The Nitrososphaerota (syn. Thaumarchaeota) are a

phylum In biology, a phylum (; : phyla) is a level of classification, or taxonomic rank, that is below Kingdom (biology), kingdom and above Class (biology), class. Traditionally, in botany the term division (taxonomy), division has been used instead ...

of the

Archaea Archaea ( ) is a Domain (biology), domain of organisms. Traditionally, Archaea only included its Prokaryote, prokaryotic members, but this has since been found to be paraphyletic, as eukaryotes are known to have evolved from archaea. Even thou ...

proposed in 2008 after the

genome A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...

of '' Cenarchaeum symbiosum'' was

sequenced In genetics and biochemistry, sequencing means to determine the primary structure (sometimes incorrectly called the primary sequence) of an unbranched biopolymer. Sequencing results in a symbolic linear depiction known as a sequence which succi ...

and found to differ significantly from other members of the

hyperthermophilic A hyperthermophile is an organism that thrives in extremely hot environments—from 60 °C (140 °F) upward. An optimal temperature for the existence of hyperthermophiles is often above 80 °C (176 °F). Hyperthermophiles are of ...

phylum

Thermoproteota The Thermoproteota are prokaryotes that have been classified as a phylum (biology), phylum of the domain Archaea. Initially, the Thermoproteota were thought to be sulfur-dependent extremophiles but recent studies have identified characteristic T ...

(formerly Crenarchaeota). Three described species in addition to ''C. symbiosum'' are '' Nitrosopumilus maritimus'', '' Nitrososphaera viennensis'', and '' Nitrososphaera gargensis''. The phylum was proposed in 2008 based on

phylogenetic In biology, phylogenetics () is the study of the evolutionary history of life using observable characteristics of organisms (or genes), which is known as phylogenetic inference. It infers the relationship among organisms based on empirical dat ...

data, such as the sequences of these organisms'

ribosomal RNA Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribosomal ...

genes, and the presence of a form of

type I topoisomerase In molecular biology Type I topoisomerases are enzymes that cut one of the two strands of double-stranded DNA, relax the strand, and reanneal the strand. They are further subdivided into two structurally and mechanistically distinct topoisomeras ...

that was previously thought to be unique to the

eukaryote The eukaryotes ( ) constitute the Domain (biology), domain of Eukaryota or Eukarya, organisms whose Cell (biology), cells have a membrane-bound cell nucleus, nucleus. All animals, plants, Fungus, fungi, seaweeds, and many unicellular organisms ...

s. 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 Nitrososphaerota, making it a potential

biomarker In biomedical contexts, a biomarker, or biological marker, is a measurable indicator of some biological state or condition. Biomarkers are often measured and evaluated using blood, urine, or soft tissues to examine normal biological processes, ...

for the phylum. Most organisms of this lineage thus far identified are chemolithoautotrophic

ammonia Ammonia is an inorganic chemical compound of nitrogen and hydrogen with the chemical formula, formula . A Binary compounds of hydrogen, stable binary hydride and the simplest pnictogen hydride, ammonia is a colourless gas with a distinctive pu ...

-oxidizers and may play important roles in

biogeochemical cycle A biogeochemical cycle, or more generally a cycle of matter, is the movement and transformation of chemical elements and compounds between living organisms, the atmosphere, and the Earth's crust. Major biogeochemical cycles include the carbon cyc ...

s, such as the

nitrogen cycle The nitrogen cycle is the biogeochemical cycle by which nitrogen is converted into multiple chemical forms as it circulates among atmosphere, atmospheric, terrestrial ecosystem, terrestrial, and marine ecosystems. The conversion of nitrogen can ...

and the

carbon cycle The carbon cycle is a part of the biogeochemical cycle where carbon is exchanged among the biosphere, pedosphere, geosphere, hydrosphere, and atmosphere of Earth. Other major biogeochemical cycles include the nitrogen cycle and the water cycl ...

Metagenomic Metagenomics is the study of all genetic material from all organisms in a particular environment, providing insights into their composition, diversity, and functional potential. Metagenomics has allowed researchers to profile the microbial co ...

sequencing In genetics and biochemistry, sequencing means to determine the primary structure (sometimes incorrectly called the primary sequence) of an unbranched biopolymer. Sequencing results in a symbolic linear depiction known as a sequence which succ ...

indicates that they constitute ~1% of the sea surface metagenome across many sites. Nitrososphaerota-derived membrane-spanning tetraether lipids (glycerol dialkyl glycerol tetraethers; GDGTs) 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 Nitrososphaerota seem to be

autotroph An autotroph is an organism that can convert Abiotic component, abiotic sources of energy into energy stored in organic compounds, which can be used by Heterotroph, other organisms. Autotrophs produce complex organic compounds (such as carbohy ...

s that fix CO₂, their GDGTs can act as a record for past

Carbon-13 Carbon-13 (13C) is a natural, stable isotope of carbon with a nucleus containing six protons and seven neutrons. As one of the environmental isotopes, it makes up about 1.1% of all natural carbon on Earth. Detection by mass spectrometry A m ...

ratios in the

dissolved inorganic carbon Dissolved inorganic carbon (DIC) is the sum of the aqueous species of inorganic carbon in a solution. Carbon compounds can be distinguished as either organic or inorganic, and as dissolved or particulate, depending on their composition. Organic c ...

pool, and thus have the potential to be used for reconstructions of the carbon cycle in the past.

Taxonomy

The currently accepted taxonomy is based on the

List of Prokaryotic names with Standing in Nomenclature List of Prokaryotic names with Standing in Nomenclature (LPSN) is an online database that maintains information on the naming and taxonomy of prokaryotes, following the taxonomy requirements and rulings of the International Code of Nomenclatu ...

(LPSN) and

National Center for Biotechnology Information The National Center for Biotechnology Information (NCBI) is part of the National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The NCBI is lo ...

(NCBI) * Class Nitrososphaeria Stieglmeier et al. 2014 onexivisphaeria Kato et al. 2020** ?"'' Cenoporarchaeum''" corrig. Zhang et al. 2019 ** ?"''Candidatus'' Gagatemarchaeum" Sheridan et al. 2023 ** ?"''Candidatus'' Giganthauma" Muller et al. 2010 ** ?"''Candidatus'' Nitrosodeserticola" Hwang et al. 2021 ** ?"''Candidatus'' Subgagatemarchaeum" Sheridan et al. 2023 ** Order " Geothermarchaeales" Adam et al. 2022 *** Family Geothermarchaeaceae Adam et al. 2022 **** "'' Geothermarchaeum''" Adam et al. 2022 **** "'' Scotarchaeum''" Adam et al. 2022 ** 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 Methylarchaeaceae Hua et al. 2019 **** ?"''Candidatus'' Methylarchaeum" Hua et al. 2019 **** ?"''Candidatus'' Methanotowutia" Ou et al. 2022 *** Family Nitrososphaeraceae Stieglmeier et al. 2014 **** "''Candidatus'' Nitrosocosmicus" Lehtovirta-Morley et al. 2016 **** "''Candidatus'' Nitrosopolaris" Pessi, Rutanen & Hultman 2022 **** '' Nitrososphaera'' Stieglmeier et al. 2014 ** Order Nitrosopumilales Qin et al. 2017 *** Family Nitrosopumilaceae Qin et al. 2017 **** "''

Cenarchaeum ''Cenarchaeum'' is a monotypic genus of archaeans in the family Cenarchaeaceae.See the NCBIbr>webpage on Cenarchaeum Data extracted from the The marine archaean ''Cenarchaeum symbiosum'' is psychrophilic and is found inhabiting marine sponges. ...

''" DeLong & Preston 1996 **** '' Nitrosarchaeum'' corrig. Jung et al. 2018 **** ?"''Candidatus'' Nitrosoabyssus" Garritano et al. 2024 **** ?"''Candidatus'' Nitrosokoinonia" Glasl et al. 2023 **** ?"''Candidatus'' Nitrosomaritimum" Zhao et al. 2024 **** "''Candidatus'' Nitrosopelagicus" Santoro et al. 2015 **** ''

Nitrosopumilus ''Nitrosopumilus'' is a genus of archaea. The type species, ''Nitrosopumilus maritimus'', is an extremely common archaeon living in seawater. It is the first member of the Group 1a Nitrososphaerota (formerly Thaumarchaeota) to be isolated in pur ...

'' Qin et al. 2017 **** ?"''Candidatus'' Nitrosospongia" Moeller et al. 2019 **** "''Candidatus'' Nitrosotalea" Lehtovirta 2011 **** "''Candidatus'' Nitrosotenuis" Li et al. 2016

Metabolism

Nitrososphaerota are important ammonia oxidizers in aquatic and terrestrial environments, and are the first archaea identified as being involved in

nitrification ''Nitrification'' is the biological oxidation of ammonia to nitrate via the intermediary nitrite. Nitrification is an important step in the nitrogen cycle in soil. The process of complete nitrification may occur through separate organisms or ent ...

. They are capable of oxidizing ammonia at much lower substrate concentrations than

ammonia-oxidizing bacteria Nitrifying bacteria are chemolithotrophic organisms that include species of genera such as ''Nitrosomonas'', ''Nitrosococcus'', ''Nitrobacter'', '' Nitrospina'', ''Nitrospira'' and '' Nitrococcus''. These bacteria get their energy from the oxidati ...

, 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 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. In addition to ammonia, at least one Nitrososphaerota strain has been shown to be able to use

urea Urea, also called carbamide (because it is a diamide of carbonic acid), is an organic compound with chemical formula . This amide has two Amine, amino groups (–) joined by a carbonyl functional group (–C(=O)–). It is thus the simplest am ...

as a substrate for nitrification. This would allow for competition with phytoplankton that also grow on urea. 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

heterotroph A heterotroph (; ) is an organism that cannot produce its own food, instead taking nutrition from other sources of organic carbon, mainly plant or animal matter. In the food chain, heterotrophs are primary, secondary and tertiary consumers, but ...

ic, indicating a potential for a diversity of metabolic lifestyles within the phylum. Marine Nitrososphaerota have also been shown to produce

nitrous oxide Nitrous oxide (dinitrogen oxide or dinitrogen monoxide), commonly known as laughing gas, nitrous, or factitious air, among others, is a chemical compound, an Nitrogen oxide, oxide of nitrogen with the Chemical formula, formula . At room te ...

, which as a

greenhouse gas Greenhouse gases (GHGs) are the gases in the atmosphere that raise the surface temperature of planets such as the Earth. Unlike other gases, greenhouse gases absorb the radiations that a planet emits, resulting in the greenhouse effect. T ...

has implications for

climate change Present-day climate change includes both global warming—the ongoing increase in Global surface temperature, global average temperature—and its wider effects on Earth's climate system. Climate variability and change, Climate change in ...

. 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. Many members of the phylum assimilate carbon by fixing HCO₃⁻. 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. Some Nitrososphaerota such as ''Nitrosopumilus maritimus'' are able to incorporate organic carbon as well as inorganic, indicating a capacity for

mixotroph A mixotroph is an organism that uses a mix of different sources of energy and carbon, instead of having a single trophic mode, on the continuum from complete autotrophy to complete heterotrophy. It is estimated that mixotrophs comprise more than ...

y. At least two isolated strains have been identified as obligate mixotrophs, meaning they require a source of organic carbon in order to grow. A study has revealed that Nitrososphaerota are most likely the dominant producers of the critical

vitamin B12 Vitamin B12, also known as cobalamin, is a water-soluble vitamin involved in metabolism. One of eight B vitamins, it serves as a vital cofactor (biochemistry), cofactor in DNA synthesis and both fatty acid metabolism, fatty acid and amino a ...

. This finding has important implications for eukaryotic

phytoplankton Phytoplankton () are the autotrophic (self-feeding) components of the plankton community and a key part of ocean and freshwater Aquatic ecosystem, ecosystems. The name comes from the Greek language, Greek words (), meaning 'plant', and (), mea ...

, many of which are

auxotrophic Auxotrophy ( "to increase"; ''τροφή'' "nourishment") is the inability of an organism to synthesize a particular organic compound required for its growth (as defined by IUPAC). An auxotroph is an organism that displays this characteristic; ''a ...

and must acquire vitamin B₁₂ from the environment; thus the Nitrososphaerota could play a role in

algal bloom An algal bloom or algae bloom is a rapid increase or accumulation in the population of algae in fresh water or marine water systems. It is often recognized by the discoloration in the water from the algae's pigments. The term ''algae'' encompass ...

s and by extension global levels of atmospheric

carbon dioxide Carbon dioxide is a chemical compound with the chemical formula . It is made up of molecules that each have one carbon atom covalent bond, covalently double bonded to two oxygen atoms. It is found in a gas state at room temperature and at norma ...

. Because of the importance of vitamin B₁₂ in biological processes such as the

citric acid cycle The citric acid cycle—also known as the Krebs cycle, Szent–Györgyi–Krebs cycle, or TCA cycle (tricarboxylic acid cycle)—is a series of chemical reaction, biochemical reactions that release the energy stored in nutrients through acetyl-Co ...

and

DNA synthesis DNA synthesis is the natural or artificial creation of deoxyribonucleic acid (DNA) molecules. DNA is a macromolecule made up of nucleotide units, which are linked by covalent bonds and hydrogen bonds, in a repeating structure. DNA synthesis occu ...

, production of it by the Nitrososphaerota may be important for a large number of aquatic organisms.

Environment

Many Nitrososphaerota, such as ''Nitrosopumilus maritimus'', are marine and live in the open ocean. Most of these

plankton Plankton are the diverse collection of organisms that drift in Hydrosphere, water (or atmosphere, air) but are unable to actively propel themselves against ocean current, currents (or wind). The individual organisms constituting plankton are ca ...

ic Nitrososphaerota, which compose the Marine Group I.1a, are distributed in the subphotic zone, between 100m and 350m. 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 Mangrove forests, also called mangrove swamps, mangrove thickets or mangals, are productive wetlands that occur in coastal intertidal zones. Mangrove forests grow mainly at tropical and subtropical latitudes because mangrove trees cannot withs ...

. Of these two species, Candidatus ''Giganthauma insulaporcus'' and Candidatus ''Giganthauma karukerense'', the latter is associated with

Gammaproteobacteria ''Gammaproteobacteria'' is a class of bacteria in the phylum ''Pseudomonadota'' (synonym ''Proteobacteria''). It contains about 250 genera, which makes it the most genus-rich taxon of the Prokaryotes. Several medically, ecologically, and scienti ...

with which it may have a

symbiotic relationship Symbiosis (Ancient Greek : living with, companionship < : together; and ''bíōsis'': living) is any type of a close and long-term biolo ...

, 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 A mesophile is an organism that grows best in moderate temperature, neither too hot nor too cold, with an optimum growth range from . The optimum growth temperature for these organisms is 37 °C (about 99 °F). The term is mainly applied ...

. Genetic analysis and the observation that the most basal identified Nitrososphaerota genomes are from hot environments suggests that the ancestor of Nitrososphaerota was

thermophilic A thermophile is a type of extremophile that thrives at relatively high temperatures, between . Many thermophiles are archaea, though some of them are bacteria and fungi. Thermophilic eubacteria are suggested to have been among the earliest bact ...

, and mesophily evolved later.

Taxonomy

Metabolism

Environment

See also

References

Further reading