A report on Nitrogen fixation and Diazotroph

Schematic representation of the nitrogen cycle. Abiotic nitrogen fixation has been omitted.
Leguminous plants used to fertilize an abandoned land
Nodules are visible on this broad bean root
A sectioned alder tree root nodule
Equipment for a study of nitrogen fixation by alpha rays (Fixed Nitrogen Research Laboratory, 1926)
Lightning heats the air around it breaking the bonds of starting the formation of nitrous acid.

Diazotrophs are bacteria and archaea that fix atmospheric nitrogen gas into a more usable form such as ammonia.

- Diazotroph

Nitrogen fixation is carried out naturally in soil by microorganisms termed diazotrophs that include bacteria, such as Azotobacter, and archaea.

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

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Overall
Structure of the FeMo cofactor showing the sites of binding to nitrogenase (the amino acids cys and his).

Nitrogenase

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Nitrogenases are enzymes that are produced by certain bacteria, such as cyanobacteria (blue-green bacteria) and rhizobacteria.

Nitrogenases are enzymes that are produced by certain bacteria, such as cyanobacteria (blue-green bacteria) and rhizobacteria.

Structure of the FeMo cofactor showing the sites of binding to nitrogenase (the amino acids cys and his).
Figure 1: Nitrogenase with key catalytic sites highlighted. There are two sets of catalytic sites within each nitrogenase enzyme.
Figure 2: Nitrogenase with one set of metal clusters magnified. Electrons travel from the Fe-S cluster (yellow) to the P cluster (red), and end at the FeMo-co (orange).
Figure 3: Key catalytic sites within nitrogenase. Atoms are colored by element. Top: Fe-S Cluster Middle: P Cluster Bottom: FeMo-co
Figure 4: Lowe-Thorneley kinetic model for reduction of nitrogen to ammonia by nitrogenase.
Figure 5: Distal vs. alternating mechanistic pathways for nitrogen fixation in nitrogenase.
Figure 6: Amino acid residues of nitrogenase that interact with MgATP during catalysis.

Nitrogenases are the only family of enzymes known to catalyze this reaction, which is a key step in the process of nitrogen fixation.

Molybdenum nitrogenase, which can be found in diazotrophs such as legume-associated rhizobia, is the nitrogenase that has been studied the most extensively and thus is the most well characterized.

Cyanobacteria

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Cyanobacteria, also known as Cyanophyta, are a phylum of Gram-negative bacteria that obtain energy via photosynthesis.

Cyanobacteria, also known as Cyanophyta, are a phylum of Gram-negative bacteria that obtain energy via photosynthesis.

Cyanobacteria are found almost everywhere. Sea spray containing marine microorganisms, including cyanobacteria, can be swept high into the atmosphere where they become aeroplankton, and can travel the globe before falling back to earth.
• Unicellular: (a) Synechocystis and (b) Synechococcus elongatus • Non-heterocytous: (c) Arthrospira maxima,• False- or non-branching heterocytous: (f) Nostoc• True-branching heterocytous: (h) Stigonema
Outer and plasma membranes are in blue, thylakoid membranes in gold, glycogen granules in cyan, carboxysomes (C) in green, and a large dense polyphosphate granule (G) in pink
Environmental impact of cyanobacteria and other photosynthetic microorganisms in aquatic systems. Different classes of photosynthetic microorganisms are found in aquatic and marine environments where they form the base of healthy food webs and participate in symbioses with other organisms. However, shifting environmental conditions can result in community dysbiosis, where the growth of opportunistic species can lead to harmful blooms and toxin production with negative consequences to human health, livestock and fish stocks. Positive interactions are indicated by arrows; negative interactions are indicated by closed circles on the ecological model.
Diagnostic Drawing: Cyanobacteria associated with tufa: Microcoleus vaginatus
(1) Cyanobacteria enter the leaf tissue through the stomata and colonize the intercellular space, forming a cyanobacterial loop. (2) On the root surface, cyanobacteria exhibit two types of colonization pattern; in the root hair, filaments of Anabaena and Nostoc species form loose colonies, and in the restricted zone on the root surface, specific Nostoc species form cyanobacterial colonies. (3) Co-inoculation with 2,4-D and Nostoc spp. increases para-nodule formation and nitrogen fixation. A large number of Nostoc spp. isolates colonize the root endosphere and form para-nodules.
Live cyanobionts (cyanobacterial symbionts) belonging to Ornithocercus dinoflagellate host consortium (a) O. magnificus with numerous cyanobionts present in the upper and lower girdle lists (black arrowheads) of the cingulum termed the symbiotic chamber. (b) O. steinii with numerous cyanobionts inhabiting the symbiotic chamber. (c) Enlargement of the area in (b) showing two cyanobionts that are being divided by binary transverse fission (white arrows).
Light microscope view of cyanobacteria from a microbial mat
Types of cell death according to the Nomenclature Committee on Cell Death (upper panel; and proposed for cyanobacteria (lower panel). Cells exposed to extreme injury die in an uncontrollable manner, reflecting the loss of structural integrity. This type of cell death is called "accidental cell death" (ACD). “Regulated cell death (RCD)” is encoded by a genetic pathway that can be modulated by genetic or pharmacologic interventions. Programmed cell death (PCD) is a type of RCD that occurs as a developmental program, and has not been addressed in cyanobacteria yet. RN, regulated necrosis.
Synechococcus uses a gliding technique to move at 25 μm/s. Scale bar is about 10 µm.
Based on data: nodes (1–10) and stars representing common ancestors from Sánchez-Baracaldo et al., 2015, timing of the Great Oxidation Event (GOE), the Lomagundi-Jatuli Excursion, and Gunflint formation. Green lines represent freshwater lineages and blue lines represent marine lineages are based on Bayesian inference of character evolution (stochastic character mapping analyses).
Tree of Life in Generelle Morphologie der Organismen (1866). Note the location of the genus Nostoc with algae and not with bacteria (kingdom "Monera")
Cyanobacteria cultured in specific media: Cyanobacteria can be helpful in agriculture as they have the ability to fix atmospheric nitrogen in soil.
Spirulina tablets
Stromatolites left behind by cyanobacteria are the oldest known fossils of life on Earth. This fossil is one billion years old.
Oncolitic limestone formed from successive layers of calcium carbonate precipitated by cyanobacteria
Oncolites from the Late Devonian Alamo bolide impact in Nevada
{{center|Cyanobacterial remains of an annulated tubular microfossil Oscillatoriopsis longa{{hsp}}<ref>{{cite journal |doi=10.1111/pala.12374 |title=First record of Cyanobacteria in Cambrian Orsten deposits of Sweden |year=2018 |last1=Castellani |first1=Christopher |last2=Maas |first2=Andreas |last3=Eriksson |first3=Mats E. |last4=Haug |first4=Joachim T. |last5=Haug |first5=Carolin |last6=Waloszek |first6=Dieter |journal=Palaeontology |volume=61 |issue=6 |pages=855–880 |s2cid=134049042}}</ref>
Cyanobacteria activity turns Coatepeque Caldera lake a turquoise color
Cyanobacterial bloom near Fiji
Cyanobacteria in Lake Köyliö.

Some species are nitrogen-fixing and live in a wide variety of moist soils and water, either freely or in a symbiotic relationship with plants or lichen-forming fungi (as in the lichen genus Peltigera).

The relationships between cyanobionts (cyanobacterial symbionts) and protistan hosts are particularly noteworthy, as some nitrogen-fixing cyanobacteria (diazotrophs) play an important role in primary production, especially in nitrogen-limited oligotrophic oceans.

Bacteria

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Bacteria (singular bacterium, common noun bacteria) are ubiquitous, mostly free-living organisms often consisting of one biological cell.

Bacteria (singular bacterium, common noun bacteria) are ubiquitous, mostly free-living organisms often consisting of one biological cell.

Rod-shaped Bacillus subtilis
Phylogenetic tree of Bacteria, Archaea and Eucarya. The vertical line at bottom represents the last universal common ancestor.
Bacteria display many cell morphologies and arrangements
The range of sizes shown by prokaryotes (Bacteria), relative to those of other organisms and biomolecules.
Structure and contents of a typical Gram-positive bacterial cell (seen by the fact that only one cell membrane is present).
An electron micrograph of Halothiobacillus neapolitanus cells with carboxysomes inside, with arrows highlighting visible carboxysomes. Scale bars indicate 100 nm.
Helicobacter pylori electron micrograph, showing multiple flagella on the cell surface
Bacillus anthracis (stained purple) growing in cerebrospinal fluid
Many bacteria reproduce through binary fission, which is compared to mitosis and meiosis in this image.
A culture of ''Salmonella
A colony of Escherichia coli
Helium ion microscopy image showing T4 phage infecting E. coli. Some of the attached phage have contracted tails indicating that they have injected their DNA into the host. The bacterial cells are ~ 0.5 µm wide.
Transmission electron micrograph of Desulfovibrio vulgaris showing a single flagellum at one end of the cell. Scale bar is 0.5 micrometers long.
The different arrangements of bacterial flagella: A-Monotrichous; B-Lophotrichous; C-Amphitrichous; D-Peritrichous
Streptococcus mutans visualised with a Gram stain.
Phylogenetic tree showing the diversity of bacteria, compared to other organisms. Here bacteria are represented by three main supergroups: the CPR ultramicrobacterias, Terrabacteria and Gracilicutes according to recent genomic analyzes (2019).
Overview of bacterial infections and main species involved.
Colour-enhanced scanning electron micrograph showing Salmonella typhimurium (red) invading cultured human cells
In bacterial vaginosis, beneficial bacteria in the vagina (top) are displaced by pathogens (bottom). Gram stain.
Antonie van Leeuwenhoek, the first microbiologist and the first person to observe bacteria using a microscope.

Bacteria are vital in many stages of the nutrient cycle by recycling nutrients such as the fixation of nitrogen from the atmosphere.

One example is that some bacteria called diazotrophs have the ability to fix nitrogen gas using the enzyme nitrogenase.

Root nodules, each containing billions of Rhizobiaceae bacteria

Rhizobia

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Root nodules, each containing billions of Rhizobiaceae bacteria
Rhizobia nodules on Vigna unguiculata

Rhizobia are diazotrophic bacteria that fix nitrogen after becoming established inside the root nodules of legumes (Fabaceae).

A cluster of Escherichia coli bacteria magnified 10,000 times

Microorganism

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Organism of microscopic size, which may exist in its single-celled form or as a colony of cells.

Organism of microscopic size, which may exist in its single-celled form or as a colony of cells.

A cluster of Escherichia coli bacteria magnified 10,000 times
Antonie van Leeuwenhoek was the first to study microscopic organisms.
Lazzaro Spallanzani showed that boiling a broth stopped it from decaying.
Vardhmana Mahavira postulated the existence of microscopic creatures in the sixth century BC.
Louis Pasteur showed that Spallanzani's findings held even if air could enter through a filter that kept particles out.
Robert Koch showed that microorganisms caused disease.
Staphylococcus aureus bacteria magnified about 10,000x
Euglena mutabilis, a photosynthetic flagellate
A tetrad of Deinococcus radiodurans, a radioresistant extremophile bacterium
The photosynthetic cyanobacterium Hyella caespitosa (round shapes) with fungal hyphae (translucent threads) in the lichen Pyrenocollema halodytes
Wastewater treatment plants rely largely on microorganisms to oxidise organic matter.
A laboratory fermentation vessel
The eukaryotic parasite Plasmodium falciparum (spiky blue shapes), a causative agent of malaria, in human blood

He was responsible for the first isolation and description of both nitrifying and nitrogen-fixing bacteria.

This is achieved by a number of diazotrophs.

Cyanothece

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

During nitrogen-fixing conditions, Cyanothece creates inclusion storage bodies under the control of a circadian rhythm.

Daniel Rutherford, discoverer of nitrogen

Nitrogen

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Chemical element with the symbol N and atomic number 7.

Chemical element with the symbol N and atomic number 7.

Daniel Rutherford, discoverer of nitrogen
The shapes of the five orbitals occupied in nitrogen. The two colours show the phase or sign of the wave function in each region. From left to right: 1s, 2s (cutaway to show internal structure), 2px, 2py, 2pz.
Table of nuclides (Segrè chart) from carbon to fluorine (including nitrogen). Orange indicates proton emission (nuclides outside the proton drip line); pink for positron emission (inverse beta decay); black for stable nuclides; blue for electron emission (beta decay); and violet for neutron emission (nuclides outside the neutron drip line). Proton number increases going up the vertical axis and neutron number going to the right on the horizontal axis.
Molecular orbital diagram of dinitrogen molecule, N2. There are five bonding orbitals and two antibonding orbitals (marked with an asterisk; orbitals involving the inner 1s electrons not shown), giving a total bond order of three.
Solid nitrogen on the plains of Sputnik Planitia on Pluto next to water ice mountains
Structure of [Ru(NH3)5(N2)]2+ (pentaamine(dinitrogen)ruthenium(II)), the first dinitrogen complex to be discovered
Mesomeric structures of borazine, (–BH–NH–)3
Standard reduction potentials for nitrogen-containing species. Top diagram shows potentials at pH 0; bottom diagram shows potentials at pH 14.
Nitrogen trichloride
Nitrogen dioxide at −196 °C, 0 °C, 23 °C, 35 °C, and 50 °C. converts to colourless dinitrogen tetroxide at low temperatures, and reverts to at higher temperatures.
Fuming nitric acid contaminated with yellow nitrogen dioxide
Schematic representation of the flow of nitrogen compounds through a land environment
A container vehicle carrying liquid nitrogen.

Nitrogen fixation by industrial processes like the Frank–Caro process (1895–1899) and Haber–Bosch process (1908–1913) eased this shortage of nitrogen compounds, to the extent that half of global food production (see Applications) now relies on synthetic nitrogen fertilisers.

Some nitrogen fixation is done by lightning strikes producing the nitrogen oxides, but most is done by diazotrophic bacteria through enzymes known as nitrogenases (although today industrial nitrogen fixation to ammonia is also significant).

Azotobacter

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Genus of usually motile, oval or spherical bacteria that form thick-walled cysts and may produce large quantities of capsular slime.

Genus of usually motile, oval or spherical bacteria that form thick-walled cysts and may produce large quantities of capsular slime.

Martinus Beijerinck (1851–1931), discoverer of the genus Azotobacter

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 (nitrogen fixation).

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.

Trichodesmium

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Genus of filamentous cyanobacteria.

Genus of filamentous cyanobacteria.

Illustration
Trichodesmium erythraeum bloom, between Vanuatu and New Caledonia, SW Pacific Ocean.
a. The N2-fixing Trichodesmium spp., which commonly occurs in tropical and sub-tropical waters, is of large environmental significance in fertilizing the ocean with important nutrients. b. Trichodesmium can establish massive blooms in nutrient poor ocean regions with high dust deposition, partly due to their unique ability to capture dust, center it, and subsequently dissolve it. c. Proposed dust-bound Fe acquisition pathway: Bacteria residing within the colonies produce siderophores (C-I) that react with the dust particles in the colony core and generate dissolved Fe (C-II). This dissolved Fe, complexed by siderophores, is then acquired by both Trichodesmium and its resident bacteria (C-III), resulting in a mutual benefit to both partners of the consortium.

Trichodesmium is a diazotroph; that is, it fixes atmospheric nitrogen into ammonium, a nutrient used by other organisms.

Fabaceae

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The Fabaceae or Leguminosae, commonly known as the legume, pea, or bean family, are a large and agriculturally important family of flowering plants.

The Fabaceae or Leguminosae, commonly known as the legume, pea, or bean family, are a large and agriculturally important family of flowering plants.

The fruit of Gymnocladus dioicus
A flower of Wisteria sinensis, Faboideae. Two petals have been removed to show stamens and pistil
Legume of Vicia sativa
Roots of Vicia with white root nodules visible.
Cross-section through a root nodule of Vicia observed through a microscope.
Indigo colorant
The Cockspur Coral Tree Erythrina crista-galli is one of many Fabaceae used as ornamental plants. In addition, it is the National Flower of Argentina and Uruguay.
Acacia baileyana (Wattle)
Loments of Alysicarpus vaginalis
Calliandra emarginata
Cassia leptophylla tree
Desmodium gangeticum
Dichrostachys cinerea Sickle Bush
Delonix regia tree
Indigofera gerardiana
Tendrils of Lathyrus odoratus (Sweet pea)
Inflorescence of Lupinus arboreus (Yellow bush lupin)
Pisum sativum (Peas); note the leaf-like stipules
Smithia conferta
Trifolium repens in Kullu District of Himachal Pradesh, India.
Kashubian vetch – Kashubia
Zornia gibbosa
Cytisus scoparius (Scotch broom)
Senna pendula (Easter cassia)
Hosackia stipularis (Stipulate Lotus)
Lupinus manus (Sky Lupine)
Vigna caracalla (snail vine) flowers
Lupinus succulentus (Arroyo Lupine Succulent)
Lupinus stiversii (Harlequin Lupine)
Virgilia oroboides (Cape lilac) mauve flowers

This process is called nitrogen fixation.

Biological nitrogen fixation (BNF, performed by the organisms called diazotrophs) is a very old process that probably originated in the Archean eon when the primitive atmosphere lacked oxygen.