Bacteria

Bacteria


Bacteria (micrometres in length, bacteria have a number of shapes, ranging from spheres to rods and spirals. Bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste,[1] and the deep portions of Earth's crust. Bacteria also live in symbiotic and parasitic relationships with plants and animals. They are also known to have flourished in manned spacecraft.[2]

There are typically 40 million bacterial fixation of nitrogen from the atmosphere and putrefaction. In the biological communities surrounding hydrothermal vents and cold seeps, bacteria provide the nutrients needed to sustain life by converting dissolved compounds, such as hydrogen sulphide and methane, to energy. On 17 March 2013, researchers reported data that suggested bacterial life forms thrive in the Mariana Trench, which with a depth of up to 11 kilometres is the deepest part of the Earth's oceans.[5][6] Other researchers reported related studies that microbes thrive inside rocks up to 580 metres below the sea floor under 2.6 kilometres of ocean off the coast of the northwestern United States.[5][7] According to one of the researchers, "You can find microbes everywhere — they're extremely adaptable to conditions, and survive wherever they are."[5]

Most bacteria have not been characterized, and only about half of the phyla of bacteria have species that can be grown in the laboratory.[8] The study of bacteria is known as bacteriology, a branch of microbiology.

There are approximately ten times as many bacterial cells in the human flora as there are human cells in the body, with the largest number of the human flora being in the gut flora, and a large number on the skin.[9] The vast majority of the bacteria in the body are rendered harmless by the protective effects of the immune system, and some are beneficial. However, several 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 per year, mostly in sub-Saharan Africa.[10] In developed countries, antibiotics are used to treat bacterial infections and are also used in farming, making antibiotic resistance a growing problem. In industry, bacteria are important in sewage treatment and the breakdown of oil spills, the production of cheese and yogurt through fermentation, and the recovery of gold, palladium, copper and other metals in the mining sector,[11] as well as in biotechnology, and the manufacture of antibiotics and other chemicals.[12]

Once regarded as evolved from an ancient common ancestor. These evolutionary domains are called Bacteria and Archaea.[13]

Contents

  • Etymology 1
  • Origin and early evolution 2
  • Morphology 3
  • Cellular structure 4
    • Intracellular structures 4.1
    • Extracellular structures 4.2
    • Endospores 4.3
  • Metabolism 5
  • Growth and reproduction 6
  • Genetics 7
    • DNA transfer 7.1
    • Bacteriophages 7.2
  • Behavior 8
    • Secretion 8.1
    • Bioluminescence 8.2
    • Multicellularity 8.3
    • Movement 8.4
  • Classification and identification 9
  • Interactions with other organisms 10
    • Predators 10.1
    • Mutualists 10.2
    • Pathogens 10.3
  • Significance in technology and industry 11
  • History of bacteriology 12
  • See also 13
  • References 14
  • Further reading 15
  • External links 16

Etymology

The word bacteria is the plural of the New Latin bacterium, which is the latinisation of the Greek βακτήριον (bakterion),[14] the diminutive of βακτηρία (bakteria), meaning "staff, cane",[15] because the first ones to be discovered were rod-shaped.[16][17]

Origin and early evolution

The ancestors of modern bacteria were unicellular microorganisms that were the Francevillian biota. Although bacterial fossils exist, such as stromatolites, their lack of distinctive morphology prevents them from being used to examine the 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.[20]

Bacteria were also involved in the second great evolutionary divergence, that of the archaea and eukaryotes. Here, eukaryotes resulted from the entering of ancient bacteria into chloroplasts in algae and plants. There are also some algae that originated from even later endosymbiotic events. Here, eukaryotes engulfed a eukaryotic algae that developed into a "second-generation" plastid.[23][24] This is known as secondary endosymbiosis.

Morphology

Bacteria display many cell morphologies and arrangements

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 0.5–5.0 micrometres in length. However, a few species are visible to the unaided eye — for example, Thiomargarita namibiensis is up to half a millimetre long[25] and Epulopiscium fishelsoni reaches 0.7 mm.[26] Among the smallest bacteria are members of the genus Mycoplasma, which measure only 0.3 micrometres, as small as the largest viruses.[27] Some bacteria may be even smaller, but these ultramicrobacteria are not well-studied.[28]

Most bacterial species are either spherical, called cocci (sing. coccus, from Greek kókkos, grain, seed), or rod-shaped, called bacilli (sing. bacillus, from Latin baculus, stick). Elongation is associated with swimming.[29] Some bacteria, called vibrio, are shaped like slightly curved rods or comma-shaped; others can be spiral-shaped, called spirilla, or tightly coiled, called spirochaetes. A small number of species even have tetrahedral or cuboidal shapes.[30] More recently, some bacteria were discovered deep under Earth's crust that grow as branching filamentous types with a star-shaped cross-section. The large surface area to volume ratio of this morphology may give these bacteria an advantage in nutrient-poor environments.[31] 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.[32][33]

A biofilm of thermophilic bacteria in the outflow of Mickey Hot Springs, Oregon, approximately 20 mm thick.

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.[34]

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.[35][36] In natural environments, such as soil or the surfaces of plants, the majority of bacteria are bound to surfaces in biofilms.[37] 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.[38]

Even more complex morphological changes are sometimes possible. For example, when starved of amino acids, differentiate into a specialised dormant state called myxospores, which are more resistant to drying and other adverse environmental conditions than are ordinary cells.[40]

Cellular structure

Structure and contents of a typical Gram positive bacterial cell (seen by the fact that only one cell membrane is present).

Intracellular structures

The bacterial cell is surrounded by a [44]

ribosomes Bacteria do not have a membrane-bound nucleus, and their

electron microscope image of carboxysomes in Halothiobacillus neapolitanus, below is an image of purified carboxysomes. On the right is a model of their structure. Scale bars are 100 nm.[52]

Many important biochemical reactions, such as energy generation, use concentration gradients across membranes. 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.[49] However, in many photosynthetic bacteria the plasma membrane is highly folded and fills most of the cell with layers of light-gathering membrane.[50] These light-gathering complexes may even form lipid-enclosed structures called chlorosomes in green sulfur bacteria.[51] Other proteins import nutrients across the cell membrane, or expel undesired molecules from the cytoplasm.

[48][47], often grouped in chains called polyribosomes, for the production of proteins, but the structure of the bacterial ribosome is different from that of eukaryotes and Archaea.[56] Bacterial ribosomes have a sedimentation rate of 70S (measured in Svedberg units): their subunits have rates of 30S and 50S. Some antibiotics bind specifically to 70S ribosomes and inhibit bacterial protein synthesis. Those antibiotics kill bacteria without affecting the larger 80S ribosomes of eukaryotic cells and without harming the host.

Some bacteria produce intracellular nutrient storage granules for later use, such as Carboxysomes are bacterial microcompartments that contain enzymes involved in carbon fixation. Magnetosomes are bacterial microcompartments, present in magnetotactic bacteria, that contain magnetic crystals.

Extracellular structures

In most bacteria, a cell wall is present on the outside of the cell membrane. The cell membrane and cell wall comprise the cell envelope. A common bacterial cell wall material is peptidoglycan (called "murein" in older sources), which is made from polysaccharide chains cross-linked by peptides containing D-amino acids.[62] Bacterial cell walls are different from the cell walls of plants and fungi, which are made of cellulose and chitin, respectively.[63] 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.[63]

There are broadly speaking two different types of cell wall in bacteria, a thick one in the gram-positives and a thinner one in the gram-negatives. The names originate from the reaction of cells to the Gram stain, a test long-employed for the classification of bacterial species.[64]

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. Lipopolysaccharides, also called endotoxins, are composed of polysaccharides and lipid A that is responsible for much of the toxicity of gram-negative bacteria. Most bacteria have the gram-negative cell wall, and only the Firmicutes and Actinobacteria have the alternative gram-positive arrangement.[65] These two groups were previously known as the low G+C and high G+C Gram-positive bacteria, respectively. 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.[66] If the bacterial cell wall is entirely removed, it is called a protoplast, whereas if it is partially removed, it is called a spheroplast. ß-Lactam antibiotics, such as penicillin, inhibit the formation of peptidoglycan cross-links in the bacterial cell wall. The enzyme lysozyme, found in human tears, also digests the cell wall of bacteria and is the body's main defense against eye infections.

Acid-fast bacteria, such as Mycobacteria, are resistant to decolorization by acids during staining procedures. The high mycolic acid content of Mycobacteria, is responsible for the staining pattern of poor absorption followed by high retention. The most common staining technique used to identify acid-fast bacteria is the Ziehl-Neelsen stain or acid-fast stain, in which the acid-fast bacilli are stained bright-red and stand out clearly against a blue background. L-form bacteria are strains of bacteria that lack cell walls. The main pathogenic bacteria in this class is Mycoplasma (not to be confused with Mycobacteria).

In many bacteria, an S-layer of rigidly arrayed protein molecules covers the outside of the cell.[67] 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.[68]

Helicobacter pylori electron micrograph, showing multiple flagella on the cell surface

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.[69]

Fimbriae (sometimes called "attachment pili") are fine filaments of protein, usually 2–10 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 involved in attachment to solid surfaces or to other cells, and are essential for the virulence of some bacterial pathogens.[70] Pili (sing. pilus) are cellular appendages, slightly larger than fimbriae, that can transfer genetic material between bacterial cells in a process called conjugation where they are called conjugation pili or "sex pili" (see bacterial genetics, below).[71] They can also generate movement where they are called type IV pili (see movement, below).

slime layer of extra-cellular polymer to a highly structured capsule. These structures can protect cells from engulfment by eukaryotic cells such as macrophages (part of the human immune system).[72] They can also act as antigens and be involved in cell recognition, as well as aiding attachment to surfaces and the formation of biofilms.[73]

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.[74]

Endospores

Bacillus anthracis (stained purple) growing in cerebrospinal fluid

Certain genera of Gram-positive bacteria, such as Bacillus, Clostridium, Sporohalobacter, Anaerobacter, and Heliobacterium, can form highly resistant, dormant structures called endospores.[75] 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.[76] Endospores have a central core of cytoplasm containing DNA and ribosomes surrounded by a cortex layer and protected by an impermeable and rigid coat. Dipicolinic acid is a chemical compound that composes 5% to 15% of the dry weight of bacterial spores. It is implicated as responsible for the heat resistance of the endospore.

Endospores show no detectable actin polymerization at one pole of their cells, they can form a kind of tail that pushes them through the host cell's cytoplasm.[135]

Classification and identification

Streptococcus mutans visualized with a Gram stain

cellular metabolism or on differences in cell components, such as DNA, fatty acids, pigments, antigens and quinones.[96] While these schemes allowed the identification and classification of bacterial strains, it was unclear whether these differences represented variation between distinct species or between strains of the same species. This uncertainty was due to the lack of distinctive structures in most bacteria, as well as lateral gene transfer between unrelated species.[136] Due to lateral gene transfer, some closely related bacteria can have very different morphologies and metabolisms. To 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.[137] Classification of bacteria is determined by publication in the International Journal of Systematic Bacteriology,[138] and Bergey's Manual of Systematic Bacteriology.[139] 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-cell 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.[13] 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.[140] 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.[8][141] For example, a few biologists argue that the Archaea and Eukaryotes evolved from Gram-positive bacteria.[142]

The 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.

green and bacteria blue. archaea are colored red, Eukaryotes [1]

The serology.

anaerobic growth), patterns of hemolysis, and staining.

As with bacterial classification, identification of bacteria is increasingly using molecular methods. Diagnostics using DNA-based tools, such as polymerase chain reaction, are increasingly popular due to their specificity and speed, compared to culture-based methods.[145] These methods also allow the detection and identification of "viable but nonculturable" cells that are metabolically active but non-dividing.[146] 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 a little less than 9,300 known species of prokaryotes, which includes bacteria and archaea;[147] but attempts to estimate the true number of bacterial diversity have ranged from 107 to 109 total species – and even these diverse estimates may be off by many orders of magnitude.[148][149]

Interactions with other organisms

Despite their apparent simplicity, bacteria can form complex associations with other organisms. These body odor.

Predators

Some species of bacteria kill and then consume other microorganisms, these species are called predatory bacteria.[150] These include organisms such as


  • MicrobeWiki, an extensive wiki about bacteria and viruses
  • Bacteria that affect crops and other plants
  • Bacterial Nomenclature Up-To-Date from DSMZ
  • Genera of the domain Bacteria – list of Prokaryotic names with Standing in Nomenclature
  • The largest bacteria
  • Tree of Life: Eubacteria
  • Videos of bacteria swimming and tumbling, use of optical tweezers and other videos.
  • Planet of the Bacteria by Stephen Jay Gould
  • On-line text book on bacteriology
  • Animated guide to bacterial cell structure.
  • Bacteria Make Major Evolutionary Shift in the Lab
  • Online collaboration for bacterial taxonomy.
  • PATRIC, a Bioinformatics Resource Center for bacterial pathogens, funded by NIAID
  • Bacterial Chemotaxis Interactive Simulator – A web-app that uses several simple algorithms to simulate bacterial chemotaxis.
  • Cell-Cell Communication in Bacteria on-line lecture by Bonnie Bassler, and TED: Discovering bacteria's amazing communication system
  • Sulfur-cycling fossil bacteria from the 1.8-Ga Duck Creek Formation provide promising evidence of evolution's null hypothesis, Proceedings of the National Academy of Sciences of the United States of AmericaSummarized in: Scientists discover bacteria that haven't evolved in more than 2 billion years, LiveScience and BusinessInsider

External links

Further reading

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return p

end

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function p._hatnote(s, options) checkType('_hatnote', 1, s, 'string') checkType('_hatnote', 2, options, 'table', true) local classes = {'hatnote'} local extraclasses = options.extraclasses local selfref = options.selfref if type(extraclasses) == 'string' then classes[#classes + 1] = extraclasses end if selfref then classes[#classes + 1] = 'selfref' end return string.format( '

function p.hatnote(frame) local args = getArgs(frame) local s = args[1] local options = {} if not s then return p.makeWikitextError( 'no text specified', 'Template:Hatnote#Errors', args.category ) end options.extraclasses = args.extraclasses options.selfref = args.selfref return p._hatnote(s, options) end


-- Hatnote -- -- Produces standard hatnote text. Implements the template.


function p._formatLink(link, display) -- Find whether we need to use the colon trick or not. We need to use the -- colon trick for categories and files, as otherwise category links -- categorise the page and file links display the file. checkType('_formatLink', 1, link, 'string') checkType('_formatLink', 2, display, 'string', true) link = removeInitialColon(link) local namespace = p.findNamespaceId(link, false) local colon if namespace == 6 or namespace == 14 then colon = ':' else colon = end -- Find whether a faux display value has been added with the | magic -- word. if not display then local prePipe, postPipe = link:match('^(.-)|(.*)$') link = prePipe or link display = postPipe end -- Find the display value. if not display then local page, section = link:match('^(.-)#(.*)$') if page then display = page .. ' § ' .. section end end -- Assemble the link. if display then return string.format('%s', colon, link, display) else return string.format('%s%s', colon, link) end end

function p.formatLink(frame) local args = getArgs(frame) local link = args[1] local display = args[2] if not link then return p.makeWikitextError( 'no link specified', 'Template:Format hatnote link#Errors', args.category ) end return p._formatLink(link, display) end


-- Format link -- -- Makes a wikilink from the given link and display values. Links are escaped -- with colons if necessary, and links to sections are detected and displayed -- with " § " as a separator rather than the standard MediaWiki "#". Used in -- the template.


function p.makeWikitextError(msg, helpLink, addTrackingCategory) -- Formats an error message to be returned to wikitext. If -- addTrackingCategory is not false after being returned from -- Module:Yesno, and if we are not on a talk page, a tracking category -- is added. checkType('makeWikitextError', 1, msg, 'string') checkType('makeWikitextError', 2, helpLink, 'string', true) yesno = require('Module:Yesno') local title = mw.title.getCurrentTitle() -- Make the help link text. local helpText if helpLink then helpText = ' (help)' else helpText = end -- Make the category text. local category if not title.isTalkPage and yesno(addTrackingCategory) ~= false then category = 'Hatnote templates with errors' category = string.format( '%s:%s', mw.site.namespaces[14].name, category ) else category = end return string.format( '%s', msg, helpText, category ) end

function p.formatPageTables(...) -- Takes a list of page/display tables and returns it as a list of -- formatted links. Nil values are not allowed. local pages = {...} local links = {} for i, t in ipairs(pages) do checkType('formatPageTables', i, t, 'table') local link = t[1] local display = t[2] links[i] = p._formatLink(link, display) end return links end

function p.formatPages(...) -- Formats a list of pages using formatLink and returns it as an array. Nil -- values are not allowed. local pages = {...} local ret = {} for i, page in ipairs(pages) do ret[i] = p._formatLink(page) end return ret end

function p.findNamespaceId(link, removeColon) -- Finds the namespace id (namespace number) of a link or a pagename. This -- function will not work if the link is enclosed in double brackets. Colons -- are trimmed from the start of the link by default. To skip colon -- trimming, set the removeColon parameter to true. checkType('findNamespaceId', 1, link, 'string') checkType('findNamespaceId', 2, removeColon, 'boolean', true) if removeColon ~= false then link = removeInitialColon(link) end local namespace = link:match('^(.-):') if namespace then local nsTable = mw.site.namespaces[namespace] if nsTable then return nsTable.id end end return 0 end

local function removeInitialColon(s) -- Removes the initial colon from a string, if present. return s:match('^:?(.*)') end

local function getArgs(frame) -- Fetches the arguments from the parent frame. Whitespace is trimmed and -- blanks are removed. mArguments = require('Module:Arguments') return mArguments.getArgs(frame, {parentOnly = true}) end


-- Helper functions


local p = {}

local libraryUtil = require('libraryUtil') local checkType = libraryUtil.checkType local mArguments -- lazily initialise Module:Arguments local yesno -- lazily initialise Module:Yesno


return p-------------------------------------------------------------------------------- -- Module:Hatnote -- -- -- -- This module produces hatnote links and links to related articles. It -- -- implements the and meta-templates and includes -- -- helper functions for other Lua hatnote modules. --

end

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function p._hatnote(s, options) checkType('_hatnote', 1, s, 'string') checkType('_hatnote', 2, options, 'table', true) local classes = {'hatnote'} local extraclasses = options.extraclasses local selfref = options.selfref if type(extraclasses) == 'string' then classes[#classes + 1] = extraclasses end if selfref then classes[#classes + 1] = 'selfref' end return string.format( '

function p.hatnote(frame) local args = getArgs(frame) local s = args[1] local options = {} if not s then return p.makeWikitextError( 'no text specified', 'Template:Hatnote#Errors', args.category ) end options.extraclasses = args.extraclasses options.selfref = args.selfref return p._hatnote(s, options) end


-- Hatnote -- -- Produces standard hatnote text. Implements the template.


function p._formatLink(link, display) -- Find whether we need to use the colon trick or not. We need to use the -- colon trick for categories and files, as otherwise category links -- categorise the page and file links display the file. checkType('_formatLink', 1, link, 'string') checkType('_formatLink', 2, display, 'string', true) link = removeInitialColon(link) local namespace = p.findNamespaceId(link, false) local colon if namespace == 6 or namespace == 14 then colon = ':' else colon = end -- Find whether a faux display value has been added with the | magic -- word. if not display then local prePipe, postPipe = link:match('^(.-)|(.*)$') link = prePipe or link display = postPipe end -- Find the display value. if not display then local page, section = link:match('^(.-)#(.*)$') if page then display = page .. ' § ' .. section end end -- Assemble the link. if display then return string.format('%s', colon, link, display) else return string.format('%s%s', colon, link) end end

function p.formatLink(frame) local args = getArgs(frame) local link = args[1] local display = args[2] if not link then return p.makeWikitextError( 'no link specified', 'Template:Format hatnote link#Errors', args.category ) end return p._formatLink(link, display) end


-- Format link -- -- Makes a wikilink from the given link and display values. Links are escaped -- with colons if necessary, and links to sections are detected and displayed -- with " § " as a separator rather than the standard MediaWiki "#". Used in -- the template.


function p.makeWikitextError(msg, helpLink, addTrackingCategory) -- Formats an error message to be returned to wikitext. If -- addTrackingCategory is not false after being returned from -- Module:Yesno, and if we are not on a talk page, a tracking category -- is added. checkType('makeWikitextError', 1, msg, 'string') checkType('makeWikitextError', 2, helpLink, 'string', true) yesno = require('Module:Yesno') local title = mw.title.getCurrentTitle() -- Make the help link text. local helpText if helpLink then helpText = ' (help)' else helpText = end -- Make the category text. local category if not title.isTalkPage and yesno(addTrackingCategory) ~= false then category = 'Hatnote templates with errors' category = string.format( '%s:%s', mw.site.namespaces[14].name, category ) else category = end return string.format( '%s', msg, helpText, category ) end

function p.formatPageTables(...) -- Takes a list of page/display tables and returns it as a list of -- formatted links. Nil values are not allowed. local pages = {...} local links = {} for i, t in ipairs(pages) do checkType('formatPageTables', i, t, 'table') local link = t[1] local display = t[2] links[i] = p._formatLink(link, display) end return links end

function p.formatPages(...) -- Formats a list of pages using formatLink and returns it as an array. Nil -- values are not allowed. local pages = {...} local ret = {} for i, page in ipairs(pages) do ret[i] = p._formatLink(page) end return ret end

function p.findNamespaceId(link, removeColon) -- Finds the namespace id (namespace number) of a link or a pagename. This -- function will not work if the link is enclosed in double brackets. Colons -- are trimmed from the start of the link by default. To skip colon -- trimming, set the removeColon parameter to true. checkType('findNamespaceId', 1, link, 'string') checkType('findNamespaceId', 2, removeColon, 'boolean', true) if removeColon ~= false then link = removeInitialColon(link) end local namespace = link:match('^(.-):') if namespace then local nsTable = mw.site.namespaces[namespace] if nsTable then return nsTable.id end end return 0 end

local function removeInitialColon(s) -- Removes the initial colon from a string, if present. return s:match('^:?(.*)') end

local function getArgs(frame) -- Fetches the arguments from the parent frame. Whitespace is trimmed and -- blanks are removed. mArguments = require('Module:Arguments') return mArguments.getArgs(frame, {parentOnly = true}) end


-- Helper functions


local p = {}

local libraryUtil = require('libraryUtil') local checkType = libraryUtil.checkType local mArguments -- lazily initialise Module:Arguments local yesno -- lazily initialise Module:Yesno


-- Module:Hatnote -- -- -- -- This module produces hatnote links and links to related articles. It -- -- implements the and meta-templates and includes -- -- helper functions for other Lua hatnote modules. --


References

See also

A major step forward in the study of bacteria came in 1977 when Carl Woese recognized that archaea have a separate line of evolutionary descent from bacteria.[196] This new phylogenetic taxonomy depended on the sequencing of 16S ribosomal RNA, and divided prokaryotes into two evolutionary domains, as part of the three-domain system.[13]

Though it was known in the nineteenth century that bacteria are the cause of many diseases, no effective antibacterial treatments were available.[193] In 1910, Paul Ehrlich developed the first antibiotic, by changing dyes that selectively stained Treponema pallidum — the spirochaete that causes syphilis — into compounds that selectively killed the pathogen.[194] 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.[195]

Robert Koch, a pioneer in medical microbiology, worked on disease, and these postulates are still used today.[192]

fermentation process, 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.[190]

Christian Gottfried Ehrenberg introduced the word "bacterium" in 1828.[187] In fact, his Bacterium was a genus that contained non-spore-forming rod-shaped bacteria,[188] as opposed to Bacillus, a genus of spore-forming rod-shaped bacteria defined by Ehrenberg in 1835.[189]

Bacteria were first observed by the Dutch microscopist animalcules" (spermatozoa) — taken seriously.

Antonie van Leeuwenhoek, the first microbiologist and the first person to observe bacteria using a microscope.

History of bacteriology

[181][180].antibodies, or growth factors, insulin bacteria for the production of therapeutic proteins, such as bioengineer This understanding of bacterial metabolism and genetics allows the use of biotechnology to [179][178] 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

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.[174] 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.[175][176]

The ability of bacteria to degrade a variety of organic compounds is remarkable and has been used in waste processing and bioremediation. Bacteria capable of digesting the hydrocarbons in petroleum are often used to clean up oil spills.[171] 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 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.[172] In the chemical industry, bacteria are most important in the production of enantiomerically pure chemicals for use as pharmaceuticals or agrichemicals.[173]

Bacteria, often lactic acid bacteria, such as Lactobacillus and Lactococcus, 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 yogurt.[169][170]

Significance in technology and industry

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.[167] 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.[168] Infections can be prevented by antiseptic measures such as sterilizing 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.

Overview of bacterial infections and main species involved.[165][166]

Each species of pathogen has a characteristic spectrum of interactions with its human 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.[162] 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.[163][164]

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.

Pathogens

Color-enhanced scanning electron micrograph showing Salmonella typhimurium (red) invading cultured human cells

In soil, microorganisms that reside in the gut flora of the intestines can contribute to gut immunity, synthesise vitamins, such as folic acid, vitamin K and biotin, convert sugars to lactic acid (see Lactobacillus), as well as fermenting complex undigestible carbohydrates.[157][158][159] 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.[160]

Certain bacteria form close spatial associations that are essential for their survival. One such mutualistic association, called interspecies hydrogen transfer, occurs between clusters of butyric acid or propionic acid, and produce hydrogen, and methanogenic Archaea that consume hydrogen.[155] 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 hydrogen-consuming Archaea keeps the hydrogen concentration low enough to allow the bacteria to grow.

Mutualists

[154] Several

Motile bacteria are attracted or repelled by certain stimuli in behaviors called taxes: these include chemotaxis, phototaxis, energy taxis, and magnetotaxis.[132][133][134] In one peculiar group, the myxobacteria, individual bacteria move together to form waves of cells that then differentiate to form fruiting bodies containing spores.[40] The myxobacteria move only when on solid surfaces, unlike E. coli, which is motile in liquid or solid media.

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-dimensional random walk.[131] (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.[126]

This motor drives the motion of the filament, which acts as a propeller. [130] across the membrane for power.electrochemical gradient The flagellum is a rotating structure driven by a reversible motor at the base that uses the [126] Bacterial species differ in the number and arrangement of flagella on their surface; some have a single flagellum (

Flagella are semi-rigid cylindrical structures that are rotated and function much like the propeller on a ship. Objects as small as bacteria operate a low Reynolds number and cylindrical forms are more efficient than the flat, paddle-like, forms appropriate at human-size scale.[129]

"Our observations redefine twitching motility as a rapid, highly organized mechanism of bacterial translocation by which Pseudomonas aeruginosa can disperse itself over large areas to colonize new territories. It is also now clear, both morphologically and genetically, that twitching motility and social gliding motility, such as occurs in Myxococcus xanthus, are essentially the same process."
— " – Semmler, Whitchurch & Mattick (1999)Pseudomonas aeruginosa"A re-examination of twitching motility in
[128]).pN as a grappling hook, repeatedly extending it, anchoring it and then retracting it with remarkable force (>80 type IV piliIn bacterial gliding and twitching motility, bacteria use their

Swimming bacteria frequently move near 10 body lengths per second and a few as fast as 100. This makes them at least as fast as fish, on a relative scale.[127]

Flagellum of Gram-negative bacteria. The base drives the rotation of the hook and filament.

Many bacteria can move using a variety of mechanisms: flagella are used for swimming through fluids; bacterial gliding and twitching motility move bacteria across surfaces; and changes of buoyancy allow vertical motion.[126]

Movement

Quorum sensing allows bacteria to coordinate gene expression, and enables them to produce, release and detect autoinducers or pheromones which accumulate with the growth in cell population.[125]

One type of inter-cellular communication by a molecular signal is called quorum sensing, which serves the purpose of determining whether there is a local population density that is sufficiently high that it is productive to invest in processes that are only successful if large numbers of similar organisms behave similarly, as in excreting digestive enzymes or emitting light.

The communal benefits of multicellular cooperation include a cellular division of labor, accessing resources that cannot effectively be utilized by single cells, collectively defending against antagonists, and optimizing population survival by differentiating into distinct cell types.[123] For example, bacteria in biofilms can have more than 500 times increased resistance to antibacterial agents than individual "planktonic" bacteria of the same species.[124]

Bacteria often function as multicellular aggregates known as biofilms, exchanging a variety of molecular signals for inter-cell communication, and engaging in coordinated multicellular behavior.[123][124]

Multicellularity

A few bacteria have chemical systems that generate light. This bioluminescence often occurs in bacteria that live in association with fish, and the light probably serves to attract fish or other large animals.[122]

Bioluminescence

Bacteria frequently secrete chemicals into their environment in order to modify it favorably. The secretions are often proteins and may act as enzymes that digest some form of food in the environment.

Secretion

Behavior

Bacteriophages are viruses that infect bacteria. 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 bacterium into a lethal pathogen.[118] Bacteria resist phage infection through restriction modification systems that degrade foreign DNA,[119] 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.[120][121] This CRISPR system provides bacteria with acquired immunity to infection.

Bacteriophages

In ordinary circumstances, transduction, conjugation, and transformation involve transfer of DNA between individual bacteria of the same species, but occasionally transfer may occur between individuals of different bacterial species and this may have significant consequences, such as the transfer of antibiotic resistance.[115] In such cases, gene acquisition from other bacteria or the environment is called horizontal gene transfer and may be common under natural conditions.[116] Gene transfer is particularly important in antibiotic resistance as it allows the rapid transfer of resistance genes between different pathogens.[117]

Transformation, unlike transduction or conjugation, depends on numerous bacterial gene products that specifically interact to perform this complex process,[109] and thus transformation is clearly a bacterial adaptation for DNA transfer. In order for a bacterium to bind, take up and recombine donor DNA into its own chromosome, it must first enter a special physiological state termed competence (see Natural competence). In Bacillus subtilis, about 40 genes are required for the development of competence.[110] The length of DNA transferred during B. subtilis transformation can be between a third of a chromosome up to the whole chromosome.[111][112] Transformation appears to be common among bacterial species, and thus far at least 60 species are known to have the natural ability to become competent for transformation.[113] The development of competence in nature is usually associated with stressful environmental conditions, and seems to be an adaptation for facilitating repair of DNA damage in recipient cells.[114]

Transduction of bacterial genes by bacteriophage appears to be a consequence of infrequent errors during intracellular assembly of virus particles, rather than a bacterial adaptation. Conjugation, in the much-studied E. coli system is determined by plasmid genes, and is an adaptation for transferring copies of the plasmid from one bacterial host to another. It is seldom that a conjugative plasmid integrates into the host bacterial chromosome, and subsequently transfers part of the host bacterial DNA to another bacterium. Plasmid-mediated transfer of host bacterial DNA also appears to be an accidental process rather than a bacterial adaptation.

Some bacteria also transfer genetic material between cells. This can occur in three main ways. First, 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 conjugation, whereby DNA is transferred through direct cell contact.

DNA transfer

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.[107] 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.[108]

Bacteria may also contain plasmids, which are small extra-chromosomal DNAs that may contain genes for antibiotic resistance or virulence factors. Plasmids replicate independently of chromosomes, so it is possible that plasmids could be lost in bacterial cell division. Against this possibility is the fact that a single bacterium can contain hundreds of copies of a single plasmid.[106]

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,[102] to 12,200,000 base pairs in the soil-dwelling bacteria Sorangium cellulosum.[103] 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.[104] 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 rarer than in eukaryotes.[105]

Genetics

Bacterial growth follows four 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.[100] The second phase of growth is the log phase, also known as the logarithmic or 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 third 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.[101] The final phase is the death phase where the bacteria run out of nutrients and die.

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 nutrient limitation has led the evolution of different growth strategies (see syntrophy).[99]

[96] In the laboratory, bacteria are usually grown using solid or liquid media. Solid

A colony of Escherichia coli[95]

Bacteria are further divided into 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, wherein the electrons taken from the reduced substrates are transferred to oxidised intermediates to generate reduced fermentation products (e.g., binary fission Unlike in multicellular organisms, increases in cell size (

Many bacteria reproduce through binary fission, which is compared to mitosis and meiosis in this image.

Growth and reproduction

Regardless of the type of metabolic process they employ, the majority of bacteria are able to take in raw materials only in the form of relatively small molecules, which enter the cell by diffusion or through molecular channels in cell membranes. The Planctomycetes are the exception (as they are in possessing membranes around their nuclear material). It has recently been shown that Gemmata obscuriglobus is able to take in large molecules via a process that in some ways resembles endocytosis, the process used by eukaryotic cells to engulf external items.[26][92]

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.[91]

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. In unusual circumstances, the gas methane can be used by methanotrophic bacteria as both a source of electrons and a substrate for carbon anabolism.[90] In both aerobic phototrophy and chemolithotrophy, oxygen is used as a terminal electron acceptor, whereas under anaerobic conditions inorganic compounds are used instead. Most lithotrophic organisms are autotrophic, whereas organotrophic organisms are heterotrophic.

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.[89] 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.

[88][87], a form of asexual reproduction.[93] Under optimal conditions, bacteria can grow and divide extremely rapidly, and bacterial populations can double as quickly as every 9.8 minutes.[94] 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.

Carbon metabolism in bacteria is either autotrophic, meaning that cellular carbon is obtained by fixing carbon dioxide. Heterotrophic bacteria include parasitic types. Typical autotrophic bacteria are phototrophic cyanobacteria, green sulfur-bacteria and some purple bacteria, but also many chemolithotrophic species, such as nitrifying or sulfur-oxidising bacteria.[86] Energy metabolism of bacteria is either based on phototrophy, the use of light through photosynthesis, or based 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).

Nutritional types in bacterial metabolism
Nutritional type Source of energy Source of carbon Examples
 Phototrophs  Sunlight  Organic compounds (photoheterotrophs) or carbon fixation (photoautotrophs)  Cyanobacteria, Green sulfur bacteria, Chloroflexi, or Purple bacteria 
 Lithotrophs Inorganic compounds  Organic compounds (lithoheterotrophs) or carbon fixation (lithoautotrophs)  Thermodesulfobacteria, Hydrogenophilaceae, or Nitrospirae 
 Organotrophs Organic compounds  Organic compounds (chemoheterotrophs) or carbon fixation (chemoautotrophs)    Bacillus, Clostridium or Enterobacteriaceae 

Bacteria exhibit an extremely wide variety of electron acceptors used for aerobic or anaerobic respiration.[85]

Metabolism

[82].tetanus endospores causes Clostridium tetani endospores, and contamination of deep puncture wounds with Bacillus anthracis can be contracted by the inhalation of anthrax Endospore-forming bacteria can also cause disease: for example, [81] According to scientist Dr. Steinn Sigurdsson, "There are viable bacterial spores that have been found that are 40 million years old on Earth — and we know they're very hardened to radiation."[80] and radiation in space.vacuum and endospores even allow bacteria to survive exposure to the [79][78]