Soil microbial diversity is often studied from the perspective of community composition, but less is known about genetic heterogeneity within species. The relative impacts of clonal interference, gene-specific selection, and recombination in many abundant but rarely cultivated soil microbes remain unknown. Here we track genome-wide population genetic variation for 19 highly abundant bacterial species sampled from across a grassland meadow. Genomic inferences about population structure are made using the millions of sequencing reads that are assembled de novo into consensus genomes from metagenomes, as each read pair describes a short genomic sequence from a cell in each population. Genomic nucleotide identity of assembled genomes was significantly associated with local geography for over half of the populations studied, and for a majority of populations within-sample nucleotide diversity could often be as high as meadow-wide nucleotide diversity. Genes involved in metabolite biosynthesis and extracellular transport were characterized by elevated nucleotide diversity in multiple species. Microbial populations displayed varying degrees of homologous recombination and recombinant variants were often detected at 7-36% of loci genome-wide. Within multiple populations we identified genes with unusually high spatial differentiation of alleles, fewer recombinant events, elevated ratios of nonsynonymous to synonymous variants, and lower nucleotide diversity, suggesting recent selective sweeps for gene variants. Taken together, these results indicate that recombination and gene-specific selection commonly shape genetic variation in several understudied soil bacterial lineages.

中文翻译：

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土壤细菌种群是通过草地草地的重组和基因特异性选择形成的。

通常从群落组成的角度研究土壤微生物多样性，但对物种内的遗传异质性知之甚少。克隆干扰、基因特异性选择和重组对许多丰富但很少栽培的土壤微生物的相对影响仍然未知。在这里，我们跟踪从草地上采样的 19 种高度丰富的细菌物种的全基因组种群遗传变异。关于种群结构的基因组推断是使用数百万个测序读数进行的，这些读数从头组装成来自宏基因组的共有基因组，因为每个读数对描述了来自每个种群中一个细胞的短基因组序列。对于超过一半的研究人群，组装基因组的基因组核苷酸身份与当地地理显着相关，对于样本内的大多数种群而言，核苷酸多样性通常可能与草甸范围内的核苷酸多样性一样高。参与代谢物生物合成和细胞外转运的基因的特点是多个物种中核苷酸多样性升高。微生物种群表现出不同程度的同源重组，重组变体通常在全基因组基因座的 7-36% 处检测到。在多个人群中，我们鉴定出具有异常高的等位基因空间分化、较少重组事件、升高的非同义变体与同义变体的比率以及较低的核苷酸多样性的基因，这表明最近对基因变体的选择性扫描。综合起来，