Marine sediments represent a vast habitat for complex microbiomes. Among these, ammonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are one of the most common, yet little explored, inhabitants, which seem extraordinarily well adapted to the harsh conditions of the subsurface biosphere. We present 11 metagenome-assembled genomes of the most abundant AOA clades from sediment cores obtained from the Atlantic Mid-Ocean ridge flanks and Pacific abyssal plains. Their phylogenomic placement reveals three independently evolved clades within the order Nitrosopumilales, of which no cultured representative is known yet. In addition to the gene sets for ammonia oxidation and carbon fixation known from other AOA, all genomes encode an extended capacity for the conversion of fermentation products that can be channeled into the central carbon metabolism, as well as uptake of amino acids probably for protein maintenance or as an ammonia source. Two lineages encode an additional (V-type) ATPase and a large repertoire of DNA repair systems that may allow to overcome the challenges of high hydrostatic pressure. We suggest that the adaptive radiation of AOA into marine sediments occurred more than once in evolution and resulted in three distinct lineages with particular adaptations to this extremely energy-limiting and high-pressure environment.

海洋沉积物代表了复杂微生物群落的广阔栖息地。其中，奇古菌门的氨氧化古细菌 (AOA) 是最常见但鲜为人知的生物之一，它们似乎非常适应地下生物圈的严酷条件。我们展示了从大西洋中洋脊侧翼和太平洋深海平原获得的沉积岩芯中最丰富的 AOA 进化枝的 11 个宏基因组组装基因组。它们的系统发育位置揭示了Nitrosopumiles 目内三个独立进化的进化枝，其中尚无文化代表。除了其他 AOA 已知的用于氨氧化和碳固定的基因组外，所有基因组都编码了发酵产物转化的扩展能力，这些发酵产物可以被引导到中心碳代谢中，以及可能用于蛋白质维持的氨基酸摄取或作为氨源。两个谱系编码一个额外的（V 型）ATP 酶和大量 DNA 修复系统，可以克服高静水压力的挑战。我们认为，AOA 对海洋沉积物的适应性辐射在进化过程中不止一次发生，并导致三个不同的谱系对这种极端能量限制和高压环境具有特殊的适应性。