[2] The phylum was proposed in 2008 based on phylogenetic data, such as the sequences of these organisms' ribosomal RNA genes, and the presence of a form of type I topoisomerase that was previously thought to be unique to the eukaryotes.

[2][5] This assignment was confirmed by further analysis published in 2010 that examined the genomes of the ammonia-oxidizing archaea Nitrosopumilus maritimus and Nitrososphaera gargensis, concluding that these species form a distinct lineage that includes Cenarchaeum symbiosum.

Nitrosopelagicus" "Cenarchaeum" Nitrosarchaeum Nitrosopumilus The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[17] and National Center for Biotechnology Information (NCBI)[18] Nitrososphaerota are important ammonia oxidizers in aquatic and terrestrial environments, and are the first archaea identified as being involved in nitrification.

[32] They are capable of oxidizing ammonia at much lower substrate concentrations than ammonia-oxidizing bacteria, and so probably dominate in oligotrophic conditions.

[34] One study of microbes from wastewater treatment plants found that not all Nitrososphaerota that express amoA genes are active ammonia oxidizers.

These Nitrososphaerota may be capable of oxidizing methane instead of ammonia, or they may be heterotrophic, indicating a potential for a diversity of metabolic lifestyles within the phylum.

[35] Marine Nitrososphaerota have also been shown to produce nitrous oxide, which as a greenhouse gas has implications for climate change.

[9] At least two isolated strains have been identified as obligate mixotrophs, meaning they require a source of organic carbon in order to grow.

This finding has important implications for eukaryotic phytoplankton, many of which are auxotrophic and must acquire vitamin B12 from the environment; thus the Nitrososphaerota could play a role in algal blooms and by extension global levels of atmospheric carbon dioxide.