Nitrogen fixation

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Nitrogen fixation is a chemical process by which molecular dinitrogen (N
2) is converted into ammonia (NH
3). [1] It occurs both biologically and abiologically in chemical industries. Biological nitrogen fixation or diazotrophy is catalyzed by enzymes called nitrogenases. [2] These enzyme complexes are encoded by the Nif genes (or Nif homologs) and contain iron, often with a second metal (usually molybdenum, but sometimes vanadium). [3]

Contents

Some nitrogen-fixing bacteria have symbiotic relationships with plants, especially legumes, mosses and aquatic ferns such as Azolla . [4] Looser non-symbiotic relationships between diazotrophs and plants are often referred to as associative, as seen in nitrogen fixation on rice roots. Nitrogen fixation occurs between some termites and fungi. [5] It occurs naturally in the air by means of NOx production by lightning. [6] [7]

Nitrogen fixation is essential to life on Earth because fixed inorganic nitrogen compounds are required for the biosynthesis of all nitrogen-containing organic compounds such as amino acids, polypeptides and proteins, nucleoside triphosphates and nucleic acids. As part of the nitrogen cycle, it is essential for soil fertility and the growth of terrestrial and semiaquatic vegetations, upon which all consumers of those ecosystems rely for biomass. Nitrogen fixation is thus crucial to the food security of human societies in sustaining agricultural yields (especially staple crops), livestock feeds (forage or fodder) and fishery (both wild and farmed) harvests. It is also indirectly relevant to the manufacture of all nitrogenous industrial products, which include fertilizers, pharmaceuticals, textiles, dyes and explosives.

History

Schematic representation of the nitrogen cycle. Abiotic nitrogen fixation has been omitted. Nitrogen Cycle.svg
Schematic representation of the nitrogen cycle. Abiotic nitrogen fixation has been omitted.

Biological nitrogen fixation was discovered by Jean-Baptiste Boussingault in 1838. [8] [9] Later, in 1880, the process by which it happens was discovered by German agronomist Hermann Hellriegel and Hermann Wilfarth  [ de ] [10] and was fully described by Dutch microbiologist Martinus Beijerinck. [11]

"The protracted investigations of the relation of plants to the acquisition of nitrogen begun by de Saussure, Ville, Lawes, Gilbert and others, and culminated in the discovery of symbiotic fixation by Hellriegel and Wilfarth in 1887." [12]

"Experiments by Bossingault in 1855 and Pugh, Gilbert & Lawes in 1887 had shown that nitrogen did not enter the plant directly. The discovery of the role of nitrogen fixing bacteria by Herman Hellriegel and Herman Wilfarth in 1886-1888 would open a new era of soil science." [13]

In 1901, Beijerinck showed that Azotobacter chroococcum was able to fix atmospheric nitrogen. This was the first species of the azotobacter genus, so-named by him. It is also the first known diazotroph, species that use diatomic nitrogen as a step in the complete nitrogen cycle. [14]

Biological

Biological nitrogen fixation (BNF) occurs when atmospheric nitrogen is converted to ammonia by a nitrogenase enzyme. [1] The overall reaction for BNF is:

N2 + 16ATP + 16H2O + 8e− + 8H+ → 2NH3 +H2 + 16ADP + 16Pi

The process is coupled to the hydrolysis of 16 equivalents of ATP and is accompanied by the co-formation of one equivalent of H
2. [15] The conversion of N
2 into ammonia occurs at a metal cluster called FeMoco, an abbreviation for the iron-molybdenum cofactor. The mechanism proceeds via a series of protonation and reduction steps wherein the FeMoco active site hydrogenates the N
2 substrate. [16] In free-living diazotrophs, nitrogenase-generated ammonia is assimilated into glutamate through the glutamine synthetase/glutamate synthase pathway. The microbial nif genes required for nitrogen fixation are widely distributed in diverse environments. [17]

For example, decomposing wood, which generally has a low nitrogen content, has been shown to host a diazotrophic community. [18] [19] The bacteria enrich the wood substrate with nitrogen through fixation, thus enabling deadwood decomposition by fungi. [20]

Nitrogenases are rapidly degraded by oxygen. For this reason, many bacteria cease production of the enzyme in the presence of oxygen. Many nitrogen-fixing organisms exist only in anaerobic conditions, respiring to draw down oxygen levels, or binding the oxygen with a protein such as leghemoglobin. [21] [22]

Importance of nitrogen

Atmospheric nitrogen is inaccessible to most organisms, [23] because its triple covalent bond is very strong. Most take up fixed nitrogen from various sources. For every 100 atoms of carbon, roughly 2 to 20 atoms of nitrogen are assimilated. The atomic ratio of carbon (C) : nitrogen (N) : phosphorus (P) observed on average in planktonic biomass was originally described by Alfred Redfield, [24] who determined the stoichiometric relationship between C:N:P atoms, The Redfield Ratio, to be 106:16:1. [24]

Nitrogenase

The protein complex nitrogenase is responsible for catalyzing the reduction of nitrogen gas (N2) to ammonia (NH3). [25] [26] In cyanobacteria, this enzyme system is housed in a specialized cell called the heterocyst. [27] The production of the nitrogenase complex is genetically regulated, and the activity of the protein complex is dependent on ambient oxygen concentrations, and intra- and extracellular concentrations of ammonia and oxidized nitrogen species (nitrate and nitrite). [28] [29] [30] Additionally, the combined concentrations of both ammonium and nitrate are thought to inhibit NFix, specifically when intracellular concentrations of 2-oxoglutarate (2-OG) exceed a critical threshold. [31] The specialized heterocyst cell is necessary for the performance of nitrogenase as a result of its sensitivity to ambient oxygen. [32]

Nitrogenase consist of two proteins, a catalytic iron-dependent protein, commonly referred to as MoFe protein and a reducing iron-only protein (Fe protein). There are three different iron dependent proteins, molybdenum-dependent, vanadium-dependent, and iron-only, with all three nitrogenase protein variations containing an iron protein component. Molybdenum-dependent nitrogenase is the most commonly present nitrogenase. [33] The different types of nitrogenase can be determined by the specific iron protein component. [34] Nitrogenase is highly conserved. Gene expression through DNA sequencing can distinguish which protein complex is present in the microorganism and potentially being expressed. Most frequently, the nifH gene is used to identify the presence of molybdenum-dependent nitrogenase, followed by closely related nitrogenase reductases (component II) vnfH and anfH representing vanadium-dependent and iron-only nitrogenase, respectively. [35] In studying the ecology and evolution of nitrogen-fixing bacteria, the nifH gene is the biomarker most widely used. [36] nifH has two similar genes anfH and vnfH that also encode for the nitrogenase reductase component of the nitrogenase complex. [37]

Evolution of Nitrogenase

Nitrogenase is thought to have evolved sometime between 1.5-2.2 billion years ago (Ga), [38] [39] although some isotopic support showing nitrogenase evolution as early as around 3.2 Ga. [40] Nitrogenase appears to have evolved from maturase-like proteins, although the function of the preceding protein is currently unknown. [41]

Nitrogenase has three different forms (Nif, Anf, and Vnf) that correspond with the metal found in the active site of the protein (Molybdenum, Iron, and Vanadium respectively). [42] Marine metal abundances over Earth’s geologic timeline are thought to have driven the relative abundance of which form of nitrogenase was most common. [43] Currently, there is no conclusive agreement on which form of nitrogenase arose first.

Microorganisms

Diazotrophs are widespread within domain Bacteria including cyanobacteria (e.g. the highly significant Trichodesmium and Cyanothece ), green sulfur bacteria, purple sulfur bacteria, Azotobacteraceae, rhizobia and Frankia. [44] [45] Several obligately anaerobic bacteria fix nitrogen including many (but not all) Clostridium spp. Some archaea such as Methanosarcina acetivorans also fix nitrogen, [46] and several other methanogenic taxa, are significant contributors to nitrogen fixation in oxygen-deficient soils. [47]

Cyanobacteria, commonly known as blue-green algae, inhabit nearly all illuminated environments on Earth and play key roles in the carbon and nitrogen cycle of the biosphere. In general, cyanobacteria can use various inorganic and organic sources of combined nitrogen, such as nitrate, nitrite, ammonium, urea, or some amino acids. Several cyanobacteria strains are also capable of diazotrophic growth, an ability that may have been present in their last common ancestor in the Archean eon. [48] Nitrogen fixation not only naturally occurs in soils but also aquatic systems, including both freshwater and marine. [49] [50] Indeed, the amount of nitrogen fixed in the ocean is at least as much as that on land. [51] The colonial marine cyanobacterium Trichodesmium is thought to fix nitrogen on such a scale that it accounts for almost half of the nitrogen fixation in marine systems globally. [52] Marine surface lichens and non-photosynthetic bacteria belonging in Proteobacteria and Planctomycetes fixate significant atmospheric nitrogen. [53] Species of nitrogen fixing cyanobacteria in fresh waters include: Aphanizomenon and Dolichospermum (previously Anabaena). [54] Such species have specialized cells called heterocytes, in which nitrogen fixation occurs via the nitrogenase enzyme. [55] [56]

Algae

One type of organelle can turn nitrogen gas into a biologically available form. This nitroplast was discovered in algae. [57]

Root nodule symbioses

Legume family

Nodules are visible on this broad bean root Root nodules on fava bean plant.jpg
Nodules are visible on this broad bean root

Plants that contribute to nitrogen fixation include those of the legume family—Fabaceae— with taxa such as kudzu, clover, soybean, alfalfa, lupin, peanut and rooibos. [45] They contain symbiotic rhizobia bacteria within nodules in their root systems, producing nitrogen compounds that help the plant to grow and compete with other plants. [58] When the plant dies, the fixed nitrogen is released, making it available to other plants; this helps to fertilize the soil. [21] [59] The great majority of legumes have this association, but a few genera (e.g., Styphnolobium ) do not. In many traditional farming practices, fields are rotated through various types of crops, which usually include one consisting mainly or entirely of clover.[ citation needed ]

Fixation efficiency in soil is dependent on many factors, including the legume and air and soil conditions. For example, nitrogen fixation by red clover can range from 50 to 200 lb/acre (56 to 224 kg/ha). [60]

Non-leguminous

A sectioned alder tree root nodule A sectioned alder root nodule gall.JPG
A sectioned alder tree root nodule

The ability to fix nitrogen in nodules is present in actinorhizal plants such as alder and bayberry, with the help of Frankia bacteria. They are found in 25 genera in the orders Cucurbitales, Fagales and Rosales, which together with the Fabales form a nitrogen-fixing clade of eurosids. The ability to fix nitrogen is not universally present in these families. For example, of 122 Rosaceae genera, only four fix nitrogen. Fabales were the first lineage to branch off this nitrogen-fixing clade; thus, the ability to fix nitrogen may be plesiomorphic and subsequently lost in most descendants of the original nitrogen-fixing plant; however, it may be that the basic genetic and physiological requirements were present in an incipient state in the most recent common ancestors of all these plants, but only evolved to full function in some of them. [61]

In addition, Trema (Parasponia), a tropical genus in the family Cannabaceae, is unusually able to interact with rhizobia and form nitrogen-fixing nodules. [62]

Non-legumious nodulating plants
FamilyGeneraSpecies
Betulaceae
Most or all species
Boraginaceae
Cannabaceae
Casuarinaceae
Coriariaceae
Datiscaceae
Elaeagnaceae
Myricaceae
Posidoniaceae
Rhamnaceae
Rosaceae

Other plant symbionts

Some other plants live in association with a cyanobiont (cyanobacteria such as Nostoc ) which fix nitrogen for them:

Some symbiotic relationships involving agriculturally-important plants are: [65]

Industrial processes

Historical

A method for nitrogen fixation was first described by Henry Cavendish in 1784 using electric arcs reacting nitrogen and oxygen in air. This method was implemented in the Birkeland–Eyde process of 1903. [67] The fixation of nitrogen by lightning is a very similar natural occurring process.

The possibility that atmospheric nitrogen reacts with certain chemicals was first observed by Desfosses in 1828. He observed that mixtures of alkali metal oxides and carbon react with nitrogen at high temperatures. With the use of barium carbonate as starting material, the first commercial process became available in the 1860s, developed by Margueritte and Sourdeval. The resulting barium cyanide reacts with steam, yielding ammonia. In 1898 Frank and Caro developed what is known as the Frank–Caro process to fix nitrogen in the form of calcium cyanamide. The process was eclipsed by the Haber process, which was discovered in 1909. [68] [69]

Haber process

Equipment for a study of nitrogen fixation by alpha rays (Fixed Nitrogen Research Laboratory, 1926) THC 2003.902.022 D. C. Bardwell Study of Nitrogen Fixation.tif
Equipment for a study of nitrogen fixation by alpha rays (Fixed Nitrogen Research Laboratory, 1926)

The dominant industrial method for producing ammonia is the Haber process also known as the Haber-Bosch process. [70] Fertilizer production is now the largest source of human-produced fixed nitrogen in the terrestrial ecosystem. Ammonia is a required precursor to fertilizers, explosives, and other products. The Haber process requires high pressures (around 200 atm) and high temperatures (at least 400 °C), which are routine conditions for industrial catalysis. This process uses natural gas as a hydrogen source and air as a nitrogen source. The ammonia product has resulted in an intensification of nitrogen fertilizer globally [71] and is credited with supporting the expansion of the human population from around 2 billion in the early 20th century to roughly 8 billion people now. [72]

Homogeneous catalysis

Much research has been conducted on the discovery of catalysts for nitrogen fixation, often with the goal of lowering energy requirements. However, such research has thus far failed to approach the efficiency and ease of the Haber process. Many compounds react with atmospheric nitrogen to give dinitrogen complexes. The first dinitrogen complex to be reported was Ru(NH
3)
5(N
2)2+. [73] Some soluble complexes do catalyze nitrogen fixation. [74]

Lightning

Lightning heats the air around it in a high-temperature plasma, breaking the bonds of N 2, starting the formation of nitrous acid (HNO 2). Lightning Pritzerbe 01 (MK).jpg
Lightning heats the air around it in a high-temperature plasma, breaking the bonds of N
2, starting the formation of nitrous acid (HNO
2).

Nitrogen can be fixed by lightning converting nitrogen gas (N
2) and oxygen gas (O
2) in the atmosphere into NOx (nitrogen oxides). The N
2 molecule is highly stable and nonreactive due to the triple bond between the nitrogen atoms. [75] Lightning produces enough energy and heat to break this bond [75] allowing nitrogen atoms to react with oxygen, forming NO
x. These compounds cannot be used by plants, but as this molecule cools, it reacts with oxygen to form NO
2, [76] which in turn reacts with water to produce HNO
2 (nitrous acid) or HNO
3 (nitric acid). When these acids seep into the soil, they make NO3- (nitrate), which is of use to plants. [77] [75]

See also

Related Research Articles

<span class="mw-page-title-main">Nitrogen cycle</span> Biogeochemical cycle by which nitrogen is converted into various chemical forms

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 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.

<i>Trichodesmium</i> Genus of bacteria

Trichodesmium, also called sea sawdust, is a genus of filamentous cyanobacteria. They are found in nutrient poor tropical and subtropical ocean waters. Trichodesmium is a diazotroph; that is, it fixes atmospheric nitrogen into ammonium, a nutrient used by other organisms. Trichodesmium is thought to fix nitrogen on such a scale that it accounts for almost half of the nitrogen fixation in marine systems globally. Trichodesmium is the only known diazotroph able to fix nitrogen in daylight under aerobic conditions without the use of heterocysts.

<span class="mw-page-title-main">Heterocyst</span>

Heterocysts or heterocytes are specialized nitrogen-fixing cells formed during nitrogen starvation by some filamentous cyanobacteria, such as Nostoc, Cylindrospermum, and Anabaena. They fix nitrogen from dinitrogen (N2) in the air using the enzyme nitrogenase, in order to provide the cells in the filament with nitrogen for biosynthesis.

Diazotrophs are bacteria and archaea that fix atmospheric nitrogen (N2) in the atmosphere into bioavailable forms such as ammonia.

<span class="mw-page-title-main">Nitrogenase</span> Class of enzymes

Nitrogenases are enzymes (EC 1.18.6.1EC 1.19.6.1) that are produced by certain bacteria, such as cyanobacteria (blue-green bacteria) and rhizobacteria. These enzymes are responsible for the reduction of nitrogen (N2) to ammonia (NH3). Nitrogenases are the only family of enzymes known to catalyze this reaction, which is a step in the process of nitrogen fixation. Nitrogen fixation is required for all forms of life, with nitrogen being essential for the biosynthesis of molecules (nucleotides, amino acids) that create plants, animals and other organisms. They are encoded by the Nif genes or homologs. They are related to protochlorophyllide reductase.

<i>Azotobacter</i> Genus of bacteria

Azotobacter is a genus of usually motile, oval or spherical bacteria that form thick-walled cysts and may produce large quantities of capsular slime. They are aerobic, free-living soil microbes that play an important role in the nitrogen cycle in nature, binding atmospheric nitrogen, which is inaccessible to plants, and releasing it in the form of ammonium ions into the soil. In addition to being a model organism for studying diazotrophs, it is used by humans for the production of biofertilizers, food additives, and some biopolymers. The first representative of the genus, Azotobacter chroococcum, was discovered and described in 1901 by Dutch microbiologist and botanist Martinus Beijerinck. Azotobacter species are Gram-negative bacteria found in neutral and alkaline soils, in water, and in association with some plants.

<i>Rhodospirillum rubrum</i> Species of bacterium

Rhodospirillum rubrum is a Gram-negative, pink-coloured bacterium, with a size of 800 to 1000 nanometers. It is a facultative anaerobe, thus capable of using oxygen for aerobic respiration under aerobic conditions, or an alternative terminal electron acceptor for anaerobic respiration under anaerobic conditions. Alternative terminal electron acceptors for R. rubrum include dimethyl sulfoxide or trimethylamine oxide.

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<span class="mw-page-title-main">Biohydrogen</span> Hydrogen that is produced biologically

Biohydrogen is H2 that is produced biologically. Interest is high in this technology because H2 is a clean fuel and can be readily produced from certain kinds of biomass, including biological waste. Furthermore some photosynthetic microorganisms are capable to produce H2 directly from water splitting using light as energy source.

The nif genes are genes encoding enzymes involved in the fixation of atmospheric nitrogen into a form of nitrogen available to living organisms. The primary enzyme encoded by the nif genes is the nitrogenase complex which is in charge of converting atmospheric nitrogen (N2) to other nitrogen forms such as ammonia which the organism can use for various purposes. Besides the nitrogenase enzyme, the nif genes also encode a number of regulatory proteins involved in nitrogen fixation. The nif genes are found in both free-living nitrogen-fixing bacteria and in symbiotic bacteria associated with various plants. The expression of the nif genes is induced as a response to low concentrations of fixed nitrogen and oxygen concentrations (the low oxygen concentrations are actively maintained in the root environment of host plants). The first Rhizobium genes for nitrogen fixation (nif) and for nodulation (nod) were cloned in the early 1980s by Gary Ruvkun and Sharon R. Long in Frederick M. Ausubel's laboratory.

Cyanobionts are cyanobacteria that live in symbiosis with a wide range of organisms such as terrestrial or aquatic plants; as well as, algal and fungal species. They can reside within extracellular or intracellular structures of the host. In order for a cyanobacterium to successfully form a symbiotic relationship, it must be able to exchange signals with the host, overcome defense mounted by the host, be capable of hormogonia formation, chemotaxis, heterocyst formation, as well as possess adequate resilience to reside in host tissue which may present extreme conditions, such as low oxygen levels, and/or acidic mucilage. The most well-known plant-associated cyanobionts belong to the genus Nostoc. With the ability to differentiate into several cell types that have various functions, members of the genus Nostoc have the morphological plasticity, flexibility and adaptability to adjust to a wide range of environmental conditions, contributing to its high capacity to form symbiotic relationships with other organisms. Several cyanobionts involved with fungi and marine organisms also belong to the genera Richelia, Calothrix, Synechocystis, Aphanocapsa and Anabaena, as well as the species Oscillatoria spongeliae. Although there are many documented symbioses between cyanobacteria and marine organisms, little is known about the nature of many of these symbioses. The possibility of discovering more novel symbiotic relationships is apparent from preliminary microscopic observations.

<span class="mw-page-title-main">Bacterioplankton</span> Bacterial component of the plankton that drifts in the water column

Bacterioplankton refers to the bacterial component of the plankton that drifts in the water column. The name comes from the Ancient Greek word πλαγκτός (planktós), meaning "wandering" or "drifting", and bacterium, a Latin term coined in the 19th century by Christian Gottfried Ehrenberg. They are found in both seawater and fresh water.

<span class="mw-page-title-main">Vanadium nitrogenase</span> Enzyme necessary for the process of nitrogen fixation

Vanadium nitrogenase is a key enzyme for nitrogen fixation found in nitrogen-fixing bacteria, and is used as an alternative to molybdenum nitrogenase when molybdenum is unavailable. Vanadium nitrogenases are an important biological use of vanadium, which is uncommonly used by life. An important component of the nitrogen cycle, vanadium nitrogenase converts nitrogen gas to ammonia, thereby making otherwise inaccessible nitrogen available to plants. Unlike molybdenum nitrogenase, vanadium nitrogenase can also reduce carbon monoxide to ethylene, ethane and propane but both enzymes can reduce protons to hydrogen gas and acetylene to ethylene.

Candidatus Atelocyanobacterium thalassa, also referred to as UCYN-A, is a nitrogen-fixing species of cyanobacteria commonly found in measurable quantities throughout the world's oceans and some seas. Members of A. thalassa are spheroid in shape and are 1-2 μm in diameter, and provide nitrogen to ocean regions by fixing non biologically available atmospheric nitrogen into biologically available ammonium that other marine microorganisms can use.

Raphidiopsis raciborskii is a freshwater cyanobacterium.

<span class="mw-page-title-main">FeMoco</span> Cofactor of nitrogenase

FeMoco (FeMo cofactor) is the primary cofactor of nitrogenase. Nitrogenase is the enzyme that catalyzes the conversion of atmospheric nitrogen molecules N2 into ammonia (NH3) through the process known as nitrogen fixation. Because it contains iron and molybdenum, the cofactor is called FeMoco. Its stoichiometry is Fe7MoS9C.

<i>Cyanothece</i> Genus of bacteria

Cyanothece is a genus of unicellular, diazotrophic, oxygenic photosynthesizing cyanobacteria.

<i>Crocosphaera watsonii</i> Species of bacterium

Crocosphaera watsonii is an isolate of a species of unicellular diazotrophic marine cyanobacteria which represent less than 0.1% of the marine microbial population. They thrive in offshore, open-ocean oligotrophic regions where the waters are warmer than 24 degrees Celsius. Crocosphaera watsonii cell density can exceed 1,000 cells per milliliter within the euphotic zone; however, their growth may be limited by the concentration of phosphorus. Crocosphaera watsonii are able to contribute to the oceanic carbon and nitrogen budgets in tropical oceans due to their size, abundance, and rapid growth rate. Crocosphaera watsonii are unicellular nitrogen fixers that fix atmospheric nitrogen to ammonia during the night and contribute to new nitrogen in the oceans. They are a major source of nitrogen to open-ocean systems. Nitrogen fixation is important in the oceans as it not only allows phytoplankton to continue growing when nitrogen and ammonium are in very low supply but it also replenishes other forms of nitrogen, thus fertilizing the ocean and allowing more phytoplankton growth.

Trichodesmium thiebautii is a cyanobacteria that is often found in open oceans of tropical and subtropical regions and is known to be a contributor to large oceanic surface blooms. This microbial species is a diazotroph, meaning it fixes nitrogen gas (N2), but it does so without the use of heterocysts. T. thiebautii is able to simultaneously perform oxygenic photosynthesis. T. thiebautii was discovered in 1892 by M.A. Gomont. T. thiebautii are important for nutrient cycling in marine habitats because of their ability to fix N2, a limiting nutrient in ocean ecosystems.

Richelia is a genus of nitrogen-fixing, filamentous, heterocystous and cyanobacteria. It contains the single species Richelia intracellularis. They exist as both free-living organisms as well as symbionts within potentially up to 13 diatoms distributed throughout the global ocean. As a symbiont, Richelia can associate epiphytically and as endosymbionts within the periplasmic space between the cell membrane and cell wall of diatoms.

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