Leibniz Institute DSMZ-German Collection of Cell Microorganisms and Cell Cultures GmbH, D-38124 Braunschweig, Germany.
Institute of Hydrobiology, Biology Center CAS, Na Sádkách 7, 37005 České Budejovice, Czech Republic.
Sci Adv. 2023 Feb 3;9(5):eadc9392. doi: 10.1126/sciadv.adc9392. Epub 2023 Feb 1.
Ammonia-oxidizing archaea (AOA) play a key role in the aquatic nitrogen cycle. Their genetic diversity is viewed as the outcome of evolutionary processes that shaped ancestral transition from terrestrial to marine habitats. However, current genome-wide insights into AOA evolution rarely consider brackish and freshwater representatives or provide their divergence timeline in lacustrine systems. An unbiased global assessment of lacustrine AOA diversity is critical for understanding their origins, dispersal mechanisms, and ecosystem roles. Here, we leveraged continental-scale metagenomics to document that AOA species diversity in freshwater systems is remarkably low compared to marine environments. We show that the uncultured freshwater AOA, " Nitrosopumilus limneticus," is ubiquitous and genotypically static in various large European lakes where it evolved 13 million years ago. We find that extensive proteome remodeling was a key innovation for freshwater colonization of AOA. These findings reveal the genetic diversity and adaptive mechanisms of a keystone species that has survived clonally in lakes for millennia.
氨氧化古菌（AOA）在水生氮循环中发挥着关键作用。它们的遗传多样性被视为塑造从陆地到海洋栖息地的祖先过渡的进化过程的结果。然而，目前对 AOA 进化的全基因组研究很少考虑到半咸水和淡水代表，也没有提供它们在湖泊系统中的分歧时间线。对湖泊 AOA 多样性进行无偏的全球评估对于了解它们的起源、扩散机制和生态系统角色至关重要。在这里，我们利用大陆尺度的宏基因组学来记录淡水系统中的 AOA 物种多样性与海洋环境相比显著较低。我们表明，未培养的淡水 AOA“Nitrosopumilus limneticus”在各种大型欧洲湖泊中普遍存在且基因型稳定，这些湖泊中的 AOA 是在 1300 万年前进化而来的。我们发现，广泛的蛋白质组重塑是 AOA 成功在淡水中定殖的关键创新。这些发现揭示了一个在湖泊中已经克隆生存了数千年的关键物种的遗传多样性和适应机制。
