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The Thaumarchaeota or Thaumarchaea (from the θαῦμα) are a phylum of the Archaea proposed in 2008 after the genome of Cenarchaeum symbiosum was sequenced and found to differ significantly from other members of the hyperthermophilic phylum Crenarchaeota. Thaumarchaea can be found in both aquatic and soil environments. Three described species in addition to C. symbosium are Nitrosopumilus maritimus, Nitrososphaera viennensis, and Nitrososphaera gargensis. The phylum was proposed 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. 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. The lipid crenarchaeol has been found only in Thaumarchaea, making it a potential biomarker for the phylum. Most organisms of this lineage thus far identified are chemolithoautotrophic ammonia-oxidizers and may play important roles in biogeochemical cycles such as the nitrogen cycle and the carbon cycle. Metagenomic sequencing indicates that they constitute ~1% of the sea surface metagenome across many sites.

Thaumarchaeota-derived GDGT lipids from marine sediments can be used to reconstruct past temperatures via the TEX86 paleotemperature proxy, as these lipids vary in structure according to temperature. Because most Thaumarchaea seem to be autotrophs that fix CO2, their GDGTs can act as a record for past Carbon-13 ratios in the dissolved inorganic carbon pool, and thus have the potential to be used for reconstructions of the carbon cycle in the past.

Metabolism
Thaumarchaea are important ammonia oxidizers in aquatic and terrestrial environments. They are capable of oxidizing ammonia at much lower substrate concentrations than ammonia-oxidizing bacteria, and so probably dominate in oligotrophic conditions. 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 Thaumarchaea 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. It has been suggested that some Thaumarchaea may use substrates other than ammonia for energy or may even be heterotrophs. One study of microbes from wastewater treatment plants found that not all Thaumarchaea that express amoA genes are active ammonia oxidizers. These Thaumarchaea may be oxidizing methane instead of ammonia or may in fact be heterotrophic, indicating a potential for a diversity of metabolic lifestyles within the phylum.

Many members of the phylum assimilate carbon by CO2 fixation, using dissolved inorganic carbon as a pool. This is done using a hydroxypropionate/hydroxybutyrate cycle similar to the Crenarchaea but which appears to have evolved independently. All Thaumarchaea that have been identified by metagenomics thus far encode this pathway. Notably, the Thaumarchaeal CO2-fixation pathway is more efficient than any known aerobic autotrophic pathway. This efficiency helps explain their ability to thrive in low-nutrient environments. Some Thaumarchaea such as Nitrosopumilus maritimus may be able to incorporate organic carbon to an extent, indicating a capacity for mixotrophy. Others may be entirely heterotrophic and assimilate organic carbon compounds.

A study has revealed that Thaumarchaea are likely dominant producers of the critical vitamin B12 in aquatic environments. This finding has important implications for eukaryotic phytoplankton, many of which are auxotrophic and must acquire vitamin B12 from the environment; thus the Thaumarchaea 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 Thaumarchaea may be important for a large number of aquatic organisms.

Environment
Many Thaumarchaea, such as Nitrosopumilus maritimus, are marine and live in the open ocean. Most of these planktonic Thaumarchaea are distributed in the subphotic zone, between 100m and 350m. Other marine Thaumarchaea live in shallower waters. One study has identified two novel Thaumarchaeota 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 Thaumarchaea, they are mesophilic. Genetic analysis and the observation that the most basal identified Thaumarchaeal genomes are from hot environments suggests that the ancestor of Thaumarchaeota was thermophilic, and mesophily evolved later.