PDF(Pubmed)
Abstract：
The evolutionary trajectory of Methylophilaceae includes habitat transitions from freshwater sediments to freshwater and marine pelagial that resulted in genome reduction (genome-streamlining) of the pelagic taxa. However, the extent of genetic similarities in the genomic structure and microdiversity of the two genome-streamlined pelagic lineages (freshwater \"Ca. Methylopumilus\" and the marine OM43 lineage) has so far never been compared. Here, we analyzed complete genomes of 91 \"Ca. Methylopumilus\" strains isolated from 14 lakes in Central Europe and 12 coastal marine OM43 strains. The two lineages showed a remarkable niche differentiation with clear species-specific differences in habitat preference and seasonal distribution. On the other hand, we observed a synteny preservation in their genomes by having similar locations and types of flexible genomic islands (fGIs). Three main fGIs were identified: a replacement fGI acting as phage defense, an additive fGI harboring metabolic and resistance-related functions, and a tycheposon containing nitrogen-, thiamine-, and heme-related functions. The fGIs differed in relative abundances in metagenomic datasets suggesting different levels of variability ranging from strain-specific to population-level adaptations. Moreover, variations in one gene seemed to be responsible for different growth at low substrate concentrations and a potential biogeographic separation within one species. Our study provides a first insight into genomic microdiversity of closely related taxa within the family Methylophilaceae and revealed remarkably similar dynamics involving mobile genetic elements and recombination between freshwater and marine family members.
摘要：
嗜甲基科的进化轨迹包括从淡水沉积物到淡水和海洋上层的栖息地过渡，这导致了上层类群的基因组减少（基因组精简）。然而,两个基因组流线型上层谱系（淡水“Ca。Methypumilus\“和海洋OM43谱系）迄今为止从未进行过比较。这里,我们分析了91“Ca的完整基因组。从中欧14个湖泊和12个沿海海洋OM43菌株中分离出的甲虫菌株。这两个谱系显示出明显的生态位分化，在栖息地偏好和季节分布方面具有明显的物种特异性差异。另一方面,通过具有相似的位置和类型的柔性基因组岛（fGI），我们观察到它们基因组中的同伦保存。确定了三个主要的fGI：替代fGI充当噬菌体防御，具有代谢和抗性相关功能的添加剂fGI，和一个含氮的typeposon-，硫胺素-,和血红素相关的功能。在宏基因组数据集中，fGI的相对丰度有所不同，这表明从菌株特异性到种群水平适应的变异性水平不同。此外，一个基因的变异似乎是在低底物浓度下生长不同的原因，以及一个物种内潜在的生物地理分离。我们的研究首次了解了嗜甲基科内密切相关的分类单元的基因组微多样性，并揭示了涉及移动遗传元件以及淡水和海洋家族成员之间重组的非常相似的动力学。
