Nitrogen fixation and Related Topics

Nitrogenase

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

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.

Leguminous plants used to fertilize an abandoned land

Diazotroph

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

Cyanobacteria

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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.

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

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).

Root nodule

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Nitrogen is the most commonly limiting nutrient in plants. Legumes use nitrogen fixing bacteria, specifically symbiotic rhizobia bacteria, within their root nodules to counter the limitation. Rhizobia bacteria convert nitrogen gas (N2) to ammonia (NH3) in a process called nitrogen fixation. Ammonia is then assimilated into nucleotides, amino acids, vitamins and flavones which are essential to the growth of the plant. The plant root cells convert sugar into organic acids which then supply to the rhizobia in exchange, hence a symbiotic relationship between rhizobia and the legumes.

Indeterminate nodules growing on the roots of Medicago italica

Diagram illustrating the different zones of an indeterminate root nodule (see text).

Cross section through a soybean root nodule. The bacterium, Bradyrhizobium japonicum, colonizes the roots and establishes a nitrogen fixing symbiosis. This high magnification image shows part of a cell with single bacteroids within their symbiosomes. In this image, endoplasmic reticulum, dictysome and cell wall can be seen.

Nitrogen-fixing nodules on a clover root.

Close up of dissected Medicago Root nodule of the Fabaceae plants family.

Root nodules are found on the roots of plants, primarily legumes, that form a symbiosis with nitrogen-fixing bacteria.

Legume

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Plant in the family Fabaceae , or the fruit or seed of such a plant.

Freshly dug peanuts (Arachis hypogaea), indehiscent legume fruits

Depending on the variety, Phaseolus vulgaris (a pulse) may be called "common bean", "kidney bean", "haricot bean", "pinto bean", or "navy bean", among other names.

Legumes are notable in that most of them have symbiotic nitrogen-fixing bacteria in structures called root nodules.

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.

A flower of Wisteria sinensis, Faboideae. Two petals have been removed to show stamens and pistil

Roots of Vicia with white root nodules visible.

Cross-section through a root nodule of Vicia observed through a microscope.

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.

Tendrils of Lathyrus odoratus (Sweet pea)

Inflorescence of Lupinus arboreus (Yellow bush lupin)

Pisum sativum (Peas); note the leaf-like stipules

Trifolium repens in Kullu District of Himachal Pradesh, India.

Lupinus succulentus (Arroyo Lupine Succulent)

Virgilia oroboides (Cape lilac) mauve flowers

This process is called nitrogen fixation.

Global cycling of reactive nitrogen including industrial fertilizer production, nitrogen fixed by natural ecosystems, nitrogen fixed by oceans, nitrogen fixed by agricultural crops, NOx emitted by biomass burning, NOx emitted from soil, nitrogen fixed by lightning, NH3 emitted by terrestrial ecosystems, deposition of nitrogen to terrestrial surfaces and oceans, NH3 emitted from oceans, ocean NO2 emissions from the atmosphere, denitrification in oceans, and reactive nitrogen burial in oceans.

Nitrogen cycle

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Biogeochemical cycle by which nitrogen is converted into multiple chemical forms as it circulates among atmosperic, terrestrial, and marine ecosystems.

ANAMMOX is anaerobic ammonium oxidation, DNRA is dissimilatory nitrate reduction to ammonium, and COMMAMOX is complete ammonium oxidation.

The main studied processes of the N cycle in different marine environments. Every coloured arrow represents a N transformation: N2 fixation (red), nitrification (light blue), nitrate reduction (violet), DNRA (magenta), denitrification (aquamarine), N-damo (green), and anammox (orange). Black curved arrows represent physical processes such as advection and diffusion.

Classical representation of nitrogen cycle

alt=Diagram of nitrogen cycle above and below ground. Atmospheric nitrogen goes to nitrogen-fixing bacteria in legumes and the soil, then ammonium, then nitrifying bacteria into nitrites then nitrates (which is also produced by lightning), then back to the atmosphere or assimilated by plants, then animals. Nitrogen in animals and plants become ammonium through decomposers (bacteria and fungi).|Flow of nitrogen through the ecosystem. Bacteria are a key element in the cycle, providing different forms of nitrogen compounds able to be assimilated by higher organisms

Simple representation of the nitrogen cycle. Blue represent nitrogen storage, green is for processes moving nitrogen from one place to another, and red is for the bacteria involved

Estimated nitrogen surplus (the difference between inorganic and organic fertilizer application, atmospheric deposition, fixation and uptake by crops) for the year 2005 across Europe.

Important processes in the nitrogen cycle include fixation, ammonification, nitrification, and denitrification.

Bacteria

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

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.

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.

Nitrogen

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Chemical element with the symbol N and atomic number 7.

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 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.