Nitrososphaerota

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[14] and National Center for Biotechnology Information (NCBI)[15]

• Class Nitrososphaeria Stieglmeier et al. 2014[16] [Conexivisphaeria Kato et al. 2020]
  •  ?"Cenoporarchaeum" corrig. Zhang et al. 2019
  •  ?"Candidatus Giganthauma" Muller et al. 2010[17]
  • Order "Geothermarchaeales"
  • Order Conexivisphaerales Kato et al. 2020
    • Family Conexivisphaeraceae Kato et al. 2020
      • Conexivisphaera Kato et al. 2020
  • Order "Nitrosocaldales" de la Torre et al. 2008
    • Family "Nitrosocaldaceae" Qin et al. 2016
      •  ?"Candidatus Nitrosothermus" Luo et al. 2021
      • "Candidatus Nitrosocaldus" de la Torre et al. 2008
  • Order Nitrososphaerales Stieglmeier et al. 2014
    • Family Methylarchaceae Hua et al. 2019
      •  ?"Candidatus Methylarchaeum" Hua et al. 2019
    • Family Nitrososphaeraceae Stieglmeier et al. 2014
      • "Candidatus Nitrosocosmicus" Lehtovirta-Morley et al. 2016
      • Nitrososphaera Stieglmeier et al. 2014[18]
  • Order Nitrosopumilales Qin et al. 2017[19]
    • Family Nitrosopumilaceae Qin et al. 2017
      •  ?"Candidatus Nitrosospongia" Moeller et al. 2019
      • "Candidatus Nitrosotalea" Lehtovirta 2011[20]
      • "Candidatus Nitrosotenuis" Li et al. 2016[21][22]
      • "Candidatus Nitrosopelagicus" Santoro et al. 2015[23]
      • "Cenarchaeum" DeLong & Preston 1996
      • Nitrosarchaeum corrig. Jung et al. 2018[24][25]
      • Nitrosopumilus Qin et al. 2017[26][27][28]

Nitrososphaerota are important ammonia oxidizers in aquatic and terrestrial environments, and are the first archaea identified as being involved in nitrification.[29] They are capable of oxidizing ammonia at much lower substrate concentrations than ammonia-oxidizing bacteria, and so probably dominate in oligotrophic conditions.[8][30] Their ammonia oxidation pathway requires less oxygen than that of ammonia-oxidizing bacteria, so they do better in environments with low oxygen concentrations like sediments and hot springs. Ammonia-oxidizing Nitrososphaerota can be identified metagenomically by the presence of archaeal ammonia monooxygenase (amoA) genes, which indicate that they are overall more dominant than ammonia oxidizing bacteria.[8] In addition to ammonia, at least one Nitrososphaerota strain has been shown to be able to use urea as a substrate for nitrification. This would allow for competition with phytoplankton that also grow on urea.[31] 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.[32] Marine Nitrososphaerota have also been shown to produce nitrous oxide, which as a greenhouse gas has implications for climate change. Isotopic analysis indicates that most nitrous oxide flux to the atmosphere from the ocean, which provides around 30% of the natural flux, may be due to the metabolic activities of archaea.[33]

Many members of the phylum assimilate carbon by fixing HCO₃⁻.[9] This is done using a hydroxypropionate/hydroxybutyrate cycle similar to the Thermoproteota but which appears to have evolved independently. All Nitrososphaerota that have been identified by metagenomics thus far encode this pathway. Notably, the Nitrososphaerota CO₂-fixation pathway is more efficient than any known aerobic autotrophic pathway. This efficiency helps explain their ability to thrive in low-nutrient environments.[30] Some Nitrososphaerota such as Nitrosopumilus maritimus are able to incorporate organic carbon as well as inorganic, indicating a capacity for mixotrophy.[9] At least two isolated strains have been identified as obligate mixotrophs, meaning they require a source of organic carbon in order to grow.[31]

A study has revealed that Nitrososphaerota are most likely the dominant producers of the critical vitamin B12. 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. Because of the importance of vitamin B₁₂ in biological processes such as the citric acid cycle and DNA synthesis, production of it by the Nitrososphaerota may be important for a large number of aquatic organisms.[34]

Many Nitrososphaerota, such as Nitrosopumilus maritimus, are marine and live in the open ocean.[9] Most of these planktonic Nitrososphaerota, which compose the Marine Group I.1a, are distributed in the subphotic zone, between 100m and 350m.[7] Other marine Nitrososphaerota live in shallower waters. One study has identified two novel Nitrososphaerota species living in the sulfidic environment of a tropical mangrove swamp. Of these two species, Candidatus Giganthauma insulaporcus and Candidatus Giganthauma karukerense, the latter is associated with Gammaproteobacteria with which it may have a symbiotic relationship, though the nature of this relationship is unknown. The two species are very large, forming filaments larger than ever before observed in archaea. As with many Nitrososphaerota, they are mesophilic.[35] Genetic analysis and the observation that the most basal identified Nitrososphaerota genomes are from hot environments suggests that the ancestor of Nitrososphaerota was thermophilic, and mesophily evolved later.[29]

• Eocyte hypothesis