The SAR11 clade of Alphaproteobacteria is the most abundant group of planktonic cells in the near-surface epipelagic waters of the ocean, but the mechanisms underlying its exceptional success have not been fully elucidated. Here, we applied a metagenomic approach to explore microdiversity patterns by measuring the accumulation of synonymous and nonsynonymous mutations as well as homologous recombination in populations of SAR11 from different aquatic habitats (marine epipelagic, bathypelagic, and surface freshwater). The patterns of mutation accumulation and recombination were compared to those of other groups of representative marine microbes with multiple ecological strategies that share the same marine habitat, namely, Cyanobacteria (Prochlorococcus and Synechococcus), Archaea (“Candidatus Nitrosopelagicus” and Marine Group II Thalassoarchaea), and some heterotrophic marine bacteria (Alteromonas and Erythrobacter). SAR11 populations showed widespread recombination among distantly related members, preventing divergence leading to a genetically stable population. Moreover, their high intrapopulation sequence diversity with an enrichment in synonymous replacements supports the idea of a very ancient divergence and the coexistence of multiple different clones. However, other microbes analyzed seem to follow different evolutionary dynamics where processes of diversification driven by geographic and ecological instability produce a higher number of nonsynonymous replacements and lower intrapopulation sequence diversity. Together, these data shed light on some of the evolutionary and ecological processes that lead to the large genomic diversity in SAR11. Furthermore, this approach can be applied to other similar microbes that are difficult to culture in the laboratory, but abundant in nature, to investigate the underlying dynamics of their genomic evolution.

中文翻译：

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从宏基因组角度分析海洋细菌 SAR11 的进化成功

Alphaproteobacteria的 SAR11 进化枝是海洋近地表上层水域中最丰富的浮游细胞群，但其非凡成功的机制尚未完全阐明。在这里，我们应用宏基因组方法通过测量来自不同水生栖息地（海洋上层、深海和表层淡水）的 SAR11 种群中同义和非同义突变的积累以及同源重组来探索微多样性模式。将突变积累和重组的模式与其他具有多种生态策略、共享相同海洋栖息地的代表性海洋微生物的模式进行比较，即蓝细菌（原绿球藻和蓝细菌），古（“暂定Nitrosopelagicus”和海洋集团II Thalassoarchaea），以及一些异养海洋细菌（交替单胞菌和赤）。SAR11 种群在远亲成员之间表现出广泛的重组，防止了导致遗传稳定种群的分歧。此外，它们的高种群内序列多样性以及同义替换的丰富性支持了非常古老的分歧和多个不同克隆共存的想法。然而，分析的其他微生物似乎遵循不同的进化动力学，其中由地理和生态不稳定性驱动的多样化过程产生更多的非同义替换和较低的种群内序列多样性。总之，这些数据揭示了导致 SAR11 中大量基因组多样性的一些进化和生态过程。此外，