Diversity and distribution of archaeal and bacterial nitrifiers in deep oceans

Thaumarchaeota and Nitrospinae are the main drivers of nitrification in global oceans. However, their vertical and horizontal distributions throughout seawater columns remain unclear. Here, we conducted high-throughput sequencing of 16S rRNA genes and quantified putative nitrifying genes of microbial communities within seawater samples from the full depths of the Central Indian Ocean and the Western Pacific Ocean waters. Thaumarchaeota and Nitrospinae exhibited clear compositional distinctions between the two oceanic regions. Vertical variation in their assemblages was also apparent among all samples and within regions. However, their core operational taxonomic units (OTUs) were shared between the two regions and belonged to diverse phylogenetic clades that coincided with specific vertical niches. Further, their relative abundances were significantly and positively associated with Acidobacteriota, SAR324, Chloroflexi, and SAR406 phyla across and within regions, suggesting potential metabolic interactions. Regardless of oceanic regions, the maximal copy numbers of Thaumarchaeotal 16S rRNA and ammonia monooxygenase subunit A genes were both observed at 150-200 m depth, approximately overlapping with the primary nitrite maximum (PNM, 150 m), just below the deep chlorophyll a maximum (DCM, 125 m and 150 m); the maximal Nitrospina 16S rRNA gene copy numbers were located deeper (500 m), where nitrate concentrations had already increased.