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Bacterium
Escherichia coli
Scientific classification
Domain:	Bacteria
Subgroups
Actinobacteria Aquificae Bacteroidetes/Chlorobi Chlamydiae/Verrucomicrobia Chloroflexi Chrysiogenetes Cyanobacteria Deferribacteres Deinococcus-Thermus Dictyoglomi Fibrobacteres/Acidobacteria Firmicutes Fusobacteria Gemmatimonadetes Nitrospirae Planctomycetes Proteobacteria Spirochaetes Thermodesulfobacteria Thermomicrobia Thermotogae

Bacteria (singular: bacterium) are microscopic, unicellular organisms. They are often spherical (with the suffix -coccus), rod-shaped (with the suffix -bacillus) or spiral-shaped. They are 0.5-5 µm in the longest dimension, although the wide diversity of bacteria can display a huge variety of morphologies. The study of bacteria is known as bacteriology, a branch of microbiology.

Bacteria are ubiquitous in the environment, living in every possible habitat on the planet including, but by no means limited to, soil, underwater, deep in the earth's crust, and even such environments as sulfuric acid and nuclear waste. There are typically ten billion bacterial cells in a gram of soil, and one hundred thousand bacterial cells in a millilitre of sea water. In all, there may be around five million trillion trillion (5 × 10) bacteria in the world. Bacteria play an important role in the cycling of nutrients in the environment, and many important steps in the nutrient cycle are catalysed exclusively by bacteria, such as the fixation of nitrogen from the atmosphere.

There are more bacterial cells on each of our bodies than there are cells of our own and bacteria are a natural component of the human body, particularly on the skin and in the mouth and intestinal tract. However, pathogenic bacteria cause many infectious diseases, including cholera, leprosy and bubonic plague. The most common bacterial disease is tuberculosis, which kills about 2 million people every year, mostly in sub-Saharan Africa. In developed countries, the use of antibiotics allows the treatment of many bacterial infections, but antibiotic resistance is becoming increasingly common.

Bacteria are also important to numerous industrial processes, such as wastewater treatment, the production of cheese and yoghurt and more recently, the industrial production of antibiotics and other chemicals.

The term "bacteria" has traditionally been generally applied to all microscopic, single-celled prokaryotes. Although this term remains in everyday use, the scientific nomenclature changed after the discovery that prokaryotic life actually consists of two very different lines of evolution (see three-domain system). Originally called Eubacteria and Archaebacteria, these evolutionary domains are now called Bacteria and Archaea.

Metabolism

Main article: Microbial metabolism

In contrast to higher organisms, bacteria exhibit an extremely wide variety of metabolic types. In fact, it is widely accepted that eukaryotic metabolism is largely a derivative of bacterial metabolism with mitochondria having descended from a lineage within the α-Proteobacteria and chloroplasts from the Cyanobacteria by ancient endosymbiotic events. The distribution of metabolic traits within a group of organisms has traditionally been used to define their taxonomy, although these traits often do not correspond with genetic techniques (see groups and identification below).

Bacterial metabolism can be divided broadly on the basis of the kind of energy used for growth, electron donors and electron acceptors and by the source of carbon used. Most bacteria are heterotrophic; using organic carbon compounds as both carbon and energy sources. In aerobic organisms, oxygen is used as the terminal electron acceptor. In anaerobic organisms other inorganic compounds, such as nitrate, sulfate or carbon dioxide as terminal electron acceptors leading to the environmentally important processes of denitrification, sulfate reduction and acetogenesis, respectively. 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. As an alternative to heterotrophy some bacteria such as cyanobacteria and purple bacteria are autotrophic, meaning that they obtain cellular carbon by fixing carbon dioxide.

Energy metabolism of bacteria is either based on phototrophy, the use of light: or on chemotrophy, the use of chemical substances for fueling life processes. Lithotrophic bacteria use inorganic electron donors for respiration (chemolithotrophs) or biosynthesis and carbon dioxide fixation (photolithotrophs). In contrast, organotrophs use organic compounds as electron donors for biosynthetic reactions. 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. In both aerobic phototrophy and chemolithotrophy oxygen is used as a terminal electron acceptor, while under anaerobic conditions inorganic compounds (see above) are used instead. Most photolithotrophic and chemolithotrophic organisms are autotrophic, whereas photoorganotrophic and chemoorganotrophic organisms are heterotrophic.

In addition to carbon, 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.

Growth and reproduction

All bacteria reproduce through asexual reproduction (one parent) binary fission, under optimal conditions bacteria can grow extremely rapidly and can double as quickly as every 9.8 minutes. Two identical clone daughter cells are produced. Some bacteria, while still reproducing asexually, form more complex reproductive structures that facilitate the dispersal of the newly-formed daughter cells. Examples include fruiting body formation by Myxococcus and arial hyphae formation by Streptomyces, or budding. Budding is resulted of a 'bud' of a cell growing from another cell, and then finally breaking away.

Only about half of the known bacterial phyla have species that can be cultured in the laboratory and our knowledge of bacteria as a whole is biased towards those organisms that can be isolated in this way. 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, when measurement of growth or large volumes of cells are required, liquid growth media are used. Growth in stirred liquid media occurs as an even cell suspension, making the cultures easy to divide and transfer compared to solid media, although isolating single bacteria from liquid media is extremely difficult.

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 indefinitely. This constant limitation of nutrients has led the evolution of different growth strategies in different types of organisms (see R/K selection theory). Some possess the ability to grow extremely rapidly when nutrients become available, such as the formation of algal (and cyanobacterial) blooms that often occur in lakes during the summer. Other organisms have devised more specialized strategies to make them more successful in a harsh environment, such as the production of multiple antibiotics by Streptomyces; that inhibit the growth of competing microorganisms. In a natural environment, many organisms live in communities (e.g. biofilms) which may allow for increased supply of nutrients and protection of environmental stresses. These relationships can be essential for growth of a particular organism or group of organisms (syntrophy).

Bacterial growth follows three distinct phases. When an old stock of bacteria is diluted into fresh media these cells need to adapt to the nutrient rich environment. The first phase of growth is the lag phase, a period of slow growth when the cells are adapting to fast growth. The lag phase has high biosynthesis rates, as enzymes needed to metabolise a variety of substrates are produced. 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 the 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 begin to reduce their metabolic activity, as well consume their own non-essential 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. The limitations of this discontinuous growth pattern can be avoided by the use of a chemostat, which maintains a bacterial culture under steady-state conditions by continuously adding nutrients and removing waste products and cells. Large chemostats are often used for industrial-scale microbial processes.

Genetic variation

Bacteria, as asexual organisms, inherit an identical copy of their parent's genes (i.e. are clonal). All bacteria, however, have the ability to evolve through selection on changes to their genetic material (DNA) which arise either through mutation or genetic recombination. Mutation occurs as a result of errors made during the replication of DNA. It occurs naturally and as a result of the presence of mutagens. Mutation rates can vary among different species of bacteria. The most frequent genetic changes in bacterial genomes come from random mutation. Some bacteria can also undergo genetic recombination. This can occur when bacteria take-up exogenous environmental DNA from closely related genera in a process called transformation. In the process of transduction, a virus can alter the DNA of a bacterium by becoming lysogenic and introducing foreign DNA into the host chromosome, which can then be transcribed and replicated. This gene acquisition from the environment is called horizontal gene transfer and may be common under natural conditions.

Because of their ability to quickly grow, and the relative ease with which they can be manipulated, bacteria have historically been the workhorses for the fields of molecular biology, genetics and biochemistry. By making mutations in bacterial DNA and examining the resulting phenotypes, scientists have been able to determine the function of many different genes and enzymes. Lessons learned from bacteria can then be applied to more complex organisms which are often more difficult to study.

Movement

Motile bacteria can move about, using flagella, bacterial gliding, or changes of buoyancy. A unique group of bacteria, the spirochaetes, have structures similar to flagella, called axial filaments, between two membranes in the periplasmic space. They have a distinctive helical body that twists about as it moves.

Bacterial flagella are arranged in many different ways. Bacteria can have a single polar flagellum at one end of a cell, clusters of many flagella at one end or flagella scattered all over the cell, as with peritrichous. Often in the close vicinity of the flagella a specialized region of the cell membrane the polar membrane can be discerned in ultrathin sections. Many bacteria (such as E. coli) have two distinct modes of movement: forward movement (swimming) and tumbling. The tumbling allows them to reorient and introduces an important element of randomness in their forward movement. (See external links below for link to videos.)

Motile bacteria are attracted or repelled by certain stimuli, behaviors called taxes - for instance, chemotaxis, phototaxis, mechanotaxis, and magnetotaxis. In one peculiar group, the myxobacteria, individual bacteria attract to form swarms and may differentiate to form fruiting bodies. The myxobacteria move only when on solid surfaces, unlike E. coli which is motile in liquid or solid media.

Groups and identification

Historically, bacteria as originally studied by botanists were classified in the same way as plants, that is, mainly by shape. Bacteria come in a variety of different cell morphologies (shapes), including bacillus (rod-shape), coccus (spherical), spirillum (helical), and vibrio (curved bacillus). However, because of their small size bacteria are relatively uniform in shape and therefore classification based on morphology was unsuccessful. The first formal classification scheme was developed following the development of the Gram stain by Hans Christian Gram which separates bacteria based on the structural characteristics of their cell walls. This scheme included:

• Gracilicutes - Gram negative staining bacteria with a second cell membrane
• Firmicutes - Gram positive staining bacteria with a thick peptidoglycan wall
• Mollicutes - Gram negative staining bacteria with no cell wall or second membrane
• Mendosicutes - atypically staining strains now known to belong to the Archaea

Further developments (essentially) based on this scheme included comparisons of bacteria based on differences in cellular metabolism as determined by a wide variety of specific tests. Bacteria were also classified based on differences in cellular chemical compounds such as fatty acids, pigments, and quinones for example. While these schemes allowed for the differentiation between bacterial strains, it was unclear whether these differences represented variation between distinct species or between strains of the same species. It was not until the utilization of genome-based techniques such as guanine cytosine ratio determination, genome-genome hybridization and gene sequencing (in particular the rRNA gene) that microbial taxonomy developed (or at least is developing) into a stable, accurate classification system. It should be noted, however, that due to the existence numerous historical classification schemes and our current poor understanding of microbial diversity, bacterial taxonomy remains a changing and expanding field.

Benefits and dangers

Bacteria are both harmful and useful to the environment and animals, including humans. The role of bacteria in disease and infection is important. Some bacteria act as pathogens and cause diseases such as tetanus, typhoid fever, diphtheria, syphilis, cholera, food-borne illness, leprosy, and tuberculosis(TB). Sepsis, a systemic infectious syndrome characterized by shock and massive vasodilation, or localized infection, can be caused by bacteria such as Streptococcus, Staphylococcus, or many gram-negative bacteria. Some bacterial infections can spread throughout the host's body and become systemic. In plants, bacteria cause leaf spot, fireblight, and wilts. The mode of infection includes contact, air, food, water, and insect-borne microorganisms. The hosts infected with the pathogens may be treated with antibiotics, which can be classified as bacteriocidal and bacteriostatic, which at concentrations that can be reached in bodily fluids either kill bacteria or hamper their growth, respectively. Antiseptic measures may be taken to prevent infection by bacteria, for example, by swabbing skin with alcohol prior to piercing the skin with the needle of a syringe. Sterilization of surgical and dental instruments is done to make them sterile or pathogen-free to prevent contamination and infection by bacteria. Sanitizers and disinfectants are used to kill bacteria or other pathogens to prevent contamination and risk of infection.

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) help in the transformation of molecular dinitrogen gas as their source of nitrogen, converting it to nitrogenous compounds in a process known as nitrogen fixation. 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 the gut flora in the human large intestine can contribute to gut immunity, synthesise vitamins such as folic acid and biotin, and ferment complex undigestable carbohydrates.

The ability of bacteria to degrade a variety of organic compounds is remarkable. Highly specialized groups of microorganisms play important roles in the mineralization of specific classes of organic compounds. For example, the decomposition of cellulose, which is one of the most abundant constituents of plant tissues, is mainly brought about by aerobic bacteria that belong to the genus Cytophaga. This ability has also been utilized by humans in industry, waste processing, and bioremediation. Bacteria capable of digesting the hydrocarbons in petroleum are often used to clean up oil spills. Some beaches in Prince William Sound were fertilized in an attempt to facilitate the growth of such bacteria after the infamous 1989 Exxon Valdez oil spill. These efforts were effective on beaches that were not too thickly covered in oil.

Bacteria, often in combination with yeasts and molds, are used in the preparation of fermented foods such as cheese, pickles, soy sauce, sauerkraut, vinegar, wine, and yogurt. Using biotechnology techniques, bacteria can be bioengineered for the production of therapeutic drugs, such as insulin, or for the bioremediation of toxic wastes.

"Friendly bacteria" is a term used to refer to those bacteria that offer some benefit to human hosts, such as Lactobacillus species, which convert milk protein to lactic acid in the gut. The presence of such bacterial colonies also inhibits the growth of potentially pathogenic bacteria (usually through competitive exclusion). Other bacteria that are helpful inside the body are many strains of E. coli, which are harmless in healthy individuals and provide Vitamin K.

See also

• Bacterial growth
• Bacteriocin
• Economic importance of bacteria
• Magnetotactic bacteria
• Microorganism
• Nanobacterium
• Transgenic bacteria

References

1. University of Georgia Campus News
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4. Drake H, Daniel S, Küsel K, Matthies C, Kuhner C, Braus-Stromeyer S (1997). "Acetogenic bacteria: what are the in situ consequences of their diverse metabolic versatilities?". Biofactors. 6 (1): 13–24. PMID 9233536.{{cite journal}}: CS1 maint: multiple names: authors list (link)
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• Some text in this entry was merged with the Nupedia article entitled Bacteria, written by Nagina Parmar; reviewed and approved by the Biology group (editor: Gaytha Langlois, lead reviewer: Gaytha Langlois, lead copyeditors: Ruth Ifcher and Jan Hogle)
•  This article incorporates public domain material from Science Primer. NCBI. Archived from the original on 2009-12-08.

Further reading

• Alcamo, I. Edward. Fundamentals of Microbiology. 5th ed. Menlo Park, California: Benjamin Cumming, 1997.
• Atlas, Ronald M. Principles of Microbiology. St. Louis, Missouri: Mosby, 1995.
• Holt, John.G. Bergey's Manual of Determinative Bacteriology. 9th ed. Baltimore, Maryland: Williams and Wilkins, 1994.
• Hugenholtz P, Goebel BM, Pace NR (1998). "Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity". J Bacteriol. 180 (18): 4765–74. PMID 9733676.{{cite journal}}: CS1 maint: multiple names: authors list (link)
• Koshland, Daniel E., Jr. (1977). "A Response Regulator Model in a Simple Sensory System". Science. 196: 1055–1063. PMID 870969.{{cite journal}}: CS1 maint: multiple names: authors list (link)
• Stanier, R.Y., J. L. Ingraham, M. L. Wheelis, and P. R. Painter. General Microbiology. 5th ed. Upper Saddle River, New Jersey: Prentice Hall, 1986.

External links

• Bacterial Nomenclature Up-To-Date from DSMZ
• Bacterial Growth and Cell Wall (Ger)
• Microminds
• The largest bacteria
• Tree of Life
• Videos of bacteria swimming and tumbling, use of optical tweezers and other fine videos.
• Planet of the Bacteria by Stephen Jay Gould
• Major Groups of Prokaryotes
• Bitter Resistance by Bruce Sterling
• On-line text book on bacteriology
• cyanobacteria in lichens

• Bacteria
• Bacteriology