Nitrososphaerota

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Nitrososphaerota
ThaspiviridaeFig1rv2.png
Nitrosopumilus maritimus , partially with virions of Nitrosopumilus spindle-shaped virus 1 ( Thaspiviridae ) attached.
Scientific classification
Domain:
Archaea
Superphylum:
"Proteoarchaeota"
Phylum:
Nitrososphaerota

Brochier-Armanet et al. 2021 [1]
Class:
Nitrososphaeria
Order
Synonyms
  • "Nitrososphaerota" Whitman et al. 2018
  • "Nitrososphaeraeota" Oren et al. 2015
  • "Thaumarchaeota" Brochier-Armanet et al. 2008 [2]

The Nitrososphaerota (syn. Thaumarchaeota) 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 Thermoproteota (formerly Crenarchaeota). [3] [2] [4] Three described species in addition to C. symbiosum are Nitrosopumilus maritimus , Nitrososphaera viennensis , and Nitrososphaera gargensis . [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. [6] The lipid crenarchaeol has been found only in Nitrososphaerota, making it a potential biomarker for the phylum. [7] [8] 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. [9]

Contents

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. [10] Because most Nitrososphaerota 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. [7]

Taxonomy

Phylogeny of Nitrososphaerota [11] [12] [13]
Phylogeny of Nitrososphaerota [14] [15] [16]
Nitrososphaeria

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]

Metabolism

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. [8] [33] 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. [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. 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. [36]

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. [33] 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. [34]

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. [37]

Environment

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. [38] 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. [32]

See also

Related Research Articles

<i>Nanoarchaeum equitans</i> Species of archaeon

Nanoarchaeum equitans is a species of marine archaea that was discovered in 2002 in a hydrothermal vent off the coast of Iceland on the Kolbeinsey Ridge by Karl Stetter. It has been proposed as the first species in a new phylum, and is the only species within the genus Nanoarchaeum. Strains of this microbe were also found on the Sub-polar Mid Oceanic Ridge, and in the Obsidian Pool in Yellowstone National Park. Since it grows in temperatures approaching boiling, at about 80 °C (176 °F), it is considered to be a thermophile. It grows best in environments with a pH of 6, and a salinity concentration of 2%. Nanoarchaeum appears to be an obligate symbiont on the archaeon Ignicoccus; it must be in contact with the host organism to survive. Nanoarchaeum equitans cannot synthesize lipids but obtains them from its host. Its cells are only 400 nm in diameter, making it the smallest known living organism, and the smallest known archaeon.

<span class="mw-page-title-main">Nanoarchaeota</span> Phylum of archaea

Nanoarchaeota is a proposed phylum in the domain Archaea that currently has only one representative, Nanoarchaeum equitans, which was discovered in a submarine hydrothermal vent and first described in 2002.

<span class="mw-page-title-main">Nitrification</span> Biological oxidation of ammonia/ammonium to nitrate

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 entirely within one organism, as in comammox bacteria. The transformation of ammonia to nitrite is usually the rate limiting step of nitrification. Nitrification is an aerobic process performed by small groups of autotrophic bacteria and archaea.

<span class="mw-page-title-main">Korarchaeota</span> Proposed phylum within the Archaea

The Korarchaeota is a proposed phylum within the Archaea. The name is derived from the Greek noun koros or kore, meaning young man or young woman, and the Greek adjective archaios which means ancient. They are also known as Xenarchaeota. The name is equivalent to Candidatus Korarchaeota, and they go by the name Xenarchaeota or Xenarchaea as well.

Methanotrophs are prokaryotes that metabolize methane as their source of carbon and chemical energy. They are bacteria or archaea, can grow aerobically or anaerobically, and require single-carbon compounds to survive.

<span class="mw-page-title-main">Nitrosopumilales</span> Order of archaea

The Nitrosopumilales are an order of the Archaea class Nitrososphaeria.

Cenarchaeum is a monotypic genus of archaeans in the family Cenarchaeaceae. The marine archaean Cenarchaeum symbiosum is psychrophilic and is found inhabiting marine sponges. Cenarchaeum symbiosum was initially detected as a major symbiotic microorganism living within the sponge Axinella mexicana. It has been ubiquitously detected in the world oceans at lower abundances, while in some genera of marine sponges it is one of the most abundant microbiome members. Its genome sequence and diversity has been investigated in detail finding unique metabolic products and its role in ammonia-oxidizing activities.

<i>Nitrosopumilus</i> Genus of archaea

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 to be isolated in pure culture. Gene sequences suggest that the Group 1a Nitrososphaerota are ubiquitous with the oligotrophic surface ocean and can be found in most non-coastal marine waters around the planet. It is one of the smallest living organisms at 0.2 micrometers in diameter. Cells in the species N. maritimus are shaped like peanuts and can be found both as individuals and in loose aggregates. They oxidize ammonia to nitrite and members of N. maritimus can oxidize ammonia at levels as low as 10 nanomolar, near the limit to sustain its life. Archaea in the species N. maritimus live in oxygen-depleted habitats. Oxygen needed for ammonia oxidation might be produced by novel pathway which generates oxygen and dinitrogen. N. maritimus is thus among organisms which are able to produce oxygen in dark.

<span class="mw-page-title-main">Archaea</span> Domain of organisms

Archaea is a domain of organisms. Traditionally, Archaea only included its prokaryotic members, but this sense has been found to be paraphyletic, as eukaryotes are now known to have evolved from archaea. Even though the domain Archaea includes eukaryotes, the term "archaea" in English still generally refers specifically to prokaryotic members of Archaea. Archaea were initially classified as bacteria, receiving the name archaebacteria, but this term has fallen out of use.

Nanohaloarchaea is a clade of diminutive archaea with small genomes and limited metabolic capabilities, belonging to the DPANN archaea. They are ubiquitous in hypersaline habitats, which they share with the extremely halophilic haloarchaea.

Nitrososphaera is a mesophilic genus of ammonia-oxidizing Crenarchaeota. The first Nitrososphaera organism was discovered in garden soils at the University of Vienna leading to the categorization of a new genus, family, order and class of Archaea. This genus is contains three distinct species: N. viennensis, Ca. N. gargensis, and Ca N. evergladensis. Nitrososphaera are chemolithoautotrophs and have important biogeochemical roles as nitrifying organisms.

The "Aigarchaeota" are a proposed archaeal phylum of which the main representative is Caldiarchaeum subterraneum. It is not yet clear if this represents a new phylum or a Nitrososphaerota order, since the genome of Caldiarchaeum subterraneum encodes several Nitrososphaerota-like features. The name "Aigarchaeota" comes from the Greek αυγή, avgí, meaning "dawn" or "aurora", for the intermediate features of hyperthermophilic and mesophilic life during the evolution of its lineage.

<span class="mw-page-title-main">Lokiarchaeota</span> Phylum of archaea

Lokiarchaeota is a proposed phylum of the Archaea. The phylum includes all members of the group previously named Deep Sea Archaeal Group, also known as Marine Benthic Group B. Lokiarchaeota is part of the superphylum Asgard containing the phyla: Lokiarchaeota, Thorarchaeota, Odinarchaeota, Heimdallarchaeota, and Helarchaeota. A phylogenetic analysis disclosed a monophyletic grouping of the Lokiarchaeota with the eukaryotes. The analysis revealed several genes with cell membrane-related functions. The presence of such genes support the hypothesis of an archaeal host for the emergence of the eukaryotes; the eocyte-like scenarios.

Nitrososphaera gargensis is a non-pathogenic, small coccus measuring 0.9 ± 0.3 μm in diameter. N. gargensis is observed in small abnormal cocci groupings and uses its archaella to move via chemotaxis. Being an Archaeon, Nitrososphaera gargensis has a cell membrane composed of crenarchaeol, its isomer, and a distinct glycerol dialkyl glycerol tetraether (GDGT), which is significant in identifying ammonia-oxidizing archaea (AOA). The organism plays a role in influencing ocean communities and food production.

<span class="mw-page-title-main">DPANN</span> A superphylum of Archaea grouping taxa that display various environmental and metabolic features

DPANN is a superphylum of Archaea first proposed in 2013. Many members show novel signs of horizontal gene transfer from other domains of life. They are known as nanoarchaea or ultra-small archaea due to their smaller size (nanometric) compared to other archaea.

"Candidatus Thorarchaeota", or simply Thorarchaeota, is a phylum within the superphylum Asgard archaea. The Asgard superphylum represents the closest prokaryotic relatives of eukaryotes. Since there is such a close relation between the two different domains, it provides further evidence to the two-domain tree of life theory which states that eukaryotes branched from the archaeal domain. Asgard archaea are single cell marine microbes that contain branch like appendages and have genes that are similar to eukarya. The asgard archaea superphylum is composed of Thorarchaeota, Lokiarchaeota, Odinarchaeota, and Heimdallarchaeota. Thorarchaeota were first identified from the sulfate-methane transition zone in tidewater sediments. Thorarcheota are widely distributed in marine and freshwater sediments.

<span class="mw-page-title-main">TACK</span> Clade of Archaea

TACK is a group of archaea, its name an acronym for Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota, the first groups discovered. They are found in different environments ranging from acidophilic thermophiles to mesophiles and psychrophiles and with different types of metabolism, predominantly anaerobic and chemosynthetic. TACK is a clade that is sister to the Asgard branch that gave rise to the eukaryotes. It has been proposed that the TACK clade be classified as Crenarchaeota and that the traditional "Crenarchaeota" (Thermoproteota) be classified as a class called "Sulfolobia", along with the other phyla with class rank or order. After including the kingdom category into ICNP, the proposed name of this group is kingdom Thermoproteati.

Crenarchaeol is a glycerol biphytanes glycerol tetraether (GDGT) biological membrane lipid. Together with archaeol, crenarcheol comprises a major component of archaeal membranes. Archaeal membranes are distinct from those of bacteria and eukaryotes because they contain isoprenoid GDGTs instead of diacyl lipids, which are found in the other domains. It has been proposed that GDGT membrane lipids are an adaptation to the high temperatures present in the environments that are home to extremophile archaea

<span class="mw-page-title-main">Marine prokaryotes</span> Marine bacteria and marine archaea

Marine prokaryotes are marine bacteria and marine archaea. They are defined by their habitat as prokaryotes that live in marine environments, that is, in the saltwater of seas or oceans or the brackish water of coastal estuaries. All cellular life forms can be divided into prokaryotes and eukaryotes. Eukaryotes are organisms whose cells have a nucleus enclosed within membranes, whereas prokaryotes are the organisms that do not have a nucleus enclosed within a membrane. The three-domain system of classifying life adds another division: the prokaryotes are divided into two domains of life, the microscopic bacteria and the microscopic archaea, while everything else, the eukaryotes, become the third domain.

Christa Schleper is a German microbiologist known for her work on the evolution and ecology of Archaea. Schleper is Head of the Department of Functional and Evolutionary Biology at the University of Vienna in Austria.

References

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