A report on Bacteria and Nitrogen fixation

Schematic representation of the nitrogen cycle. Abiotic nitrogen fixation has been omitted.
Rod-shaped Bacillus subtilis
Nodules are visible on this broad bean root
Phylogenetic tree of Bacteria, Archaea and Eucarya. The vertical line at bottom represents the last universal common ancestor.
A sectioned alder tree root nodule
Bacteria display many cell morphologies and arrangements
Equipment for a study of nitrogen fixation by alpha rays (Fixed Nitrogen Research Laboratory, 1926)
The range of sizes shown by prokaryotes (Bacteria), relative to those of other organisms and biomolecules.
Lightning heats the air around it breaking the bonds of starting the formation of nitrous acid.
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.

- Bacteria

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

- Nitrogen fixation

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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

Two of the three domains, Archaea and Bacteria, only contain microorganisms.

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

Leguminous plants used to fertilize an abandoned land

Diazotroph

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Leguminous plants used to fertilize an abandoned land

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

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

Nitrogenase

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

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

Archaea

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Archaea (singular archaeon ) constitute a domain of single-celled organisms.

Archaea (singular archaeon ) constitute a domain of single-celled organisms.

Archaea were found in volcanic hot springs. Pictured here is Grand Prismatic Spring of Yellowstone National Park.
The ARMAN are a group of archaea recently discovered in acid mine drainage.
Membrane structures. Top, an archaeal phospholipid: 1, isoprene chains; 2, ether linkages; 3, L-glycerol moiety; 4, phosphate group. Middle, a bacterial or eukaryotic phospholipid: 5, fatty acid chains; 6, ester linkages; 7, D-glycerol moiety; 8, phosphate group. Bottom: 9, lipid bilayer of bacteria and eukaryotes; 10, lipid monolayer of some archaea.
Bacteriorhodopsin from Halobacterium salinarum. The retinol cofactor and residues involved in proton transfer are shown as ball-and-stick models.
Sulfolobus infected with the DNA virus STSV1. Bar is 1 micrometer.
Archaea that grow in the hot water of the Morning Glory Hot Spring in Yellowstone National Park produce a bright colour
Methanogenic archaea form a symbiosis with termites.

Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebacteria kingdom), but this term has fallen out of use.

This includes both reactions that remove nitrogen from ecosystems (such as nitrate-based respiration and denitrification) as well as processes that introduce nitrogen (such as nitrate assimilation and nitrogen fixation).

In a cleaning symbiosis the clownfish feeds on small invertebrates, that otherwise have potential to harm the sea anemone, and the fecal matter from the clownfish provides nutrients to the sea anemone. The clownfish is protected from predators by the anemone's stinging cells, to which the clownfish is immune, and the clownfish emits a high pitched sound that deters butterfly fish, which would otherwise eat the anemone. The relationship is therefore classified as mutualistic.

Symbiosis

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Any type of a close and long-term biological interaction between two different biological organisms, be it mutualistic, commensalistic, or parasitic.

Any type of a close and long-term biological interaction between two different biological organisms, be it mutualistic, commensalistic, or parasitic.

In a cleaning symbiosis the clownfish feeds on small invertebrates, that otherwise have potential to harm the sea anemone, and the fecal matter from the clownfish provides nutrients to the sea anemone. The clownfish is protected from predators by the anemone's stinging cells, to which the clownfish is immune, and the clownfish emits a high pitched sound that deters butterfly fish, which would otherwise eat the anemone. The relationship is therefore classified as mutualistic.
Diagram of the six possible types of symbiotic relationship, from mutual benefit to mutual harm.
Alder tree root nodule houses endosymbiotic nitrogen-fixing bacteria.
Male-male interference competition in red deer
Hermit crab, Calcinus laevimanus, with sea anemone.
Bryoliths document a mutualistic symbiosis between a hermit crab and encrusting bryozoans.
Commensal mites travelling (phoresy) on a fly (Pseudolynchia canariensis)
Head (scolex) of tapeworm Taenia solium is adapted to parasitism with hooks and suckers to attach to its host.
The black walnut secretes a chemical from its roots that harms neighboring plants, an example of antagonism.
Leafhoppers protected by meat ants
Pollination is a mutualism between flowering plants and their animal pollinators.
A fig is pollinated by the fig wasp, Blastophaga psenes.
Pseudomyrmex ant on bull thorn acacia (Vachellia cornigera) with Beltian bodies that provide the ants with protein

Examples include diverse microbiomes: rhizobia, nitrogen-fixing bacteria that live in root nodules on legume roots; actinomycetes, nitrogen-fixing bacteria such as Frankia, which live in alder root nodules; single-celled algae inside reef-building corals; and bacterial endosymbionts that provide essential nutrients to about 10%–15% of insects.

A spectacular example of obligate mutualism is the relationship between the siboglinid tube worms and symbiotic bacteria that live at hydrothermal vents and cold seeps.

Green sulfur bacteria

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Reductive TCA Cycle Diagram

The green sulfur bacteria are a phylum of obligately anaerobic photoautotrophic bacteria that metabolize sulfur.

Nitrogen fixation among green sulfur bacteria is generally typical of an anoxygenic phototroph, and requires the presence of light.

Pseudomonadota

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Major phylum of Gram-negative bacteria.

Major phylum of Gram-negative bacteria.

Others are free-living (nonparasitic) and include many of the bacteria responsible for nitrogen fixation.