''Nitrosopumilus'' is a

genus Genus (; : genera ) is a taxonomic rank above species and below family (taxonomy), family as used in the biological classification of extant taxon, living and fossil organisms as well as Virus classification#ICTV classification, viruses. In bino ...

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 ...

. The type species, ''Nitrosopumilus maritimus'', is an extremely common

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

living in seawater. It is the first member of the Group 1a

Nitrososphaerota 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 Thermopr ...

(formerly Thaumarchaeota) 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 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 ...

nitrite The nitrite polyatomic ion, ion has the chemical formula . Nitrite (mostly sodium nitrite) is widely used throughout chemical and pharmaceutical industries. The nitrite anion is a pervasive intermediate in the nitrogen cycle in nature. The name ...

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. This organism was isolated from sediment in a tropical tank at the

Seattle Aquarium The Seattle Aquarium is a public aquarium in Seattle, Washington, United States, located on Pier 59 and 60 on the Elliott Bay waterfront. The aquarium opened in 1977 and is accredited by the Association of Zoos and Aquariums (AZA). The aquari ...

by a group led by David Stahl (

University of Washington The University of Washington (UW and informally U-Dub or U Dub) is a public research university in Seattle, Washington, United States. Founded in 1861, the University of Washington is one of the oldest universities on the West Coast of the Uni ...

Biology

Lipid membranes

Populations of ''N. maritimus'' are probably the main source of

glycerol dialkyl glycerol tetraether Glycerol dialkyl glycerol tetraether lipids (GDGTs) are a class of membrane lipids synthesized by archaea and some bacteria, making them useful biomarkers for these organisms in the geological record. Their presence, structure, and relative abundan ...

s (GDGTs) in the ocean, a compound which constitutes their monolayer lipidic

cell membranes The cell membrane (also known as the plasma membrane or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biological membrane that separates and protects the interior of a cell from the outside environment (the extra ...

as ''intact polar lipids (IPLs)'' together with

crenarcheol Crenarchaeol is a (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 GDGT ...

. This membrane structure is thought to maximise

proton motive force Chemiosmosis is the movement of ions across a semipermeable membrane bound structure, down their electrochemical gradient. An important example is the formation of adenosine triphosphate (ATP) by the movement of hydrogen ions (H+) across a membra ...

. The compounds found in the membrane of these organisms, such as GDGTs, IPLs, and crenarcheol, can be useful as

biomarkers 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, p ...

for the presence of organisms belonging to the

group in the water column. These archaea have also been found to change their membrane's composition in relation to temperature (by GDGT cyclization), growth, metabolic status, and, even if less dramatically, to pH.

Cell division

All known Archaea use

cell division Cell division is the process by which a parent cell (biology), cell divides into two daughter cells. Cell division usually occurs as part of a larger cell cycle in which the cell grows and replicates its chromosome(s) before dividing. In eukar ...

to duplicate.

Euryarchaeota Methanobacteriota is a phylum in the domain Archaea. Taxonomy The phylum ''Methanobacteriota'' was introduced to prokaryotic nomenclature in 2023. It contains following classes: *Archaeoglobi Garrity & Holt (2002) *Halobacteria Grant ''et al ...

and

Bacteria Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...

use the

FtsZ FtsZ is a protein encoded by the ''ftsZ'' gene that assembles into a ring at the future site of bacterial cell division (also called the Z ring). FtsZ is a prokaryotic homologue of the eukaryotic protein tubulin. The initials FtsZ mean "Filame ...

mechanism in

, while

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 ...

divide using the Cdv machinery. However,

such as ''N. maritimus'' adopts both mechanisms,

and Cdv. Nevertheless, after further researches, ''N. maritimus'' was found to use mainly Cdv proteins rather than

during

. In this case, Cdv is the primary system in

for ''N. maritimus''. Therefore, to replicate a

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 1.645Mb, ''N. maritimus'' spends 15 to 18 hours.

Physiology

Genome

Ammonia-oxidizing bacteria (AOB) are known to have chemolithoautotrophic growth by using inorganic carbon, ''N. maritimus'', an Ammonia-oxidizing archaea (AOA) use a similar process of growth. While AOB uses Calvin–Bassham–Benson cycle with the -fixing enzyme ribulose bisphosphate carboxylase/oxygenase (

RubisCO Ribulose-1,5-bisphosphate carboxylase/oxygenase, commonly known by the abbreviations RuBisCo, rubisco, RuBPCase, or RuBPco, is an enzyme () involved in the light-independent (or "dark") part of photosynthesis, including the carbon fixation by wh ...

) as the key enzyme; ''N. maritimus'' seems to grow and use an alternative pathway due to the lack of genes and enzymes. Therefore, a variant of the 3-hydroxypropionate/4-hydroxybutyrate is used by ''N. maritimus'' to develop autotrophically, which allows its capacity to assimilate inorganic carbon. Using the 3-hydroxypropionate/4-hydroxybutyrate pathway method instead of the

Calvin cycle The Calvin cycle, light-independent reactions, bio synthetic phase, dark reactions, or photosynthetic carbon reduction (PCR) cycle of photosynthesis is a series of chemical reactions that convert carbon dioxide and hydrogen-carrier compounds into ...

, ''N. maritimus'' could provide a growth advantage as the process is more energy-efficient. Due to its originality, ''N. maritimus'' plays an essential role in the carbon and nitrogen cycle

Ammonia oxidation

The isolation and the sequencing of ''N. maritimus''s genome have allowed to extend the insight into the

physiology Physiology (; ) is the science, scientific study of function (biology), functions and mechanism (biology), mechanisms in a life, living system. As a branches of science, subdiscipline of biology, physiology focuses on how organisms, organ syst ...

of the organisms belonging to the

group. ''N. maritimus'' was the first

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

with an ''ammonia oxidizing metabolism'' to be studied. This organism is common in the marine environment especially at the bottom of the

photic zone The photic zone (or euphotic zone, epipelagic zone, or sunlight zone) is the uppermost layer of a body of water that receives sunlight, allowing phytoplankton to perform photosynthesis. It undergoes a series of physical, chemical, and biological ...

where the amount of Ammonium and Iron is enough to support its growth. The physiology of ''N. maritimus'' remains unclear under certain aspects. It conserves energy for its vital functions, from the

oxidation Redox ( , , reduction–oxidation or oxidation–reduction) is a type of chemical reaction in which the oxidation states of the reactants change. Oxidation is the loss of electrons or an increase in the oxidation state, while reduction is ...

of ''Ammonia'' () and the reduction of ''Oxygen'' (), with the formation of ''Nitrite''. ' is the carbon source. It is fixed and assimilated by the microorganism through the '' 3-hydroxypropinate/4-hydroxybutyrate carbon cycle''. ''N. maritimus'' carries out the first step of

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 ...

, by acting in a key role in 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 ...

along the water column. Since this oxidizing reaction releases just a little amount of energy, the growth of this microorganism is slow. ''N. maritimus’''s genome includes the amoA gene, encoding for the

Ammonia Monooxygenase Ammonia monooxygenase (, ''AMO'') is an enzyme, which catalysis, catalyses the following chemical reaction : ammonia + AH2 + O2 \rightleftharpoons NH2OH + A + H2O Ammonia monooxygenase contains copper and possibly nonheme iron. AMO is the first ...

(AMO) enzyme. This latter allows the oxidation of ammonia to hydroxylamine (). Instead, the genome lacks the gene encoding for

Hydroxylamine Oxidoreductase Hydroxylamine oxidoreductase (HAO) is an enzyme found in the prokaryotic genus '' Nitrosomonas.'' It plays a critically important role in the biogeochemical nitrogen cycle as part of the metabolism of ammonia-oxidizing bacteria. The substrate is ...

(HAO) responsible for oxidizing the intermediate () to nitrite. The hydroxylamine is produced as a

metabolite In biochemistry, a metabolite is an intermediate or end product of metabolism. The term is usually used for small molecules. Metabolites have various functions, including fuel, structure, signaling, stimulatory and inhibitory effects on enzymes, c ...

, and it is immediately consumed during the metabolic reaction. Other intermediates produced during this metabolic pathway are: the nitric oxide (NO), the

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 ...

(), the nitoxyl (HNO). These are toxic at high concentration. The enzyme responsible for oxidizing the hydroxylamine to nitrite is not well-known yet. Two hypotheses are suggested for the metabolic pathway of ''N. maritimus'' that involve two types of

enzymes An enzyme () is a protein that acts as a biological catalyst by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as pro ...

: the copper-based enzyme (Cu-ME) and the nitrite reductase enzyme (nirK) and its reverse: *In the first one ammonia is oxidized through AMO forming the hydroxylamine; the latter, plus a molecule of nitric oxide, are, in turn, oxidized by a copper-based enzyme (Cu-ME) producing two molecules of nitrite. One of these is reduced to NO by the nitrite reductase (nirK) and goes back to the cu-ME enzyme. An electrons translocation occurs producing a Proton Motive Force (PMF) and allowing

ATP synthesis ATP synthase is an enzyme that catalyzes the formation of the energy storage molecule adenosine triphosphate (ATP) using adenosine diphosphate (ADP) and inorganic phosphate (Pi). ATP synthase is a molecular machine. The overall reaction catalyzed ...

. *In the second one ammonia is oxidized through AMO making up the hydroxylamine and then the two enzymes, nirK and Cu-ME, oxidize the hydroxylamine to nitric oxide and this to nitrite. The proper roles and the order at which these enzymes work, have to be clarified. The

S-layer An S-layer (surface layer) is a part of the cell envelope found in almost all archaea, as well as in many types of bacteria. The S-layers of both archaea and bacteria consists of a Monolayer, monomolecular layer composed of only one (or, in a few c ...

of ''N. maritimus'' is found to form into multiple layers of channels that allow

ammonium Ammonium is a modified form of ammonia that has an extra hydrogen atom. It is a positively charged (cationic) polyatomic ion, molecular ion with the chemical formula or . It is formed by the protonation, addition of a proton (a hydrogen nucleu ...

() cations to flow through. Additionally, ''nitrous oxide'' is released by this type of metabolism. It is an important

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 ...

that likely is produced as result of abiotic

denitrification Denitrification is a microbially facilitated process where nitrate (NO3−) is reduced and ultimately produces molecular nitrogen (N2) through a series of intermediate gaseous nitrogen oxide products. Facultative anaerobic bacteria perform denitr ...

of metabolites.

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). Incertae sedis: * "''Ca.'' Nitrosopumilus brisbanensis" Prabhu et al. 2024 * "''Nitrosopumilus cymbastelae''" corrig. Zhang et al. 2019 * "''Nitrosopumilus detritiferus''" Zhang et al. 2019 * "''Nitrosopumilus hexadellae''" corrig. Zhang et al. 2019

Ecology

Habitats

Characteristic of the

phylum, ''N. maritimus'' is mainly found in oligotrophic (poor environment in nutrients) open ocean, within the Pelagic zone.Walker, C. B., J. R. de la Torre, M. G. Klotz, H. Urakawa, N. Pinel, D. J. Arp, C. Brochier-Armanet, et al. "Nitrosopumilus Maritimus Genome Reveals Unique Mechanisms for Nitrification and Autotrophy in Globally Distributed Marine Crenarchaea." Proceedings of the National Academy of Sciences of the United States of America 107, no. 19 (May 11, 2010): 8818–23. https://doi.org/10.1073/pnas.0913533107. Initially discovered in Seattle, in an aquarium,Könneke, Martin, Anne E. Bernhard, José R. de la Torre, Christopher B. Walker, John B. Waterbury, and David A. Stahl. "Isolation of an Autotrophic Ammonia-Oxidizing Marine Archaeon." Nature 437, no. 7058 (September 2005): 543–46. https://doi.org/10.1038/nature03911. today ''N. maritimus'' can populate numerous environment such as the subtropical North Pacific and South Atlantic Ocean or the mesopelagic zone in the Pacific Ocean. ''N. maritimus'' is an aerobic archeon able to grow even with an extremely low concentration of nutrients,Martens-Habbena, Willm, Paul M. Berube, Hidetoshi Urakawa, José R. de la Torre, and David A. Stahl. "Ammonia Oxidation Kinetics Determine Niche Separation of Nitrifying Archaea and Bacteria." Nature 461, no. 7266 (October 2009): 976–79. like in dark-deep open ocean, in which ''N. maritimus'' as an important impact.Meador, Travis B., Niels Schoffelen, Timothy G. Ferdelman, Osmond Rebello, Alexander Khachikyan, and Martin Könneke. "Carbon Recycling Efficiency and Phosphate Turnover by Marine Nitrifying Archaea." Science Advances 6, no. 19 (May 8, 2020): eaba1799. https://doi.org/10.1126/sciadv.aba1799.

Contributions

Nitrification of the ocean

Members of the species ''N. maritimus'' can oxidize ammonia to form nitrite, which is the first step of 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 ...

. Ammonia and nitrate are the two nutrients which form the inorganic pool of nitrogen. Populating poor environments (lacking of organic energy sources and sunlight), the oxidation of ammonia could contribute to primary productivity . In fact, nitrate fuels half of the primary production of phytoplankton but not only phytoplankton needs nitrate. The high ammonia's affinity allows ''N. maritimus'' to largely compete with the other marine phototrophs and chemotrophs. Regarding the ammonium turnover per unit biomass, ''N. maritimus'' would be around 5 times higher than oligotrophic heterotrophs' turnover, and around 30 times higher than most of the oligotrophic diatoms known turnover. Computing these two observations nitrification by ''N. maritimus'' plays a key role in the marine nitrogen cycle.Wuchter, Cornelia, Ben Abbas, Marco J. L. Coolen, Lydie Herfort, Judith van Bleijswijk, Peer Timmers, Marc Strous, et al. "Archaeal Nitrification in the Ocean." Proceedings of the National Academy of Sciences of the United States of America 103, no. 33 (August 15, 2006): 12317–22. https://doi.org/10.1073/pnas.0600756103.

Carbon and phosphorus implications

Its ability to fix inorganic carbon via an alternative pathway (3-hydroxypropionate/4-hydroxybutyrate pathway) allows ''N. maritimus'' to participate efficiently in the flux of the global carbon budget. Coupling with the ammonia-oxidizing pathway, ''N. maritimus'' and the other marine thaumarchaea, approximately, recycle 4.5% of the organic carbon mineralized in the oceans and transform 4.3% of detrital phosphorus into new phosphorus substances.