Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow
Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow
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DOI：
10.1038/s41396-020-0655-x
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发表时间：
2020-04-23
期刊：
影响因子：
11
通讯作者：
Banfield, Jillian F.
中科院分区：
文献类型：
--
作者：
Crits-Christoph, Alexander;Olm, Matthew R.;Banfield, Jillian F.
土壤微生物多样性通常从群落组成的角度进行研究，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数量丰富但很少栽培的土壤微生物的相对影响尚不清楚。在这里，我们跟踪了从草原草甸采集的19种高度丰富的细菌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，这些测序读数从头开始组装成来自元基因组的共识基因组，因为每个读取对描述了来自每个种群中的一个细胞的短基因组序列。对于所研究的种群中，超过一半的种群的基因组核苷酸同源性与当地地理显著相关，对于大多数种群而言，样本内的核苷酸多样性往往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胞外运输的基因在多个物种中具有核苷酸多样性增加的特点。微生物种群表现出不同程度的同源重组，重组变异体经常在全基因组7-36%的基因座上被检测到。在多个群体中，我们发现了等位基因空间分化异常高、重组事件较少、非同义变种与同义变种比率升高、核苷酸多样性较低的基因，这表明最近对基因变种的选择性扫描。综上所述，这些结果表明，重组和基因特异性选择共同形成了几个未被研究的土壤细菌谱系的遗传变异。
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.