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Background  Marine Group I (MGI)  Thaumarchaeota , which play key roles in the global biogeochemical cycling of nitrogen and carbon (ammonia oxidizers), thrive in the aphotic deep sea with massive populations. Recent studies have revealed that MGI  Thaumarchaeota  were present in the deepest part of oceans—the hadal zone (depth > 6000 m, consisting almost entirely of trenches), with the predominant phylotype being distinct from that in the “shallower” deep sea. However, little is known about the metabolism and distribution of these ammonia oxidizers in the hadal water.    Results  In this study, metagenomic data were obtained from 0–10,500 m deep seawater samples from the Mariana Trench. The distribution patterns of  Thaumarchaeota  derived from metagenomics and 16S rRNA gene sequencing were in line with that reported in previous studies: abundance of  Thaumarchaeota  peaked in bathypelagic zone (depth 1000–4000 m) and the predominant clade shifted in the hadal zone. Several metagenome-assembled thaumarchaeotal genomes were recovered, including a near-complete one representing the dominant hadal phylotype of MGI. Using comparative genomics, we predict that unexpected genes involved in bioenergetics, including two distinct ATP synthase genes (predicted to be coupled with H +  and Na +  respectively), and genes horizontally transferred from other extremophiles, such as those encoding putative di-myo-inositol-phosphate (DIP) synthases, might significantly contribute to the success of this hadal clade under the extreme condition. We also found that hadal MGI have the genetic potential to import a far higher range of organic compounds than their shallower water counterparts. Despite this trait, hadal MDI ammonia oxidation and carbon fixation genes are highly transcribed providing evidence they are likely autotrophic, contributing to the primary production in the aphotic deep sea.    Conclusions  Our study reveals potentially novel adaptation mechanisms of deep-sea thaumarchaeotal clades and suggests key functions of deep-sea  Thaumarchaeota  in carbon and nitrogen cycling.Video Abstract

Novel insights into the Thaumarchaeota in the deepest oceans: their metabolism and potential adaptation mechanisms