Kopac Sarah, Wang Zhang, Wiedenbeck Jane, Sherry Jessica, Wu Martin, Cohan Frederick M
Department of Biology, Wesleyan University, Middletown, Connecticut, USA.
Department of Biology, University of Virginia, Charlottesville, Virginia, USA.
Appl Environ Microbiol. 2014 Aug;80(16):4842-53. doi: 10.1128/AEM.00576-14. Epub 2014 Jun 6.
Closely related bacterial genomes usually differ in gene content, suggesting that nearly every strain in nature may be ecologically unique. We have tested this hypothesis by sequencing the genomes of extremely close relatives within a recognized taxon and analyzing the genomes for evidence of ecological distinctness. We compared the genomes of four Death Valley isolates plus the laboratory strain W23, all previously classified as Bacillus subtilis subsp. spizizenii and hypothesized through multilocus analysis to be members of the same ecotype (an ecologically homogeneous population), named putative ecotype 15 (PE15). These strains showed a history of positive selection on amino acid sequences in 38 genes. Each of the strains was under a different regimen of positive selection, suggesting that each strain is ecologically unique and represents a distinct ecological speciation event. The rate of speciation appears to be much faster than can be resolved with multilocus sequencing. Each PE15 strain contained unique genes known to confer a function for bacteria. Remarkably, no unique gene conferred a metabolic system or subsystem function that was not already present in all the PE15 strains sampled. Thus, the origin of ecotypes within this clade shows no evidence of qualitative divergence in the set of resources utilized. Ecotype formation within this clade is consistent with the nanoniche model of bacterial speciation, in which ecotypes use the same set of resources but in different proportions, and genetic cohesion extends beyond a single ecotype to the set of ecotypes utilizing the same resources.
亲缘关系密切的细菌基因组通常在基因内容上存在差异，这表明自然界中几乎每一个菌株在生态上可能都是独特的。我们通过对一个公认分类单元内的极近缘菌株的基因组进行测序，并分析基因组以寻找生态差异的证据，来检验这一假设。我们比较了四个死亡谷分离株以及实验室菌株W23的基因组，所有这些菌株先前都被归类为枯草芽孢杆菌斯皮兹亚种，并通过多位点分析推测为同一生态型（一个生态上同质的群体）的成员，命名为假定生态型15（PE15）。这些菌株在38个基因的氨基酸序列上显示出正选择的历史。每个菌株都处于不同的正选择模式下，这表明每个菌株在生态上都是独特的，代表了一个独特的生态物种形成事件。物种形成的速度似乎比多位点测序所能解析的要快得多。每个PE15菌株都包含已知赋予细菌功能的独特基因。值得注意的是，没有一个独特基因赋予所有采样的PE15菌株中都不存在的代谢系统或子系统功能。因此，该进化枝内生态型的起源没有显示出在利用的资源集上存在质的差异的证据。该进化枝内的生态型形成与细菌物种形成的纳米生态位模型一致，在该模型中，生态型使用相同的资源集，但比例不同，并且遗传凝聚力超出单个生态型，延伸到利用相同资源的一组生态型。
