Microbiology

Overview
Microbiology is the study of microorganisms, which are unicellular or cell-cluster microscopic organisms. This includes eukaryotes such as fungi and protists, and prokaryotes such as bacteria and certain algae. Viruses, though not strictly classed as living organisms, are also studied. Microbiology is a broad term which includes many branches like virology, mycology, parasitology and others. A person who specializes in the area of microbiology is called a microbiologist.

Although much is now known in the field of microbiology, advances are being made regularly. We have probably only studied about 1% of all of the microbes on Earth. Thus, despite the fact that over three hundred years have passed since the discovery of microbes, the field of microbiology could be said to be in its infancy relative to other biological disciplines such as zoology, botany and entomology.

History
The existence of microorganisms was hypothesized during the late Middle Ages but they were not observed or proven until the invention of the microscope in the 17th century. In The Canon of Medicine (1020), Abū Alī ibn Sīnā (Avicenna) stated that bodily secretion is contaminated by foul foreign earthly bodies before being infected, but he did not view them as primary causes of disease. When the Black Death bubonic plague reached al-Andalus in the 14th century, Ibn Khatima and Ibn al-Khatib hypothesized that infectious diseases are caused by microorganisms which enter the human body.

Bacteria were first observed by Anton van Leeuwenhoek in 1676 using a single-lens microscope of his own design. The name "bacterium" was introduced much later, by Ehrenberg in 1828, derived from the Greek βακτηριον meaning "small stick". While van Leeuwenhoek is often cited as the first microbiologist, the first recorded microbiological observation, that of the fruiting bodies of molds, was made earlier in 1665 by Robert Hooke.

The field of bacteriology (later a subdiscipline of microbiology) is generally considered to have been founded by Ferdinand Cohn (1828–1898), 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. Pasteur (1822–1895) and Robert Koch (1843–1910) were contemporaries of Cohn’s and are often considered to be the founders of medical microbiology. 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. Pasteur also designed methods for food preservation (pasteurization) and vaccines against several diseases such as anthrax, fowl cholera and rabies. Koch is best known for his contributions to the germ theory of disease, proving that specific diseases were caused by specific pathogenic microorganisms. 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.

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 microorganisms having direct medical relevance. It was not until the work of Martinus Beijerinck (1851–1931) and Sergei Winogradsky (1856–1953), the founders of general microbiology (an older term encompassing aspects of microbial physiology, diversity and ecology), that the true breadth of microbiology was revealed. Beijerinck made two major contributions to microbiology: the discovery of viruses and the development of enrichment culture techniques. 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 microorganisms in geochemical processes. He was responsible for the first isolation and description of both nitrifying and nitrogen-fixing bacteria.

Types
The field of microbiology can be generally divided into several subdisciplines:
 * Microbial physiology: The study of how the microbial cell functions biochemically. Includes the study of microbial growth, microbial metabolism and microbial cell structure.
 * Microbial genetics: The study of how genes are organised and regulated in microbes in relation to their cellular functions. Closely related to the field of molecular biology.
 * Medical microbiology: The study of 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.
 * 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. Includes the study of microbial ecology, microbially-mediated nutrient cycling, geomicrobiology, microbial diversity and bioremediation. Characterisation of key bacterial habitats such as the rhizosphere and phyllosphere, soil and groundwater ecosystems, open oceans or extreme environments (extremophiles).
 * Evolutionary microbiology: The study of the evolution of microbes. Includes the study of bacterial systematics and taxonomy.
 * 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.
 * Aeromicrobiology: The study of airborne microorganisms.
 * Food Microbiology: The study of microorganisms causing food spoilage.
 * Pharmaceutical microbiology: the study of microorganisms causing pharmaceutical contamination and spoilage.

Benefits
While microbes are often viewed negatively due to their association with many human illnesses, microbes are also responsible for many beneficial processes such as industrial fermentation (e.g. the production of alcohol and dairy products), antibiotic production and as vehicles for cloning in higher 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.

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 most sites are typically comprised of 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.

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).

General

 * Online Microbiology textbook
 * Todar's Bacteriology textbook
 * Online Medical Microbiology textbook

Journals

 * Nature Reviews Microbiology (journal home)

Professional organizations

 * American Society for Microbiology
 * Society for General Microbiology
 * Fondation Mérieux

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