Genome-resolved metagenomics reveals lineage-specific metabolic strategies within marine nitrifier subpopulations

Nitrification in the marine environment is predominantly attributed to two microbial groups: ammonia-oxidizing archaea of the phylum Thaumarchaeota and nitrite-oxidizing Nitrospinae bacteria. Recent biogeochemical and ‘omic-based analyses have established these two groups of nitrifiers as important players in the marine carbon cycle as well as the nitrogen cycle. Various sub-lineages have been described for each phylum in the marine realm that are suggested to inhabit distinct niche spaces within the water column. However, features that confer the ability to occupy differing nutrient and/or physicochemical regimes in the pelagic environment to each subgroup are largely unknown.

Here we present a comparative genomic analysis of metagenome-assembled genomes (MAGs) belonging to major uncultured lineages within marine Thaumarchaeota and Nitrospinae, assembled from metagenomes obtained from Monterey Bay, an upwelling-influenced, non-estuarine embayment on the central coast of California. We highlight differences in metabolic potential and nutrient acquisition strategies among lineages and examine the expression profiles of each MAG during a spring upwelling period in Monterey Bay. Our results significantly expand our understanding of the metabolic diversity and versatility of subgroups within the two phyla, with important implications for nutrient cycling in the coastal ocean.