Nitrogen Metabolism

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Biological Nitrogen Fixation

 

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 Enzyme

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Metabolism 

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Metabolism is the sum of all chemical transformations taking place in a cell or organism.

It occurs through a series of enzyme-catalyzed reactions that constitute metabolic pathway.

In this multistep sequence, the product of one step serves as the substrate for the next step. These metabolic intermediates are called metabolites.

Multiple metabolic pathways remain interconnected to form a meaningful well-coordinated network that determines the overall functioning of the cell.

Complexity of metabolic pathways as depicted in KEGG: Kyoto Encyclopedia of Genes and Genomes

 

             

Catabolism

• The degradative phase of metabolism 
• Organic nutrient molecules (carbohydrates, fats, and proteins) are converted into smaller, simpler end products (such as lactic acid, CO2, NH3) 
• Release energy:
• A part is conserved in the form of ATP and reduced electron carriers (NADH, NADPH, and FADH2)
• The rest is lost as heat

Anabolism

• The biosynthetic phase of metabolism
• Small, simple precursors are built up into larger and more complex molecules (lipids, polysaccharides, proteins, and nucleic acids)
• Require input of energy (phosphoryl group transfer potential of ATP and reducing power of NADH, NADPH, and FADH2)

Some pathways can be either anabolic or catabolic, depending on the energy conditions in the cell. They are referred to as amphibolic pathways.

Example: Citric acid cycle

Metabolic pathways may linear, branched or cyclic.

Catabolic pathways are convergent and anabolic pathways divergent.

• Converging catabolism: convert several starting materials into a single product
• Diverging anabolism: yielding multiple useful end products from a single precursor
• Cyclic pathway: one starting component is regenerated in a series of reactions that converts another starting component into a product

Metabolic processes are regulated in three principal ways:

• by controlling the accessibility of substrates
• by controlling the amounts of enzymes
• by controlling their catalytic activities

Controlling the accessibility of substrates

• At low substrate concentration (near or below Km), rate of reaction depends on substrate concentration.
• Controlling the flux of substrates also regulates metabolism. 
• The transfer of substrates from one compartment of a cell to another (e.g., from the cytosol to mitochondria) can serve as a control point.
• Compartmentalization segregates opposed reactions. For example, fatty acid oxidation takes place in mitochondria, whereas fatty acid synthesis takes place in the cytosol. 

Controlling the amounts of enzymes

• The amount of a particular enzyme depends on:
• its rate of synthesis
• its rate of degradation
• The level of most enzymes is adjusted primarily by changing the rate of transcription of the genes encoding them.

Controlling their catalytic activities

The catalytic activity of enzymes is controlled by: 

• Reversible allosteric control: Key enzymes in many biosynthetic pathways is allosterically inhibited by a metabolic intermediate or coenzyme or the  ultimate product of the pathway. 
• Reversible covalent modification: Activation/deactivation of enzymes by phosphorylation/deposphorylation of particular residues.
• Hormones-mediated reversible modification of key enzymes: Hormones or growth factors coordinate metabolic relations between different tissues, often by regulating the reversible modification of key enzymes.

Classification of the Bryophytes (Goffinet, Buck and Shaw; 2008)

Mosses display a wide range of structural diversity from which relationships and lineages can be inferred. Historically, bryophyte systematics has focused on peristome teeth complexity and sex organ distribution to define taxonomic units.

Modern classifications reflect systematic concepts proposed by Fleischer (1920) and Brotherus (1924, 1925), wherein the peristomate mosses were classified as follows:

• Nematodontous
• Arthrodontous

Based on the position of perichaetia, arthrodontous mosses were sub-divided into:

• Acrocarpous 
• Pleurocarpous

Based on the architecture of the outer ring of peristome teeth, arthrodontous mosses were sub-divided into:

• Haplolepideous
• Diplolepideous

Sphagnum, Andreaea, Andreaeobryum, and Takakia represent additional groupings distinguished by the presence of a pseudopodium and the mode of sporangial dehiscence.

The classification of the Bryophyta is undergoing constant revisions, particularly in the light of phylogenetic inferences. The classification proposed by Goffinet, Buck, and Shaw (2008) builds on those presented by Buck & Goffinet (2000) and Goffinet & Buck (2004). Their classification is outlined below:

BRYOPHYTA

        SUPERCLASS I

                CLASS TAKAKIOPSIDA: Leaves divided into terete filaments; capsules dehiscent by a single longitudinal spiral slit; stomata lacking. Example: Takakia

Takakia sp.

        SUPERCLASS II

                        CLASS SPHAGNOPSIDA: Branches usually in fascicles; leaves composed of a network of chlorophyllose and hyaline cells; setae lacking; capsules elevated on a pseudopodium; stomata lacking. Example: Sphagnum

Sphagnum

        SUPERCLASS III

                CLASS ANDREAEOPSIDA: Plants on acidic rocks, generally autoicous; cauline central strand absent; calyptrae small; capsules valvate, with four valves attached at apex; seta absent, pseudopodium present; stomata lacking. Example: Andreaea

Andreaea

                CLASS ANDREAEOBRYOPSIDA: Plants on calcareous rocks, dioicous; cauline central strand lacking; calyptrae large and covering whole capsule; capsules valvate, apex eroding and valves free when old; stomata lacking; seta present. Example: Andreaeobryum

Andreaeobryum

        SUPERCLASS V

         CLASS OEDIPODIOPSIDA: Leaves unicostate; calyptrae cucullate; capsule symmetric and erect, neck very long; stomata lacking; capsules gymnostomous. Example: Oedipodium

Oedipodium

                    CLASS POLYTRICHOPSIDA: Plants typically robust, dioicous; cauline central strand present; stems typically rhizomatous; costa broad, with adaxial chlorophyllose lamellae; peristome nematodontous, mostly of (16)32–64 teeth. Example: Polytrichum

Polytrichum

                    CLASS TETRAPHIDOPSIDA: Leaves unicostate; calyptrae small conic; capsule symmetric and erect, neck short; peristome nematodontous, of four erect teeth. Example: Tetraphis

Tetraphis

                       CLASS BRYOPSIDA: Plants small to robust; leaves costate or not, typically lacking lamellae; capsules operculate; peristome at least partially arthrodontous. Example: Bryum

Bryum

Features of the classification system:

• The rank of superclass is adopted to unite all arthrodontous mosses in one taxon (i.e. Superclass V).
• Although this system of classification aimed at accepting only monophyletic taxa, given the limited number of ranks available, paraphyletic taxa were incorporated (e.g. Bryanae). 
• Effort was made to resolve the relationships among genera of the Hypnanae.
• Due to the lack of sequence data and availability of information of many taxa at regional level only, the authors have been unable to expand their classification system to a global scale.                                        

Further reading: 

Buck WR, Shaw AJ, Goffinet B. Morphology, anatomy, and classification of the Bryophyta. In: Bryophyte Biology: Second Edition, ed. B. Goffinet & A. J. Shaw. Cambridge University Press; 2008. p. 55–138.

Economic Importance of Bryophyte

Medicinal Importance of Bryophytes

Bryophytes have been found to possess medicinal properties, making them a valuable resource for traditional and modern medicine.

Antibacterial and Antiviral Properties:

Many bryophyte species, such as Sphagnum, Marchantia, and Conocephalum, have been found to exhibit antibacterial and antiviral activities. These properties make them useful for treating bacterial infections.

Antifungal and Antiparasitic Properties:

Bryophytes, such as Polytrichum and Neckera, have been found to possess antifungal and antiparasitic properties. These properties make them useful for treating fungal infections and parasitic diseases.

Anti-Inflammatory and Antioxidant Properties:

Many bryophyte species, such as Marchantia and Conocephalum, have been found to exhibit anti-inflammatory and antioxidant activities and are used to treat inflammatory diseases and prevent oxidative stress.

Wound Healing and Surgical Dressings:

Sphagnum has been used for centuries as a wound dressing and surgical material due to its high absorptive power and antiseptic properties. Other bryophytes, such as Polytrichum, have also been found to promote wound healing.

Treatment of Respiratory Diseases:

Marchantia, Neckera, and Polytrichum has been traditionally used to treat respiratory diseases, such as pulmonary tuberculosis and bronchitis. Conocephalum has also been found to exhibit anti-inflammatory and antioxidant activities that may help alleviate respiratory diseases.

Treatment of Liver and Kidney Diseases:

Polytrichum has been traditionally used to treat kidney and gall bladder stones. Other bryophytes, such as Marchantia, have also been found to exhibit hepatoprotective and nephroprotective activities.

Anticancer Properties:

Some bryophyte species, such as Conocephalum, have been found to exhibit anticancer properties, although more research is needed to confirm these findings.

Active component of medicinally important bryophytes:

Marchantia: marchantin A

Polytrichum: polytrichumol

Conocephalum: conocephalumol

Neckera: neckeral

Sphagnum: sphagnol

Importance of Bryophytes in Ornamental Purposes

Bryophytes are gaining popularity for their unique textures and colors, making them ideal for ornamental purposes. Bryophytes can be used in a range of ornamental applications, including:

• Terrariums and vivariums
• Floral arrangements and bouquets
• Ground cover and landscaping
• Indoor and outdoor containers

Key Benefits:

• Unique textures and colors
• Low maintenance
• Versatile
• Sustainable and eco-friendly
• Air purification

Examples of Ornamental Bryophytes

Sphagnum

Hypnum

Polytrichum

Rhytidiadelphus

Bryophytes in Peat Formation

Bryophytes, especially Sphagnum, play a crucial role in peat formation, which has significant economic and environmental importance.

Fuel Source: Peat is used as a fuel source, particularly in power plants and for domestic heating.

Horticulture: Peat is used as a soil amendment in horticulture, due to its high water-holding capacity and acidity.

Other Uses: Peat is also used in water filtration, as a component in potting mixes, and in the production of activated carbon.

Bryophytes as a Food Source

Bryophytes, including mosses, liverworts, and hornworts, are a vital food source for various animals and humans.

Animal feed:

Deers, reindeers, caribou, musk ox, arctic geese, lemmings, rodents, birds like such as grouse and ptarmigan and insects like springtails and beetles feed on mosses and liverworts, particularly during winter when other food sources are scarce.

Human Consumption:

• Traditional Medicine: In some cultures, bryophytes are used in traditional medicine to treat various ailments.
• Food Source: In some parts of the world, like Japan and Hawaii, mosses are considered a delicacy and are eaten raw or cooked.
• Supplements: Some bryophytes, like Sphagnum, are used as dietary supplements due to their high nutritional value.

Nutritional Value: Bryophytes are rich in fiber, protein and vitamins and minerals making them a valuable food source.

Bryophytes as Indicators

Bryophytes can serve as early warning systems for environmental pollution and degradation. Hence, they are used to monitor environmental health and track changes over time.

Types of Indicators:

• Air Quality Indicators
• Water Quality Indicators
• Soil Quality Indicators

How Bryophytes Indicate Environmental Health

• Heavy Metal Accumulation: Bryophytes can accumulate heavy metals, such as lead and mercury, in their tissues, indicating pollution levels.
• pH Tolerance: Bryophytes can tolerate a wide range of pH levels, making them useful indicators of soil and water acidity.
• Sensitivity to Pollutants: Bryophytes are sensitive to pollutants, such as sulfur dioxide and ozone, making them useful indicators of air pollution.

Examples of Indicator Bryophytes:

• Sphagnum: Indicates acidic and oxygen-poor conditions.
• Polytrichum: Indicates dry and nutrient-poor conditions.
• Marchantia: Indicates moist and nutrient-rich conditions

Bryophytes as Packing and Construction Materials

Bryophytes have been used for centuries as packing and construction materials due to their unique properties.

Packing Materials:

• Dried Mosses: Dried mosses, such as Sphagnum, have been used as packing materials for fragile items, like glassware and electronics.
• Insulation: Bryophytes have been used as insulation materials in buildings, reducing heat loss and energy consumption.
• Shipping Live Materials: Bryophytes have been used to keep live materials, like plants and animals, moist and secure during shipping.

Construction Materials:

• Chinking Material: Bryophytes, like Sphagnum, have been used as chinking materials to seal gaps between logs in log cabins.
• Roofing Material: Bryophytes have been used as roofing materials, providing insulation and waterproofing.
• Wall Construction: Bryophytes have been used as a component in wall construction, providing insulation and structural support.
• Fire prevention: Nordic people used the aquatic moss Fontinalis antipyretica between the chimney and walls to prevent fires.

Benefits:

• Sustainable
• Eco-Friendly
• Insulation Properties
• Fire Resistance

Examples: Sphagnum, Polytrichum, Hypnum

Bryophyte as Absorbent Material

• A layer of Sphagnum is used in hiking boots for cushioning the foot and absorbing moisture and odor. Dry Sphagnum is used in diapers and in cradles to keep babies clean and warm.
• It is also used to make beddings, mattresses, cushions, and pillows by stuffing mosses into coarse linen sacks.

Research and Education

• Bryophytes are used as model organisms in scientific research, particularly in the fields of ecology, evolution, and developmental biology.
• They are also used in educational settings to teach students about plant biology, ecology, and conservation.

Role of Bryophytes in Ecology and Plant Succession

The ability of bryophytes to stabilize soil, to trap and hold moisture, to exchange cations, and to tolerate desiccation together with their high totipotency makes them a very important contributor in plant succession and ecology.

Succession is an orderly sequence of changes in an open habitat in which organisms interact with the environment for development of a stable and climax community.

Plant succession taking place on a particular habitat is called a sere, its various intermediate stages are called seral stages, and the communities representing the stages are called seral communities.

The importance of bryophytes in ecology and plant succession is outlined below: 

As aids in soil conservation: 

Mosses prevent sheet erosion of soil. They grow densely forming a mat or carpet-like structure. It bears the impact of the falling raindrops, holds much of the rainwater, and thus the amount of run-off water is considerably reduced. The intertwined moss stems and the underground rhizoids firmly binds the soil particles together to a considerable depth of around 6 to 8 inches. This minimizes soil erosion even on steep hill sides.

Formation of soil and vegetation cover: 

In a xeric succession which begins on a bare rock surface the bryophytes, mosses in particular, form an important seral community. The bryophytes and the lichens in the primary succession led to soil formation through accumulation of organic matters and prepare rocky out crops for secondary succession of herbs, shrubs, and trees. The pioneer community is the crustose lichen and followed by the first seral community, the folios lichen. Acid secreted by lichens attack the rock and provide bits of soil. Additional soil particles maybe formed by weathering or be blown in from somewhere else. Thus, the accumulation of soil particles, organic matter, and humus results in the development of a fine soil layer over the underlying rock. This favors the entrance and colonization of mosses, thus beginning the moss stage.

Funaria hygrometrica is the first to colonize the high pH and high potash substratum. It is followed by Polytricum juniperinum, P. piliferum, Ceratodon sp., Tortula sp., and Grimmia sp. These mosses have an added advantage due to presence of minute green leaf-like structures with accelerated photosynthesis and presence of slender multicellular branched rhizoids that compete with folios lichens for absorption of water and nutrients. The increased rate of photosynthesis and absorption produces organic matter at higher pace thus accelerating the soil formation process.

Bog succession: 

Mosses play an important role in bog succession from open water to climax forest. Moses, like Sphagnum, grow over the water surface with their intertwined stems forming a thick mat together with the dead and partiality decayed gametophytic tissue. This provides a substratum for the germination of seeds or propagules of many floating and rooted hydrophytes. In course of time the partially decomposed Sphagnum and the hydrophytes form a dense surface covering over the water forming the so-called quacking bogs. Later bogs are converted into swamps capable of supporting relatively large trees and eventually such swamps are replaced by forest growth. The 'feather mosses' like Hylocomium splendens and Thuidium delicatulum, serve as seed beds for native forest trees and wildflowers.

Rock builders: 

Certain mosses growing in association with other aquatic plants contain large amount of calcium carbonate. The plants bring about decomposition of bicarbonate ions by abstracting free carbon dioxide. The insoluble calcium carbonate precipitates and hardens, forming calcareous rock like deposits. This deposition grows and extends over areas of several 100 square feet. This travertine rock deposits are extensively used as building stone. 

Peatland ecology:

Bryophytes play an important role information of peatland. The factors for the development of peat as follows:

Nutrient absorption capacity: Nitrates and phosphate are the limiting factors in peat formation. Bryophytes can absorb nitrates and phosphate very easily then other vascular plants. 

Water holding capacity: Bryophytes can absorb water and hold it for longer period of time. Some morphological structures help them in this purpose. This enables continuous photosynthetic activity even in the dry season. 

Decomposition: In peat and, growth rate of peat moses is greater than their decomposition rate. This happens only if there is oligotrophication.

Acidification: Some peat moses like Sphagnum secret uronic acids. Protons are liberated from the uronic acid resulting in acidification of the environment.

Water Retention and Purification:

Bryophytes have the ability to absorb and retain large amounts of water, helping to regulate water cycles. They also aid in purifying water by filtering out impurities and excess nutrients.