Ammonia-oxidizing archaea (AOA) are ubiquitous canonical chemolithoautotrophs that contribute to global nitrogen and carbon cycles. In marine environments, AOA are mainly represented by the members of the family Nitrosopumilaceae, yet their diversity, activity, and ecological differentiation in coastal wetlands remain incompletely resolved, especially in oxygen-limited sediments. This gap is particularly relevant to intertidal wetlands, where steep gradients in salinity, oxygen, organic matter, and porewater exchange create biogeochemically active interfaces for nitrogen transformation.
In a recent genome-resolved metagenomic study of saltmarsh intertidal aquifers in the Yancheng Coastal Wetland, China, we identified a previously overlooked AOA genus, Candidatus Nitrosomaritimum. By integrating phylogenomics, amoA gene phylogeny, metatranscriptomics, and amoA amplicon profiling, we showed that Nitrosomaritimum is an abundant and active AOA group broadly distributed across estuarine-coastal environments and marine sediments. Comparative genomics suggested adaptation to diffusion-limited intertidal aquifers, including capacities for urea utilization, phosphate acquisition via Pst or Phn transporters, and a putative nitrous oxide reductase that may contribute to N₂O reduction in an anoxic ammonia oxidation pathway coupled with intracellular oxygen production.
Despite this progress, the ecological role of Nitrosomaritimum has likely been underestimated because of taxonomic bias in marker-gene databases and the lack of lineage-specific quantification tools. By integrating SILVA 16S rRNA references with genome-derived GTDB sequences, we refined the phylogeny of Nitrosopumilaceae and identified a monophyletic Nitrosomaritimum clade. This corrected the mis-annotation of ~16% of SILVA references previously assigned to Nitrosopumilus. Based on this refined taxonomy, we developed a 16S rRNA gene classifier and a specific amoA qPCR primer set (AOAnm3bF-AOAnm3aR) for sensitive relative and absolute quantification of Nitrosomaritimum. Applying this integrated toolkit to intertidal wetlands revealed clear niche differentiation: Nitrosopumilus predominated in oxygenated seawater, whereas Nitrosomaritimum was enriched in anoxic, diffusion-limited coastal sediments, indicating distinct redox and hydrological niches. This pattern suggests that sediment-adapted AOA lineages may play disproportionate roles in ammonia oxidation, nitrogen retention, and nitrogen loss at land-ocean interfaces.
Together, our findings bridge the genome-resolved discovery of Nitrosomaritimum with quantitative ecological validation across marker-gene and functional-gene scales. This work revises a long-standing taxonomic bias in marine AOA research, clarifies the hidden contribution of Nitrosomaritimum to nitrogen transformation in coastal sediments, and provides a transferable strategy for resolving microbial lineages whose ecological importance is masked by incomplete reference taxonomy.

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