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The Role of Microorganisms in Cycling

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In nature there are repeated cycles of substances that are essential for plant life and animals. Especially important is transformation of substances that make up living matter - the so-called organogenic. It is carbon, nitrogen, sulfur, phosphorus, oxygen and hydrogen, from which protein, fat, carbohydrates are built.

In the cycle of matter in nature a great role belongs to green plants and various microorganisms. With the most active participation of microorganisms in nature, mainly in the soil and the hydrosphere, two opposing processes are ongoing: the synthesis of complex organic mineral compounds and, on the contrary, the decomposition of organic matter to the mineral. The unity of these opposing processes is the basis of the biological role of microorganisms in the cycle of matter in nature. Due to their biochemical activity less complex chemical compounds become more complex, organic, and, conversely, more complex organic compounds break down into simple chemical elements. Planet green plants and photosynthetic microorganisms use the carbon dioxide of air, water, minerals, soil and energy of sunlight to synthesize organic compounds, which make up the various components of cells. The organic matter of vegetable origin is used in the food of herbivores. In turn carnivores and people are using organic materials as food. Once an animal or plant dies, organic compounds that make up its cells  break down into simpler forms are re-used for the synthesis of plant organisms (Heritage, Evans & Killington, 2000).

The most important role microorganisms perform in the cycle of carbon, nitrogen, phosphorus and iron.

It is known, that cycling of matter is a set of transformations of the chemical elements, which make up living organisms. The main factors that determine the dominant role of microbes in the cycle of matter are the wide spread of microorganisms (e.g., a layer of fertile soil thickness of 15 cm can contain up to 5 tons of microbial biomass per hectare) and their extraordinary metabolic flexibility at high baud rate. Of great importance is the narrow specialization of individual groups of microorganisms with respect to disposition of substances. Therefore, some of the steps of the cycle of substances can be carried out only by prokaryotes. In nature, all organisms are divided into three groups. Producers are green plants and micro-organisms that synthesize organic matter, using the  energy of sun, carbon dioxide and water. Consumers (consuments) are animals, which spend a significant part of the primary biomass to build their bodies (Berner & Berner, 1996).

Also we should mention destructors, bacteria (including actinomycetes) and fungi, that decompose the dead animals and plants, with organic materials are transformed into inorganic, that is why there is mineralization (Uroz, Calvarus, Turpault, Frey-Klett, 2009).

The carbon cycle. The role of bacteria in the exchange of carbon

The relationship of living organisms on Earth is particularly expressed in the carbon cycle. Atmospheric air contains about 0.03% C02, but the productivity of green plants is so great that the entire stock of carbon dioxide in the atmosphere (2600-109 m C02) would be spent during 20 years - the term which is negligible in the short-scale evolution. Photosynthesis would be stopped if the microorganisms, plants and animals do not provide a return of C02 into the atmosphere as a result of continuous mineralization of organic matter. Cyclic conversion of carbon and oxygen are mostly implemented in two different directions of the process: oxygenic photosynthesis and respiration (or burning in non-biological reactions).

In green plants and cyanobacteria, oxygen aerobic photosynthesis uses carbon dioxide (CO2) and water, releasing oxygen as a waste product. Although anaerobic purple and green bacteria can restore C02 to organic substances, oxidizing compounds other than water (NH3, NO2, H2, Fe2 +, reduced sulfur compounds), the contribution of these processes to the overall fixation of CO is negligible. As a result of photosynthetic fixation of C02, sugars and other compounds are produced. Most of the fixed carbon is deposited in the form of plant polymeric carbohydrates (starch, cellulose). Therefore, sugar plays a leading role in the nutrition of all living organisms, which need organic food (heterotrophic organisms), and are the preferred nutrient for most heterotrophic microorganisms.

In the presence of oxygen, the complete oxidation of organic matter to CO is executed by many aerobic (Pseudomonas, Bacillus) and facultative anaerobic (actinomycetes) bacteria, fungi, and animals. As examples of incomplete oxidation we can mention oxidation of sugar acetic acid bacteria (Acetobacter, Gluconobacter) with the formation of acetate, lactate formation by fungi, belonging to the order Mucorales (Rhizopus oryzae, R. nigricans, etc.), gluconic acid formation, using cells of Aspergillus and species of Penicillium (Florian, 2002).

Under anaerobic conditions, organic compounds are degraded by fermentation (yeast, lactic acid bacteria, propionic acid bacteria, the bacteria from the family Enterobacteriaceae), or oxidized in the process of anaerobic respiration in the presence of hydrogen acceptors. In the role of hydrogen acceptors are the nitrates, sulfates, carbonates, fumarate, Fe3 +: respectively produced by denitrifying, methane-producing bacteria. Methanogenic bacteria (Methanobacterium, Methanococcus, Methanosarcina) are strict anaerobes that constitute the last link in the anaerobic food chain. Emissions of methane under aerobic conditions can be oxidized to C02 methylotrophic bacteria (Methylomonas, Methytosinus, Methylococcus). (Allsopp, Kenneth & Gaylarde, 2004)

Carbon is taken from the cycle in different ways. Carbonate ions contained in seawater, are combined with dissolved ions Ca2 + and precipitated as CaC03 (calcium carbonate). The latter is also formed in biological way in the limestone structures of simple corals and shellfish, depositing as limestone rocks. Deposition of non-mineralized organic matter in high humidity and lack of oxygen leads to the accumulation of humus, the formation of peat and coal. Another type to produce organic carbon from the cycle is using deposits of oil and natural gas (methane).

Human activity steadily shifts the balance toward the formation of carbon C02. On the one hand, this is due to the intense combustion of oil, coal and natural gas, and, on the other hand, this is due to the decrease of photosynthetic carbon fixation through the destruction of forests, soil degradation and pollution of the ocean (Dugdale, & Duglale, 1962).

The most important element, which is part of the protein and, therefore, is of paramount importance for life,  is nitrogen. In living beings that inhabit the planet, there are about 15-20 billion tons of nitrogen, in the soil (30-cm layer) for each hectare there is an average 5-15 tons of nitrogen.

In the nitrogen cycle in nature, involving microorganisms, the following stages can be distinguished: the assimilation of atmospheric nitrogen, ammonification, nitrification, denitrification.

We should mention also assimilation of nitrogen from the air nitrogen-fixing bacteria. Among microbes that assimilate atmospheric nitrogen, two groups can be distinguished- the free-living and nodule bacteria.

Free-living nitrogen-fixing bacteria live and fix nitrogen in the soil, regardless of the plants. The main types of bacteria are Azotobacter chroococcum, Cl. pasteurianum. Azotobacter in an area of 1 ha in the year fixes from 20 to 50 kg of nitrogen gas, increasing soil fertility. This process is most intensive in case of good soil aeration.

Nodule bacteria are produces in the process of fixing atmospheric nitrogen in symbiosis with legumes. The presence of bacteria in the nodules of legumes was discovered by Voronin. In pure culture these microbes were isolated by Beijerinck in 1888.

Ammonification is nitrogen mineralization of organic matter, which flows under the influence of ammonifying microbes that produce proteolytic enzymes. Thanks to ammonification of representatives of flora and fauna and their waste products (urea, faeces), soil is enriched with nitrogen and other compounds. Simultaneously ammonifying microbes perform an enormous sanitary role, cleaning soil and hydrosphere of decomposing organic substrate. Among this group the most important are the following microorganisms:

- aerobic spore - mesentericus (potato bacillus), megatherium (cabbage bacillus), subtilis (Bacillus subtilis), mycoides (mushroom bacillus).

- aerobic ammonifiers which do not form spores —E. coli, Proteus vulgaris, Ps. fluorescens.

- anaerobic spore ammonifiers, which include Cl. putrificum, Cl. sporogenes.

Ammonification is also caused by actinomycetes and fungi living in the soil.

Nitrification is the next stage of the transformation of  nitrogen by microorganisms. This process is the oxidation of ammonia formed during the decomposition of organic nitrogen compounds.

Denitrification, which flows under the influence of microbes, is the reduction of nitrates with formation of molecular nitrogen as the final product, returning from the soil into the atmosphere. This process is caused by denitrifying bacteria. The most common of these in the nature are the following: Tiolacillus denitrificans, a– bacillus that does not form spores, a facultative anaerobic organism; Ps. fluorescens - bacillus that highlights green pigment and decomposes nitrates; Ps. aeruginosa - a bacterium similar to the previous one; Ps. Stutzeri - a small bacillus that forms chains and decomposes nitrates under anaerobic conditions.

The role of microbes in the carbon cycle

Major organogenic element, which forms part of microbes, plants and animals, is carbon. In the cellular material that element compounds about 50% of dry matter. Autotrophic bacteria used for converting carbon dioxide, which has no energy properties, into organic compounds need energy from thermal sources, which is solar or chemical energy produced by oxidation of minerals. The assimilation of carbon by using solar energy is called photosynthesis, and by using chemical energy - chemosynthesis. Thus, under influence of autotrophic bacteria, using solar or chemical energy, carbon dioxide is converted into organic matter. The basic process that returns the carbon dioxide in the atmosphere is the decomposition of organic compounds under the influence of microorganisms. This process of decomposition of organic compounds is called fermentation. In nature, there are many types of fermentation caused by certain types of bacteria. We will only give the ones which are of the greatest importance for the carbon cycle.

Fermentation of fiber. In nature, large carbon reserves are concentrated in the tissue (pulp) of plants. After their death there is decomposition of cellulose to release carbon in the form of carbon dioxide back to the atmosphere. The fermentation of fiber can be aerobic and anaerobic.

Anaerobic fermentation of fiber. Fiber fermenters were identified in 1889 and described as agents of hydrogen and methane fermentation (Cl. omelianskii, Cl. Cellobioparum). Anaerobic fermentation of cellulose takes place in two stages:

- The first phase - saccharification of cellulose;

- The second stage - expansion of sugar, depending on the type of fermentation to alcohol, lactic acid, butyric acid, carbon dioxide, hydrogen, methane, etc.

Hydrogen and methane decomposition occurs in the proventricular tissues of cattle by eating lots of green beans, especially moisture, which causes the development of acute bloat scar (Heritage, Evans& Killington, 1999).

Aerobic fermentation of cellulose is the most intensive under the influence of the following three types of micro-organisms that are common in nature: Cytophaga - moving long bacillus with sharp ends, Ceivirio - long curved bacillus, Cetacicula - short bacillus with sharp edges. Under aerobic conditions, fiber is decomposed also by actinomycetes and fungi genera Aspergillus, Penicillium, etc.

Cellulose-decomposing microorganisms perform huge sanitary role, expanding the tissue of dead plants, increasing the fertility of soil.

Fermentation of pectin. A lot of microorganisms take an active part in the process of destruction of dead plants; as a result these   microorganisms cause fermentation of pectin intercellular substance that binds plant cells. When heated, pectin acquires jelly-like consistency (pektis - jelly). Activators of this fermentation are Cl. Pectinovorum, spore moving large bacillus. Great practical importance pektin-acid fermentation has for retting fiber crops (flax, hemp). Cellulose fibers of these plants are glued to the surrounding tissues by pectin.

Alcoholic fermentation is the process utilizing fungi, yeast form. They decompose sugar to form of ethyl alcohol and carbon dioxide.

Wild yeasts are widespread in nature; they live in the flowers, leaves and stems of plants, especially in large numbers in fruits. Cultural yeasts are used in bread making. Kefir is also made using yeast. Production of ethanol, various wines, and beers is based on the activity of yeast. In livestock liquid and dry yeasts are used, as they are rich in protein, fat and vitamins.

Saccharomyces cerevisiae, the yeast commonly used as baker's yeast, –is an oval cell with length of 8-10 micron. This yeast causes top fermentation. Top fermentation takes place with a slight increase in temperature to 20 ... 280C. After 5 to 7 days fermentation ends and yeast settles to the bottom. Bottom-fermenting yeast (S. vini) is developed in anaerobic conditions and at lower temperature (120C  ...), so the process is slower.

Lactic fermentation. Microbiological nature of the process was founded by L. Pasteur. As a result of lactic acid fermentation, mostly sugars or polyols and proteins are broken down to lactic acid.

Depending on what products are formed during the fermentation of glucose, just a lactic acid or also other organic products and CO2, lactic acid bacteria are divided into homofermentative and heterofermentative bacteria.

Homofermentative lactic fermentation.

Homofermentative lactobacilli include coccoid microorganisms of the genus Streptococcus (Str. lactis, Str. Cremoris, Str. Thermophilus, Str. Diacetilactis) and rod-shaped bacteria of the genus Lactobacterium (Lact. bulgaricum, Lact.lactis, Lact. Acidophilus), which form only a lactic acid during fermentation.

Heterofermentative lactic fermentation. It is caused by the genera Leuconostoc (spherical cells located singly or in pairs, facultative anaerobic, gram-positive, immobile), Lactobacterium (small gram-positive rods) and Bifidobacterium (direct branched bacillus, still, Gram-positive anaerobes, permanent residents of the intestine of humans and animals). All lactic acid bacteria are antagonists of putrefactive microorganisms. This phenomenon is due to the action of lactic acid, which is actively produced by lactic acid bacteria, as well as the ability to produce antibiotic substances. This is the basis of dietary milk products for prevention and treatment of gastrointestinal diseases caused by putrefactive microbes in humans and newborn animals.

Acetic fermentation is a microbial oxidation of ethanol to acetic acid. The nature of this process was first founded by L. Pasteur, proving the leading role of the bacteria in it. Last are widely distributed in nature; they are found in soil, air, plants, in homes and livestock farms.

Genus of acetic acid bacteria, Acetobacter, is represented by 11 species, typical representatives of which are A. aceti and A. pasteurianurn. These are short, aerobic rods, located in isolation.

In case of long-term storage of beer, dry (no alcohol fortified) wines, A. aceti forms a wrinkled film on their surface. It consists of three acetic acid bacteria, which are most common in the nature: Acetobacter aceti, A. pasteurianurn and A. kutringianurn. In industry, microorganisms of the genus Acetobacter are used for the production of edible vinegar from wine and alcohol. Acetic fermentation is of practical importance in silage fodder.

Butyric fermentation is caused by butyric microorganisms, decomposing carbohydrates with the formation of butyric acid.

Activators of butyric fermentation are mostly anaerobes; they are widely distributed in nature, they are found in soil, water, air, plants, food, etc. Simultaneously with carbohydrate they break down fats and proteins, and initially intermediates are formed (pyruvic acid, acetaldehyde), and then butyric acid and by-products are formed (acetone, butyl alcohol, carbon dioxide, hydrogen). Butyric fermentation is caused by about 25 types of microorganisms.

The main ones: Cl. pasteurianum, Cl. pectinovorum, Cl. felsineum. These are large movable rods with rounded ends; they are able to form spores, acquiring the characteristic spindle shape.  Cytoplasm of these microbes contains glycogen and granulosis, so they are well painted with a solution of iodine in blue and brown. Microbial spores are highly resistant to heat and can endure sterilization at 120 ° C, staying alive, for example, in meat and fish. When canned, they form gases that cause swelling of cells (bombazh). At the same time toxic substances are accumulated in these products. Therefore, canned food with bombazh is unsuitable.

Butyric fermentation is often the cause of rancidity of sunflower seeds, soybeans, vegetable oils and rancidity of fats of animal origin. When butyric acid is accumulated in the silo in an amount of 0.3-0.4%, animals don’t want to it. Butyric acid bacteria are involved in hay self heating.

Microbial transformation of phosphorus, iron and sulfur. Phosphorus is part of proteins and lipids. Especially a lot of it is contained in the nuclei of cells, the humans and animals` brain. The microorganisms involved in the conversion of phosphorus, live in the soil and water. Their role is limited to two processes: mineralization of phosphorus, a component of organic matter, and the transformation of poorly soluble phosphates into soluble. Phosphorus mineralization is caused by putrefaction bacteria, especially megatherium. Phosphoric acid, formed in this process, binds with alkaline soil and is then transformed to poorly soluble calcium, iron, magnesium, and therefore it is not easily accessible to plants. In the future, under the influence of acid-forming soil bacteria, particularly nitrification, these salts are converted into soluble compounds of phosphoric acid, available to plants.

Iron is a part of the protein hemoglobin contained in red blood cells, and respiratory enzymes (cytochrome). This explains its important role in human and animal respiration. In nature, iron is part of many organic and inorganic compounds in the form of insoluble ferric Fe3 + and soluble ferrous Fe2 +. Conversion of iron from one form to another is carried out by iron bacteria.

The main representatives of iron bacteria are filamentous bacteria of the genera Crenothrix, Leptothrix. Iron bacteria are aerobic and are found in most water bodies; in the process of their activities iron oxide is generated. Upon the death of bacteria marsh and lake-iron ore is formed, and can be found tens or hundreds square meters away from islands. Iron bacteria play an important role in the formation of iron-manganese deposits in nature.

The structure of a protein of plant and animal origin also includes sulfur, which explains the importance of this element in the cycle of matter. Bacteria assimilating sulfur compounds are called sulfur bacteria. They live in the soil, water and manure. During the decomposition of soil organic sulfur compounds, as well as during the recovery of salts of sulfuric, sulfurous acid, hydrogen sulfide is formed, and it is toxic for plants and animals. This gas is converted into harmless compounds, available for plants, by sulfur bacteria. Filamentous sulfur bacteria are divided into filamentous (Beggiatoa, Thiothrix), thione (Thiobaccilus), photosynthetic purple and green. Filamentous bacteria are long filaments composed of many cells; they are aerobes, able to oxidize hydrogen sulfide to sulfuric acid (Ivanov, 1957). Thiobacteria are moving bacteria, which do not form spores; they are gram-negative rods, capable of oxidizing sulfur and its compounds. Photosynthetic sulfur bacteria have different morphological forms (cocci, rods, spirillum); they are strict anaerobes and are developed in the light in a medium with hydrogen sulfide or sodium triosulfate.

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