Microbial nitrification is a critical process governing nitrogen availability in aquatic systems. Freshwater nitrifiers have received little attention, leaving many unanswered questions about their taxonomic distribution, functional potential, and ecological interactions. Here, we reconstructed genomes to infer the metabolism and ecology of free-living picoplanktonic nitrifiers across the Laurentian Great Lakes, a connected series of five of Earth’s largest lakes. Surprisingly, ammonia oxidizing Bacteria (AOB) related to Nitrosospira dominated over ammonia oxidizing Archaea (AOA) at nearly all stations, with distinct ecotypes prevailing in the transparent, oligotrophic upper lakes compared to Lakes Erie and Ontario. Unexpectedly, one ecotype of Nitrosospira encodes proteorhodopsin, which could enhance survival in conditions where ammonia oxidation is inhibited or substrate limited. Nitrite oxidizing Bacteria (NOB) Ca. Nitrotoga and Nitrospira fluctuated in dominance, with the latter prevailing in deeper, less productive basins. Genome reconstructions reveal highly reduced genomes and features consistent with genome streamlining, along with diverse adaptations to sunlight and oxidative stress and widespread capacity for organic nitrogen use. Our findings expand the known functional diversity of nitrifiers and establish their ecological genomics in large lake ecosystems. By elucidating links between microbial biodiversity and biogeochemical cycling, our work also informs ecosystem models of the Laurentian Great Lakes, a critical freshwater resource experiencing rapid environmental change.

中文翻译：

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淡水硝化菌中的基因组精简、蛋白视紫红质和有机氮代谢

微生物硝化作用是控制水生系统中氮可用性的关键过程。淡水硝化菌很少受到关注，在它们的分类分布、功能潜力和生态相互作用方面留下了许多悬而未决的问题。在这里，我们重建了基因组，以推断 Laurentian 五大湖（地球上五个最大的湖泊的一系列相连）中自由生活的微型浮游硝化菌的代谢和生态。令人惊讶的是，与亚硝化螺旋体相关的氨氧化细菌 (AOB)在几乎所有站点上均占氨氧化古细菌 (AOA) 的主导地位，与伊利湖和安大略湖相比，在透明、贫营养的上层湖泊中普遍存在不同的生态型。出乎意料的是，亚硝化螺属的一种生态型编码视紫红质蛋白，它可以在氨氧化受到抑制或底物有限的条件下提高存活率。亚硝酸盐氧化细菌 (NOB) Ca。Nitrotoga 和Nitrospira主导地位波动，后者盛行于更深、生产力较低的盆地。基因组重建揭示了高度减少的基因组和与基因组精简一致的特征，以及对阳光和氧化应激的不同适应以及有机氮使用的广泛能力。我们的发现扩展了硝化菌的已知功能多样性，并在大型湖泊生态系统中建立了它们的生态基因组学。通过阐明微生物多样性与生物地球化学循环之间的联系，我们的工作还为劳伦大湖的生态系统模型提供了信息，劳伦大湖是一个正在经历快速环境变化的重要淡水资源。