Unique phylogenies and metabolic adaptations of novel lineage III and comammox <i>Nitrospira</i> species from deep-sea sediments

The genus <i>Nitrospira</i>, which includes canonical nitrite-oxidizing bacteria (NOB) and species capable of complete ammonia oxidation (comammox), plays an important role in the global biogeochemical nitrogen cycle. Typically, lineage IV <i>Nitrospira</i> predominate in marine environments, and other lineages are thought to be less abundant and remain poorly characterized in oceanic systems. Here, we recovered five novel metagenome-assembled genomes (MAGs) affiliated with <i>Nitrospira</i> lineage II-IV from deep-sea sediments. Notably, two of these MAGs represent members of lineage III and comammox <i>Nitrospira</i>, respectively, suggesting the presence of previously uncharacterized lineages in the deep sea. Phylogenetic and gene locus analyses indicated that deep-sea lineage III and comammox <i>Nitrospira</i> form distinct evolutionary clades that diverge from their terrestrial and coastal relatives, and we therefore designate these two marine-derived groups as "lineage III clade B" and "comammox clade A4", respectively. Comparative read recruitment analyses revealed that these lineages exhibit potential pan-oceanic distribution in deep-sea sediments and waters, albeit at very low abundances. Furthermore, the identification of genes encoding <i>amtB</i>-type ammonium transporters (<i>amtB</i>), the ABC-type glycerol-3-phosphate transport system (<i>ugpABCE</i>), a multi-subunit Na⁺/H⁺ antiporter (<i>mnh</i>), and betaine transporters (<i>BetT</i>, <i>opuABC</i>) suggests that these newly discovered <i>Nitrospira</i> species possess adaptive capabilities to thrive in oligotrophic and saline marine environments. These findings provide novel insights into the occurrence, metabolic features, and adaptation strategies of lineage III and comammox <i>Nitrospira</i>, expand our understanding of <i>Nitrospira</i> diversity in the deep sea, and offer valuable perspectives on the evolutionary history of various <i>Nitrospira</i> lineages.