An agar plate streaked with microorganisms

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Microbiology (from Greek μῑκρος, mīkros, "small"; βίος, bios, "life"; and -λογία, -logia) is the study of microscopic organisms, which are defined as any living organism that is either a single cell (unicellular), a cell cluster, or has no cells at all (acellular).^[1] This includes eukaryotes, such as fungi and protists, and prokaryotes. Viruses^[2] and prions, though not strictly classed as living organisms, are also studied. Microbiology typically includes the study of the immune system, or immunology. Generally, immune systems interact with pathogenic microbes; these two disciplines often intersect which is why many colleges offer a paired degree such as "Microbiology and Immunology".

Microbiology is a broad term which includes virology, mycology, parasitology, bacteriology, immunology and other branches. A microbiologist is a specialist in microbiology and these related topics.

Microbiological procedures usually must be aseptic, and use a variety of tools such as light microscopes with a combination of stains and dyes.The most commonly used stains are called basic dyes, and are composed of positively charged molecules. Two types of basic dyes are simple stains and differential stains. Simple stains consist of one dye and identify the shape and multicell arrangement of bacteria. Methylene blue, carbolfuchsin, safranin, and crystal violet are some of the most commonly used stains. Differential stains on the other hand, use two or more dyes and help us to distinguish between two or more organisms or two or different parts of the organism. Types of differential stains are gram, Ziehl-Neelsen acid fast, negative, flagella, and endospore. Specific constraints apply to particular fields of microbiology, such as parasitology, which heavily utilizes the light microscopy, whereas microscopy's utility in bacteriology is limited due to the similarity is many cells physiology. Indeed, most means of differentiating bacteria is based on growth or biochemical reactions. Virology has very little need for light microscopes, relying on almost entirely molecular means. Mycology relies on all technologies the most evenly, from macroscopy to molecular techniques.

Microbiology is actively researched, and the field is advancing continuously. It is estimated that only about one percent of the microorganisms present in a given environmental sample are culturable^[3] and the number of bacterial cells and species on Earth is still not possible to be determined, recent estimates indicate that it can be extremely high (5 Exp 30 cells on Earth, unknown number of species). Although microbes were directly observed over three hundred years ago, the precise determination, quantitation and description of its functions is far to be complete, given the overwhelming diversity detected by genetic and culture-independent means.

History[link]

Ancient[link]

The existence of microorganisms was hypothesized for many centuries before their actual discovery. The existence of unseen microbiological life was postulated by Jainism which is based on Mahavira’s teachings as early as 6th century BCE.^[4] Paul Dundas notes that Mahavira asserted existence of unseen microbiological creatures living in earth, water, air and fire.^[5] Jain scriptures also describe nigodas which are sub-microscopic creatures living in large clusters and having a very short life and are said to pervade each and every part of the universe, even in tissues of plants and flesh of animals.^[6] The Roman Marcus Terentius Varro made references to microbes when he warned against locating a homestead in the vicinity of swamps "because there are bred certain minute creatures which cannot be seen by the eyes, which float in the air and enter the body through the mouth and nose and there by cause serious diseases."^{[7][citation needed]}

In 1546 Girolamo Fracastoro proposed that epidemic diseases were caused by transferable seedlike entities that could transmit infection by direct or indirect contact, or vehicle transmission.^[8]

However, early claims about the existence of microorganisms were speculative, and not based on microscopic observation. Actual observation and discovery of microbes had to await the invention of the microscope in the 17th century.

Modern[link]

Anton van Leeuwenhoek, is considered to be the first to observe microorganisms using a microscope.

In 1676, Anton van Leeuwenhoek observed bacteria and other microorganisms, using a single-lens microscope of his own design.^[1] While Van Leeuwenhoek is often cited as the first to observe microbes, Robert Hooke made the first recorded microscopic observation, of the fruiting bodies of molds, in 1665.^[9] The first observation of microbes using a microscope is generally credited to the Dutch draper and haberdasher, Antonie van Leeuwenhoek, who lived for most of his life in Delft, Holland. It has, however, been suggested that a Jesuit priest called Athanasius Kircher was the first to observe micro-organisms.^[10] He was among the first to design magic lanterns for projection purposes, so he must have been well acquainted with the properties of lenses.^[10] One of his books contains a chapter in Latin, which reads in translation – ‘Concerning the wonderful structure of things in nature, investigated by Microscope. Here, he wrote ‘who would believe that vinegar and milk abound with an innumerable multitude of worms.’ He also noted that putrid material is full of innumerable creeping animalcule. These observations antedate Robert Hooke’s Micrographia by nearly 20 years and were published some 29 years before van Leeuwenhoek saw protozoa and 37 years before he described having seen bacteria.^[10]

Innovative laboratory glassware and experimental methods developed by Louis Pasteur and other biologists contributed to the young field of bacteriology in the late 19th century.

The field of bacteriology (later a subdiscipline of microbiology) was founded in the 19th century by Ferdinand Cohn, a botanist whose studies on algae and photosynthetic bacteria led him to describe several bacteria including Bacillus and Beggiatoa. Cohn was also the first to formulate a scheme for the taxonomic classification of bacteria and discover spores.^[11] Louis Pasteur and Robert Koch were contemporaries of Cohn’s and are often considered to be the father of microbiology^[10] and medical microbiology, respectively.^[12] Pasteur is most famous for his series of experiments designed to disprove the then widely held theory of spontaneous generation, thereby solidifying microbiology’s identity as a biological science.^[13] Pasteur also designed methods for food preservation (pasteurization) and vaccines against several diseases such as anthrax, fowl cholera and rabies.^[1] Koch is best known for his contributions to the germ theory of disease, proving that specific diseases were caused by specific pathogenic micro-organisms. He developed a series of criteria that have become known as the Koch's postulates. Koch was one of the first scientists to focus on the isolation of bacteria in pure culture resulting in his description of several novel bacteria including Mycobacterium tuberculosis, the causative agent of tuberculosis.^[1]

While Pasteur and Koch are often considered the founders of microbiology, their work did not accurately reflect the true diversity of the microbial world because of their exclusive focus on micro-organisms having direct medical relevance. It was not until the late 19th century and the work of Martinus Beijerinck and Sergei Winogradsky, the founders of general microbiology (an older term encompassing aspects of microbial physiology, diversity and ecology), that the true breadth of microbiology was revealed.^[1] Beijerinck made two major contributions to microbiology: the discovery of viruses and the development of enrichment culture techniques.^[14] While his work on the Tobacco Mosaic Virus established the basic principles of virology, it was his development of enrichment culturing that had the most immediate impact on microbiology by allowing for the cultivation of a wide range of microbes with wildly different physiologies. Winogradsky was the first to develop the concept of chemolithotrophy and to thereby reveal the essential role played by micro-organisms in geochemical processes.^[15] He was responsible for the first isolation and description of both nitrifying and nitrogen-fixing bacteria.^[1]

Branches[link]

The branches of microbiology can be classified into pure and applied sciences.^[16] Microbiology can be also classified based on taxonomy, in the cases of bacteriology, mycology, protozoology, and phycology. There is considerable overlap between the specific branches of microbiology with each other and with other disciplines.

Pure microbiology[link]

Taxonomic arrangement[link]

• Bacteriology: The study of bacteria.
• Mycology: The study of fungi.
• Protozoology: The study of protozoa.
• Phycology (or algology): The study of algae.
• Parasitology: The study of parasites.
• Immunology: The study of the immune system.
• Virology: The study of the viruses.
• Nematology:The study of the nematodes

Integrative arrangement[link]

• Microbial cytology: The study of microscopic and submicroscopic details of microorganisms.
• Microbial physiology: The study of how the microbial cell functions biochemically. Includes the study of microbial growth, microbial metabolism and microbial cell structure.
• Microbial ecology: The relationship between microorganisms and their environment.
• Microbial genetics: The study of how genes are organized and regulated in microbes in relation to their cellular functions. Closely related to the field of molecular biology.
• Cellular microbiology: A discipline bridging microbiology and cell biology.
• Evolutionary microbiology: The study of the evolution of microbes. This field can be subdivided into:
  • Microbial taxonomy: The naming and classification of microorganisms.
  • Microbial systematics: The study of the diversity and genetic relationship of microorganisms.
• Generation microbiology: The study of those microorganisms that have the same characters as their parents.
• Systems microbiology: A discipline bridging systems biology and microbiology.
• Molecular microbiology: The study of the molecular principles of the physiological processes in microorganisms.

Other[link]

• Nano microbiology: The study of those microgasims
• Exo microbiology (or Astro microbiology): The study of microorganisms in outer space.

Applied microbiology[link]

• Medical microbiology: The study of the pathogenic microbes and the role of microbes in human illness. Includes the study of microbial pathogenesis and epidemiology and is related to the study of disease pathology and immunology.
• Pharmaceutical microbiology: The study of microorganisms that are related to the production of antibiotics, enzymes, vitamins,vaccines, and other pharmaceutical products and that cause pharmaceutical contamination and spoil.
• Industrial microbiology: The exploitation of microbes for use in industrial processes. Examples include industrial fermentation and wastewater treatment. Closely linked to the biotechnology industry. This field also includes brewing, an important application of microbiology.
• Microbial biotechnology: The manipulation of microorganisms at the genetic and molecular level to generate useful products.
• Food microbiology and Dairy microbiology: The study of microorganisms causing food spoilage and foodborne illness. Using microorganisms to produce foods, for example by fermentation.
• Agricultural microbiology: The study of agriculturally relevant microorganisms. This field can be further classified into the following:
  • Plant microbiology and Plant pathology: The study of the interactions between microorganisms and plants and plant pathogens.
  • Soil microbiology: The study of those microorganisms that are found in soil.
• Veterinary microbiology: The study of the role in microbes in veterinary medicine or animal taxonomy.
• Environmental microbiology: The study of the function and diversity of microbes in their natural environments. This involves the characterization of key bacterial habitats such as the rhizosphere and phyllosphere, soil and groundwater ecosystems, open oceans or extreme environments (extremophiles). This field includes other branches of microbiology such as:
  • Microbial ecology
  • Microbially-mediated nutrient cycling
  • Geomicrobiology
  • Microbial diversity
  • Bioremediation
• Water microbiology (or Aquatic microbiology): The study of those microorganisms that are found in water.
• Aeromicrobiology (or Air microbiology): The study of airborne microorganisms.
• Epidemiology: The study of the incidence, spread, and control of disease.

Benefits[link]

Fermenting tanks with yeast being used to brew beer

Whilst there are undoubtedly some who fear all microbes due to the association of some microbes with various human illnesses, many microbes are also responsible for numerous beneficial processes such as industrial fermentation (e.g. the production of alcohol, vinegar and dairy products), antibiotic production and as vehicles for cloning in more complex organisms such as plants. Scientists have also exploited their knowledge of microbes to produce biotechnologically important enzymes such as Taq polymerase, reporter genes for use in other genetic systems and novel molecular biology techniques such as the yeast two-hybrid system.

Bacteria can be used for the industrial production of amino acids. Corynebacterium glutamicum is one of the most important bacterial species with an annual production of more than two million tons of amino acids, mainly L-glutamate and L-lysine.^[17]

A variety of biopolymers, such as polysaccharides, polyesters, and polyamides, are produced by microorganisms. Microorganisms are used for the biotechnological production of biopolymers with tailored properties suitable for high-value medical application such as tissue engineering and drug delivery. Microorganisms are used for the biosynthesis of xanthan, alginate, cellulose, cyanophycin, poly(gamma-glutamic acid), levan, hyaluronic acid, organic acids, oligosaccharides and polysaccharide, and polyhydroxyalkanoates.^[18]

Microorganisms are beneficial for microbial biodegradation or bioremediation of domestic, agricultural and industrial wastes and subsurface pollution in soils, sediments and marine environments. The ability of each microorganism to degrade toxic waste depends on the nature of each contaminant. Since sites typically have multiple pollutant types, the most effective approach to microbial biodegradation is to use a mixture of bacterial species and strains, each specific to the biodegradation of one or more types of contaminants.^[19]

There are also various claims concerning the contributions to human and animal health by consuming probiotics (bacteria potentially beneficial to the digestive system) and/or prebiotics (substances consumed to promote the growth of probiotic microorganisms).^[20]

Recent research has suggested that microorganisms could be useful in the treatment of cancer. Various strains of non-pathogenic clostridia can infiltrate and replicate within solid tumors. Clostridial vectors can be safely administered and their potential to deliver therapeutic proteins has been demonstrated in a variety of preclinical models.^[21]

See also[link]

References[link]

External links[link]

At Wikiversity you can learn more and teach others about Microbiology at: The Department of Microbiology

• Microbiology on In Our Time at the BBC. (listen now)
• Bacteriology Made Easy | Medchrome
• Online lectures in microbiology University of South Carolina
• Microbiology Online
• Online Microbiology textbook
• Online Medical Microbiology textbook
• Institute of Microbiology of the Swiss Federal Institute of Technology
• Annual Review of Microbiology