''Nitrososphaera gargensis'' is a non-

pathogen In biology, a pathogen ( el, πάθος, "suffering", "passion" and , "producer of") in the oldest and broadest sense, is any organism or agent that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a germ ...

ic, small

coccus A coccus (plural cocci) is any bacterium or archaeon that has a spherical, ovoid, or generally round shape. Bacteria are categorized based on their shapes into three classes: cocci (spherical-shaped), bacillus (rod-shaped) and spiral ( of whi ...

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 Chemotaxis (from '' chemo-'' + ''taxis'') is the movement of an organism or entity in response to a chemical stimulus. Somatic cells, bacteria, and other single-cell or multicellular organisms direct their movements according to certain chemica ...

. Being an

Archaeon Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebact ...

, ''Nitrososphaera gargensis'' has a

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

composed of crenarchaeol, its

isomer In chemistry, isomers are molecules or polyatomic ions with identical molecular formulae – that is, same number of atoms of each element – but distinct arrangements of atoms in space. Isomerism is existence or possibility of isomers. Iso ...

, and a distinct

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 ...

(GDGT), which is significant in identifying ammonia-oxidizing archaea (AOA). The organism plays a role in influencing ocean communities and food production.Courtens, Emilie Np, Eva Spieck, Ramiro Vilchez-Vargas, Samuel Bodé, Pascal Boeckx, Stefan Schouten, Ruy Jauregui, Dietmar H. Pieper, Siegfried E. Vlaeminck, and Nico Boon. "A Robust Nitrifying Community in a Bioreactor at 50 °C Opens up the Path for Thermophilic Nitrogen Removal." ''The ISME Journal'' (2016) http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej20168a.htm

Discovery

''Nitrososphaera gargensis'' was discovered in a Garga hot spring in

Siberia Siberia ( ; rus, Сибирь, r=Sibir', p=sʲɪˈbʲirʲ, a=Ru-Сибирь.ogg) is an extensive geographical region, constituting all of North Asia, from the Ural Mountains in the west to the Pacific Ocean in the east. It has been a part of ...

by Hatzenpichler and associates in 2008. The organism was isolated from a sample taken from the Siberian

hot spring A hot spring, hydrothermal spring, or geothermal spring is a spring produced by the emergence of geothermally heated groundwater onto the surface of the Earth. The groundwater is heated either by shallow bodies of magma (molten rock) or by circ ...

s that was actually located in a

microbial mat A microbial mat is a multi-layered sheet of microorganisms, mainly bacteria and archaea, or bacteria alone. Microbial mats grow at interfaces between different types of material, mostly on submerged or moist surfaces, but a few survive in deserts. ...

. Hatzenpichler et al. later grew the culture aerobically at 46℃ with

ammonium The ammonium cation is a positively-charged polyatomic ion with the chemical formula or . It is formed by the protonation of ammonia (). Ammonium is also a general name for positively charged or protonated substituted amines and quaternary a ...

and

bicarbonate In inorganic chemistry, bicarbonate (IUPAC-recommended nomenclature: hydrogencarbonate) is an intermediate form in the deprotonation of carbonic acid. It is a polyatomic anion with the chemical formula . Bicarbonate serves a crucial biochemic ...

. In 2007, the first indications of ''Nitrososphaera gargensis'' were found through testing a hot spring sample for ammonia oxidizers. The researchers found ammonia-oxidizing archaea instead of the expected bacteria with this capability since no previous archaea had been found to be able to complete this process. Through analyzing 16S rRNA gene sequences and performing the scientific methods of catalyzed reporter deposition (CARD)-

FISH Fish are aquatic, craniate, gill-bearing animals that lack limbs with digits. Included in this definition are the living hagfish, lampreys, and cartilaginous and bony fish as well as various extinct related groups. Approximately 95% of li ...

(fluorescence ''in situ'' hybridization) and microautoradiography, the researchers determined that the organism in the sample was an ammonia-oxidizing archaea and classified this organism as ''Candidatus Nitrososphaera gargensis''.

Genomics

''Nitrososphaera gargensis genome is 2.83 Mb in size with a

GC content In molecular biology and genetics, GC-content (or guanine-cytosine content) is the percentage of nitrogenous bases in a DNA or RNA molecule that are either guanine (G) or cytosine (C). This measure indicates the proportion of G and C bases out o ...

of 48%, which is much larger than most other ammonia-oxidizing archaea. The organism encodes for 3565

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...

gene In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...

s and 37

RNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...

genes.KEGG GENOME: Candidatus Nitrososphaera Gargensis. KEGG GENOME: Candidatus Nitrososphaera Gargensis. KEGG, 2012. http://www.genome.jp/kegg-bin/show_organism?org=nga ''N. gargensis'' also contains a

CRISPR CRISPR () (an acronym for clustered regularly interspaced short palindromic repeats) is a family of DNA sequences found in the genomes of prokaryotic organisms such as bacteria and archaea. These sequences are derived from DNA fragments of bacte ...

-Cas type I system able to target viral DNA,

gene duplication Gene duplication (or chromosomal duplication or gene amplification) is a major mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene. ...

s in its chaperones, and numerous

transposase A transposase is any of a class of enzymes capable of binding to the end of a transposon and catalysing its movement to another part of a genome, typically by a cut-and-paste mechanism or a replicative mechanism, in a process known as transposition ...

genes.

Taxonomy and phylogeny

''N. gargensis'' neighbors ''

Nitrosopumilus maritimus ''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 pure culture. Gene sequences suggest that the Group 1a Nitrososp ...

'' and ''Nitrososphaera viennensis'' on the

phylogenetic tree A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological spec ...

.Brochier-Armanet, Céline, et al. "Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota." Nature Reviews Microbiology6.3 (2008): 245-252. https://www.researchgate.net/publication/5576617_Brochier-Armanet_C_Boussau_B_Gribaldo_S_Forterre_P_Mesophilic_Crenarchaeota_proposal_for_a_third_archaeal_phylum_the_Thaumarchaeota_Nat_Rev_Microbiol_6_245-252 Like ''Nitrososphaera gargensis'', both of these organisms are

chemolithoautotrophic A lithoautotroph is an organism which derives energy from reactions of reduced compounds of mineral (inorganic) origin. Two types of lithoautotrophs are distinguished by their energy source; photolithoautotrophs derive their energy from light while ...

ammonia-oxidizers that thrive in hot and humid habitats. Spang et al. elucidated, in 2012, the notable similarities between ''N. gargensis'' and ''N. viennensis'' through their nitrification ability and PHA (putatively polyhydroxybutyrate) production along with other elements.

Nitrification and metabolism

As a chemolithoautotroph, ''Nitrososphaera gargensis'' performs aerobic oxidation of

ammonia Ammonia is an inorganic compound of nitrogen and hydrogen with the formula . A stable binary hydride, and the simplest pnictogen hydride, ammonia is a colourless gas with a distinct pungent smell. Biologically, it is a common nitrogenous was ...

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 breaks down

cyanate Cyanate is an anion with the structural formula , usually written . It also refers to any salt containing it, such as ammonium cyanate. It is an isomer of the much less stable fulminate anion .William R. Martin and David W. Ball (2019): "Small ...

for energy. ''N. gargensis'' also encompasses a flexible carbon

metabolism Metabolism (, from el, μεταβολή ''metabolē'', "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run cell ...

, allowing for the uptake of

organic material Organic matter, organic material, or natural organic matter refers to the large source of carbon-based compounds found within natural and engineered, terrestrial, and aquatic environments. It is matter composed of organic compounds that have c ...

Nitrification ''Nitrification'' is the biological oxidation of ammonia to nitrite followed by the oxidation of the nitrite to nitrate occurring through separate organisms or direct ammonia oxidation to nitrate in comammox bacteria. The transformation of amm ...

, the process of oxidizing ammonia to

nitrate Nitrate is a polyatomic ion A polyatomic ion, also known as a molecular ion, is a covalent bonded set of two or more atoms, or of a metal complex, that can be considered to behave as a single unit and that has a net charge that is not zer ...

, is a significant step in the

nitrogen cycle The nitrogen cycle is the biogeochemical cycle by which nitrogen is converted into multiple chemical forms as it circulates among atmospheric, terrestrial, and marine ecosystems. The conversion of nitrogen can be carried out through both biologi ...

. Since nitrogen is limited in marine environments, the recent discovery of ammonia-oxidizing archaea proves to be an active source of study for researchers. ''N. gargensis'' possesses ammonia monooxygenase, which is the enzyme that enables the organism the ability to oxidize ammonia, or

urea Urea, also known as carbamide, is an organic compound with chemical formula . This amide has two amino groups (–) joined by a carbonyl functional group (–C(=O)–). It is thus the simplest amide of carbamic acid. Urea serves an important r ...

and potentially cyanate as other sources of ammonia.

Habitat

''Nitrososphaera gargensis'' was discovered in a Garga hot spring and most commonly resides in similar heavy metal-containing thermal springs or can be isolated from microbial mats near hot springs. Besides hot springs, other ammonia-oxidizing archaea are commonly found in soil, freshwater, and the sediments in freshwater. ''N. gargensis'' grows best at 46℃ and thrives on the presence of ammonia or other nitrogen sources, and it utilizes flagella to move via chemotaxis.

Current research

Crenarchaeol isomer

The membrane composition of ammonia-oxidizing archaea, specifically through a crenarchaeol isomer, can be used to identify them as an AOA. ''N. gargensis'' was the first cultivated organism with the ability to produce a significant quantity of the crenarchaeol isomer. With its ability to synthesize crenarchaeol, ''N. gargensis'' allows scientists to expand this synthesis also to the Group I.1b Crenarchaeota. These discoveries indicate that these organisms are significant sources of crenarchaeol in their habitats of

thermophilic A thermophile is an organism—a type of extremophile—that thrives at relatively high temperatures, between . Many thermophiles are archaea, though they can be bacteria or fungi. Thermophilic eubacteria are suggested to have been among the earl ...

and terrestrial environments and corroborate the association between AOA and crenarchaeol.

Marine nitrogen cycles

Furthermore, ''Nitrososphaera gargensis'' influence as an ammonia-oxidizing archaea expands from land to water since its nitrification ability plays a role in the nitrogen cycles that are present in the ocean. The nitrogen cycle determines the interplay of organisms in marine

ecosystem An ecosystem (or ecological system) consists of all the organisms and the physical environment with which they interact. These biotic and abiotic components are linked together through nutrient cycles and energy flows. Energy enters the syste ...

s and the activity of the ocean.

Food production and fertilizers

Along with influencing the structure of soils and ocean communities, ''Nitrososphaera gargensis'' also plays a role in food production. Since nitrogen is required for food production, fertilizers containing nitrogen are used. This leads to pollution that can harm the environment and end up in wastewater. Therefore, researchers are trying to develop ways to remove the nitrogen from the affected areas. Organisms similar to ''Nitrososphaera gargensis'' were found to oxidize ammonia in this study, and with this knowledge, the researchers plan on coupling this ability with other processes in the nitrogen cycle in order to remove the form of nitrogen that is polluting the area. Such couplings could occur due to the fact that AOA are not affected by

nitrous acid Nitrous acid (molecular formula ) is a weak and monoprotic acid known only in Solution (chemistry), solution, in the gas phase and in the form of nitrite () salts. Nitrous acid is used to make diazonium salts from amines. The resulting diazoni ...

concentrations whereas nitrite-oxidizing bacteria are inhibited by this

chemical A chemical substance is a form of matter having constant chemical composition and characteristic properties. Some references add that chemical substance cannot be separated into its constituent elements by physical separation methods, i.e., wi ...

. In this difference, techniques could be developed to foster deammonification, which is more cost-effective. Overall, in these studies, researchers are trying to find the correct balance in a thermophilic

bioreactor A bioreactor refers to any manufactured device or system that supports a biologically active environment. In one case, a bioreactor is a vessel in which a chemical reaction, chemical process is carried out which involves organisms or biochemistry, ...

in order to eliminate nitrogen.