Microorganisms are living organisms which are very small and not visible to the naked eye. They are various microorganisms they include bacteria, fungi, archaea, and protists. Microbes live in a wide range of habitats: from hot springs, to the human body and the depths of the ocean, individual species are highly adapted to ecological niches. Bacteria and archaea are prokaryotes, they lack a cell nucleus and the other membrane bound organelles. They are almost always unicellular but bacteria which live in soil (myxobacteria) have large genomes, relative to other bacteria. They can aggregate into complex structures as part of their life cycle. Other bacteria can function and reproduce as individual cells, but often aggregate in multicellular colonies. Their genome is usually a single loop of DNA and they also have DNA inside the plasmids. Bacteria are surrounded by a cell wall, which provides strength and rigidity to their cells. They reproduce by binary fission and sometimes by budding, but they do not undergo sexual reproduction. Archaea are also single-celled organisms that lack nuclei. Archaea and bacteria are different because both their genetics and biochemistry are different. Protists are unicellular or multicellular without specialized tissues, they live in almost any environment that contains liquid water. Fungi are also eukaryotes; the difference between fungi and other eukaryotes is that fungal cells have cell walls that contain chitin, unlike the cell walls of plants, which contain cellulose.
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Pathogenic microbes are harmful, since they invade and grow within other organisms, causing diseases. However, most microorganisms are important in an ecosystem because they act as decomposers and they play an important role in nutrient recycling. They are involved in major processes such as biogeochemical cycles, water purification and biotechnology.
There are four major biochemical cycle: sulphur, nitrogen, carbon and iron cycle. Every organism on earth needs carbon either for structure, energy or both. Carbon dioxide fixation is carried out by phototrophic (bacteria can be aerobic or anaerobic) or lithotrophic bacteria (bacteria that oxidize or reduce inorganic substrates), which reduce CO2 to form glucose and methanogens, reduce CO2 to form methane. The digestion of cellulose in ruminants occurs through microbial activity. Microbes which live inside ruminant release enzyme cellulase to hydrolyse cellulose to produce cellobiose and glucose. Glucose then undergoes bacterial fermentation and form volatile fatty acids, CO2 and methane. The relationship between the ruminant and microbes is symbiosis because both of them benefits from each other. Other microorganisms play a part in the carbon cycle. For example the sulphur bacteria are able to use the energy they gain from the degradation of a compound called hydrogen sulphide to degrade carbon compounds. Other bacteria such as Thiobacillus ferrooxidans uses the energy gained from the removal of an electron from iron-containing compounds to convert carbon. The anaerobic degradation of carbon is done only by microorganisms. This degradation is a combined effort of several bacteria. Examples of the bacteria include Bacteroides succinogenes, Clostridium butyricum, and Syntrophomonas sp. This bacterial relationship is responsible for the mass of the carbon dioxide and methane that is released to the atmosphere. Figure 1 shows illustrate carbon cycle.
Figure 1: http://www.fas.org/irp/imint/docs/rst/Sect16/originals/Fig16_14.jpg
Nitrogen is a naturally occurring element that is essential for growth and reproduction in both plants and animals. It is found in amino acids that make up proteins, in nucleic acids, in DNA, and in many other organic and inorganic compounds. In addition, nitrogen comprises about 80% of the Earth's atmosphere. Azotobacter and Rhizobium are nitrogen fixation bacteria; they convert nitrogen from the air into ammonia. Nitrosomonas and Nitrobacter bacteria convert ammonia into nitrite followed by the oxidation of these nitrites into nitrates. Nitrifying bacteria work in aerobic condition. Denitrification is carried out by denitrifying bacteria, in this process nitrate is reduced to either nitrous oxide or nitrogen gas, which is then released into the atmosphere. Examples of denitrifying bacteria are Paracoccus denitrificans and various Pseudomonas. These bacteria only work in anaerobic conditions. This is shown in figure 2.
Figure 2: Nitrogen cycle
Sulphur is one of the constituents of many proteins, vitamins and hormones. Plants absorb sulphur when it is dissolved in water. Animals consume these plants, so that they take up enough sulphur to maintain their health. Most of the earth's sulphur is fixed in rocks and salts or buried deep in the ocean in oceanic sediments. Sulphur can also be found in the atmosphere. It reduces the amount of solar energy entering the earth, thereby contributing to a cooling of the planet. Both aerobes (Beggiatoa, Sulfolobus, Thiobacillus, Thiothrix) and anaerobes (Thiospirillum, Thiocapsa, Chromatium, Chlorobium, Prosthecocloris) oxidize sulphide to sulphur and then oxidize it to sulphate. Desulfovibrio reduce reduces SO42 to H2S. This is summarised below.
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Figure 3: Sulphur cycle
Iron is the fourth most abundant element in the earth's crust. Microbial metal transformations are essential for the production of metallic ores. Iron is the key component of many enzymes, as well as being the main component of haemoglobin, in human blood. Iron oxidizing bacteria (Thiobacillus ferrooxidans, Gallionella), oxidisation of ferrous iron to ferric iron does not provide sufficient electrochemical potential to allow ATP generation or NADPH formation therefore, many iron bacteria also derive electrons from oxidation of hydrogen sulphide, sulphur and thiosulfate. Thiobacillus ferrooxidans uses the natural proton gradient in its low pH environment to generate ATP via ATP synthase. Iron reducing bacteria (Pseudomonas, Geobacter) reduce ferric iron to ferrous ion via anaerobic process.
Biotechnology uses microorganisms such as bacteria to perform industrial or manufacturing processes. Milk fermentation is usually caused by Streptococci and Lactobacilli bacteria. These bacteria cause the breakdown of lactose to lactic acid. Fermented milk products include yoghurts, chesses and butter. The lactic acid bacteria such as Streptococci and Lactobacilli and other microorganisms which present in the cheese contribute enzymes which breakdown fats, sugar and proteins during cheese making. Lactic acid bacteria are naturally present in milk, therefore before the cheese making; the milk is pasteurized by heating at 62oC for 30minutes. This heat treatment will destroy most lactic acid bacteria in the milk and will also kill other pathogenic bacteria which cause illness. Bacteria Streptococcus thermophilus and Lactobacillus bulgaricus are responsible for yoghurt production. The process of yoghurt production is similar to cheese making.
The other important type of fermentation is alcoholic fermentation. Alcoholic fermentation is made by yeast (fungi) and other kinds of bacteria. These microorganisms convert simple sugar such as glucose into ethanol and CO2. Glucose is broken down into pyruvic acid and then it is converted to ethanol and CO2. Bread, beer and wine are the products of alcoholic fermentation, the same microorganisms is used to produce these products.
Genomic, molecular makers, cloning and genetic modification are part of modern biotechnology. Microorganisms such as Escherichia coli or yeast are used in the production of substances like insulin and antibiotics. Insulin is widely used for the treatment of diabetes, people with diabetes produce less insulin so artificial synthesis of insulin which is made by recombinant DNA technology helps diabetic patients to reduce blood glucose level. Insulin is extracted from the pancreas of cattle or pig then the insulin gene is joined with a plasmid vector, and then there are inserted into E.coli bacterium to replicate and to produce more insulin for treatment. The use of microbes in insulin production lowers the cost of the product. This example indicates both the health and economic benefits of the use of microbes. Human growth hormone, clotting factors for hemophiliacs, fertility drugs and other drugs are made by modern biotechnology.
Gene therapy uses an adenovirus vector to modify DNA in a human cell. A gene is inserted into an adenovirus vector and if the treatment is successful, the gene will make a functional protein. Gene therapy is used treat genetic and other diseases like cancer and AIDs by using normal gene to replace defective genes.
Microorganisms are also very important in waste water treatment. They are responsibleÂ for many different chemical reactions, as the bacteria metabolize,Â grow and divide they produce enzymes, which break down organic matters in sewage. Anoxic microorganisms convert macromolecular waster into soluble products using enzymes such as proteases and lipases. Then the soluble products undergo fermentation to produce ethanoic acid, CO2 and H2 and in the end methanogenic archaea make methane and CO2. Methane is used as a fuel and CO2 is recycled as mentioned above in carbon cycle. The second step of water treatment uses bacteria, fungi, protists and other organisms helps in the purification of water.
Human flora is collection of microorganism such as bacteria, archaea and fungi which live on the surface of skin, in the saliva and in the gastrointestinal tracts. Most microorganisms in human are mutualistic because they are harmless to human and both host and microorganisms benefit from the relationship. Normal flora helps by competing with pathogens such as Salmonella, they provide vitamins and Bacteroides is present in human, these bacteria benefit their host by excluding potential pathogens from colonizing the gut. Biofilms are collection of bacteria enclosed in a mucoid polysaccharide structure which attaches the community to a surface. Having a biofilms helps defend human against foreign microorganisms.
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In agriculture, the use of bacterial insecticides has reduced the use of chemical insecticides, which is both a cost savings to the producer and less stressful on the environment. Other bacterial enzymes and parts of the organisms are used to produce materials such as plastic.
Some pathogenic microorganisms cause diseases and cancer however, on the whole most microorganisms are harmless and beneficial to human. As i mentioned above microorganisms used in industry mainly for the production of enzymes, antibiotics, vitamins, insulin and they are also involved in the food production such as cheese, yoghurt bread and alcohol. Most importantly microorganisms are helpful in waste water treatment and other waster product degradation as they are also natural decomposers. Biofuels are extracted from microbes. Microbes are also involved in agriculture. Microbes are beneficial for health, environment, social and economy. To conclude, microorganisms are everywhere and we cannot live without them.