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The nitrogen cycle is the biogeochemical cycle by which nitrogen is converted into multiple chemical forms as it circulates among atmosphere, terrestrial, and marine ecosystems. The conversion of nitrogen can be carried out through both biological and physical processes. Important processes in the nitrogen cycle include fixation, ammonification, nitrification, and denitrification. The majority of Earth's atmosphere (78%) is atmospheric nitrogen, making it the largest source of nitrogen. However, atmospheric nitrogen has limited availability for biological use, leading to a scarcity of usable nitrogen in many types of ecosystems.
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 ammonia to nitrite is usually the rate limiting step of nitrification. Nitrification is an important step in the nitrogen cycle in soil. Nitrification is an aerobic process performed by small groups of autotrophic bacteria and archaea.
Nicotinamide adenine dinucleotide (NAD) is a coenzyme central to metabolism. Found in all living cells, NAD is called a dinucleotide because it consists of two nucleotides joined through their phosphate groups. One nucleotide contains an adenine nucleobase and the other nicotinamide. NAD exists in two forms: an oxidized and reduced form, abbreviated as NAD+ and NADH (H for hydrogen), respectively.
The nitrite ion has the chemical formula NO−
2. Nitrite is widely used throughout chemical and pharmaceutical industries. The nitrite anion is a pervasive intermediate in the nitrogen cycle in nature. The name nitrite can also refer to organic compounds with the – ONO group, which are esters of nitrous acid.
Anaerobic respiration is respiration using electron acceptors other than molecular oxygen (O2). Although oxygen is not the final electron acceptor, the process still uses a respiratory electron transport chain.
Anammox, an abbreviation for anaerobic ammonium oxidation, is a globally important microbial process of the nitrogen cycle that takes place in many natural environments. The bacteria mediating this process were identified in 1999, and were a great surprise for the scientific community. In the anammox reaction, nitrite and ammonium ions are converted directly into diatomic nitrogen and water.
Sergei Nikolaievich Winogradsky was a Ukrainian microbiologist, ecologist and soil scientist who pioneered the cycle-of-life concept.
Nitrobacter is a genus comprising rod-shaped, gram-negative, and chemoautotrophic bacteria. The name Nitrobacter derives from the Latin neuter gender noun nitrum, nitri, alkalis; the Ancient Greek noun βακτηρία, βακτηρίᾱς, rod. They are non-motile and reproduce via budding or binary fission. Nitrobacter cells are obligate aerobes and have a doubling time of about 13 hours.
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 oxidation of inorganic nitrogen compounds. Types include ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB). Many species of nitrifying bacteria have complex internal membrane systems that are the location for key enzymes in nitrification: ammonia monooxygenase, hydroxylamine oxidoreductase, and nitrite oxidoreductase.
Nitrospira translate into “a nitrate spiral” is a genus of bacteria within the monophyletic clade of the Nitrospirota phylum. The first member of this genus was described 1986 by Watson et al. isolated from the Gulf of Maine. The bacterium was named Nitrospira marina. Populations were initially thought to be limited to marine ecosystems, but it was later discovered to be well-suited for numerous habitats, including activated sludge of wastewater treatment systems, natural biological marine settings, water circulation biofilters in aquarium tanks, terrestrial systems, fresh and salt water ecosystems, and hot springs. Nitrospira is a ubiquitous bacterium that plays a role in the nitrogen cycle by performing nitrite oxidation in the second step of nitrification. Nitrospira live in a wide array of environments including but not limited to, drinking water systems, waste treatment plants, rice paddies, forest soils, geothermal springs, and sponge tissue. Despite being abundant in many natural and engineered ecosystems Nitrospira are difficult to culture, so most knowledge of them is from molecular and genomic data. However, due to their difficulty to be cultivated in laboratory settings, the entire genome was only sequenced in one species, Nitrospira defluvii. In addition, Nitrospira bacteria's 16s rRNA sequences are too dissimilar to use for PCR primers, thus some members go unnoticed. In addition, members of Nitrospira with the capabilities to perform complete nitrification has also been discovered and cultivated.
Nitrosopumilus maritimus is an extremely common archaeon living in seawater. It is the first member of the Group 1a Thaumarchaeota to be isolated in pure culture. Gene sequences suggest that the Group 1a Thaumarchaeota 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. N. maritimus cells are shaped like peanuts and can be found both as individuals and in loose aggregates. It lives by oxidizing ammonia to nitrite. N. maritimus is capable of oxidizing ammonia at levels as low as 10 nanomolar, near the limit to sustain its life. N. maritimus lives 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.
Nitrite oxidoreductase is an enzyme involved in nitrification. It is the last step in the process of aerobic ammonia oxidation, which is carried out by two groups of nitrifying bacteria: ammonia oxidizers such as Nitrosospira, Nitrosomonas and Nitrosococcus convert ammonia to nitrite, while nitrite oxidizers such as Nitrobacter and Nitrospira oxidize nitrite to nitrate.
Nitrobacter vulgaris is a rod-shaped, Gram-negative, and a chemoautotrophic bacterium. It plays an important role in the nitrogen cycle by oxidizing nitrite into nitrate in soil. It cannot tolerate highly alkaline (NH4+) conditions.
The Nitrobacteraceae are a family of gram-negative, aerobic bacteria. They include plant-associated bacteria such as Bradyrhizobium, a genus of rhizobia associated with some legumes. It also contains animal-associated bacteria such as Afipia felis, formerly thought to cause cat-scratch disease. Others are free-living, such as Rhodopseudomonas, a purple bacterium found in marine water and soils. The strain Rhodopseudomonas palustris DX-1 can generate an electric current with no hydrogen production, a trait being explored in the development of the microbial fuel cell. The genus Afipia has also been found in the atmosphere, where it uses methylsulfonylmethane as a carbon source.
Nitrospirota is a phylum of bacteria. It includes multiple genera, such as Nitrospira, the largest. The first member of this phylum, Nitrospira marina, was discovered in 1985. The second member, Nitrospira moscoviensis, was discovered in 1995.
Nitrospira moscoviensis was the second bacterium classified under the most diverse nitrite-oxidizing bacteria phylum, Nitrospirae. It is a gram-negative, non-motile, facultative lithoauthotropic bacterium that was discovered in Moscow, Russia in 1995. The genus name, Nitrospira, originates from the prefix “nitro” derived from nitrite, the microbe’s electron donor and “spira” meaning coil or spiral derived from the microbe’s shape. The species name, moscoviensis, is derived from Moscow, where the species was first discovered. N. moscoviensis could potentially be used in the production of bio-degradable polymers.
Nitrobacter alkalicus is a nitrite-oxidizing bacteria from the genus of Nitrobacter.
Urine patches in cattle pastures generate large concentrations of the greenhouse gas nitrous oxide through nitrification and denitrification processes in urine-contaminated soils. Over the past few decades, the cattle population has increased more rapidly than the human population. Between the years 2000 and 2050, the cattle population is expected to increase from 1.5 billion to 2.6 billion. When large populations of cattle are packed into pastures, excessive amounts of urine soak into soils. This increases the rate at which nitrification and denitrification occur and produce nitrous oxide. Currently, nitrous oxide is one of the single most important ozone-depleting emissions and is expected to remain the largest throughout the 21st century.
NC10 is a bacterial phylum with candidate status, meaning its members remain uncultured to date. The difficulty in producing lab cultures may be linked to low growth rates and other limiting growth factors.
Nitrospinota is a bacterial phylum. Despite only few described species, members of this phylum are major nitrite-oxidizing bacteria in surface waters in oceans. By oxidation of nitrite to nitrate they are important in the process of nitrification in marine environments.
References
- ↑ LPSN lpsn.dsmz.de
- 1 2 UniProt
- ↑ Starkenburg, S. R.; Chain, P. S.; Sayavedra-Soto, L. A.; Hauser, L; Land, M. L.; Larimer, F. W.; Malfatti, S. A.; Klotz, M. G.; Bottomley, P. J.; Arp, D. J.; Hickey, W. J. (2006). "Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium Nitrobacter winogradskyi Nb-255". Applied and Environmental Microbiology. 72 (3): 2050–63. doi:10.1128/AEM.72.3.2050-2063.2006. PMC 1393235 . PMID 16517654.