General Microbiology

COMPILED ARTICLES FROM WIKIPEDIA
MICROBIOLOGY AN : INTRODUCTION
COMPILED BY WARIH NUGROHO, DVM
SCHOOL OF AGRICULTURE FOR DEVELOPMENT PELAIHARI-SOUTH KALIMANTAN 2009
Microbiology - Wikipedia, the free encyclopedia
http://en.wikipedia.org/wiki/Microbiology
Microbiology
From Wikipedia, the free encyclopedia
Microbiology (from Greek , mkros, "small"; , bios, "life"; and -, -logia) is the study of microorganisms, which are unicellular or cell-cluster microscopic organisms.[1] This includes eukaryote such as fungi and protists, and prokaryotes, which are bacteria and archaea. Viruses, though not strictly classed as living organisms, are also studied.[2] In short; microbiology refers to the study of life and organisms that are too small to be seen with the naked eye. Microbiology is a broad term which includes virology, mycology, parasitology, bacteriology and other branches. A microbiologist is a specialist in microbiology.
An agar plate streaked with microorganisms
Microbiology is researched actively, and the field is advancing continually. We have probably only studied about one percent of all of the microbe species on Earth.[3] Although microbes were first observed over three hundred years ago, the field of microbiology can be said to be in its infancy relative to older biological disciplines such as zoology and botany.
Contents
1 History 1.1 Ancient 1.2 Modern 2 Types 3 Benefits 4 References 4.1 Further reading 5 See also 6 External links 6.1 General 6.2 Journals 6.3 Professional organizations
History
Ancient
The existence of microorganisms was hypothesized for many centuries before their actual discovery in the 17th century. In 600 BCE, the ancient Indian surgeon Susruta held microbes responsible for several diseases and explained in Sushruta Samhita that they can be transmitted through contact, air or water. Theories on
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microorganisms was made by Roman scholar Marcus Terentis Varro in a book titled On Agriculture in which he warns against locating a homestead in the vicinity of swamps:
...and 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 cause serious diseases.[4]
This passage seems to indicate that the ancients were aware of the possibility that diseases could be spread by yet unseen organisms. In The Canon of Medicine (1020), Ab Al ibn Sn (Avicenna) stated that bodily secretion is contaminated by foul foreign earthly bodies before being infected.[5] He also hypothesized on the contagious nature of tuberculosis and other infectious diseases, and used quarantine as a means of limiting the spread of contagious diseases.[6] When the Black Death bubonic plague reached al-Andalus in the 14th century, Ibn Khatima hypothesized that infectious diseases are caused by "minute bodies" which enter the human body and cause disease.[5] In 1546 Girolamo Fracastoro proposed that epidemic diseases were caused by transferable seedlike entities that could transmit infection by direct or indirect contact or even without contact over long distances. All these early claims about the existence of microorganisms were speculative in nature and not based on any data or science. Microorganisms were neither proven, observed, and correctly and accurately described until the 17th century. The reason for this was that all these early inquiries lacked the most fundamental tool in order for microbiology and bacteriology to exist as a science, and that was the microscope.
Modern
Bacteria, and other microorganisms, were first observed by Antonie van Leeuwenhoek in 1676 using a single-lens microscope of his own design. In doing so Leeuwenhoek made one of the most important discoveries in biology and initiated the scientific fields of bacteriology and microbiology.[1] The name "bacterium" was introduced much later, by Ehrenberg in 1828, derived from the Greek 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.[7] The field of bacteriology (later a subdiscipline of microbiology) is generally considered to have been founded by Ferdinand Cohn Antonie van Leeuwenhoek, the first (18281898), a botanist whose studies on algae and photosynthetic microbiologist and the first to observe bacteria led him to describe several bacteria including Bacillus and microorganisms using a microscope. Beggiatoa. Cohn was also the first to formulate a scheme for the Known as the 'Father of Microbiology'. Whilst he did not invent the microscope, taxonomic classification of bacteria.[8] Louis Pasteur (18221895) he greatly developed it. and Robert Koch (18431910) were contemporaries of Cohns and are often considered to be the founders of medical microbiology.[9] Pasteur is most famous for his series of experiments designed to disprove the then widely held theory of spontaneous generation, thereby solidifying microbiologys identity as a biological science.[10] Pasteur also
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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 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.[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 microorganisms having direct medical relevance. It was not until the work of Martinus Beijerinck (18511931) and Sergei Winogradsky (18561953), 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.[11] 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.[12] He was responsible for the first isolation and description of both nitrifying and nitrogen-fixing bacteria.[1]
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 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. 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 and foodborne illness. Using microorganisms to produce foods, for example by fermentation. Pharmaceutical microbiology: the study of microorganisms causing pharmaceutical contamination and spoilage. Oral microbiology: the study of microorganisms of the mouth in particular those causing caries and periodontal disease.
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Benefits
Whilst there are undoubtedly some who fear all microbes due to the association of some microbes with many human illnesses, many 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.
Fermenting tanks with yeast being used to brew beer
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. [13] 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(gammaglutamic acid), levan, hyaluronic acid, organic acids, oligosaccharides and polysaccharide, and polyhydroxyalkanoates.[14] 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.[15] 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).[16] 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.[17]
References
1. ^ a b c d e f Madigan M, Martinko J (editors) (2006). Brock Biology of Microorganisms (11th ed.). Prentice Hall. ISBN 0-13-144329-1. 2. ^ Rice G (2007-03-27). "Are Viruses Alive?". http://serc.carleton.edu/microbelife/yellowstone /viruslive.html. Retrieved on 2007-07-23. 3. ^ Amann RI, Ludwig W, Schleifer KH (1995). "Phylogenetic identification and in situ detection of individual microbial cells without cultivation". Microbiol. Rev. 59: 143169. http://www.ncbi.nlm.nih.gov/entrez /query.fcgi?cmd=Retrieve&db=pubmed&
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dopt=Abstract&list_uids=7535888. 4. ^ Varro On Agriculture 1,xii Loeb 5. ^ a b Ibrahim B. Syed, Ph.D. (2002). "Islamic Medicine: 1000 years ahead of its times", Journal of the Islamic Medical Association 2, p. 2-9. 6. ^ David W. Tschanz, MSPH, PhD (August 2003). "Arab Roots of European Medicine", Heart Views 4 (2). 7. ^ Gest H (2005). "The remarkable vision of Robert Hooke (1635-1703): first observer of the microbial world". Perspect. Biol. Med. 48 (2): 26672. doi:10.1353/pbm.2005.0053. PMID 15834198. 8. ^ Drews G (1999). "Ferdinand Cohn, a Founder of Modern Microbiology". ASM News 65 (8). http://www.asm.org/Articles/Ferdinand.html. 9. ^ Ryan KJ, Ray CG (editors) (2004). Sherris Medical Microbiology (4th ed.). McGraw Hill. ISBN 0-8385-8529-9. 10. ^ Bordenave G (2003). "Louis Pasteur (1822-1895)". Microbes Infect. 5 (6): 55360. PMID 12758285. 11. ^ Johnson J (1998-07-01). "Martinus Willem Beijerinck". American Phytopathological Society. http://www.apsnet.org/Education/feature /TMV/intro.html. Retrieved on 2007-07-23. 12. ^ Paustian T, Roberts G. "Beijerinck and
13.
14.
15.
16.
17.
Winogradsky initiate the field of environmental microbiology". The Microbial World. http://www.microbiologytext.com /index.php?module=Book&func=displayarticle& art_id=32. Retrieved on 2007-07-23. ^ Burkovski A (editor). (2008). Corynebacteria: Genomics and Molecular Biology. Caister Academic Press. ISBN 978-1-904455-30-1. http://www.horizonpress.com/cory. ^ Rehm BHA (editor). (2008). Microbial Production of Biopolymers and Polymer Precursors: Applications and Perspectives. Caister Academic Press. ISBN 978-1-904455-36-3. http://www.horizonpress.com/biopolymers. ^ Diaz E (editor). (2008). Microbial Biodegradation: Genomics and Molecular Biology (1st ed.). Caister Academic Press. ISBN 978-1-904455-17-2. http://www.horizonpress.com /biod. ^ Tannock GW (editor). (2005). Probiotics and Prebiotics: Scientific Aspects. Caister Academic Press. ISBN 978-1-904455-01-1. http://www.horizonpress.com/pro3. ^ Mengesha et al (2009). "Clostridia in Anti-tumor Therapy". Clostridia: Molecular Biology in the Post-genomic Era. Caister Academic Press. ISBN 978-1-904455-38-7.
Further reading
Lerner, Brenda Wilmoth & K. Lee Lerner (eds) (2006). Medicine, health, and bioethics : essential primary sources (1st ed.). Thomson Gale. ISBN 1414406231. Witzany, Guenther (2008). Bio-Communication of Bacteria and its Evolutionary Interrelations to Natural Genome Editing Competences of Viruses.. Nature Precedings. hdl:10101/npre.2008.1738.1.
See also
Archaea Bacteria Biochemistry Biomilling Biosafety Biotechnology Environmental microbiology Eukaryote Food microbiology Genetics Geomicrobiology Good Hygiene Practice Good Microbiological Practice Immunology Important publications in microbiology Industrial microbiology Medical technologist Medicine Mycology Oral microbiology Bacteriophage meetings Prokaryote Virology
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External links
General
Online lectures in microbiology (http://media.med.sc.edu/microbiology2007/) University of South Carolina Microbiology Online (http://www.ocean.edu/academics/programs_of_study/science /MicrobiologyOnline.htm) Online Microbiology textbook (http://www.microbiologytext.com/index.php?module=Book&func=toc& book_id=4) Todar's Bacteriology textbook (http://www.textbookofbacteriology.net/) Online Medical Microbiology textbook (http://pathmicro.med.sc.edu/book/welcome.htm)
Journals
Annual Review of Microbiology (http://arjournals.annualreviews.org/loi/micro/) Critical Reviews in Microbiology (journal home (http://www.informaworld.com/crmicrobiology) ) International Journal of Systematic and Evolutionary Microbiology Journal of Bacteriology Nature Reviews Microbiology (journal home (http://www.nature.com/nrmicro/index.html) ) Springer Protocols in Microbiology
Professional organizations
Information portal For Microbiology Students (http://www.microbiologystudents.com/) American Society for Microbiology (http://www.asm.org/) Society for General Microbiology (http://www.socgenmicrobiol.org.uk/) Society for Industrial Microbiology (http://www.simhq.org/) Retrieved from "http://en.wikipedia.org/wiki/Microbiology" Categories: Microbiology | Subjects taught in medical school Hidden categories: Articles containing non-English language text | Articles needing additional references from July 2007 This page was last modified on 4 February 2009, at 12:31. All text is available under the terms of the GNU Free Documentation License. (See Copyrights for details.) Wikipedia is a registered trademark of the Wikimedia Foundation, Inc., a U.S. registered 501(c)(3) tax-deductible nonprofit charity.
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Virus - Wikipedia, the free encyclopedia
http://en.wikipedia.org/wiki/Virus
Virus
A virus (from the Latin virus meaning toxin or poison) is a sub-microscopic infectious agent that is unable to grow or reproduce outside a host cell. Viruses infect all cellular life. The first known virus, tobacco mosaic virus, was discovered by Martinus Beijerinck in 1899,[1] and now more than 5,000 types of virus have been described.[2] The study of viruses is known as virology, and is a branch of microbiology. Viruses consist of two or three parts: all viruses have genes made from either DNA or RNA, long molecules that carry genetic information; all have a protein coat that protects these genes; and some have an envelope of fat that surrounds them when they are outside a cell. Viruses vary in shape from simple helical and icosahedral shapes, to more complex structures. They are about 100 times smaller than bacteria.[3] The origins of viruses are unclear: some may have evolved from plasmidspieces of DNA that can move between cellsothers may have evolved from bacteria. Viruses spread in many ways; plant viruses are often transmitted from plant to plant by insects that feed on sap, such as aphids, while animal viruses can be carried by blood-sucking insects. These disease-bearing organisms are known as vectors. Influenza viruses are spread by coughing and sneezing, and others such as norovirus, are transmitted by the faecal-oral route, when they contaminate hands, food or water. Rotaviruses are often spread by direct contact with infected children. HIV is one of several viruses that are transmitted through sex.
Viruses
Rotavirus
Virus classification Group: IVII Groups I: dsDNA viruses II: ssDNA viruses III: dsRNA viruses IV: (+)ssRNA viruses V: ()ssRNA viruses VI: ssRNA-RT viruses VII: dsDNA-RT viruses
Not all viruses cause disease, as many viruses reproduce without causing any obvious harm to the infected organism. Some viruses such as HIV can cause life-long or chronic infections, and the viruses continue to replicate in the body despite the hosts' defence mechanisms. However, viral infections in animals usually cause an immune response, which can completely eliminate a virus. These immune responses can also be produced by vaccines that give lifelong immunity to a viral infection. Microorganisms such as bacteria also have defences against viral infection, such as restriction modification systems. Antibiotics have no effect on viruses, but antiviral drugs have been developed to treat life-threatening and more minor infections.
Contents
1 Etymology 2 History 3 Origins 4 Structure 4.1 Helical 4.2 Icosahedral
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4.3 Enveloped 4.4 Complex 5 Genomes 5.1 Genetic change 6 Replication 6.1 Replication cycle 6.1.1 DNA viruses 6.1.2 RNA viruses 6.1.3 Reverse transcribing viruses 7 Effects on the host cell 8 Classification 8.1 ICTV classification 8.2 Baltimore classification 9 Viruses and human disease 9.1 Epidemiology 9.2 Epidemics and pandemics 9.3 Cancer 9.4 Host defence mechanisms 9.5 Prevention and treatment 9.5.1 Vaccines 9.5.2 Antiviral drugs 10 Infection in other species 10.1 Plants 10.2 Bacteria 10.3 Archaea 11 Applications 11.1 Life sciences and medicine 11.2 Materials science and nanotechnology 11.3 Weapons 12 External links 13 References 13.1 Notes 13.2 Bibliography
Etymology
The word is from the Latin virus referring to poison and other noxious substances, first used in English in 1392.[4] Virulent, from Latin virulentus (poisonous) dates to 1400.[5] A meaning of "agent that causes infectious disease" is first recorded in 1728,[4] before the discovery of viruses by Dmitry Ivanovsky in 1892. The adjective viral dates to 1948.[6] The term virion is also used to refer to a single infective viral particle. The plural of virus is "viruses".
History
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In 1884, the French microbiologist Charles Chamberland invented a filter, (known today as the Chamberland filter or Chamberland-Pasteur filter), with pores smaller than bacteria. Thus, he could pass a solution containing bacteria through the filter and completely remove them from the solution.[7] In 1892 the Russian biologist Dimitri Ivanovski used this filter to study what is now known to be tobacco mosaic virus. His experiments showed that the crushed leaf extracts from infected tobacco plants are still infectious after filtration. Ivanovski suggested the infection might be caused by a toxin produced by bacteria, but did not pursue the idea.[8] At the time it was thought that all infectious agents could be retained by filters and grown on a nutrient mediumthis was part of the germ theory of disease.[9] In 1899 the Dutch microbiologist Martinus Beijerinck repeated the experiments and became convinced that this was a new form of infectious agent.[10] He went on to observe that the agent multiplied only in dividing cells, but as his experiments Martinus Beijerinck in his laboratory in 1921 did not show that it was made of particles, he called it a contagium vivum [8] fluidum (soluble living germ) and re-introduced the word virus. Beijerinck maintained that viruses were liquid in nature, a theory later discredited by Wendell Stanley, who proved they were particulate.[8] In the same year, 1899, Friedrich Loeffler and Frosch passed the agent of foot and mouth disease (aphthovirus) through a similar filter and ruled out the possibility of a toxin because of the high dilution; they concluded that the agent could replicate.[8] In the early 20th century, the English bacteriologist Frederick Twort discovered the viruses that infect bacteria, which are now called bacteriophages,[11] and the French-Canadian microbiologist Flix d'Herelle described viruses that, when added to bacteria growing on agar, would produce areas of dead bacteria. He accurately diluted a suspension of these viruses and discovered that the highest dilutions, rather than killing all the bacteria, formed discrete areas of dead organisms. Counting these areas and multiplying by the dilution factor allowed him to calculate the number of viruses in the suspension.[12] By the end of the nineteenth century, viruses were defined in terms of their infectivity, filterability, and their requirement for living hosts. Viruses had only been grown in plants and animals. In 1906, Harrison invented a method for growing tissue in lymph, and, in 1913, E. Steinhardt, C. Israeli and R. A. Lambert used this method to grow vaccinia virus in fragments of guinea pig corneal tissue.[13] In 1928, H. B. Maitland and M. C. Maitland grew vaccinia virus in suspensions of minced hens' kidneys. Their method was not widely adopted until the 1950s, when poliovirus was grown on a large scale for vaccine production.[14] Another breakthrough came in 1931, when the American pathologist Ernest William Goodpasture grew influenza and several other viruses in fertilised chickens' eggs.[15] In 1949 John F. Enders, Thomas Weller and Frederick Robbins grew polio virus in cultured human embryo cells, the first virus to be grown without using solid animal tissue or eggs. This work enabled Jonas Salk to make an effective polio vaccine.[16]
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With the invention of electron microscopy in 1931 by the German engineers Ernst Ruska and Max Knoll came the first images of viruses.[17] In 1935 American biochemist and virologist Wendell Stanley examined the Tobacco mosaic virus and found it to be mostly made from protein.[18] A short time later, this virus was separated into protein and RNA parts.[19] Tobacco mosaic virus was the first one to be crystallised and whose structure could therefore be elucidated in detail. The first X-ray diffraction pictures of the crystallised virus were obtained by Bernal and Fankuchen in 1941. Based on her pictures, Rosalind Franklin discovered the full structure of the virus in 1955.[20] In the same year, Heinz Fraenkel-Conrat and Robley Williams showed that purified Tobacco mosaic virus RNA and its coat protein can assemble by themselves to form functional viruses, suggesting that this simple mechanism was probably how viruses assembled within their host cells.[21]
Rosalind Franklin
The second half of the twentieth century was the golden age of virus discovery and most of the 2,000 recognised species of animal, plant and bacterial viruses were discovered during these years.[1][22] In 1957, equine arterivirus and the cause of Bovine virus diarrhea (a pestivirus) were discovered. In 1963, the hepatitis B virus was discovered by Baruch Blumberg,[23] and in 1965, Howard Temin described the first retrovirus. Reverse transcriptase, the key enzyme that retroviruses use to translate their RNA into DNA, was first described in 1970, independently by Howard Temin and David Baltimore.[24] In 1983 Luc Montagnier's team at the Pasteur Institute in France, first isolated the retrovirus now called HIV.[25]
Origins
Viruses are found wherever there is life and have probably existed since living cells first evolved.[26] The origin of viruses is unclear because they do not form fossils, so molecular techniques have been the most useful means of investigating how they arose.[27] These techniques rely on the availability of ancient viral DNA or RNA, but, unfortunately, most of the viruses that have been preserved and stored in laboratories are less than 90 years old.[28][29] There are three main theories of the origins of viruses:[30][31] Regressive theory: Viruses may have once been small cells that parasitised larger cells. Over time, genes not required by their parasitism were lost. The bacteria rickettsia and chlamydia are living cells that, like viruses, can reproduce only inside host cells. They lend credence to this theory, as their dependence on parasitism is likely to have caused the loss of genes that enabled them to survive outside a cell. This is also called the degeneracy theory.[32][33] Cellular origin theory (sometimes called the vagrancy theory):[32][34] Some viruses may have evolved from bits of DNA or RNA that "escaped" from the genes of a larger organism. The escaped DNA could have come from plasmidspieces of naked DNA that can move between cells or transposons. These are molecules of DNA that replicate and move around to different positions within the genes of the cell.[35] Once called "jumping genes", these are examples of mobile genetic elements and could be the origin of some viruses. Transposons were discovered in maize by Barbara McClintock in 1950.[36] Coevolution theory: Viruses may have evolved from complex molecules of protein and nucleic acid at the same time as cells first appeared on earth and would have been dependent on cellular life for many millions of years. Viroids are molecules of RNA that are not classified as viruses because they lack a protein coat. However, they have characteristics that are common to several viruses and are often called subviral agents.[37] Viroids are important pathogens of plants.[38] They do not code for proteins but
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interact with the host cell and use the host machinery for their replication.[39] The hepatitis delta virus of humans has an RNA genome similar to viroids but has protein coat derived from hepatitis B virus and cannot produce one of its own. It is therefore a defective virus and cannot replicate without the help of hepatitis B virus.[40] The Virophage 'sputnik' infects the Mimivirus and the related Mamavirus which in turn infect the protozooan Acanthamoeba castellanii.[41] These viruses that are dependent on other virus species are called satellites and may represent evolutionary intermediates of viroids and viruses.[42][43] Prions are infectious protein molecules that do not contain DNA or RNA.[44] They cause an infection in sheep called scrapie and cattle bovine spongiform encephalopathy ("mad cow" disease). In humans they cause kuru and Creutzfeld-Jacob disease.[45] They are able to replicate because some proteins can exist in two different shapes and the prion changes the normal shape of a host protein into the prion shape. This starts a chain reaction where each prion protein converts many host proteins into more prions, and these new prions then go on to convert even more protein into prions. Although they are fundamentally different from viruses and viroids, their discovery gives credence to theory that viruses could have evolved from self-replicating molecules.[46] Computer analysis of viral and host DNA sequences is giving a better understanding of the evolutionary relationships between different viruses and may help identify the ancestors of modern viruses. To date, such analyses have not helped to decide on which of the theories are correct. However, it seems unlikely that all currently known viruses have a common ancestor and viruses have probably arisen numerous times in the past by one or more mechanisms.[47] Opinions differ on whether viruses are a form of life, or organic structures that interact with living organisms. They have been described as "organisms at the edge of life",[48] since they resemble organisms in that they possess genes and evolve by natural selection,[49] and reproduce by creating multiple copies of themselves through self-assembly. However, although they have genes, they do not have a cellular structure, which is often seen as the basic unit of life. Additionally, viruses do not have their own metabolism, and require a host cell to make new products. They therefore cannot reproduce outside a host cell (though bacterial species such as rickettsia and chlamydia are considered living organisms despite the same limitation). Accepted forms of life use cell division to reproduce, whereas viruses spontaneously assemble within cells, which is analogous to the autonomous growth of crystals. Virus self-assembly within host cells has implications for the study of the origin of life,[50] as it lends further credence to the hypothesis that life could have started as self-assembling organic molecules.[51]
Structure
Viruses display a wide diversity of shapes and sizes, called morphologies. Viruses are about 100 times smaller than bacteria. Most viruses which have been studied have a diameter between 10 and 300 nanometres. Some filoviruses have a total length of up to 1400 nm, however their diameters are only about 80 nm.[3] Most viruses are unable to be seen with a light microscope so scanning and transmission electron microscopes are used to visualise virus particles.[52] To increase the contrast between viruses and the background, electron-dense "stains" are used. These are solutions of salts of heavy metals such as tungsten, that scatter the electrons from regions covered with the stain. When virus particles are coated with stain (positive staining), fine detail is obscured. Negative staining overcomes this problem by staining the background
Diagram of how a virus capsid can be constructed using multiple copies of just two protein molecules
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only.[53] A complete virus particle, known as a virion, consists of nucleic acid surrounded by a protective coat of protein called a capsid. These are formed from identical protein subunits called capsomers.[54] Viruses can have a lipid "envelope" derived from the host cell membrane. The capsid is made from proteins encoded by the viral genome and its shape serves as the basis for morphological distinction.[55][56] Virally coded protein subunits will self-assemble to form a capsid, generally requiring the presence of the virus genome. However, complex viruses code for proteins which assist in the construction of their capsid. Proteins associated with nucleic acid are known as nucleoproteins, and the association of viral capsid proteins with viral nucleic acid is called a nucleocapsid. In general, there are four main morphological virus types:
Helical
Helical capsids are composed of a single type of capsomer stacked around a central axis to form a helical structure which may have a central cavity, or hollow tube. This arrangement results in rod-shaped or filamentous virions: these can be short and highly rigid, or long and very flexible. The genetic material, generally single-stranded RNA, but ssDNA in some cases, is bound into the protein helix, by interactions between the negatively-charged nucleic acid and positive charges on the protein. Overall, the length of a helical capsid is related to the length of the nucleic acid contained within it and the diameter is dependent on the size and arrangement of capsomers. The well-studied Tobacco mosaic virus is an example of a helical virus.[57]
Most animal viruses are icosahedral or near-spherical with icosahedral symmetry. A regular icosahedron is the optimum way of forming a closed shell from identical sub-units. The minimum number of identical capsomers required is twelve, each composed of five identical sub-units. Many viruses, such as rotavirus, have more than twelve capsomers and appear spherical but they retain this symmetry. Capsomers at the apices are surrounded by five other capsomers and are called pentons. Capsomers on the triangular faces are surround by six others and are call hexons.[58]
Diagram of the structure of tobacco mosaic virus: the viral RNA is coiled inside the helix formed by repeating protein sub-units
Icosahedral
Electron micrograph of icosahedral viruses (adenovirus)
Enveloped
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Some species of virus envelope themselves in a modified form of one of the cell membranes, either the outer membrane surrounding an infected host cell, or internal membranes such as nuclear membrane or endoplasmic reticulum, thus gaining an outer lipid bilayer known as a viral envelope. This membrane is studded with proteins coded for by the viral genome and host genome; the lipid membrane itself and any carbohydrates present are entirely host-coded. The influenza virus and HIV use this strategy. Most enveloped viruses are dependent on the envelope for their infectivity.[59]
Electron micrograph of negatively-stained herpes zoster virusnote the envelope around the virus particle
Complex
These viruses possess a capsid which is neither purely helical, nor purely icosahedral, and which may possess extra structures such as protein tails or a complex outer wall. Some bacteriophages have a complex structure consisting of an icosahedral head bound to a helical tail which may have a hexagonal base plate with protruding protein tail fibres. The poxviruses are large, complex viruses which have an unusual morphology. The viral genome is associated with proteins within a central disk structure known as a The structure of a nucleoid. The nucleoid is surrounded by a membrane and two lateral bodies of typical bacteriophage unknown function. The virus has an outer envelope with a thick layer of protein studded over its surface. The whole particle is slightly pleiomorphic, ranging from ovoid to brick shape.[60] Mimivirus is the largest known virus, with a capsid diameter of 400 nm. Protein filaments measuring 100 nm project from the surface. The capsid appears hexagonal under an electron microscope, therefore the capsid is probably icosahedral.[61]
Genomes
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An enormous variety of genomic structures can be seen among viral species; as a group they contain more structural genomic diversity than the entire kingdoms of either plants, animals, or bacteria. A virus has either DNA or RNA genes and are called DNA viruses and RNA viruses respectively. By far most viruses have RNA. Plant viruses tend to have single-stranded RNA and bacteriophages tend to have double-stranded DNA.[62] Viral genomes are circular, such as polyomaviruses, or linear, such as adenoviruses. The type of nucleic acid is irrelevant to the shape of the genome. Among RNA viruses, the genome is often divided up into separate parts within the virion and is called segmented. Each segment often codes for one protein and they are usually found together in one capsid. Every segment is not required to be in the same virion for the overall virus to be infectious, as demonstrated by the brome mosaic virus.[3] A viral genome, irrespective of nucleic acid type, is either singlestranded or double-stranded. Single-stranded genomes consist of an unpaired nucleic acid, analogous to one-half of a ladder split down the middle. Double-stranded genomes consist of two complementary paired nucleic acids, analogous to a ladder. Some viruses, such as those belonging to the Hepadnaviridae, contain a genome which is partially double-stranded and partially single-stranded.[62] For viruses with RNA or single-stranded DNA, the strands are said to be either positive-sense (called the plus-strand) or negative-sense (called the minus-strand), depending on whether it is complementary to the viral messenger RNA (mRNA). Positive-sense viral RNA is identical to viral mRNA and thus can be immediately translated by the host cell. Negative-sense viral RNA is complementary to mRNA and thus must be converted to positive-sense RNA by an RNA polymerase before translation. DNA nomenclature is similar to RNA nomenclature, in that the coding strand for the viral mRNA is complementary to it (), and the non-coding strand is a copy of it (+).[62] Genome size varies greatly between species. The smallest viral genomes code for only four proteins and weigh about 106 Daltons; the largest weigh about 108 Daltons and code for over one hundred proteins.[62] RNA viruses generally have smaller genome sizes than DNA viruses due to a higher error-rate when replicating, and have a maximum upper size limit. Beyond this limit, errors in the genome when replicating render the virus useless or uncompetitive. To compensate for this, RNA viruses often have segmented genomes where the genome is split into smaller molecules, thus reducing the chance of error. In contrast, DNA viruses generally have larger genomes due to the high fidelity of their replication enzymes.[63]
Genomic diversity among viruses Property Parameters DNA RNA Both DNA and RNA
Nucleic acid
Shape
Linear Circular Segmented
Strandedness
Single-stranded Double-stranded Double-stranded with regions of singlestrandedness
Sense
Positive sense (+) Negative sense () Ambisense (+/)
Genetic change
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Viruses undergo genetic change by several mechanisms. These include a process called genetic drift where individual bases in the DNA or RNA mutate to other bases. Most of these point mutations are silent in that they do not change the protein that the gene encodes, but others can confer evolutionary advantages such as resistance to antiviral drugs.[64] Antigenic shift is where there is a major change in the genome of the virus. This occurs as a result of recombination or reassortment. When this happens with influenza viruses, pandemics may result.[65] RNA viruses often exist as quasispecies or swarms of viruses of the same species but with slightly different genome nucleoside sequences. Such quasispecies are a prime target for natural selection.[66] Segmented genomes confer evolutionary advantages; different strains of a virus with a segmented genome can shuffle and combine genes and produce progeny viruses or (offspring) that have unique characteristics. This is called reassortment or viral sex.[67]
How antigenic shift, or reassortment, can result in novel and highly pathogenic strains of human influenza
Genetic recombination is the process by which a strand of DNA is broken and then joined to the end of a different DNA molecule. This can occur when viruses infect cells simultaneously and studies of viral evolution have shown that recombination has been rampant in the species studied.[68] Recombination is common to both RNA and DNA viruses.[69][70]
Replication
Viral populations do not grow through cell division, because they are acellular; instead, they use the machinery and metabolism of a host cell to produce multiple copies of themselves, and they assemble in the cell.
Replication cycle
The life cycle of viruses differs greatly between species but there are six basic stages in the life cycle of viruses:[71] Attachment is a specific binding between viral capsid proteins and specific receptors on the host cellular surface. This specificity determines the host range of a virus. For example, HIV infects only human T cells, because its surface protein, gp120, can interact with CD4 and receptors on the T cell's surface. This mechanism has evolved to favour those viruses that only infect cells in which they are A typical virus replication cycle capable of replication. Attachment to the receptor can induce the viral-envelope protein to undergo changes that results in the fusion of viral and cellular membranes. Penetration follows attachment; viruses enter the host cell through receptor mediated endocytosis or membrane fusion. This is often called viral entry. The infection of plant cells is different to that of animal cells. Plants have a rigid cell wall made of cellulose and viruses can only get inside the cells following trauma to the cell wall.[72] Viruses such as tobacco mosaic virus can also move directly in plants, from cell-to-cell, through pores called plasmodesmata.[73] Bacteria, like plants, have strong cell walls which a virus must breach to infect the cell. Some viruses have evolved mechanisms which inject their genome into the bacterial cell while the viral capsid remains outside.[74]
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Uncoating is a process in which the viral capsid is degraded by viral enzymes or host enzymes thus releasing the viral genomic nucleic acid. Replication involves synthesis of viral messenger RNA (mRNA) for viruses except positive sense RNA viruses (see above), viral protein synthesis and assembly of viral proteins and viral genome replication. Following the assembly of the virus particles, post-translational modification of the viral proteins often occurs. In viruses such as HIV, this modification, (sometimes called maturation), occurs after the virus has been released from the host cell.[75] Some bacteriophages inject their Viruses are released from the host cell by lysisa process that kills genomes into bacterial cells the cell by bursting its membrane. Enveloped viruses (e.g., HIV) typically are released from the host cell by budding. During this process the virus acquires its envelope, which is a modified piece of the host's plasma membrane. DNA viruses The genome replication of most DNA viruses takes place in the cell's nucleus. If the cell has the appropriate receptor on its surface, these viruses enter the cell by fusion with the cell membrane or by endocytosis. Most DNA viruses are entirely dependent on the host cell's DNA and RNA synthesising machinery, and RNA processing machinery. The viral genome must cross the cell's nuclear membrane to access this machinery.[76][77] RNA viruses RNA viruses are unique because their genetic information is encoded in RNA. Replication usually takes place in the cytoplasm. RNA viruses can be placed into about four different groups depending on their modes of replication. The polarity (whether or not it can be used directly to make proteins) of the RNA largely determines the replicative mechanism, and whether the genetic material is single-stranded or double-stranded. RNA viruses use their own RNA replicase enzymes to create copies of their genomes.[78] Reverse transcribing viruses Reverse transcribing viruses replicate using reverse transcription, which is the formation of DNA from an RNA template. Reverse transcribing viruses containing RNA genomes use a DNA intermediate to replicate, whereas those containing DNA genomes use an RNA intermediate during genome replication. Both types use the reverse transcriptase enzyme to carry out the nucleic acid conversion. Retroviruses often integrate the DNA produced by reverse transcription into the host genome. They are susceptible to antiviral drugs that inhibit the reverse transcriptase enzyme, e.g. zidovudine and lamivudine. An example of the first type is HIV which is a retrovirus. Examples of the second type are the Hepadnaviridae, which includes Hepatitis B virus.[79]
Effects on the host cell

The range of structural and biochemical effects that viruses have on the hosts cell is extensive.[80] These are called cytopathic effects. [81] Most virus infections eventually result in the death of the host cell. The causes of death include cell lysis, alterations to the cell's surface membrane and apoptosis.[82] Often cell death is caused by cessation of its normal activities due to suppression by virus-specific proteins, not all of which are components of the virus particle.[83] Some viruses cause no apparent changes to the infected cell. Cells in which the virus is latent and inactive show
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few signs of infection and often function normally.[84] This causes persistent infections and the virus is often dormant for many months or years. This is often the case with herpes viruses.[85][86] Viruses, such as Epstein-Barr virus often cause cells to proliferate without causing malignancy, [87] but viruses, such as papillomaviruses are an established cause of cancer.[88]
Classification
Classification seeks to describe the diversity of viruses by naming and grouping them based on similarities. In 1962, Andr Lwoff, Robert Horne, and Paul Tournier were the first to develop a means of virus classification, based on the Linnaean hierarchical system.[89] This system bases classification on phylum, class, order, family, genus, and species. Viruses were grouped according to their shared properties (not of their hosts) and the type of nucleic acid forming their genomes.[90] later the International Committee on Taxonomy of Viruses was formed.
ICTV classification
The International Committee on Taxonomy of Viruses (ICTV) developed the current classification system and wrote guidelines that put a greater weight on certain virus properties to maintain family uniformity. A universal system for classifying viruses, and a unified taxonomy, has been established since 1966. The 7th lCTV Report formalised for the first time the concept of the virus species as the lowest taxon (group) in a branching hierarchy of viral taxa.[91] However, at present only a small part of the total diversity of viruses has been studied, with analyses of samples from humans finding that about 20% of the virus sequences recovered have not been seen before, and samples from the environment, such as from seawater and ocean sediments, finding that the large majority of sequences are completely novel.[92] The general taxonomic structure is as follows: Order (-virales) Family (-viridae) Subfamily (-virinae) Genus (-virus) Species (-virus) In the current (2008) ICTV taxonomy, five orders have been established, the Caudovirales, Herpesvirales, Mononegavirales, Nidovirales, and Picornavirales. The committee does not formally distinguish between subspecies, strains, and isolates. In total there are 5 orders, 82 families, 11 subfamilies, 307 genera, 2,083 species and about 3,000 types yet unclassified.[93][94]
Baltimore classification
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The Nobel Prize-winning biologist David Baltimore devised the Baltimore classification system.[95][24] The ICTV classification system is used in conjunction with the Baltimore classification system in modern virus classification.[96][97][98] The Baltimore classification of viruses is based on the mechanism of mRNA production. Viruses must generate mRNAs from their genomes to produce proteins and replicate themselves, but different mechanisms are used to achieve this in each virus family. Viral genomes may be single-stranded (ss) or doublestranded (ds), RNA or DNA, and may or may not use reverse transcriptase (RT). Additionally, ssRNA viruses may be either sense (+) or antisense (-). This classification places viruses into seven groups: I: dsDNA viruses (e.g. Adenoviruses, Herpesviruses, Poxviruses) II: ssDNA viruses (+)sense DNA (e.g. Parvoviruses) III: dsRNA viruses (e.g. Reoviruses) IV: (+)ssRNA viruses (+)sense RNA (e.g. Picornaviruses, Togaviruses) V: (-)ssRNA viruses (-)sense RNA (e.g. Orthomyxoviruses, Rhabdoviruses) VI: ssRNA-RT viruses (+)sense RNA with DNA intermediate in life-cycle (e.g. Retroviruses) VII: dsDNA-RT viruses (e.g. Hepadnaviruses) As an example of viral classification, the chicken pox virus, varicella zoster (VZV), belongs to the order Herpesvirales, family Herpesviridae, subfamily Alphaherpesvirinae, and genus Varicellovirus. VZV is in Group I of the Baltimore Classification because it is a dsDNA virus that does not use reverse transcriptase.
The Baltimore Classification of viruses is based on the method of viral mRNA synthesis.
Viruses and human disease

Examples of common human diseases caused by viruses include the common cold, influenza, chickenpox and cold sores. Many serious diseases such as ebola, AIDS, avian influenza and SARS are caused by viruses. The relative ability of viruses to cause disease is described in terms of virulence. Other diseases are under investigation as to whether they too have a virus as the causative agent, such as the possible connection between human herpes virus six (HHV6) and neurological diseases such as multiple sclerosis and chronic fatigue syndrome. There is current controversy over whether the borna virus, previously thought to cause neurological diseases in horses, could be responsible for psychiatric illnesses in humans.[99]
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A child with chickenpox
Viruses have different mechanisms by which they produce disease in an organism, which largely depends on the viral species. Mechanisms at the cellular level primarily include cell lysis, the breaking open and subsequent death of the cell. In multicellular organisms, if enough cells die the whole organism will start to suffer the effects. Although viruses cause disruption of healthy homeostasis, resulting in disease, they may exist relatively harmlessly within an organism. An example would include the ability of the herpes simplex virus, which cause cold sores, to remain in a dormant state within the human body. This is called latency[100] and is a characteristic of the all herpes viruses including the Epstein-Barr virus, which causes glandular fever, and the varicella zoster virus, which causes chicken pox. Latent chickenpox infections return in later life as the disease called shingles.
Some viruses can cause life-long or chronic infections, where the viruses continue to replicate in the body despite the hosts' defence mechanisms.[101] This is common in hepatitis B virus and hepatitis C virus infections. People chronically infected are known as carriers, as they serve as reservoirs of infectious virus.[102] In populations with a high proportion of carriers, the disease is said to be endemic.[103]
Epidemiology
Viral epidemiology is the branch of medical science that deals with the transmission and control of virus infections in humans. Transmission of viruses can be vertical, that is from mother to child, or horizontal, which means from person to person. Examples of vertical transmission include hepatitis B virus and HIV where the baby is born already infected with the virus.[104] Another, more rare, example is the varicella zoster virus, which although causing relatively mild infections in humans, can be fatal to the foetus and newly born baby.[105] Horizontal transmission is the most common mechanism of spread of viruses in populations. Transmission can be exchange of blood by sexual activity, e.g. HIV, hepatitis B and hepatitis C; by mouth by exchange of saliva, e.g. Epstein-Barr virus, or from contaminated food or water, e.g. norovirus; by breathing in viruses in the form of aerosols, e.g. influenza virus; and by insect vectors such as mosquitoes, e.g. dengue. The rate or speed of transmission of viral infections depends on factors that include population density, the number of susceptible individuals, (i.e. those who are not immune),[106] the quality of health care and the weather.[107] Epidemiology is used to break the chain of infection in populations during outbreaks of viral diseases.[108] Control measures are used which are based on knowledge of how the virus is transmitted. It is important to find the source, or sources, of the outbreak and to identify the virus. Once the virus has been identified, the chain of transmission can sometimes be broken by vaccines. When vaccines are not available sanitation and disinfection can be effective. Often infected people are isolated from the rest of the community and those that have been exposed to the virus placed in quarantine.[109] To control the outbreak of foot and mouth disease in cattle in Britain in 2001, thousands of cattle were slaughtered.[110] Most viral infections of humans and other animals have incubation periods during which the infection causes no signs or symptoms.[111] Incubation periods for viral diseases range from a few days to weeks but are known for most infections.[112] Following the incubation period there is a period of communicability; a time when an infected individual or animal is contagious and can infect another person or animal.[113] This too is known for many viral infections and knowledge the length of both periods is important in the control of outbreaks.[114] When outbreaks cause an unusually high proportion of cases in a population, community or region they are called epidemics. If outbreaks spread worldwide they are called pandemics.[115]
Epidemics and pandemics
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For more details on this topic, see List of epidemics. Native American populations were devastated by contagious diseases, particularly smallpox, brought to the Americas by European colonists. It is unclear how many Native Americans were killed by foreign diseases after the arrival of Columbus in the Americas, but the numbers have been estimated to be close to 70% of the indigenous population. The damage done by this disease significantly aided European attempts to displace and conquer the native population.[116]
A pandemic is a worldwide epidemic. The 1918 flu pandemic, commonly referred to as the Spanish flu, was a category 5 influenza pandemic caused by an unusually severe and deadly influenza A virus. The victims were often healthy young adults, in contrast to most influenza outbreaks which predominantly affect juvenile, elderly, or otherwise weakened patients.[117] The Spanish flu pandemic lasted from 1918 to 1919. Older estimates say it killed 4050 million people,[118] while more recent research suggests that it may have killed as many as 100 million people, or 5% of the world's population in 1918.[119] Most researchers believe that HIV originated in sub-Saharan Africa during the twentieth century;[120] it is now a pandemic, with an estimated 38.6 million people now living with the disease worldwide.[121] The Joint United Nations Programme on HIV/AIDS (UNAIDS) and the World Health Organization (WHO) estimate that AIDS has killed more than 25 million people since it was first recognised on June 5, 1981, making it one of the most destructive epidemics in recorded history.[122] In 2007 there were 2.7 million new HIV infections and 2 million HIV-related deaths.[123] Several highly lethal viral pathogens are members of the Filoviridae. Filoviruses are filament-like viruses that cause viral hemorrhagic fever, and include the ebola and marburg viruses. The Marburg virus attracted widespread press attention in April 2005 for an outbreak in Angola. Beginning in October 2004 and continuing into 2005, the outbreak was the world's worst epidemic of any kind of viral hemorrhagic fever.[124]
The reconstructed 1918 influenza virus
Cancer
For more details on this topic, see Oncovirus.
The Marburg virus
Viruses are an established cause of malignancy(cancer) in humans and other species. The main viruses associated with human cancers are human papillomavirus, hepatitis B virus, Epstein-Barr virus, and human T-lymphotropic virus. Hepatitis viruses can induce a chronic viral infection that leads to liver cancer.[125][126] Infection by human T-lymphotropic virus can lead to tropical spastic paraparesis and adult T-cell leukemia.[127] Human papillomaviruses are an established cause of cancers of cervix, skin, anus, and penis.[128] Within the Herpesviridae, Kaposi's sarcoma-associated herpesvirus causes Kaposi's sarcoma and body cavity lymphoma, and EpsteinBarr virus causes Burkitt's lymphoma, Hodgkins lymphoma, B lymphoproliferative disorder and nasopharyngeal carcinoma.[129]
Host defence mechanisms

See also: Immune system The body's first line of defence against viruses is the innate immune system. This comprises cells and other
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mechanisms that defend the host from infection in a non-specific manner. This means that the cells of the innate system recognise, and respond to, pathogens in a generic way, but unlike the adaptive immune system, it does not confer long-lasting or protective immunity to the host.[130] RNA interference is an important innate defence against viruses.[131] Many viruses have a replication strategy that involves double-stranded RNA (dsRNA). When such a virus infects a cell, it releases its RNA molecule or molecules, which immediately bind to a protein complex called dicer that cuts the RNA into smaller pieces. A biochemical pathway called the RISC complex is activated which degrades the viral mRNA and the cell survives the infection. Rotaviruses avoid this mechanism by not uncoating fully inside the cell and by releasing newly produced mRNA through pores in the particle's inner capsid. The genomic dsRNA remains protected inside the core of the virion.[132][133] When the adaptive immune system of a vertebrate encounters a virus, it produces specific antibodies which bind to the virus and render it non-infectious. This is called humoral immunity. Two types of antibodies are important. The first called IgM is highly effective at neutralizing viruses but is only produced by the cells of the immune system for a few weeks. The second, called, IgG is produced indefinitely. The presence of IgM in the blood of the host is used to test for acute infection, whereas IgG indicates an infection sometime in the past.[134] IgG antibody is measured when tests for immunity are carried out.[135] A second defence of vertebrates against viruses is called cell-mediated immunity and involves immune cells known as T cells. The body's cells constantly display short fragments of their proteins on the cell's surface, and if a T cell recognises a suspicious viral fragment there, the host cell is destroyed by T killer cells and the virus-specific T-cells proliferate. Cells such as the macrophage are specialists at this antigen presentation.[136] The production of interferon is an important host defence mechanism. This is a hormone produced by the body when viruses are present. Its role in immunity is complex, but it eventually stops the viruses from reproducing by killing the infected cell and its close neighbours[137]
Two rotaviruses: the one on the right is coated with antibodies which stop its attaching to cells and infecting them
Not all virus infections produce a protective immune response in this way. HIV evades the immune system by constantly changing the amino acid sequence of the proteins on the surface of the virion. These persistent viruses evade immune control by sequestration, blockade of antigen presentation, cytokine resistance, evasion of natural killer cell activities, escape from apoptosis, and antigenic shift.[138] Other viruses, called neurotropic viruses, are disseminated by neural spread where the immune system may be unable to reach them.
Prevention and treatment

Because viruses use the machinery of a host cell to reproduce and reside within them, they are difficult to eliminate without killing the host cell. The most effective medical approaches to viral diseases so far are vaccinations to provide resistance to infection, and antiviral drugs. Vaccines For more details on this topic, see Vaccination. Vaccination is a cheap and effective way of preventing infections by viruses. Vaccines were used to prevent viral infections long before the discovery of the actual viruses. Their use has resulted in a dramatic decline in morbidity (illness) and mortality (death) associated with viral infections such as polio, measles, mumps and
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rubella.[139] Smallpox infections have been eradicated.[140] Currently vaccines are available to prevent over thirteen viral infections of humans,[141] and more are used to prevent viral infections of animals.[142] Vaccines can consist of live-attenuated or killed viruses, or viral proteins (antigens).[143] Live vaccines contain weakened forms of the virus that causes the disease. Such viruses are called attenuated. Live vaccines can be dangerous when given to people with a weak immunity, (who are described as immunocompromised), because in these people, the weakened virus can cause the original disease.[144] Biotechnology and genetic engineering techniques are used to produce subunit vaccines. These vaccines use only the capsid proteins of the virus. Hepatitis B vaccine is an example of this type of vaccine.[145] Subunit vaccines are safe for immunocompromised patients because they cannot cause the disease.[146] However, the yellow fever virus vaccine, a live-attenuated strain called 17D, is probably the safest and most effective vaccine ever generated.[147] Antiviral drugs For more details on this topic, see Antiviral drug. Over the past twenty years, the development of antiviral drugs has increased rapidly. This has been driven by the AIDS epidemic. Antiviral drugs are often nucleoside analogues, (fake DNA building blocks), which viruses incorporate into their genomes during replication. The life-cycle of the virus is then halted because the newly synthesised DNA is inactive. This is because these analogues lack the hydroxyl groups which along with phosphorus atoms, link together to form the strong "backbone" of the DNA molecule. This is called DNA chain termination.[148] Examples of nucleoside analogues are aciclovir for Herpes simplex virus infections and lamivudine for HIV and Hepatitis B virus infections. Aciclovir is one of the oldest and most frequently prescribed antiviral drugs.[149] Other antiviral drugs in use target different stages of the viral life cycle. HIV is dependent on a proteolytic enzyme called the HIV-1 protease for it to become fully infectious. There is a large class of drugs called protease inhibitors that inactivate this enzyme.
Guanosine
The guanosine analogue Aciclovir
Hepatitis C is caused by an RNA virus. In 80% of people infected, the disease is chronic, and without treatment, they are infected for the remainder of their lives. However, there is now an effective treatment that uses the nucleoside analogue drug ribavirin combined with interferon.[150] The treatment of chronic carriers of the hepatitis B virus by using a similar strategy using lamivudine has been developed.[151]
Infection in other species

Viruses infect all cellular life and, although viruses occur universally, each cellular species has its own specific range that often only infect that species.[152] Viruses are important pathogens of livestock. Diseases such as Foot and Mouth Disease and bluetongue, are caused by viruses.[153] Companion animals such as cats, dogs and horses, if not vaccinated, are susceptible to serious viral infections. Canine parvovirus is caused by a small DNA virus and infections are often fatal in pups.[154] Like all invertebrates, the honey bee is susceptible to many viral infections.[155] Fortunately, most viruses co-exist harmlessly in their host and cause no signs or symptoms of disease.[9]
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Plants
There are many types of plant virus, but often they only cause a loss of yield, and it is not economically viable to try to control them. Plant viruses are often spread from plant to plant by organisms, known as vectors. These are normally insects, but some fungi, nematode worms and single-celled organisms have been shown to be vectors. When control of plant virus infections is considered economical, (for perennial fruits for example), efforts are concentrated on killing the vectors and removing alternate hosts such as weeds.[156] Plant viruses are harmless to humans and other animals because they can only reproduce in living plant cells.[157]
Plants have elaborate and effective defence mechanisms against viruses. One of the most effective is the presence of so-called resistance (R) genes. Each R gene confers resistance to a particular virus by triggering localised areas of cell death around the infected cell, which can often be seen with the unaided eye as large spots. This stops the infection from spreading.[158] RNA interference is also an effective defence in plants.[159] When they are infected, plants often produce natural disinfectants which kill viruses, such as salicylic acid, nitric oxide and reactive oxygen molecules.[160]
Peppers infected by mild mottle virus
Bacteria
Bacteriophages are an extremely common and diverse group of viruses. For example, bacteriophages are the most common form of biological entity in aquatic environments, with up to ten times more of these viruses in the oceans than bacteria,[161] reaching levels of 250,000,000 bacteriophages per millilitre of seawater.[162] These viruses infect specific bacteria by binding to surface receptor molecules and then entering the cell. Within a short amount of time, in some cases just minutes, bacterial polymerase starts translating viral mRNA into protein. These proteins go on to become either new virions within the cell, helper proteins which help assembly of new virions, or proteins involved in cell lysis. Viral enzymes aid in the breakdown of the cell membrane, and, in the case of the T4 phage, in just over twenty minutes after injection over three hundred phages could be released.[163]
The major way bacteria defend themselves from bacteriophages is by producing enzymes which destroy foreign DNA. These enzymes, called restriction endonucleases, cut up the viral DNA that bacteriophages inject into bacterial cells.[164] Bacteria also contain a system that uses CRISPR sequences to retain fragments of the genomes of viruses that the bacteria have come into contact with in the past, which allows them to block the virus's replication through a form of RNA interference.[165][166] This genetic system provides bacteria with acquired immunity to infection.
Transmission electron micrograph of multiple bacteriophages attached to a bacterial cell wall
Archaea
Some viruses replicate within archaea: these are double-stranded DNA viruses that appear to be unrelated to any other form of virus and have a variety of unusual shapes, with some resembling bottles, hooked rods, or teardrops.[167] These viruses have been studied in most detail in the thermophilic archaea, particularly the orders Sulfolobales and Thermoproteales.[168] Defences against these viruses may involve RNA interference from
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repetitive DNA sequences within archaean genomes that are related to the genes of the viruses.[169][170]
Applications
Life sciences and medicine
Viruses are important to the study of molecular and cellular biology as they provide simple systems that can be used to manipulate and investigate the functions of cells.[171] The study and use of viruses have provided valuable information about aspects of cell biology.[172] For example, viruses have been useful in the study of genetics and helped our understanding of the basic mechanisms of molecular genetics, such as DNA replication, transcription, RNA processing, translation, protein transport, and immunology. Geneticists often use viruses as vectors to introduce genes into cells that they are studying. This is useful for making the cell produce a foreign substance, or to study the effect of introducing a new gene into the genome. In similar fashion, virotherapy uses viruses as vectors to treat various diseases, as they can specifically target cells and DNA. It shows promising use in the treatment of cancer and in gene therapy. Eastern European scientists have used phage therapy as an alternative to antibiotics for some time, and interest in this approach is increasing, due to the high level of antibiotic resistance now found in some pathogenic bacteria.[173]
Materials science and nanotechnology

Current trends in nanotechnology promise to make much more versatile use of viruses. From the viewpoint of a materials scientist, viruses can be regarded as organic nanoparticles. Their surface carries specific tools designed to cross the barriers of their host cells. The size and shape of viruses, and the number and nature of the functional groups on their surface, is precisely defined. As such, viruses are commonly used in materials science as scaffolds for covalently linked surface modifications. A particular quality of viruses is that they can be tailored by directed evolution. The powerful techniques developed by life sciences are becoming the basis of engineering approaches towards nanomaterials, opening a wide range of applications far beyond biology and medicine.[174] Because of their size, shape, and well-defined chemical structures, viruses have been used as templates for organizing materials on the nanoscale. Recent examples include work at the Naval Research Laboratory in Washington, DC, using Cowpea Mosaic Virus (CPMV) particles to amplify signals in DNA microarray based sensors. In this application, the virus particles separate the fluorescent dyes used for signaling in order to prevent the formation of non-fluorescent dimers that act as quenchers.[175] Another example is the use of CPMV as a nanoscale breadboard for molecular electronics.[176]
Weapons
For more details on this topic, see Biological warfare.
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The ability of viruses to cause devastating epidemics in human societies has led to the concern that viruses could be weaponised for biological warfare. Further concern was raised by the successful recreation of the infamous 1918 influenza virus in a laboratory.[177] The smallpox virus devastated numerous societies throughout history before its eradication. It currently exists in several secure laboratories around the world, and fears that it may be used as a weapon are not totally unfounded. The vaccine for smallpox is not safe, and during the years before the eradication of smallpox disease more people became seriously ill as a result of vaccination than did people from smallpox[178] and smallpox vaccination is no longer universally practiced.[179] Thus, much of the modern human population has almost no established resistance to smallpox; if it were to be released, a massive loss of life could be sustained before the virus is brought under control.
Smallpox
External links
Vaccine Research Center (http://www.vrc.nih.gov) Information regarding preventative vaccine clinical trials
References
Notes
1. ^ a b Norrby E (2008). "Nobel Prizes and the emerging virus concept". Arch. Virol. 153 (6): 110923. doi:10.1007/s00705-008-0088-8. PMID 18446425. 2. ^ Dimmock p. 49 3. ^ a b c Collier pp. 3355 4. ^ a b "virus". The Online Etymology Dictionary. http://www.etymonline.com/index.php?term=virus. Retrieved on 2008-09-12. 5. ^ "virulent, a.". The Oxford English Dictionary Online. http://dictionary.oed.com. Retrieved on 2008-09-12. 6. ^ "viral, a.". The Oxford English Dictionary Online. http://dictionary.oed.com. Retrieved on 2008-09-12. 7. ^ Shors pp. 7677 8. ^ a b c d Collier p. 3 9. ^ a b Dimmock p. 4 10. ^ Dimmock p.45 11. ^ Shors p. 589 12. ^ D'Herelle F (September 2007). "On an invisible microbe antagonistic toward dysenteric bacilli": brief note by Mr. F. D'Herelle, presented by Mr. Roux. 1917. Res. Microbiol. 158(7):5534. Epub 2007 Jul 28. PMID 17855060 13. ^ Steinhardt, E; Israeli, C; and Lambert, R.A. (1913) "Studies on the cultivation of the virus of vaccinia" J. Inf Dis. 13, 294300 14. ^ Collier p. 4 15. ^ Goodpasture EW, Woodruff AM, Buddingh GJ (1931). "The cultivation of vaccine and other viruses in the chorioallantoic membrane of chick embryos". Science 74, pp. 371372 PMID 17810781 16. ^ Rosen FS (2004). "Isolation of poliovirusJohn Enders and the Nobel Prize". New England Journal of Medicine, 351, pp. 148183 PMID 15470207 17. ^ From Nobel Lectures, Physics 19811990, (1993) Editor-in-Charge Tore Frngsmyr, Editor Gsta Ekspng, World Scientific Publishing Co., Singapore. In 1887, Buist visualised one of the largest, Vaccinia virus, by optical microscopy after staining it. Vaccinia was not known to be a virus at that time. (Buist J.B. Vaccinia and Variola: a study of their life history Churchill, London) 18. ^ Stanley WM, Loring HS (1936). "The isolation of crystalline tobacco mosaic virus protein from diseased tomato plants". Science, 83, p.85 PMID 17756690 19. ^ Stanley WM, Lauffer MA (1939). "Disintegration of tobacco mosaic virus in urea solutions". Science 89, pp.
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Bibliography
Collier, Leslie; Balows, Albert; Sussman, Max (1998) Topley and Wilson's Microbiology and Microbial Infections ninth edition, Volume 1, Virology, volume editors: Mahy, Brian and Collier, Leslie. Arnold. ISBN 0340663162 Dimmock, N.J; Easton, Andrew J; Leppard, Keith (2007) Introduction to Modern Virology sixth edition, Blackwell Publishing, ISBN 1405136456 Knipe, David M; Howley, Peter M; Griffin, Diane E; Lamb, Robert A; Martin, Malcolm A; Roizman, Bernard; Straus Stephen E. (2007) Fields Virology Lippincott Williams & Wilkins. ISBN 0781760607 Shors, Teri (2008). Understanding Viruses. Jones and Bartlett Publishers. ISBN 0763729329
Retrieved from "http://en.wikipedia.org/wiki/Virus" Categories: Articles with separate introductions | Featured articles | Virology | Viruses | Microbiology Hidden category: Wikipedia indefinitely move-protected pages This page was last modified on 18 February 2009, at 03:30. All text is available under the terms of the GNU Free Documentation License. (See Copyrights for details.) Wikipedia is a registered trademark of the Wikimedia Foundation, Inc., a U.S. registered 501(c)(3) tax-deductible nonprofit charity.
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Bacteria - Wikipedia, the free encyclopedia
http://en.wikipedia.org/wiki/Bacteria
Bacteria
The Bacteria [bk t r ] (singular: bacterium)[] are a large group of unicellular microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals. Bacteria are ubiquitous in every habitat on Earth, growing in soil, acidic hot springs, radioactive waste,[2] water, and deep in the Earth's crust, as well as in organic matter and the live bodies of plants and animals. There are typically 40 million bacterial cells in a gram of soil and a million bacterial cells in a millilitre of fresh water; in all, there are approximately five nonillion (51030) bacteria on Earth,[3] forming much of the world's biomass.[4] Bacteria are vital in recycling nutrients, with many important steps in nutrient cycles depending on these organisms, such as the fixation of nitrogen from the atmosphere and putrefaction. However, most bacteria have not been characterized, and only about half of the phyla of bacteria have species that can be cultured in the laboratory.[5] The study of bacteria is known as bacteriology, a branch of microbiology. There are approximately ten times as many bacterial cells as human cells in the human body, with large numbers of bacteria on the skin and in the digestive tract.[6] The vast majority of the bacteria in the body are rendered harmless by the protective effects of the immune system, and a few are beneficial. However, a few species of bacteria are pathogenic and cause infectious diseases, including cholera, syphilis, anthrax, leprosy and bubonic plague. The most common fatal bacterial diseases are respiratory infections, with tuberculosis alone killing about 2 million people a year, mostly in sub-Saharan Africa.[7] In developed countries, antibiotics are used to treat bacterial infections and in various agricultural processes, so antibiotic resistance is becoming common. In industry, bacteria are important in processes such as sewage treatment, the production of cheese and yoghurt through fermentation, as well as biotechnology, and the manufacture of antibiotics and other chemicals.[8] Once regarded as plants constituting the class Schizomycetes, bacteria are now classified as prokaryotes. Unlike cells of animals and other eukaryotes, bacterial cells do not contain a nucleus and rarely harbour membrane-bound organelles. Although the term bacteria traditionally included all prokaryotes, the scientific classification changed after the discovery in the 1990s that prokaryotic life consists of two very different groups of organisms that evolved independently from an ancient common ancestor. These evolutionary domains are called Bacteria and Archaea.[9]
Bacteria
Fossil range: Archean or earlier Recent
Escherichia coli image is 8 micrometres wide.
Scientific classification Domain: Bacteria Phyla[1] gram positive/no outer membrane Actinobacteria (high-G+C) Firmicutes (low-G+C) Tenericutes (no wall) gram negative/outer membrane present Aquificae Bacteroidetes/Chlorobi Chlamydiae/Verrucomicrobia Deinococcus-Thermus Fusobacteria Gemmatimonadetes Nitrospirae Proteobacteria Spirochaetes Synergistetes unknown/ungrouped Acidobacteria Chloroflexi
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Contents
1 History of bacteriology 2 Origin and early evolution 3 Morphology 4 Cellular structure 4.1 Intracellular structures 4.2 Extracellular structures 4.3 Endospores 5 Metabolism 6 Growth and reproduction 7 Genetics 8 Movement 9 Classification and identification 10 Interactions with other organisms 10.1 Predators 10.2 Mutualists 10.3 Pathogens 11 Significance in technology and industry 12 See also 13 Footnotes 14 References 15 Further reading 16 External links
Chrysiogenetes Cyanobacteria Deferribacteres Dictyoglomi Fibrobacteres Planctomycetes Thermodesulfobacteria Thermotogae
History of bacteriology
Bacteria were first observed by Antonie van Leeuwenhoek in 1676, using a single-lens microscope of his own design.[10] He called them "animalcules" and published his observations in a series of letters to the Royal Society.[11][12][13] The name bacterium was introduced much later, by Christian Gottfried Ehrenberg in 1838.[14] Louis Pasteur demonstrated in 1859 that the fermentation process is caused by the growth of microorganisms, and that this growth is not due to spontaneous generation. (Yeasts and molds, commonly associated with fermentation, are not bacteria, but rather fungi.) Along with his contemporary, Robert Koch, Pasteur was an early advocate of the germ theory of disease.[15] Robert Koch was a pioneer in medical microbiology and worked on cholera, anthrax and tuberculosis. In his research into tuberculosis, Koch finally proved the germ theory, for which he was awarded a Nobel Prize in 1905.[16] In Koch's postulates, he set out criteria to test if an organism is the cause of a disease; these postulates are still used today.[17]
Antonie van Leeuwenhoek, the first microbiologist and the first person to observe bacteria using a microscope.
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Though it was known in the nineteenth century that bacteria are the cause of many diseases, no effective antibacterial treatments were available.[18] In 1910, Paul Ehrlich developed the first antibiotic, by changing dyes that selectively stained Treponema pallidumthe spirochaete that causes syphilisinto compounds that selectively killed the pathogen.[19] Ehrlich had been awarded a 1908 Nobel Prize for his work on immunology, and pioneered the use of stains to detect and identify bacteria, with his work being the basis of the Gram stain and the Ziehl-Neelsen stain.[20] A major step forward in the study of bacteria was the recognition in 1977 by Carl Woese that archaea have a separate line of evolutionary descent from bacteria.[21] This new phylogenetic taxonomy was based on the sequencing of 16S ribosomal RNA, and divided prokaryotes into two evolutionary domains, as part of the threedomain system.[22]
Origin and early evolution

Further information: Timeline of evolution The ancestors of modern bacteria were single-celled microorganisms that were the first forms of life to develop on earth, about 4 billion years ago. For about 3 billion years, all organisms were microscopic, and bacteria and archaea were the dominant forms of life.[23][24] Although bacterial fossils exist, such as stromatolites, their lack of distinctive morphology prevents them from being used to examine the past history of bacterial evolution, or to date the time of origin of a particular bacterial species. However, gene sequences can be used to reconstruct the bacterial phylogeny, and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage.[25] The most recent common ancestor of bacteria and archaea was probably a hyperthermophile that lived about 2.5 billion3.2 billion years ago.[26][27] Bacteria were also involved in the second great evolutionary divergence, that of the archaea and eukaryotes. Here, eukaryotes resulted from ancient bacteria entering into endosymbiotic associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea.[28][29] This involved the engulfment by proto-eukaryotic cells of alpha-proteobacterial symbionts to form either mitochondria or hydrogenosomes, which are still being found in all known Eukarya (sometimes in highly reduced form, e.g. in ancient "amitochondrial" protozoa). Later on, an independent second engulfment by some mitochondria-containing eukaryotes of cyanobacterial-like organisms led to the formation of chloroplasts in algae and plants. There are even some algal groups known that clearly originated from subsequent events of endosymbiosis by heterotrophic eukaryotic hosts engulfing a eukaryotic algae that developed into "second-generation" plastids.[30][31]
Morphology
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Bacteria display a wide diversity of shapes and sizes, called morphologies. Bacterial cells are about one tenth the size of eukaryotic cells and are typically 0.55.0 micrometres in length. However, a few speciesfor example Thiomargarita namibiensis and Epulopiscium fishelsoniare up to half a millimetre long and are visible to the unaided eye.[32] Among the smallest bacteria are members of the genus Mycoplasma, which measure only 0.3 micrometres, as small as the largest viruses.[33] Some bacteria may be even smaller, but these ultramicrobacteria are not well-studied.[34] Most bacterial species are either spherical, called cocci (sing. coccus, from Greek kkkos, grain, seed) or rod-shaped, called bacilli (sing. bacillus, from Latin baculus, stick). Some rod-shaped bacteria, called vibrio, are slightly curved or Bacteria display a large diversity of cell morphologies and comma-shaped; others, can be spiral-shaped, arrangements called spirilla, or tightly coiled, called spirochaetes. A small number of species even have tetrahedral or cuboidal shapes.[35] More recently, deep subsurface bacteria have been discovered that grow as long rods with a star-shaped cross-section. The large surface area to volume ratio conferred by this morphology may give these bacteria an advantage in nutrient-poor environments.[36] This wide variety of shapes is determined by the bacterial cell wall and cytoskeleton, and is important because it can influence the ability of bacteria to acquire nutrients, attach to surfaces, swim through liquids and escape predators.[37][38] Many bacterial species exist simply as single cells, others associate in characteristic patterns: Neisseria form diploids (pairs), Streptococcus form chains, and Staphylococcus group together in "bunch of grapes" clusters. Bacteria can also be elongated to form filaments, for example the Actinobacteria. Filamentous bacteria are often surrounded by a sheath that contains many individual cells; certain types, such as species of the genus Nocardia, even form complex, branched filaments, similar in appearance to fungal mycelia.[39]
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The range of sizes shown by prokaryotes, relative to those of other organisms and biomolecules
Bacteria often attach to surfaces and form dense aggregations called biofilms or bacterial mats. These films can range from a few micrometers in thickness to up to half a meter in depth, and may contain multiple species of bacteria, protists and archaea. Bacteria living in biofilms display a complex arrangement of cells and extracellular components, forming secondary structures such as microcolonies, through which there are networks of channels to enable better diffusion of nutrients.[40][41] In natural environments, such as soil or the surfaces of plants, the majority of bacteria are bound to surfaces in biofilms.[42] Biofilms are also important in medicine, as these structures are often present during chronic bacterial infections or in infections of implanted medical devices, and bacteria protected within biofilms are much harder to kill than individual isolated bacteria.[43]
Even more complex morphological changes are sometimes possible. For example, when starved of amino acids, Myxobacteria detect surrounding cells in a process known as quorum sensing, migrate towards each other, and aggregate to form fruiting bodies up to 500 micrometres long and containing approximately 100,000 bacterial cells.[44] In these fruiting bodies, the bacteria perform separate tasks; this type of cooperation is a simple type of multicellular organisation. For example, about one in 10 cells migrate to the top of these fruiting bodies and differentiate into a specialised dormant state called myxospores, which are more resistant to drying and other adverse environmental conditions than are ordinary cells.[45]
Cellular structure
Further information: Bacterial cell structure
Intracellular structures
The bacterial cell is surrounded by a lipid membrane, or cell membrane, which encloses the contents of the cell and acts as a barrier to hold nutrients, proteins and other essential components of the cytoplasm within the cell. As they are prokaryotes, bacteria do not tend to have membrane-bound organelles in their cytoplasm and thus contain few large intracellular structures. They consequently lack a nucleus, mitochondria, chloroplasts and the other organelles present in eukaryotic cells, such as the Golgi apparatus and endoplasmic reticulum.[46] Bacteria were once seen as simple bags of cytoplasm, but elements such as prokaryotic cytoskeleton, Structure and contents of a typical bacterial cell [47][48] and the localization of proteins to specific locations within the cytoplasm[49] have been found to show levels of complexity. These subcellular compartments have been called "bacterial hyperstructures".[50] Micro-compartments such as carboxysome[51] provides a further level of organization, which are compartments
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within bacteria that are surrounded by polyhedral protein shells, rather than by lipid membranes.[52] These "polyhedral organelles" localize and compartmentalize bacterial metabolism, a function performed by the membrane-bound organelles in eukaryotes.[53][54] Many important biochemical reactions, such as energy generation, occur by concentration gradients across membranes, a potential difference also found in a battery. The general lack of internal membranes in bacteria means reactions such as electron transport occur across the cell membrane between the cytoplasm and the periplasmic space.[55] However, in many photosynthetic bacteria the plasma membrane is highly folded and fills most of the cell with layers of light-gathering membrane.[56] These light-gathering complexs may even form lipid-enclosed structures called chlorosomes in green sulfur bacteria.[57] Other proteins import nutrients across the cell membrane, or to expel undesired molecules from the cytoplasm. Bacteria do not have a membrane-bound nucleus, and their genetic material is typically a single circular chromosome located in the cytoplasm in an irregularly shaped body called the nucleoid.[59] The nucleoid contains the chromosome with associated proteins and RNA. The order Planctomycetes are an exception to the general absence of internal membranes in bacteria, because they have a membrane Carboxysomes are protein-enclosed bacterial organelles. Top left is an electron around their nucleoid and contain microscope image of carboxysomes in Halothiobacillus neapolitanus, below is other membrane-bound cellular an image of purified carboxysomes. On the right is a model of their structure. Scale bars are 100 nm.[58] structures.[60] Like all living organisms, bacteria contain ribosomes for the production of proteins, but the structure of the bacterial ribosome is different from those of eukaryotes and Archaea.[61] Some bacteria produce intracellular nutrient storage granules, such as glycogen,[62] polyphosphate,[63] sulfur[64] or polyhydroxyalkanoates.[65] These granules enable bacteria to store compounds for later use. Certain bacterial species, such as the photosynthetic Cyanobacteria, produce internal gas vesicles, which they use to regulate their buoyancy - allowing them to move up or down into water layers with different light intensities and nutrient levels.[66]
Extracellular structures
Further information: Cell envelope Around the outside of the cell membrane is the bacterial cell wall. Bacterial cell walls are made of peptidoglycan (called murein in older sources), which is made from polysaccharide chains cross-linked by unusual peptides containing D-amino acids.[67] Bacterial cell walls are different from the cell walls of plants and fungi, which are made of cellulose and chitin, respectively.[68] The cell wall of bacteria is also distinct from that of Archaea, which do not contain peptidoglycan. The cell wall is essential to the survival of many bacteria, and the antibiotic penicillin is able to kill bacteria by inhibiting a step in the synthesis of peptidoglycan.[68]
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There are broadly speaking two different types of cell wall in bacteria, called Gram-positive and Gram-negative. The names originate from the reaction of cells to the Gram stain, a test long-employed for the classification of bacterial species.[69] Gram-positive bacteria possess a thick cell wall containing many layers of peptidoglycan and teichoic acids. In contrast, Gram-negative bacteria have a relatively thin cell wall consisting of a few layers of peptidoglycan surrounded by a second lipid membrane containing lipopolysaccharides and lipoproteins. Most bacteria have the Gram-negative cell wall, and only the Firmicutes and Actinobacteria (previously known as the low G+C and high G+C Gram-positive bacteria, respectively) have the alternative Gram-positive arrangement.[70] These differences in structure can produce differences in antibiotic susceptibility; for instance, vancomycin can kill only Gram-positive bacteria and is ineffective against Gram-negative pathogens, such as Haemophilus influenzae or Pseudomonas aeruginosa.[71] In many bacteria an S-layer of rigidly arrayed protein molecules covers the outside of the cell.[72] This layer provides chemical and physical protection for the cell surface and can act as a macromolecular diffusion barrier. S-layers have diverse but mostly poorly understood functions, but are known to act as virulence factors in Campylobacter and contain surface enzymes in Bacillus stearothermophilus.[73] Flagella are rigid protein structures, about 20 nanometres in diameter and up to 20 micrometres in length, that are used for motility. Flagella are driven by the energy released by the transfer of ions down an electrochemical gradient across the cell membrane.[74] Fimbriae are fine filaments of protein, just 210 nanometres in diameter and up to several micrometers in length. They are distributed over the surface of the cell, and resemble fine hairs when seen under the electron microscope. Fimbriae are believed to be Helicobacter pylori electron micrograph, involved in attachment to solid surfaces or to other cells and are showing multiple flagella on the cell surface essential for the virulence of some bacterial pathogens.[75] Pili (sing. pilus) are cellular appendages, slightly larger than fimbriae, that can transfer genetic material between bacterial cells in a process called conjugation (see bacterial genetics, below).[76] Capsules or slime layers are produced by many bacteria to surround their cells, and vary in structural complexity: ranging from a disorganised slime layer of extra-cellular polymer, to a highly structured capsule or glycocalyx. These structures can protect cells from engulfment by eukaryotic cells, such as macrophages.[77] They can also act as antigens and be involved in cell recognition, as well as aiding attachment to surfaces and the formation of biofilms.[78] The assembly of these extracellular structures is dependent on bacterial secretion systems. These transfer proteins from the cytoplasm into the periplasm or into the environment around the cell. Many types of secretion systems are known and these structures are often essential for the virulence of pathogens, so are intensively studied.[79]
Endospores
Further information: Endospores
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Certain genera of Gram-positive bacteria, such as Bacillus, Clostridium, Sporohalobacter, Anaerobacter and Heliobacterium, can form highly resistant, dormant structures called endospores.[80] In almost all cases, one endospore is formed and this is not a reproductive process, although Anaerobacter can make up to seven endospores in a single cell.[81] Endospores have a central core of cytoplasm containing DNA and ribosomes surrounded by a cortex layer and protected by an impermeable and rigid coat. Endospores show no detectable metabolism and can survive Bacillus anthracis (stained purple) growing extreme physical and chemical stresses, such as high levels of UV in cerebrospinal fluid light, gamma radiation, detergents, disinfectants, heat, pressure and desiccation.[82] In this dormant state, these organisms may remain viable for millions of years,[83][84] and endospores even allow bacteria to survive exposure to the vacuum and radiation in space.[85] Endospore-forming bacteria can also cause disease: for example, anthrax can be contracted by the inhalation of Bacillus anthracis endospores, and contamination of deep puncture wounds with Clostridium tetani endospores causes tetanus.[86]
Metabolism
Further information: Microbial metabolism In contrast to higher organisms, bacteria exhibit an extremely wide variety of metabolic types.[87] The distribution of metabolic traits within a group of bacteria has traditionally been used to define their taxonomy, but these traits often do not correspond with modern genetic classifications.[88] Bacterial metabolism is classified into nutritional groups on the basis of three major criteria: the kind of energy used for growth, the source of carbon, and the electron donors used for growth. An additional criterion of respiratory microorganisms are the electron acceptors used for aerobic or anaerobic respiration.[89] Nutritional types in bacterial metabolism Nutritional type Phototrophs Source of energy Sunlight Inorganic compounds Organic compounds Source of carbon Examples
Organic compounds Cyanobacteria, Green sulfur bacteria, (photoheterotrophs) or carbon fixation Chloroflexi, or Purple bacteria (photoautotrophs) Organic compounds Thermodesulfobacteria, (lithoheterotrophs) or carbon fixation Hydrogenophilaceae, or Nitrospirae (lithoautotrophs) Organic compounds Bacillus, Clostridium or (chemoheterotrophs) or carbon fixation Enterobacteriaceae (chemoautotrophs)
Lithotrophs
Organotrophs
Carbon metabolism in bacteria is either heterotrophic, where organic carbon compounds are used as carbon sources, or autotrophic, meaning that cellular carbon is obtained by fixing carbon dioxide. Heterotrophic bacteria include parasitic types. Typical autotrophic bacteria are phototrophic cyanobacteria, green sulfur-
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bacteria and some purple bacteria, but also many chemolithotrophic species, such as nitrifying or sulfuroxidising bacteria.[90] Energy metabolism of bacteria is either based on phototrophy, the use of light through photosynthesis, or on chemotrophy, the use of chemical substances for energy, which are mostly oxidised at the expense of oxygen or alternative electron acceptors (aerobic/anaerobic respiration). Finally, bacteria are further divided into lithotrophs that use inorganic electron donors and organotrophs that use organic compounds as electron donors. Chemotrophic organisms use the respective electron donors for energy conservation (by aerobic/anaerobic respiration or fermentation) and biosynthetic reactions (e.g. carbon dioxide fixation), whereas phototrophic organisms use them only for biosynthetic purposes. Respiratory organisms use chemical compounds as a source of energy by taking electrons from the reduced substrate and transferring them to a terminal electron acceptor in a redox reaction. This reaction releases energy that can be used to synthesise ATP and drive metabolism. In aerobic organisms, oxygen is used as the Filaments of photosynthetic cyanobacteria electron acceptor. In anaerobic organisms other inorganic compounds, such as nitrate, sulfate or carbon dioxide are used as electron acceptors. This leads to the ecologically important processes of denitrification, sulfate reduction and acetogenesis, respectively. Another way of life of chemotrophs in the absence of possible electron acceptors is fermentation, where the electrons taken from the reduced substrates are transferred to oxidised intermediates to generate reduced fermentation products (e.g. lactate, ethanol, hydrogen, butyric acid). Fermentation is possible, because the energy content of the substrates is higher than that of the products, which allows the organisms to synthesise ATP and drive their metabolism.[91][92] These processes are also important in biological responses to pollution; for example, sulfate-reducing bacteria are largely responsible for the production of the highly toxic forms of mercury (methyl- and dimethylmercury) in the environment.[93] Non-respiratory anaerobes use fermentation to generate energy and reducing power, secreting metabolic by-products (such as ethanol in brewing) as waste. Facultative anaerobes can switch between fermentation and different terminal electron acceptors depending on the environmental conditions in which they find themselves. Lithotrophic bacteria can use inorganic compounds as a source of energy. Common inorganic electron donors are hydrogen, carbon monoxide, ammonia (leading to nitrification), ferrous iron and other reduced metal ions, and several reduced sulfur compounds. Unusually, the gas methane can be used by methanotrophic bacteria as both a source of electrons and a substrate for carbon anabolism.[94] In both aerobic phototrophy and chemolithotrophy, oxygen is used as a terminal electron acceptor, while under anaerobic conditions inorganic compounds are used instead. Most lithotrophic organisms are autotrophic, whereas organotrophic organisms are heterotrophic. In addition to fixing carbon dioxide in photosynthesis, some bacteria also fix nitrogen gas (nitrogen fixation) using the enzyme nitrogenase. This environmentally important trait can be found in bacteria of nearly all the metabolic types listed above, but is not universal.[95]
Growth and reproduction

Further information: Bacterial growth Unlike multicellular organisms, increases in the size of bacteria (cell growth) and their reproduction by cell
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division are tightly linked in unicellular organisms. Bacteria grow to a fixed size and then reproduce through binary fission, a form of asexual reproduction.[96] Under optimal conditions, bacteria can grow and divide extremely rapidly, and bacterial populations can double as quickly as every 9.8 minutes.[97] In cell division, two identical clone daughter cells are produced. Some bacteria, while still reproducing asexually, form more complex reproductive structures that help disperse the newly-formed daughter cells. Examples include fruiting body formation by Myxobacteria and aerial hyphae formation by Streptomyces, or budding. Budding involves a cell forming a protrusion that breaks away and produces a daughter cell. In the laboratory, bacteria are usually grown using solid or liquid media. Solid growth media such as agar plates are used to isolate pure cultures of a bacterial strain. However, liquid growth media are used when measurement of growth or large volumes of cells are required. Growth in stirred liquid media occurs as an even cell suspension, making the cultures easy to divide and transfer, although isolating single bacteria from liquid media is difficult. The use of selective media (media with specific nutrients added or deficient, or with antibiotics added) can help identify specific organisms.[99] Most laboratory techniques for growing bacteria use high levels of nutrients to produce large amounts of cells cheaply and quickly. However, in natural environments nutrients are limited, meaning that bacteria cannot continue to reproduce A growing colony of Escherichia coli cells[98] indefinitely. This nutrient limitation has led the evolution of different growth strategies (see r/K selection theory). Some organisms can grow extremely rapidly when nutrients become available, such as the formation of algal (and cyanobacterial) blooms that often occur in lakes during the summer.[100] Other organisms have adaptations to harsh environments, such as the production of multiple antibiotics by Streptomyces that inhibit the growth of competing microorganisms.[101] In nature, many organisms live in communities (e.g. biofilms) which may allow for increased supply of nutrients and protection from environmental stresses.[42] These relationships can be essential for growth of a particular organism or group of organisms (syntrophy).[102] Bacterial growth follows three phases. When a population of bacteria first enter a high-nutrient environment that allows growth, the cells need to adapt to their new environment. The first phase of growth is the lag phase, a period of slow growth when the cells are adapting to the high-nutrient environment and preparing for fast growth. The lag phase has high biosynthesis rates, as proteins necessary for rapid growth are produced.[103] The second phase of growth is the logarithmic phase (log phase), also known as the exponential phase. The log phase is marked by rapid exponential growth. The rate at which cells grow during this phase is known as the growth rate (k), and the time it takes the cells to double is known as the generation time (g). During log phase, nutrients are metabolised at maximum speed until one of the nutrients is depleted and starts limiting growth. The final phase of growth is the stationary phase and is caused by depleted nutrients. The cells reduce their metabolic activity and consume non-essential cellular proteins. The stationary phase is a transition from rapid growth to a stress response state and there is increased expression of genes involved in DNA repair, antioxidant metabolism and nutrient transport.[104]
Genetics
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Further information: Plasmid, Genome Most bacteria have a single circular chromosome that can range in size from only 160,000 base pairs in the endosymbiotic bacteria Candidatus Carsonella ruddii,[105] to 12,200,000 base pairs in the soil-dwelling bacteria Sorangium cellulosum.[106] Spirochaetes of the genus Borrelia are a notable exception to this arrangement, with bacteria such as Borrelia burgdorferi, the cause of Lyme disease, containing a single linear chromosome.[107] The genes in bacterial genomes are usually a single continuous stretch of DNA and although several different types of introns do exist in bacteria, these are much more rare than in eukaryotes.[108] Bacteria may also contain plasmids, which are small extra-chromosomal DNAs that may contain genes for antibiotic resistance or virulence factors. Another type of bacterial DNA are integrated viruses (bacteriophages). Many types of bacteriophage exist, some simply infect and lyse their host bacteria, while others insert into the bacterial chromosome. A bacteriophage can contain genes that contribute to its host's phenotype: for example, in the evolution of Escherichia coli O157:H7 and Clostridium botulinum, the toxin genes in an integrated phage converted a harmless ancestral bacteria into a lethal pathogen.[109] Bacteria resist phage infection through restriction modification systems that degrade foreign DNA,[110] and a system that uses CRISPR sequences to retain fragments of the genomes of phage that the bacteria have come into contact with in the past, which allows them to block virus replication through a form of RNA interference.[111][112] This CRISPR system provides bacteria with acquired immunity to infection. Bacteria, as asexual organisms, inherit identical copies of their parent's genes (i.e., they are clonal). However, all bacteria can evolve by selection on changes to their genetic material DNA caused by genetic recombination or mutations. Mutations come from errors made during the replication of DNA or from exposure to mutagens. Mutation rates vary widely among different species of bacteria and even among different clones of a single species of bacteria.[113] Genetic changes in bacterial genomes come from either random mutation during replication or "stress-directed mutation", where genes involved in a particular growth-limiting process have an increased mutation rate.[114] Some bacteria also transfer genetic material between cells. This can occur in three main ways. Firstly, bacteria can take up exogenous DNA from their environment, in a process called transformation. Genes can also be transferred by the process of transduction, when the integration of a bacteriophage introduces foreign DNA into the chromosome. The third method of gene transfer is bacterial conjugation, where DNA is transferred through direct cell contact. This gene acquisition from other bacteria or the environment is called horizontal gene transfer and may be common under natural conditions.[115] Gene transfer is particularly important in antibiotic resistance as it allows the rapid transfer of resistance genes between different pathogens.[116]
Movement
Further information: Chemotaxis, Flagella, Pilus Motile bacteria can move using flagella, bacterial gliding, twitching motility or changes of buoyancy.[117] In twitching motility, bacterial use their type IV pili as a grappling hook, repeatedly extending it, anchoring it and then retracting it with remarkable force (>80 pN).[118]
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Bacterial species differ in the number and arrangement of flagella on their surface; some have a single flagellum (monotrichous), a flagellum at each end (amphitrichous), clusters of flagella at the poles of the cell (lophotrichous), while others have flagella distributed over the entire surface of the cell (peritrichous). The bacterial flagella is the best-understood motility structure in any organism and is made of about 20 proteins, with approximately another 30 proteins required for its regulation and assembly.[117] The flagellum is a rotating structure driven by a reversible motor at the base that uses the electrochemical gradient across the membrane for power.[119] This motor drives the motion of the filament, which acts as a propeller. Many bacteria (such as E. coli) have two distinct modes of movement: forward movement (swimming) and tumbling. The tumbling allows them to reorient and makes their movement a three[120] dimensional random walk. (See external links below for link to videos.) The flagella of a unique group of bacteria, the spirochaetes, are found between two membranes in the periplasmic space. They have a distinctive helical body that twists about as it moves.[117]
Flagellum of Gram-negative Bacteria. The base drives the rotation of the hook and filament.
Motile bacteria are attracted or repelled by certain stimuli in behaviors called taxes: these include chemotaxis, phototaxis and magnetotaxis.[121][122] In one peculiar group, the myxobacteria, individual bacteria move together to form waves of cells that then differentiate to form fruiting bodies containing spores.[45] The myxobacteria move only when on solid surfaces, unlike E. coli which is motile in liquid or solid media. Several Listeria and Shigella species move inside host cells by usurping the cytoskeleton, which is normally used to move organelles inside the cell. By promoting actin polymerization at one pole of their cells, they can form a kind of tail that pushes them through the host cell's cytoplasm.[123]
Classification and identification

Further information: Scientific classification, Systematics and Clinical pathology Classification seeks to describe the diversity of bacterial species by naming and grouping organisms based on similarities. Bacteria can be classified on the basis of cell structure, cellular metabolism or on differences in cell components such as DNA, fatty acids, pigments, antigens and quinones.[99] While these schemes allowed the identification and classification of bacterial strains, it was unclear whether these differences represented Streptococcus mutans visualized variation between distinct species or between strains of the same species. with a Gram stain This uncertainty was due to the lack of distinctive structures in most bacteria, as well as lateral gene transfer between unrelated species.[124] Due to lateral gene transfer, some closely related bacteria can have very different morphologies and metabolisms. To
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overcome this uncertainty, modern bacterial classification emphasizes molecular systematics, using genetic techniques such as guanine cytosine ratio determination, genome-genome hybridization, as well as sequencing genes that have not undergone extensive lateral gene transfer, such as the rRNA gene.[125] Classification of bacteria is determined by publication in the International Journal of Systematic Bacteriology,[126] and Bergey's Manual of Systematic Bacteriology.[127] The International Committee on Systematic Bacteriology (ICSB) maintains international rules for the naming of bacteria and taxonomic categories and for the ranking of them in the International Code of Nomenclature of Bacteria. The term "bacteria" was traditionally applied to all microscopic, single-celled prokaryotes. However, molecular systematics showed prokaryotic life to consist of two separate domains, originally called Eubacteria and Archaebacteria, but now called Bacteria and Archaea that evolved independently from an ancient common ancestor.[9] The archaea and eukaryotes are more closely-related to each other than either is to the bacteria. These two domains, along with Eukarya, are the basis of the three-domain system, which is currently the most widely used classification system in microbiolology.[128] However, due to the relatively recent introduction of molecular systematics and a rapid increase in the number of genome sequences that are available, bacterial classification remains a changing and expanding field.[5][129] For example, a few biologists argue that the Archaea and Eukaryotes evolved from Gram-positive bacteria.[130] Identification of bacteria in the laboratory is particularly relevant in medicine, where the correct treatment is determined by the bacterial species causing an infection. Consequently, the need to identify human pathogens was a major impetus for the development of techniques to identify bacteria. The Gram stain, developed in 1884 by Hans Christian Gram, characterises bacteria based on the structural characteristics of their cell walls.[69] The thick layers of peptidoglycan in the "Gram-positive" cell wall stain purple, while the thin "Gram-negative" cell wall appears pink. By combining morphology and Gram-staining, most bacteria can be classified as belonging to one of four groups (Gram-positive cocci, Gram-positive bacilli, Gram-negative cocci and Gram-negative bacilli). Some organisms are best identified by stains other than the Gram stain, particularly mycobacteria or Nocardia, which show acid-fastness on ZiehlNeelsen or similar stains.[132] Other organisms may need to be identified by their growth in special media, or by other techniques, such
Phylogenetic tree showing the diversity of bacteria, compared to other organisms.[131] Eukaryotes are colored red, archaea green and bacteria blue.
as serology. Culture techniques are designed to promote the growth and identify particular bacteria, while restricting the growth of the other bacteria in the sample. Often these techniques are designed for specific specimens; for example, a sputum sample will be treated to identify organisms that cause pneumonia, while stool specimens are cultured on selective media to identify organisms that cause diarrhoea, while preventing growth of non-pathogenic bacteria. Specimens that are normally sterile, such as blood, urine or spinal fluid, are cultured under conditions designed to grow all possible organisms.[133][99] Once a pathogenic organism has been
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isolated, it can be further characterised by its morphology, growth patterns such as (aerobic or anaerobic growth, patterns of hemolysis) and staining. As with bacterial classification, identification of bacteria is increasingly using molecular methods. Diagnostics using such DNA-based tools, such as polymerase chain reaction, are increasingly popular due to their specificity and speed, compared to culture-based methods.[134] These methods also allow the detection and identification of "viable but nonculturable" cells that are metabolically active but non-dividing.[135] However, even using these improved methods, the total number of bacterial species is not known and cannot even be estimated with any certainty. Following present classification, there are fewer than 9,000 known species of bacteria (including cyanobacteria)[136], but attempts to estimate bacterial diversity have ranged from 107 to 109 total species - and even these diverse estimates may be off by many orders of magnitude.[137][138]
Interactions with other organisms

Despite their apparent simplicity, bacteria can form complex associations with other organisms. These symbiotic associations can be divided into parasitism, mutualism and commensalism. Due to their small size, commensal bacteria are ubiquitous and grow on animals and plants exactly as they will grow on any other surface. However, their growth can be increased by warmth and sweat, and large populations of these organisms in humans are the cause of body odor.
Predators
Some species of bacteria kill and then consume other microorganisms, these species called predatory bacteria.[139] These include organisms such as Myxococcus xanthus, which forms swarms of cells that kill and digest any bacteria they encounter.[140] Other bacterial predators either attach to their prey in order to digest them and absorb nutrients, such as Vampirococcus, or invade another cell and multiply inside the cytosol, such as Daptobacter.[141] These predatory bacteria are thought to have evolved from saprophages that consumed dead microorganisms, through adaptations that allowed them to entrap and kill other organisms.[142]
Mutualists
Certain bacteria form close spatial associations that are essential for their survival. One such mutualistic association, called interspecies hydrogen transfer, occurs between clusters of anaerobic bacteria that consume organic acids such as butyric acid or propionic acid and produce hydrogen, and methanogenic Archaea that consume hydrogen.[143] The bacteria in this association are unable to consume the organic acids as this reaction produces hydrogen that accumulates in their surroundings. Only the intimate association with the hydrogenconsuming Archaea keeps the hydrogen concentration low enough to allow the bacteria to grow. In soil, microorganisms which reside in the rhizosphere (a zone that includes the root surface and the soil that adheres to the root after gentle shaking) carry out nitrogen fixation, converting nitrogen gas to nitrogenous compounds.[144] This serves to provide an easily absorbable form of nitrogen for many plants, which cannot fix nitrogen themselves. Many other bacteria are found as symbionts in humans and other organisms. For example, the presence of over 1,000 bacterial species in the normal human gut flora of the intestines can contribute to gut immunity, synthesise vitamins such as folic acid, vitamin K and biotin, convert milk protein to lactic acid (see Lactobacillus), as well as fermenting complex undigestible carbohydrates.[145][146][147] The presence of this gut flora also inhibits the growth of potentially pathogenic bacteria (usually through competitive exclusion) and these beneficial bacteria are consequently sold as probiotic dietary supplements.[148]
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Pathogens
If bacteria form a parasitic association with other organisms, they are classed as pathogens. Pathogenic bacteria are a major cause of human death and disease and cause infections such as tetanus, typhoid fever, diphtheria, syphilis, cholera, foodborne illness, leprosy and tuberculosis. A pathogenic cause for a known medical disease may only be discovered many years after, as was the case with Helicobacter pylori and peptic ulcer disease. Bacterial diseases are also important in agriculture, with bacteria causing leaf spot, fire blight and wilts in plants, as well as Johne's disease, mastitis, salmonella and anthrax in farm animals. Each species of pathogen has a characteristic spectrum of Color-enhanced scanning electron interactions with its human hosts. Some organisms, such as micrograph showing Salmonella Staphylococcus or Streptococcus, can cause skin infections, typhimurium (red) invading cultured human pneumonia, meningitis and even overwhelming sepsis, a systemic cells inflammatory response producing shock, massive vasodilation and death.[149] Yet these organisms are also part of the normal human flora and usually exist on the skin or in the nose without causing any disease at all. Other organisms invariably cause disease in humans, such as the Rickettsia, which are obligate intracellular parasites able to grow and reproduce only within the cells of other organisms. One species of Rickettsia causes typhus, while another causes Rocky Mountain spotted fever. Chlamydia, another phylum of obligate intracellular parasites, contains species that can cause pneumonia, or urinary tract infection and may be involved in coronary heart disease.[150] Finally, some species such as Pseudomonas aeruginosa, Burkholderia cenocepacia, and Mycobacterium avium are opportunistic pathogens and cause disease mainly in people suffering from immunosuppression or cystic fibrosis.[151][152] Bacterial infections may be treated with antibiotics, which are classified as bacteriocidal if they kill bacteria, or bacteriostatic if they just prevent bacterial growth. There are many types of antibiotics and each class inhibits a process that is different in the pathogen from that found in the host. An example of how antibiotics produce selective toxicity are chloramphenicol and puromycin, which inhibit the bacterial ribosome, but not the structurally different eukaryotic ribosome.[153] Antibiotics are used both in treating human disease and in intensive farming to promote animal growth, where they may be contributing to the rapid development of antibiotic resistance in bacterial populations.[154] Infections can be prevented by antiseptic measures such as sterilizating the skin prior to piercing it with the needle of a syringe, and by proper care of indwelling catheters. Surgical and dental instruments are also sterilized to prevent contamination by bacteria. Disinfectants such as bleach are used to kill bacteria or other pathogens on surfaces to prevent contamination and further reduce the risk of infection.
Significance in technology and industry

Further information: Economic importance of bacteria Bacteria, often Lactobacillus in combination with yeasts and molds, have been used for thousands of years in the preparation of fermented foods such as cheese, pickles, soy sauce, sauerkraut, vinegar, wine and yoghurt.
[155][156]
The ability of bacteria to degrade a variety of organic compounds is remarkable and has been used in waste
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processing and bioremediation. Bacteria capable of digesting the hydrocarbons in petroleum are often used to clean up oil spills.[157] Fertilizer was added to some of the beaches in Prince William Sound in an attempt to promote the growth of these naturally occurring bacteria after the infamous 1989 Exxon Valdez oil spill. These efforts were effective on beaches that were not too thickly covered in oil. Bacteria are also used for the bioremediation of industrial toxic wastes.[158] In the chemical industry, bacteria are most important in the production of enantiomerically pure chemicals for use as pharmaceuticals or agrichemicals.[159] Bacteria can also be used in the place of pesticides in the biological pest control. This commonly involves Bacillus thuringiensis (also called BT), a Gram-positive, soil dwelling bacterium. Subspecies of this bacteria are used as a Lepidopteran-specific insecticides under trade names such as Dipel and Thuricide.[160] Because of their specificity, these pesticides are regarded as environmentally friendly, with little or no effect on humans, wildlife, pollinators and most other beneficial insects.[161][162] Because of their ability to quickly grow and the relative ease with which they can be manipulated, bacteria are the workhorses for the fields of molecular biology, genetics and biochemistry. By making mutations in bacterial DNA and examining the resulting phenotypes, scientists can determine the function of genes, enzymes and metabolic pathways in bacteria, then apply this knowledge to more complex organisms.[163] This aim of understanding the biochemistry of a cell reaches its most complex expression in the synthesis of huge amounts of enzyme kinetic and gene expression data into mathematical models of entire organisms. This is achievable in some well-studied bacteria, with models of Escherichia coli metabolism now being produced and tested. [164][165] This understanding of bacterial metabolism and genetics allows the use of biotechnology to bioengineer bacteria for the production of therapeutic proteins, such as insulin, growth factors, or antibodies.
[166][167]
See also
Biotechnology Extremophiles Transgenic bacteria Psychrotrophic bacteria Microorganism International Code of Nomenclature of Bacteria
Footnotes
. ^ The word bacteria derives from the Greek , baktrion, meaning "small staff".
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(http://www.environment.gov.au/biodiversity /abrs/publications/other/species-numbers/02-execsummary.html#allspecies) ^ Curtis T, Sloan W, Scannell J (2002). "Estimating prokaryotic diversity and its limits". Proc Natl Acad Sci U S a 99 (16): 104949. doi:10.1073/pnas.142680199. PMID 12097644. http://www.pubmedcentral.nih.gov /articlerender.fcgi?tool=pubmed& pubmedid=12097644. ^ Schloss P, Handelsman J (2004). "Status of the microbial census". Microbiol Mol Biol Rev 68 (4): 68691. doi:10.1128/MMBR.68.4.686-691.2004. PMID 15590780. http://www.pubmedcentral.nih.gov /articlerender.fcgi?tool=pubmed& pubmedid=15590780#r6. ^ Martin MO (September 2002). "Predatory prokaryotes: an emerging research opportunity". J. Mol. Microbiol. Biotechnol. 4 (5): 46777. PMID 12432957. ^ Velicer GJ, Stredwick KL (August 2002). "Experimental social evolution with Myxococcus xanthus". Antonie Van Leeuwenhoek 81 (1-4): 15564. PMID 12448714. ^ Guerrero R, Pedros-Alio C, Esteve I, Mas J, Chase D, Margulis L (April 1986). "Predatory prokaryotes: predation and primary consumption evolved in bacteria". Proc. Natl. Acad. Sci. U.S.A. 83: 213842. PMID 11542073. PMC: 323246. http://www.pnas.org/cgi/pmidlookup?view=long& pmid=11542073. ^ Velicer GJ, Mendes-Soares H (January 2009). "Bacterial predators". Current Biology 19 (2): R55-R56. doi:10.1016/j.cub.2008.10.043. ^ Stams A, de Bok F, Plugge C, van Eekert M, Dolfing J, Schraa G (2006). "Exocellular electron transfer in anaerobic microbial communities". Environ Microbiol 8 (3): 37182. doi:10.1111/j.1462-2920.2006.00989.x. PMID 16478444. ^ Barea J, Pozo M, Azcn R, Azcn-Aguilar C (2005). "Microbial co-operation in the rhizosphere". J Exp Bot 56 (417): 176178. doi:10.1093/jxb /eri197. PMID 15911555. http://jxb.oxfordjournals.org/cgi/content/full/56 /417/1761. ^ O'Hara A, Shanahan F (2006). "The gut flora as a forgotten organ". EMBO Rep 7 (7): 68893. doi:10.1038/sj.embor.7400731. PMID 16819463. ^ Zoetendal E, Vaughan E, de Vos W (2006). "A microbial world within us". Mol Microbiol 59 (6): 163950. doi:10.1111/j.1365-2958.2006.05056.x. PMID 16553872. ^ Gorbach S (1990). "Lactic acid bacteria and human health". Ann Med 22 (1): 3741.
doi:10.3109/07853899009147239. PMID 2109988. 148. ^ Salminen S, Gueimonde M, Isolauri E (2005). "Probiotics that modify disease risk". J Nutr 135 (5): 12948. PMID 15867327. http://jn.nutrition.org /cgi/content/full/135/5/1294. 149. ^ Fish D. "Optimal antimicrobial therapy for sepsis". Am J Health Syst Pharm 59 Suppl 1: S139. PMID 11885408. 150. ^ Belland R, Ouellette S, Gieffers J, Byrne G (2004). "Chlamydia pneumoniae and atherosclerosis". Cell Microbiol 6 (2): 11727. doi:10.1046/j.1462-5822.2003.00352.x. PMID 14706098. 151. ^ Heise E (1982). "Diseases associated with immunosuppression". Environ Health Perspect 43: 919. doi:10.2307/3429162. PMID 7037390. http://www.pubmedcentral.nih.gov /picrender.fcgi?artid=1568899&blobtype=pdf. 152. ^ Saiman, L. "Microbiology of early CF lung disease". Paediatr Respir Rev.volume=5 Suppl a: S367369. PMID 14980298 153. ^ Yonath A, Bashan A (2004). "Ribosomal crystallography: initiation, peptide bond formation, and amino acid polymerization are hampered by antibiotics". Annu Rev Microbiol 58: 23351. doi:10.1146/annurev.micro.58.030603.123822. PMID 15487937. 154. ^ Khachatourians G (1998). "Agricultural use of antibiotics and the evolution and transfer of antibiotic-resistant bacteria". CMAJ 159 (9): 112936. PMID 9835883. http://www.pubmedcentral.nih.gov /articlerender.fcgi?tool=pubmed& pubmedid=9835883. 155. ^ Johnson M, Lucey J (2006). "Major technological advances and trends in cheese". J Dairy Sci 89 (4): 11748. PMID 16537950. 156. ^ Hagedorn S, Kaphammer B (1994). "Microbial biocatalysis in the generation of flavor and fragrance chemicals". Annu. Rev. Microbiol. 48: 773800. doi:10.1146/annurev.mi.48.100194.004013. PMID 7826026. 157. ^ Cohen Y (2002). "Bioremediation of oil by marine microbial mats". Int Microbiol 5 (4): 18993. doi:10.1007/s10123-002-0089-5. PMID 12497184. 158. ^ Neves LC, Miyamura TT, Moraes DA, Penna TC, Converti A (2006). "Biofiltration methods for the removal of phenolic residues". Appl. Biochem. Biotechnol. 129-132: 13052. doi:10.1385/ABAB:129:1:130. PMID 16915636. 159. ^ Liese A, Filho M (1999). "Production of fine chemicals using biocatalysis". Curr Opin Biotechnol 10 (6): 595603. doi:10.1016/S0958-1669(99)00040-3. PMID 10600695.
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160. ^ Aronson AI, Shai Y (2001). "Why Bacillus thuringiensis insecticidal toxins are so effective: unique features of their mode of action". FEMS Microbiol. Lett. 195 (1): 18. doi:10.1111/j.1574-6968.2001.tb10489.x. PMID 11166987. 161. ^ Bozsik A (2006). "Susceptibility of adult Coccinella septempunctata (Coleoptera: Coccinellidae) to insecticides with different modes of action". Pest Manag Sci 62 (7): 6514. doi:10.1002/ps.1221. PMID 16649191. 162. ^ Chattopadhyay A, Bhatnagar N, Bhatnagar R (2004). "Bacterial insecticidal toxins". Crit Rev Microbiol 30 (1): 3354. doi:10.1080/10408410490270712. PMID 15116762. 163. ^ Serres M, Gopal S, Nahum L, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome". Genome Biol 2 (9): RESEARCH0035. doi:10.1186/gb-2001-2-9research0035. PMID 11574054. http://www.pubmedcentral.nih.gov
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/articlerender.fcgi?tool=pubmed& pubmedid=11574054. ^ Almaas E, Kovcs B, Vicsek T, Oltvai Z, Barabsi A (2004). "Global organization of metabolic fluxes in the bacterium Escherichia coli". Nature 427 (6977): 83943. doi:10.1038/nature02289. PMID 14985762. ^ Reed JL, Vo TD, Schilling CH, Palsson BO (2003). "An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)". Genome Biol. 4 (9): R54. doi:10.1186/gb-2003-4-9-r54. PMID 12952533. ^ Walsh G (2005). "Therapeutic insulins and their large-scale manufacture". Appl Microbiol Biotechnol 67 (2): 1519. doi:10.1007/s00253-004-1809-x. PMID 15580495. ^ Graumann K, Premstaller A (2006). "Manufacturing of recombinant therapeutic proteins in microbial systems". Biotechnol J 1 (2): 16486. doi:10.1002/biot.200500051. PMID 16892246.
Further reading
Alcamo IE (2001). Fundamentals of microbiology. Boston: Jones and Bartlett. ISBN 0-7637-1067-9. Atlas RM (1995). Principles of microbiology. St. Louis: Mosby. ISBN 0-8016-7790-4. Martinko JM, Madigan MT (2005). Brock Biology of Microorganisms (11th ed. ed.). Englewood Cliffs, N.J: Prentice Hall. ISBN 0-13-144329-1. Holt JC, Bergey DH (1994). Bergey's manual of determinative bacteriology (9th ed. ed.). Baltimore: Williams & Wilkins. ISBN 0-683-00603-7. Hugenholtz P, Goebel BM, Pace NR (1998). "Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity". J Bacteriol 180 (18): 476574. PMID 9733676. http://jb.asm.org/cgi/content/full/180/18/4765?view=full&pmid=9733676. Funke BR, Tortora GJ, Case CL (2004). Microbiology: an introduction (8th ed ed.). San Francisco: Benjamin Cummings. ISBN 0-8053-7614-3. Shively, Jessup M. (2006). Complex Intracellular Structures in Prokaryotes (Microbiology Monographs). Berlin: Springer. ISBN 3-540-32524-7. Witzany G, (2008). "Bio-Communication of Bacteria and their Evolutionary Roots in Natural Genome Editing Competences of Viruses". Open Evol J 2: 4454. doi:10.2174/1874404400802010044.
External links
Bacterial Nomenclature Up-To-Date from DSMZ (http://www.dsmz.de/bactnom/bactname.htm) Genera of the domain Bacteria (http://www.bacterio.cict.fr/eubacteria.html) - list of Prokaryotic names with Standing in Nomenclature The largest bacteria (http://www.sciencenews.org/pages/sn_arc99/4_17_99/fob5.htm) Tree of Life: Eubacteria (http://tolweb.org/tree?group=Eubacteria&contgroup=Life_on_Earth) Videos (http://www.rowland.harvard.edu/labs/bacteria/index_movies.html) of bacteria swimming and tumbling, use of optical tweezers and other videos. Planet of the Bacteria (http://www.stephenjaygould.org/library/gould_bacteria.html) by Stephen Jay Gould
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On-line text book on bacteriology (http://www.textbookofbacteriology.net/) Animated guide to bacterial cell structure. (http://www.blackwellpublishing.com/trun/artwork/Animations /Overview/overview.html) Bacteria Make Major Evolutionary Shift in the Lab (http://www.newscientist.com/channel/life/dn14094bacteria-make-major-evolutionary-shift-in-the-lab.html) Cell-Cell Communication in Bacteria (http://ascb.org/ibioseminars/Bassler/Bassler1.cfm) on-line lecture by Bonnie Bassler Retrieved from "http://en.wikipedia.org/wiki/Bacteria" Categories: Featured articles | Bacteria | Bacteriology | Microbiology Hidden categories: Wikipedia pages semi-protected against vandalism | Wikipedia protected pages without expiry | Articles including recorded pronunciations This page was last modified on 16 February 2009, at 19:17. All text is available under the terms of the GNU Free Documentation License. (See Copyrights for details.) Wikipedia is a registered trademark of the Wikimedia Foundation, Inc., a U.S. registered 501(c)(3) tax-deductible nonprofit charity.
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Mycology - Wikipedia, the free encyclopedia
http://en.wikipedia.org/wiki/Mycology
Mycology
Mycology (from the Greek , meaning "fungus") is the branch of biology concerned with the study of fungi, including their genetic and biochemical properties, their taxonomy, and their use to humans as a source for tinder, medicinals (e.g., penicillin), food (e.g., beer, wine, cheese, edible mushrooms) and entheogens, as well as their dangers, such as poisoning or infection. Mycology is that branch of life science,which deals with the study of fungus in terms of their genetics,biochemistry,taxonomy,use to humans as well as dangers. From mycology arose the field of phytopathology, the study of plant diseases, and the two disciplines remain closely related because the vast majority of plant pathogens are fungi. A biologist who studies mycology is called a mycologist.
A mushroom is a reproductive structure of a fungus.
Historically, mycology was a branch of botany (fungi are evolutionarily more closely related to animals than to plants but this was not recognized until a few decades ago). Pioneer mycologists included Elias Magnus Fries, Christian Hendrik Persoon, Anton de Bary and Lewis David von Schweinitz. Today, the most comprehensively studied and understood fungi are the yeasts and eukaryotic model organisms Saccharomyces cerevisiae and Schizosaccharomyces pombe. Many fungi produce toxins, antibiotics, and other secondary metabolites. For example, the cosmopolitan (worldwide) genus Fusarium and their toxins associated with fatal outbreaks of alimentary toxic aleukia in humans were extensively studied by Abraham Joffe. Fungi are fundamental for life on earth in their roles as symbionts, e.g. in the form of mycorrhizae, insect symbionts and lichens as well as their potency in breaking down complex organic biomolecules such as lignin, the more durable component of wood , as well as xenobiotics, a critical step in the global carbon cycle. Fungi and other organisms traditionally recognized as fungi, such as oomycetes and myxomycetes (slime molds), often are economically and socially important as some cause diseases of animals (such as histoplasmosis) as well as plants (such as Dutch elm disease and Rice blast). Field meetings to find interesting species of fungi are known as 'forays', after the first such meeting organized by the Woolhope Naturalists' Field Club in 1868 and entitled "a foray among the fungi." Some fungi can cause disease in humans or other organisms. The study of pathogenic fungi is referred to as medical mycology.[1]
See also
Mycotoxicology List of mycologists Pathogenic fungi Fungal Biochemical Tests
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References
1. ^ San-Blas G; Calderone RA (editors). (2008). Pathogenic Fungi. Caister Academic Press. ISBN 978-1-904455-32-5 . http://www.horizonpress.com/pat2.
Elias Magnus Fries, Systema mycologicum (1821) [1] (http://books.google.com /books?vid=OCLC10462820&id=5BMAAAAAQAAJ) Hawksworth, D. L. Mycologist's Handbook. (1974) Kew: U.K., CAB International.
External links
Professional organizations BMS: British Mycological Society (http://www.britmycolsoc.org.uk/) (United Kingdom) Centre for Research in Fungal Diversity (http://www.hku.hk/ecology/mycology/) (Hong Kong, China) La societ di micoterapia (http://www.funghi-vitalia.it/) (Italia) Medicinal Mushroom Society (http://vitalpilze.de/Introduction_1.html) MSA: Mycological Society of America (http://www.msafungi.org) (North America) Amateur organizations Mycological Society of San Francisco (http://www.mssf.org/) North American Mycological Association North American Truffling Society (http://www.natruffling.org/) Oregon Mycological Society (http://www.wildmushrooms.org/) Miscellaneous links Online lectures in mycology (http://media.med.sc.edu/microbiology2007/) University of South Carolina Shroomtalk Mycology Forums (http://www.shroomtalk.com) The WWW Virtual Library: Mycology (http://mycology.cornell.edu/) MykoWeb links page (http://www.mykoweb.com/links.html) Pacific Northwest Fungi Online Journal (http://pnwfungi.org/) Mycological Glossary at the Illinois Mycological Association (http://www.ilmyco.gen.chicago.il.us /Terms/TermsFrame.html) The Fifth Kingdom (http://www.mycolog.com/fifthtoc.html) Acta Fungorum (http://www.actafungorum.org/) (Italy) Fungi (http://www.tolweb.org/Fungi/2377) in the Tree of Life web project Fungal Cell Biology Group (http://129.215.156.68/index.html) at University of Edinburgh, UK. Mycological Marvels (http://exhibits.mannlib.cornell.edu/mycological/) Cornell University, Mann Library The Mushroom Project Game (http://www.yeoldelog.com/games/mushproj/mushproj2.shtml) Learn to identify mushrooms using this in depth, well-structured game. Retrieved from "http://en.wikipedia.org/wiki/Mycology" Category: Mycology This page was last modified on 17 February 2009, at 10:37. All text is available under the terms of the GNU Free Documentation License. (See Copyrights for details.) Wikipedia is a registered trademark of the Wikimedia Foundation, Inc., a U.S. registered 501(c)(3) tax-deductible nonprofit charity.
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Parasitism - Wikipedia, the free encyclopedia
http://en.wikipedia.org/wiki/Parasites
Parasitism
(Redirected from Parasites) Parasitism is a type of symbiotic relationship between two different organisms where one organism, the parasite, takes from the host, sometimes for a prolonged time. In general, parasites are much smaller than their hosts, show a high degree of specialization for their mode of life, and reproduce more quickly and in greater numbers than their hosts. Classic examples of parasitism include interactions between vertebrate hosts and diverse animals such as tapeworms, flukes, the Plasmodium species, and scabs. Parasitism is differentiated from parasitoidism, a relationship in which the host is always killed by the parasite such as moths, butterflies, ants, flies and others. The harm and benefit in parasitic interactions concern the biological fitness of the organisms involved. Parasites reduce host fitness in many ways, ranging from general or specialized pathology (such as castration), impairment of secondary sex characteristics, to the modification of host behaviour. Parasites increase their fitness by exploiting hosts for food, habitat and dispersal. Although the concept of parasitism applies unambiguously to many cases in nature, it is best considered part of a continuum of types of interactions between species, rather than an exclusive category. Particular interactions between species may satisfy some but not all parts of the definition. In many cases, it is difficult to demonstrate that the host is harmed. In others, there may be no apparent specialization on the part of the parasite, or the interaction between the organisms may be short-lived. In medicine, only eukaryotic organisms are considered parasites, with the exclusion of bacteria and viruses. Some branches of biology, however, regard members of these groups as parasitic.
Contents
1 Types of parasitism 2 Evolutionary aspects 2.1 Co-speciation 3 Ecology 3.1 Quantitative ecology 3.2 Diversity ecology 4 Adaptation 4.1 Transmission 4.2 Roles in ecosystems 5 See also 6 References 7 Further reading 8 External links
Mites parasitising a harvestman
Types of parasitism
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For more details on parasitic conjoined twins, see Parasitic twin. Parasites are classified based on a variety of aspects of their interactions with their hosts and on their life cycles. Those that live on its surface are called ectoparasites (e.g. some mites) and those that live inside the host are called endoparasites (e.g. hookworms). Endoparasites can exist in one of two forms: intercellular (inhabiting spaces in the hosts body) or intracellular (inhabiting cells in the hosts body). Flea bites on a human. Intracellular parasites, such as bacteria or viruses, tend to rely on a third organism which is generally known as the carrier or vector. The vector does the job of transmitting them to the host. An example of this interaction is the transmission of malaria, caused by a protozoan of the genus Plasmodium, to humans by the bite of an anopheline mosquito. An epiparasite is one that feeds on another parasite. This relationship is also sometimes referred to as hyperparasitism which may be exemplified by a protozoan (the hyperparasite) living in the digestive tract of a flea living on a dog. Parasitoids are organisms whose larval development occurs within another organism's body, resulting in the death of the host.[1] Thus, the interaction between the parasitoid and the host is fundamentally different from true parasites and their host, and shares some characteristics with predation. Social parasites take advantage of interactions between members of social organisms such as ants or termites. In kleptoparasitism, parasites appropriate food gathered by the host. An example is the brood parasitism practiced by many species of cuckoo and cowbird, which do not build nests of their own but rather deposit their eggs in nests of other species and abandon them there. The host behaves as a "babysitter" as they raise the young as their own. The cowbirds parasitism does not necessarily harm its hosts brood, however the cuckoo may remove one or more host eggs to avoid detection, furthermore the young cuckoo may heave the hosts eggs and nestlings from the nest. Parasitism can take the form of isolated cheating or exploitation among more generalized mutualistic interactions. For example, broad classes of plants and fungi exchange carbon and nutrients in common mutualistic mycorrhizal relationships; however, some plant species known as myco-heterotrophs "cheat" by taking carbon from a fungus rather than donating it.
A female Catolaccus grandis wasp is attracted by a boll weevil larva.
Evolutionary aspects
Biotrophic parasitism is an extremely common mode of life that has arisen independently many times in the course of evolution. Depending on the definition used, as many as half of all animals have at least one parasitic phase in their life cycles,[2] and it is also frequent in plants and fungi. Moreover, almost all free-living animals are host to one or more parasite taxa.[2] Parasites evolve in response to defense mechanisms of their hosts. Examples of host defenses include the toxins produced by plants to deter parasitic fungi and bacteria, the complex vertebrate immune system, which can target parasites through contact with bodily fluids, and behavioural defenses. An example of the latter is the avoidance by sheep of open pastures during spring, when roundworm eggs accumulated over the previous year
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hatch en masse. As a result of these and other host defenses, some parasites evolve adaptations that are specific to a particular host taxon and specialize to the point where they infect only a single species. Such narrow host specificity can be costly over evolutionary time, however, if the host species becomes extinct. Thus, many parasites are capable of infecting a variety of host species that are more or less closely related, with varying success. Host defenses also evolve in response to attacks by parasites. Theoretically, parasites may have an advantage in this evolutionary arms race because of their more rapid generation time. Hosts reproduce less quickly than parasites, and therefore have fewer chances to adapt than their parasites do over a given span of time. In some cases, a parasite species may coevolve with its host taxa. In theory, long-term coevolution should lead to a relatively stable relationship tending to commensalism or mutualism, in that it is in the evolutionary interest of the parasite that its host thrives. A parasite may evolve to become less harmful for its host or a host may evolve to cope with the unavoidable presence of a parasite to the point that the parasite's absence causes the host harm. For example, although animals infected with parasitic worms are often clearly harmed, and therefore parasitized, such infections may also reduce the prevalence and effects of autoimmune disorders in animal hosts, including humans.[3] The presumption of a shared evolutionary history between parasites and hosts can sometimes elucidate how host taxa are related. For instance, there has been dispute about whether flamingos are more closely related to the storks and their allies, or to ducks, geese and their relatives. The fact that flamingos share parasites with ducks and geese is evidence these groups may be more closely related to each other than either is to storks. Parasitism is part of one explanation for the evolution of secondary sex characteristics seen in breeding males throughout the animal world, such as the plumage of male peacocks and manes of male lions. According to this theory, female hosts select males for breeding based on such characteristics because they indicate resistance to parasites and other disease.
Co-speciation
In rare cases, a parasite may even undergo co-speciation with its host. One particularly remarkable example of co-speciation exists between the simian foamy virus (SFV) and its primate hosts. In one study, the phylogenies of SFV polymerase and the mitochondrial cytochrome oxidase subunit II from African and Asian primates were compared.[4] Surprisingly, the phylogenetic trees were very congruent in branching order and divergence times. Thus, the simian foamy viruses may have co-speciated with Old World primates for at least 30 million years.
Ecology
Quantitative ecology
When considering the distribution of a single parasite species, one finds that they exhibit an aggregated distribution among host individuals. This means that most hosts harbour few parasites, while a few hosts carry the vast majority of parasite individuals. This poses considerable problems for students of parasite ecology: the use of parametric statistics should be avoided. Log-transformation of data before the application of parametric test, or the use of non-parametric statistics is recommended by several authors. However, these give rise to further problems. Therefore, modern day quantitative parasitology is based on more advanced biostatistical methods.
Diversity ecology
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Hosts represent discrete habitat patches that can be occupied by parasites. A hierarchical set of terminology has come into use to describe parasite assemblages at different host scales. Infrapopulation All the parasites of one species in a single individual host. Metapopulation All the parasites of one species in a host population. Infracommunity All the parasites of all species in a single individual host. Component community All the parasites of all species in a host population. Compound community All the parasites of all species in all host species in an ecosystem. The diversity ecology of parasites differs markedly from that of free-living organisms. For free-living organisms, diversity ecology features many strong conceptual frameworks including Robert MacArthur and E. O. Wilson's theory of island biogeography, Jared Diamond's assembly rules and, more recently, null models such as Stephen Hubbell's unified neutral theory of biodiversity and biogeography. Frameworks are not so well-developed for parasites and in many ways they do not fit the free-living models. For example, island biogeography is predicated on fixed spatial relationships between habitat patches ("sinks"), usually with reference to a mainland ("source"). Parasites inhabit hosts, which represent mobile habitat patches with dynamic spatial relationships. There is no true "mainland" other than the sum of hosts (host population), so parasite component communities in host populations are metacommunities. Nonetheless, different types of parasite assemblages have been recognised in host individuals and populations, and many of the patterns observed for free-living organisms are also pervasive among parasite assemblages. The most prominent of these is the interactive-isolationist continuum. This proposes that parasite assemblages occur along a cline from interactive communities, where niches are saturated and interspecific competition is high, to isolationist communities, where there are many vacant niches and interspecific interaction is not as important as stochastic factors in providing structure to the community. Whether this is so, or whether community patterns simply reflect the sum of underlying species distributions (no real "structure" to the community), has not yet been established.
Adaptation
Parasites infect hosts that exist within their same greographical area (sympatric) more effectively. This phenomenon supports the "Red Queen hypothesis - which states that interactions between species (such as host an parasites) lead to constant natural selection for adaptation and counter adaptation."[5] The parasites track the locally common host phenotypes, therefore the parasites are less infective to allopatric (from different geographical region) hosts. Experiments published in 2002 discuss the analysis of two different snail populations from two different sources- Lake Ianthe and Lake Poerua in New Zealand. The populations were exposed to two pure parasites (digenetic trematode) taken from the same lakes. In the experiment, the snails were infected by their sympatric parasites, allopatric parasites and mixed sources of parasites. The results suggest that the parasites were more highly effective in infecting their sympatric snails than their allopatric snails. Though the allopatric snails were still infected by the parasites, the infectivity was much less when compared to the sympatric snails. Hence, the parasites were found to have adapted to infecting local populations of snails.[5]
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Transmission
Parasites inhabit living organisms and therefore face problems that free-living organisms do not. Hosts, the only habitats in which parasites can survive, actively try to avoid, repel, and destroy parasites. Parasites employ numerous strategies for getting from one host to another, a process sometimes referred to as parasite transmission or colonization. Some endoparasites infect their host by penetrating its external surface, while others must be ingested. Once inside the host, adult endoparasites need to shed offspring into the external environment in order to infect other hosts. Many adult endoparasites reside in the hosts gastrointestinal tract, where offspring can be shed along with host excreta. Adult stages of tapeworms, thorny-headed worms and most flukes use this method.
Life cycle of Entamoeba histolytica, an anaerobic parasitic protozoan.
Among protozoan endoparasites, such as the malarial parasites and trypanosomes, infective stages in the hosts blood are transported to new hosts by biting-insects or vectors. Larval stages of endoparasites often infect sites in the host other than the blood or gastrointestinal tract. In many such cases, larval endoparasites require their host to be consumed by the next host in the parasites life cycle in order to survive and reproduce. Alternatively, larval endoparasites may shed free-living transmission stages that migrate through the hosts tissue into the external environment, where they actively search for or await ingestion by other hosts. The foregoing strategies are used, variously, by larval stages of tapeworms, thorny-headed worms, flukes and parasitic roundworms. Some ectoparasites, such as monogenean worms, rely on direct contact between hosts. Ectoparasitic arthropods may rely on host-host contact (e.g. many lice), shed eggs that survive off the host (e.g. fleas), or wait in the external environment for an encounter with a host (e.g. ticks). Some aquatic leeches locate hosts by sensing movement and only attach when certain temperature and chemical cues are present. Some parasites modify host behaviour to make transmission to other hosts more likely. For example, in California salt marshes the fluke Euhaplorchis californiensis reduces the ability of its killifish host to avoid predators.[6] This parasite matures in egrets, which are more likely to feed on infected killifish than on uninfected fish. Another example is the protozoan Toxoplasma gondii, a parasite that matures in cats but can be carried by many other mammals. Uninfected rats avoid cat odours, but rats infected with T. gondii are drawn to this scent, a change which may increase transmission to feline hosts.[7]
Roles in ecosystems
Modifying the behaviour of infected hosts to make transmission to other hosts more likely is one way parasites can affect the structure of ecosystems. For example, in the case of Euhaplorchis californiensis (discussed above) it is plausible that the abundance of local predator and prey species would be different if this parasite were absent from the system. Although parasites are often omitted in depictions of food webs, they usually occupy the top position. Parasites can function like keystone species, reducing the dominance of superior competitors and allowing competing species to co-exist. Many parasites require multiple hosts of different species to complete their life cycles and rely on predator-prey or other stable ecological interactions to get from one host to another. In this sense, the parasites in an
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ecosystem reflect the "health" of that system.
See also
Intestinal parasite List of parasitic organisms List of parasites (human) List of human parasitic diseases Macroparasite Myco-heterotrophy Pathogen Parasitic plant Parasitoid wasp Pinworm Plasmodium Superparasitism Symbiosis Teratology Toxoplasmosis The Extended Phenotype
References
1. ^ H. Charles & J. Godfray (2004). "Parasitoids". Current Biology Magazine 14 (12): R456. doi:10.1016/j.cub.2004.06.004. [1] (http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRT4CNT0D6-4&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0& _userid=10&md5=3c7a3e2fbf44ccce8f7e74d13c1a72a9) 2. ^ a b Price, P.W. 1980. Evolutionary Biology of Parasites. Princeton University Press, Princeton 3. ^ Rook, G.A.W. (2007). "The hygiene hypothesis and the increasing prevalence of chronic inflammatory disorders". Transactions of the Royal Society of Tropical Medicine and Hygiene 101: 10724. doi:10.1016/j.trstmh.2007.05.014. 4. ^ SwitzerWM, Salemi M, Shanmugam V, Gao F, Cong ME, Kuiken C, Bhullar V, Beer BE, Vallet D, Gautier-Hion A, Tooze Z, Villinger F, Holmes EC, Heneine W. Ancient co-speciation of simian foamy viruses and primates. Nature. 2005 Mar 17; 434(7031):376-80. 5. ^ a b Lively, Curtis M. and Dybdahl, Mark F. "Parasite adaptation to locally common host genotypes." Nature. Vol. 405. 8 June 2000. 6. ^ Lafferty, K. D. and A. K. Morris. 1996. Altered behavior of parasitized killifish increases susceptibility to predation by bird final hosts. Ecology 77: 7. ^ Berdoy M, Webster JP, Macdonald DW (2000). "Fatal attraction in rats infected with Toxoplasma gondii". Proc. Biol. Sci. 267 (1452): 15914. doi:10.1098/rspb.2000.1182. http://www.pubmedcentral.nih.gov /articlerender.fcgi?tool=pubmed&pubmedid=.
Further reading
Zimmer, Carl 2001. Parasite Rex. Free Press. ISBN -X Combes, Claude 2005. The Art of Being a Parasite. The University of Chicago Press. ISBN-10: Desowitz, Robert 1998. Who Gave Pinta to the Santa Maria? Harvest Books. ISBN-10:
External links
[Parasitism knol [2] (http://knol.google.com/k/klaus-rohde/parasitism-an-introductionto/xk923bc3gp4/51#) ] Toxoplasmosis (http://www.cdc.gov/toxoplasmosis/) Parasitology Parasites Zoonoses (http://www.parazytologia.pl) - (Polish/English) over 50 movies (Filmoteka) and over 250 photos (Fotogaleria/Photogallery) with human and animal parasites. Aberystwyth University: Parasitology (http://www.aber.ac.uk/~mpgwww/Edu/EduIndex.html) class
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outline with links to full text articles on parasitism and parasitology. KSU: Parasitology Research (http://www.k-state.edu/parasitology) - parasitology articles and links. Medical Parasitology (http://pathmicro.med.sc.edu/book/parasit-sta.htm) online textbook. Division of Parasitic Diseases (http://www.cdc.gov/ncidod/dpd/) , Centers for Disease Control and Prevention VCU Virtual Parasite Project (http://www.vcu.edu/csbc/vpp/) - Virtual Parasite Project at Virginia Commonwealth University's Center for the Study of Biological Complexity Retrieved from "http://en.wikipedia.org/wiki/Parasitism" Categories: Parasitology | Symbiosis | Parasitism Hidden categories: All articles with unsourced statements | Articles with unsourced statements since February 2008 | Articles with unsourced statements since December 2008 This page was last modified on 13 February 2009, at 23:26. All text is available under the terms of the GNU Free Documentation License. (See Copyrights for details.) Wikipedia is a registered trademark of the Wikimedia Foundation, Inc., a U.S. registered 501(c)(3) tax-deductible nonprofit charity.
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General Microbiology

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COMPILED ARTICLES FROM WIKIPEDIA

COMPILED BY WARIH NUGROHO, DVM

SCHOOL OF AGRICULTURE FOR DEVELOPMENT PELAIHARI-SOUTH KALIMANTAN 2009

Microbiology - Wikipedia, the free encyclopedia

An agar plate streaked with microorganisms

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Microbiology - Wikipedia, the free encyclopedia

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Fermenting tanks with yeast being used to brew beer

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Virus - Wikipedia, the free encyclopedia

Virus - Wikipedia, the free encyclopedia

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Electron micrograph of icosahedral viruses (adenovirus)

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Linear Circular Segmented

Single-stranded Double-stranded Double-stranded with regions of singlestrandedness

Positive sense (+) Negative sense () Ambisense (+/)

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Effects on the host cell

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Viruses and human disease

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A child with chickenpox

Epidemics and pandemics

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The Marburg virus

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Prevention and treatment

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The guanosine analogue Aciclovir

Infection in other species

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Transmission electron micrograph of multiple bacteriophages attached to a bacterial cell wall

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Materials science and nanotechnology

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156. 157. 158. 159. 160. 161.

162. 163. 164. 165. 166. 167. 168.

173. 174. 175.

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Escherichia coli image is 8 micrometres wide.

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Origin and early evolution