomic-island acquisition of Bradyrhizobium with superior catabolic capabilities

Root nodule forming rhizobia exhibit a bipartite lifestyle, replicating in soil and also within plant cells where they fix nitrogen for legume hosts. Host control models posit that legume hosts act as a predominant selective force on rhizobia, but few studies have examined rhizobial fitness in natural populations. Here, we genotyped and phenotyped Bradyrhizobium isolates across >800km of the native Acmispon strigosus host range. We sequenced chromosomal genes expressed under free-living conditions and accessory symbiosis loci expressed in planta and encoded on an integrated ‘symbiosis island’. We uncovered a massive clonal expansion restricted to the Bradyrhizobium chromosome, with a single chromosomal haplotype dominating populations, ranging >700km, and acquiring 42 divergent symbiosis island haplotypes, none of which were spatially widespread. For focal genotypes we quantified utilization of 190 sole-carbon sources relevant to soil fitness. Chromosomal haplotypes that were both...

结瘤根瘤菌（root nodule-forming rhizobia）具有两阶段生活史，既能在土壤中增殖，也能在植物细胞内为豆科宿主固氮。宿主控制模型（host control models）提出，豆科宿主是根瘤菌的主要选择压力来源，但目前鲜有研究考察自然种群中的根瘤菌适合度。本研究对分布在原生宿主细茎山黧豆（Acmispon strigosus）超过800公里分布范围内的慢生根瘤菌（Bradyrhizobium）分离株进行了基因分型与表型鉴定。我们对自由生活状态下表达的染色体基因，以及在植物体内表达、整合于"共生岛（symbiosis island）"上的附属共生基因座进行了测序。研究发现了一次局限于慢生根瘤菌染色体的大规模克隆扩张：单一染色体单倍型在种群中占据主导地位，分布范围超过700公里，并演化出42种不同的共生岛单倍型，这些单倍型均未出现空间上的广泛传播。针对核心基因型，我们量化了190种与土壤适合度相关的唯一碳源利用情况。染色体单倍型同时...