View source for Bacteria

{{Taxobox
| color = lightgrey
| name = Bacteria
| fossil_range = [[Archean]] or earlier - Recent
| image = EscherichiaColi NIAID.jpg
| image_width = 210px
| image_caption = ''[[Escherichia coli]]'' cells magnified 25,000 times
| domain = '''Bacteria'''
| subdivision_ranks = Phyla
| subdivision =
[[Acidobacteria]]<br />
[[Actinobacteria]]<br />
[[Aquificae]]<br />
[[Bacteroidetes]]<br />
[[Chlamydiae]]<br />
[[Chlorobi]]<br />
[[Chloroflexi]]<br />
[[Chrysiogenetes]]<br />
[[Cyanobacteria]]<br />
[[Deferribacteraceae|Deferribacteres]]<br />
[[Deinococcus-Thermus]]<br />
[[Dictyoglomi]]<br />
[[Fibrobacteres]]<br />
[[Firmicutes]]<br />
[[Fusobacteria]]<br />
[[Gemmatimonadetes]]<br />
[[Nitrospirae]]<br />
[[Planctomycetes]]<br />
[[Proteobacteria]]<br />
[[Spirochaete]]s<br />
[[Thermodesulfobacteria]]<br />
[[Thermomicrobia]]<br />
[[Thermotogae]]<br />
[[Verrucomicrobia]]
}}

{{SI}}

{{CMG}}

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'''Bacteria''' (singular: '''bacterium''') are unicellular [[microorganism]]s. Typically a few [[micrometre]]s in length, bacteria have a wide range of shapes, ranging from spheres to rods to spirals. Bacteria are ubiquitous in every habitat on Earth, growing in soil, Hot spring|acidic hot springs, radioactive waste,<ref>{{cite journal |author=Fredrickson J, Zachara J, Balkwill D, ''et al'' |title=Geomicrobiology of high-level nuclear waste-contaminated vadose sediments at the Hanford site, Washington state | url=http://aem.asm.org/cgi/content/full/70/7/4230?view=long&pmid=15240306 |journal=Appl Environ Microbiol |volume=70 |issue=7 |pages=4230&ndash;41 |year=2004 |pmid=15240306}}</ref> seawater, and deep in the Earth's crust. There are typically 40 million bacterial [[cell (biology)|cells]] in a gram of soil and a million bacterial cells in a millilitre of fresh water; in all, there are approximately five [[Names of large numbers#The "standard dictionary numbers"|nonillion]] (5×10<sup>30</sup>) bacteria on Earth,<ref>{{cite journal |author=Whitman W, Coleman D, Wiebe W |title=Prokaryotes: the unseen majority | url=http://www.pnas.org/cgi/content/full/95/12/6578 |journal=Proc Natl Acad Sci U S A |volume=95 |issue=12 |pages=6578&ndash;83 |year=1998|pmid = 9618454}}</ref> forming much of the world's [[biomass (ecology)|biomass]].<ref>{{cite journal |author=Whitman W, Coleman D, Wiebe W |title=Prokaryotes: the unseen majority |url=http://www.pnas.org/cgi/content/full/95/12/6578 |journal=Proc Natl Acad Sci U S A |volume=95 |issue=12 |pages=6578–83 |year=1998|pmid=9618454}}</ref> Bacteria are vital in recycling nutrients, and many important steps in [[nutrient cycle]]s depend on bacteria, such as the [[nitrogen fixation|fixation of nitrogen]] from the [[Earth's atmosphere|atmosphere]]. However, most of these bacteria have not been characterized, and only about half of the [[phylum|phyla]] of bacteria have species that can be [[microbiological culture|cultured]] in the [[laboratory]].<ref name=Rappe>{{cite journal |author=Rappé MS, Giovannoni SJ |title=The uncultured microbial majority |journal=Annu. Rev. Microbiol. |volume=57 |issue= |pages=369-94 |year=2003 |pmid=14527284 |doi=10.1146/annurev.micro.57.030502.090759}}</ref> 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 [[gastrointestinal tract|digestive tract]].<ref>{{cite journal |author=Sears CL |title=A dynamic partnership: celebrating our gut flora |journal=Anaerobe |volume=11 |issue=5 |pages=247-51 |year=2005 |pmid=16701579 |doi=10.1016/j.anaerobe.2005.05.001}}</ref> Although the vast majority of these bacteria are rendered harmless by the protective effects of the [[immune system]], and a few are [[probiotic|beneficial]], some are [[pathogenic bacteria]] and cause [[infectious disease]]s, including [[cholera]], [[syphilis]], [[anthrax]], [[leprosy]] and [[bubonic plague]]. The most common fatal bacterial diseases are [[respiratory infection]]s, with [[tuberculosis]] alone killing about 2 million people a year, mostly in [[sub-Saharan Africa]].<ref>{{cite web  | url = http://www.who.int/healthinfo/bodgbd2002revised/en/index.html | title = 2002 WHO mortality data | accessdate = 2007-01-20}}</ref> In [[developed country|developed countries]], [[antibiotic]]s 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]], and the manufacture of antibiotics and other chemicals.<ref>{{cite journal |author=Ishige T, Honda K, Shimizu S |title=Whole organism biocatalysis |journal=Curr Opin Chem Biol |volume=9 |issue=2 |pages=174&ndash;80 |year=2005 |pmid=15811802}}</ref>

Bacteria are [[prokaryote]]s. Unlike cells of animals and other [[eukaryote]]s, bacterial cells do not contain a [[cell nucleus|nucleus]] and rarely harbour [[cell membrane|membrane-bound]] [[organelle]]s. 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 [[evolution|evolved]] independently from an ancient common ancestor. These [[domain (biology)|evolutionary domains]] are called Bacteria and [[Archaea]].<ref>{{cite journal |author=Woese C, Kandler O, Wheelis M |title=Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya| url=http://www.pnas.org/cgi/reprint/87/12/4576 |journal=Proc Natl Acad Sci U S A |volume=87 |issue=12 |pages=4576&ndash;9 |year=1990 |pmid=2112744}}</ref>

==History of bacteriology==
{{see|Microbiology}}

[[Image:Antoni van Leeuwenhoek.png|thumb|240px|left|[[Antonie van Leeuwenhoek]], the first [[microbiologist]] and the first person to observe bacteria using a [[microscope]].]]

Bacteria were first observed by [[Antonie van Leeuwenhoek]] in 1676, using a single-lens [[microscope]] of his own design.<ref>{{cite journal |author=Porter JR |title=Antony van Leeuwenhoek: Tercentenary of his discovery of bacteria |journal=Bacteriological reviews |volume=40 |issue=2 |pages=260-269 |year=1976 |pmid=786250 |url = http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=413956 | accessdate = 2007-08-19}}</ref> He called them "animalcules" and published his observations in a series of letters to the [[Royal Society]].<ref>{{cite journal |author=van Leeuwenhoek A |title=An abstract of a letter from Mr. Anthony Leevvenhoek at Delft, dated Sep. 17, 1683, Containing Some Microscopical Observations, about Animals in the Scurf of the Teeth, the Substance Call'd Worms in the Nose, the Cuticula Consisting of Scales| url=http://www.journals.royalsoc.ac.uk/content/120136/?k=Sep.+17%2c+1683 |journal=Philosophical Transactions (1683–1775) |volume=14 |pages=568-574 |year=1684| accessdate = 2007-08-19}}</ref><ref>{{cite journal |author=van Leeuwenhoek A |title=Part of a Letter from Mr Antony van Leeuwenhoek, concerning the Worms in Sheeps Livers, Gnats, and Animalcula in the Excrements of Frogs | url=http://www.journals.royalsoc.ac.uk/link.asp?id=4j53731651310230 |journal=Philosophical Transactions (1683–1775) |volume=22 |pages=509-518 |year=1700| accessdate = 2007-08-19}}</ref><ref>{{cite journal |author=van Leeuwenhoek A |title=Part of a Letter from Mr Antony van Leeuwenhoek, F. R. S. concerning Green Weeds Growing in Water, and Some Animalcula Found about Them | url=http://www.journals.royalsoc.ac.uk/link.asp?id=fl73121jk4150280 |journal=Philosophical Transactions (1683-1775) |volume=23 |pages=1304–11|year = 1702| accessdate = 2007-08-19}}</ref> The name ''bacterium'' was introduced much later, by [[Christian Gottfried Ehrenberg]] in 1838, and is derived from the [[List of Greek words with English derivatives|Greek word]] βακτήριον -α , ''bacterion -a'' , meaning "small staff".<ref>{{cite web | url = http://www.etymonline.com/index.php?term=bacteria | title = Etymology of the word "bacteria" | work = Online Etymology dictionary | accessdate = 2006-11-23}}</ref>

[[Louis Pasteur]] demonstrated in 1859 that the [[fermentation (food)|fermentation]] process is caused by the growth of microorganisms, and that this growth is not due to [[spontaneous generation]]. ([[Yeast]]s and [[mold]]s, commonly associated with fermentation, are not bacteria, but rather [[fungus|fungi]].) Along with his contemporary, [[Robert Koch]], Pasteur was an early advocate of the [[germ theory of disease]].<ref>{{cite web | url = http://biotech.law.lsu.edu/cphl/history/articles/pasteur.htm#paperII | title = Pasteur's Papers on the Germ Theory | publisher = LSU Law Center's Medical and Public Health Law Site, Historic Public Health Articles | accessdate = 2006-11-23}}</ref>
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 Physiology or Medicine|Nobel Prize]] in 1905.<ref>{{cite web | url = http://nobelprize.org/nobel_prizes/medicine/laureates/1905/ | title = The Nobel Prize in Physiology or Medicine 1905 | publisher =  Nobelprize.org | accessdate = 2006-11-22}}</ref> 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.<ref>{{cite journal |author=O'Brien S, Goedert J |title=HIV causes AIDS: Koch's postulates fulfilled |journal=Curr Opin Immunol |volume=8 |issue=5 |pages=613-618 |year=1996 |pmid=8902385}}</ref>

Though it was known in the nineteenth century that bacteria are the cause of many diseases, no effective [[antiseptic|antibacterial]] treatments were available.<ref>{{cite journal |author=Thurston A |title=Of blood, inflammation and gunshot wounds: the history of the control of sepsis |journal=Aust N Z J Surg |volume=70 |issue=12 |pages=855-61 |year=2000 |pmid=11167573}}</ref> 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.<ref>{{cite journal |author=Schwartz R |title=Paul Ehrlich's magic bullets |journal=N Engl J Med |volume=350 |issue=11 |pages=1079–80 |year=2004|id = PMID 15014180}}</ref> 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]].<ref>{{cite web | url = http://nobelprize.org/nobel_prizes/medicine/laureates/1908/ehrlich-bio.html | title = Biography of Paul Ehrlich | publisher =  Nobelprize.org | accessdate = 2006-11-26}}</ref>

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.<ref>{{cite journal |author=Woese C, Fox G |title=Phylogenetic structure of the prokaryotic domain: the primary kingdoms |journal=Proc Natl Acad Sci U S A |volume=74 |issue=11 |pages=5088-5090 |year=1977|id = PMID 270744}}</ref> This new [[phylogenetic]] [[taxonomy]] was based on the [[sequencing]] of [[16S ribosomal RNA]], and divided prokaryotes into two evolutionary domains, as part of the [[three-domain system]].<ref name=Woese>{{cite journal |author=Woese C, Kandler O, Wheelis M |title=Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya | url=http://www.pnas.org/cgi/reprint/87/12/4576 |journal=Proc Natl Acad Sci U S A |volume=87 |issue=12 |pages=4576-4579 |year=1990 |pmid=2112744}}</ref>

==Origin and early evolution==
{{further|[[Timeline of evolution]]}}

The ancestors of modern bacteria were single-celled microorganisms that were the [[Abiogenesis|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.<ref>{{cite journal |author=Schopf J |title=Disparate rates, differing fates: tempo and mode of evolution changed from the Precambrian to the Phanerozoic | url=http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=44277&blobtype=pdf |journal=Proc Natl Acad Sci U S A |volume=91 |issue=15 |pages=6735–42 |year=1994 |pmid=8041691}}</ref><ref>{{cite journal |author=DeLong E, Pace N |title=Environmental diversity of bacteria and archaea |journal=Syst Biol |volume=50 |issue=4 |pages=470–78 |year=2001|id = PMID 12116647}}</ref> Although bacterial [[fossil]]s exist, such as [[stromatolite]]s, their lack of distinctive [[morphology (biology)|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 [[phylogenetics|phylogeny]], and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage.<ref>{{cite journal |author=Brown JR, Doolittle WF |title=Archaea and the prokaryote-to-eukaryote transition |journal=Microbiol. Mol. Biol. Rev. |volume=61 |issue=4 |pages=456-502 |year=1997 |pmid=9409149 |url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9409149}}</ref> The [[most recent common ancestor]] of bacteria and archaea was probably a [[thermophile|hyperthermophile]] that lived about 2.5 billion–3.2 billion years ago.<ref>{{cite journal |author=Di Giulio M |title=The universal ancestor and the ancestor of bacteria were hyperthermophiles |journal=J Mol Evol |volume=57 |issue=6 |pages=721–30 |year=2003 |pmid=14745541}}</ref><ref>{{cite journal |author=Battistuzzi F, Feijao A, Hedges S |title=A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. | url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15535883 |journal=BMC Evol Biol |volume=4 |issue=|pages=44 |year=|pmid=15535883}}</ref>

Bacteria were also involved in the second great evolutionary divergence, that of the archaea and eukaryotes. Here, eukaryotes resulted from ancient bacteria entering into [[endosymbiont|endosymbiotic]] associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea.<ref>{{cite journal |author=Poole A, Penny D |title=Evaluating hypotheses for the origin of eukaryotes |journal=Bioessays |volume=29 |issue=1 |pages=74–84 |year=2007 |pmid=17187354}}</ref><ref name=Dyall>{{cite journal |author=Dyall S, Brown M, Johnson P |title=Ancient invasions: from endosymbionts to organelles |journal=Science |volume=304 |issue=5668 |pages=253&ndash;7 |year=2004 |pmid=15073369}}</ref> This involved the engulfment by proto-eukaryotic cells of alpha-proteobacterial symbionts to form either [[mitochondrion|mitochondria]] or [[hydrogenosome]]s, 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 [[chloroplast]]s 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.<ref>{{cite journal |author=Lang B, Gray M, Burger G |title=Mitochondrial genome evolution and the origin of eukaryotes |journal=Annu Rev Genet |volume=33 |issue= |pages=351-97 |year= |pmid=10690412}}</ref><ref>{{cite journal |author=McFadden G |title=Endosymbiosis and evolution of the plant cell |journal=Curr Opin Plant Biol |volume=2 |issue=6 |pages=513-9 |year=1999 |pmid=10607659}}</ref>

==Morphology==
[[Image:Bacterial morphology diagram.svg|left|thumb|360px|Bacteria display a large diversity of cell [[morphology (biology)|morphologies]] and arrangements]]

Bacteria display a wide diversity of shapes and sizes, called ''[[morphology (biology)|morphologies]]''. Bacterial cells are about one tenth the size of eukaryotic cells and are typically 0.5–5.0&nbsp;[[micrometre]]s in length. However, a few species–for example ''[[Thiomargarita namibiensis]]'' and ''[[Epulopiscium fishelsoni]]''–are up to half a [[millimetre]] long and are visible to the unaided eye.<ref>{{cite journal |author=Schulz H, Jorgensen B |title=Big bacteria |journal=Annu Rev Microbiol |volume=55 |issue=|pages=105&ndash;37 |year=|pmid=11544351}}</ref> Among the smallest bacteria are members of the genus ''[[Mycoplasma]]'', which measure only 0.3&nbsp;micrometres, as small as the largest [[virus]]es.<ref>{{cite journal |author=Robertson J, Gomersall M, Gill P. |title=Mycoplasma hominis: growth, reproduction, and isolation of small viable cells |journal=J Bacteriol. |volume=124 |issue=2 |pages=1007&ndash;18 |year=1975 |pmid=1102522}}</ref>

Most bacterial species are either spherical, called [[coccus|cocci]] (''sing''. coccus, from Greek ''kókkos'', grain, seed) or rod-shaped, called [[bacillus|bacilli]] (''sing''. bacillus, from [[Latin]] ''baculus'', stick). Some rod-shaped bacteria, called [[vibrio]], are slightly curved or comma-shaped; others, can be spiral-shaped, called [[spirillum|spirilla]], or tightly coiled, called [[spirochaete]]s. A small number of species even have tetrahedral or cuboidal shapes.<ref>{{cite journal |author=Fritz I, Strömpl C, Abraham W |title=Phylogenetic relationships of the genera Stella, Labrys and Angulomicrobium within the 'Alphaproteobacteria' and description of Angulomicrobium amanitiforme sp. nov | url=http://ijs.sgmjournals.org/cgi/content/full/54/3/651 |journal=Int J Syst Evol Microbiol |volume=54 |issue=Pt 3 |pages=651-7 |year=2004|id = PMID 15143003}}</ref> 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 [[predation|predators]].<ref>{{cite journal |author=Cabeen M, Jacobs-Wagner C |title=Bacterial cell shape |journal=Nat Rev Microbiol |volume=3 |issue=8 |pages=601&ndash;10 |year=2005 |pmid=16012516}}</ref><ref>{{cite journal |author=Young K |title=The selective value of bacterial shape |journal=Microbiol Mol Biol Rev |volume=70 |issue=3 |pages=660&ndash;703 |year=2006 |pmid=16959965}}</ref>

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 [[Mycelium|mycelia]].<ref>{{cite journal |author=Douwes K, Schmalzbauer E, Linde H, Reisberger E, Fleischer K, Lehn N, Landthaler M, Vogt T |title=Branched filaments no fungus, ovoid bodies no bacteria: Two unusual cases of mycetoma |journal=J Am Acad Dermatol |volume=49 |issue=2 Suppl Case Reports |pages=S170&ndash;3 |year=2003 |pmid=12894113}}</ref>

[[Image:Relative scale.svg|thumb|310px|left|The range of sizes shown by [[prokaryote]]s, relative to those of other organisms and [[biomolecule]]s]]

Bacteria often attach to surfaces and form dense aggregations called [[biofilm]]s or [[bacterial mat]]s. 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, [[protist]]s 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.<ref>{{cite journal |author=Donlan R |title=Biofilms: microbial life on surfaces |journal=Emerg Infect Dis |volume=8 |issue=9 |pages=881–90 |year=2002 |pmid=12194761}}</ref><ref>{{cite journal |author=Branda S, Vik S, Friedman L, Kolter R |title=Biofilms: the matrix revisited |journal=Trends Microbiol |volume=13 |issue=1 |pages=20–26 |year=2005 |pmid=15639628}}</ref> In natural environments, such as soil or the surfaces of plants, the majority of bacteria are bound to surfaces in biofilms.<ref name=Davey>{{cite journal |author=Davey M, O'toole G |title=Microbial biofilms: from ecology to molecular genetics |journal=Microbiol Mol Biol Rev |volume=64 |issue=4 |pages=847–67 |year=2000|id = PMID 11104821}}</ref> Biofilms are also important for chronic bacterial infections and infections of [[implant (medicine)|implanted]] medical devices, as bacteria protected within these structures are much harder to kill than individual bacteria.<ref>{{cite journal |author=Donlan RM, Costerton JW |title=Biofilms: survival mechanisms of clinically relevant microorganisms |journal=Clin Microbiol Rev |volume=15 |issue=2 |pages=167–93 |year=2002 |pmid=11932229}}</ref>

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&nbsp;micrometres long and containing approximately 100,000 bacterial cells.<ref>{{cite journal |author=Shimkets L |title=Intercellular signaling during fruiting-body development of Myxococcus xanthus. |journal=Annu Rev Microbiol |volume=53 |issue=|pages=525–49 | year =|id = PMID 10547700}}</ref> In these fruiting bodies, the bacteria perform separate tasks; this type of cooperation is a simple type of [[multicellular organism|multicellular]] organisation. For example, about one in 10 cells migrate to the top of these fruiting bodies and [[cellular differentiation|differentiate]] into a specialised dormant state called myxospores, which are more resistant to desiccation and other adverse environmental conditions than are ordinary cells.<ref>{{cite journal |author=Kaiser D |title=Signaling in myxobacteria |journal=Annu Rev Microbiol |volume=58 |issue=|pages=75–98 |year=|pmid=15487930}}</ref>

==Cellular structure ==
{{further|[[Bacterial cell structure]]}}

[[Image:Average prokaryote cell- en.svg|thumb|320px|left|Diagram of the cellular structure of a typical bacterial cell]]

===Intracellular structures===
The bacterial cell is surrounded by a [[lipid]] membrane, or [[cell membrane]], which encompasses the contents of the cell and acts as a barrier to hold nutrients, [[protein]]s and other essential components of the [[cytoplasm]] within the cell. As they are [[prokaryote]]s, bacteria do not tend to have membrane-bound [[organelle]]s in their cytoplasm and thus contain few intracellular structures. They consequently lack a [[cell nucleus|nucleus]], [[mitochondrion|mitochondria]], [[chloroplast]]s and the other organelles present in eukaryotic cells, such as the [[Golgi apparatus]] and [[endoplasmic reticulum]].<ref name=Stryer>{{cite book | author = Berg JM, Tymoczko JL Stryer L | title = Molecular Cell Biology | edition = 5th ed. | publisher = WH Freeman | year = 2002 | isbn = 0-7167-4955-6}}</ref> However, recent research is identifying increasing amounts of structural complexity in bacteria, such as the discovery of the [[prokaryotic cytoskeleton]].<ref>{{cite journal |author=Gitai Z |title=The new bacterial cell biology: moving parts and subcellular architecture |journal=Cell |volume=120 |issue=5 |pages=577–86 |year=2005 |pmid=15766522}}</ref><ref>{{cite journal |author=Shih YL, Rothfield L |title=The bacterial cytoskeleton |journal=Microbiol. Mol. Biol. Rev. |volume=70 |issue=3 |pages=729–54 |year=2006 |pmid=16959967 |url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16959967}}</ref>

Many important [[biochemistry|biochemical]] reactions, such as [[Energy#Biology|energy]] generation, occur due to [[diffusion|concentration gradient]]s across membranes, creating a potential difference analogous to a [[battery (electricity)|battery]]. The absence of internal membranes in bacteria means these reactions, such as [[electron transport chain|electron transport]], occur across the cell membrane, between the cytoplasm and the [[periplasmic space]].<ref>{{cite journal |author=Harold F |title=Conservation and transformation of energy by bacterial membranes | url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=4261111 |journal=Bacteriol Rev |volume=36 |issue=2 |pages=172–230 |year=1972 |pmid=4261111}}</ref>  Additionally, while some transporter proteins consume chemical energy, others harness concentration gradients to import nutrients across the cell membrane or to expel undesired molecules from the cytoplasm.

Bacteria do not have a membrane-bound nucleus, and their [[gene]]tic material is typically a single circular [[chromosome]] located in the cytoplasm in an irregularly shaped body called the [[nucleoid]].<ref>{{cite journal |author=Thanbichler M, Wang S, Shapiro L |title=The bacterial nucleoid: a highly organized and dynamic structure |journal=J Cell Biochem |volume=96 |issue=3 |pages=506–21 |year=2005 |pmid=15988757}}</ref> The nucleoid contains the chromosome with associated proteins and [[RNA]]. Like all living organisms, bacteria contain [[ribosome]]s for the production of proteins, but the structure of the bacterial ribosome is different from those of [[eukaryote]]s and [[Archaea]].<ref>{{cite journal |author=Poehlsgaard J, Douthwaite S |title=The bacterial ribosome as a target for antibiotics |journal=Nat Rev Microbiol |volume=3 |issue=11 |pages=870–81 |year=2005|id = PMID 16261170}}</ref> The order [[Planctomycetes]] are an exception to the general absence of internal membranes in bacteria, because they have a membrane around their nucleoid and contain other membrane-bound cellular structures.<ref>{{cite journal |author=Fuerst J |title=Intracellular compartmentation in planctomycetes |journal=Annu Rev Microbiol |volume=59 |pages=299–328 |year=2005 |pmid=15910279}}</ref>

Some bacteria produce intracellular nutrient storage granules, such as [[glycogen]],<ref>{{cite journal |author=Yeo M, Chater K |title=The interplay of glycogen metabolism and differentiation provides an insight into the developmental biology of Streptomyces coelicolor | url=http://mic.sgmjournals.org/cgi/content/full/151/3/855?view=long&pmid=15758231 |journal=Microbiology |volume=151 |issue=Pt 3 |pages=855–61 |year=2005 |pmid=15758231}}</ref> [[polyphosphate]],<ref>{{cite journal |author=Shiba T, Tsutsumi K, Ishige K, Noguchi T |title=Inorganic polyphosphate and polyphosphate kinase: their novel biological functions and applications | url=http://protein.bio.msu.ru/biokhimiya/contents/v65/full/65030375.html |journal=Biochemistry (Mosc) |volume=65 |issue=3 |pages=315–23 |year=2000 |pmid=10739474}}</ref> [[sulfur]]<ref>{{cite journal |author=Brune DC. |title=Isolation and characterization of sulfur globule proteins from Chromatium vinosum and Thiocapsa roseopersicina | url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=7575095&dopt=Abstract   |journal=Arch Microbiol |volume=163 |issue=6 |pages=391–99 |year=1995 |pmid=7575095}}</ref> or [[polyhydroxyalkanoates]].<ref>{{cite journal |author=Kadouri D, Jurkevitch E, Okon Y, Castro-Sowinski S. |title=Ecological and agricultural significance of bacterial polyhydroxyalkanoates | url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15986831&query_hl=13&itool=pubmed_DocSum |journal=Crit Rev Microbiol |volume=31 |issue=2 |pages=55–67 |year=2005|pmid = 15986831}}</ref> These granules enable bacteria to store compounds for later use. Certain bacterial species, such as the [[Photosynthesis#Bacterial variations|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.<ref>{{cite journal |author=Walsby A |title=Gas vesicles | url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=8177173 |journal=Microbiol Rev |volume=58 |issue=1 |pages=94–144 |year=1994 |pmid=8177173}}</ref>

===Extracellular structures===
{{further|[[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 [[peptide]]s containing D-[[amino acid]]s.<ref>{{cite journal |author=van Heijenoort J |title=Formation of the glycan chains in the synthesis of bacterial peptidoglycan | url=http://glycob.oxfordjournals.org/cgi/content/full/11/3/25R |journal=Glycobiology |volume=11 |issue=3 |pages=25R&ndash;36R |year=2001 |pmid=11320055}}</ref> Bacterial cell walls are different from the cell walls of [[plant]]s and [[fungus|fungi]], which are made of [[cellulose]] and [[chitin]], respectively.<ref name=Koch>{{cite journal |author=Koch A |title=Bacterial wall as target for attack: past, present, and future research | url=http://cmr.asm.org/cgi/content/full/16/4/673?view=long&pmid=14557293 |journal=Clin Microbiol Rev |volume=16 |issue=4 |pages=673&ndash;87 |year=2003|id = PMID 14557293}}</ref> 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.<ref name=Koch/>

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.<ref name=Gram>{{cite journal | last = Gram | first =  HC | authorlink = Hans Christian Gram |year=1884 |title=Über die isolierte Färbung der Schizomyceten in Schnitt- und Trockenpräparaten |journal=Fortschr. Med. |volume=2 |pages=185&ndash;189 }}</ref>

Gram-positive bacteria possess a thick cell wall containing many layers of peptidoglycan and [[teichoic acid]]s. 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 [[lipopolysaccharide]]s and [[lipoprotein]]s. 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.<ref>{{cite journal |author=Hugenholtz P |title=Exploring prokaryotic diversity in the genomic era | url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=11864374 |journal=Genome Biol |volume=3 |issue=2 |pages=REVIEWS0003 |year=2002|id = PMID 11864374}}</ref> 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 [[pathogen]]s, such as ''[[Haemophilus influenzae]]'' or ''[[Pseudomonas aeruginosa]]''.<ref>{{cite journal |author=Walsh F, Amyes S |title=Microbiology and drug resistance mechanisms of fully resistant pathogens. |journal=Curr Opin Microbiol |volume=7 |issue=5 |pages=439-44 |year=2004 |pmid=15451497}}</ref>

In many bacteria an [[S-layer]] of rigidly arrayed protein molecules covers the outside of the cell.<ref>{{cite journal |author=Engelhardt H, Peters J |title=Structural research on surface layers: a focus on stability, surface layer homology domains, and surface layer-cell wall interactions |journal=J Struct Biol |volume=124 |issue=2&ndash;3 |pages=276–302 |year=1998|id = PMID 10049812}}</ref> This layer provides chemical and physical protection for the cell surface and can act as a [[macromolecule|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 [[enzyme]]s in ''[[Bacillus stearothermophilus]]''.<ref>{{cite journal |author=Beveridge T, Pouwels P, Sára M, Kotiranta A, Lounatmaa K, Kari K, Kerosuo E, Haapasalo M, Egelseer E, Schocher I, Sleytr U, Morelli L, Callegari M, Nomellini J, Bingle W, Smit J, Leibovitz E, Lemaire M, Miras I, Salamitou S, Béguin P, Ohayon H, Gounon P, Matuschek M, Koval S |title=Functions of S-layers |journal=FEMS Microbiol Rev |volume=20 |issue=1&ndash;2 |pages=99&ndash;149 |year=1997 |pmid=9276929}}</ref>

[[Image:EMpylori.jpg|thumb|250px|left|''[[Helicobacter pylori]]'' electron micrograph, showing multiple flagella on the cell surface]]

[[Flagellum|Flagella]] are rigid protein structures, about 20&nbsp;[[metre|nanometre]]s in diameter and up to 20&nbsp;micrometres in length, that are used for motility. Flagella are driven by the energy released by the transfer of [[ion]]s down an [[electrochemical gradient]] across the cell membrane.<ref>{{cite journal |author=Kojima S, Blair D |title=The bacterial flagellar motor: structure and function of a complex molecular machine |journal=Int Rev Cytol |volume=233 |issue=|pages=93&ndash;134 |year=|pmid=15037363}}</ref>

[[Fimbria (bacteriology)|Fimbriae]] are fine filaments of protein, just 2–10&nbsp;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.<ref>{{cite journal |author=Beachey E |title=Bacterial adherence: adhesin-receptor interactions mediating the attachment of bacteria to mucosal surface |journal=J Infect Dis |volume=143 |issue=3 |pages=325&ndash;45 |year=1981|id = PMID 7014727}}</ref> [[Pilus|Pili]] (''sing''. pilus) are cellular appendages, slightly larger than fimbriae, that can transfer genetic material between bacterial cells in a process called [[bacterial conjugation|conjugation]] (see bacterial genetics, below).<ref>{{cite journal |author=Silverman P |title=Towards a structural biology of bacterial conjugation |journal=Mol Microbiol |volume=23 |issue=3 |pages=423&ndash;9 |year=1997 |pmid=9044277}}</ref>

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 (microbiology)|capsule]] or [[glycocalyx]]. These structures can protect cells from engulfment by eukaryotic cells, such as [[macrophage]]s.<ref>{{cite journal |author=Stokes R, Norris-Jones R, Brooks D, Beveridge T, Doxsee D, Thorson L |title=The glycan-rich outer layer of the cell wall of Mycobacterium tuberculosis acts as an antiphagocytic capsule limiting the association of the bacterium with macrophages | url=http://iai.asm.org/cgi/content/full/72/10/5676?view=long&pmid=15385466 |journal=Infect Immun |volume=72 |issue=10 |pages=5676&ndash;86 |year=2004 |pmid=15385466}}</ref> They can also act as antigens and be involved in cell recognition, as well as aiding attachment to surfaces and the formation of biofilms.<ref>{{cite journal |author=Daffé M, Etienne G |title=The capsule of Mycobacterium tuberculosis and its implications for pathogenicity |journal=Tuber Lung Dis |volume=79 |issue=3 |pages=153&ndash;69 |year=1999 |pmid=10656114}}</ref>

The assembly of these extracellular structures is dependent on bacterial [[secretion|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.<ref>{{cite journal |author=Finlay B, Falkow S |title=Common themes in microbial pathogenicity revisited | url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9184008 |journal=Microbiol Mol Biol Rev |volume=61 |issue=2 |pages=136&ndash;69 |year=1997 |pmid=9184008}}</ref>

===Endospores===
{{further|[[Endospore]]s}}

[[Image:Gram Stain Anthrax.jpg|thumb|250px|right|''[[Bacillus anthracis]]'' (stained purple) growing in [[cerebrospinal fluid]]]]

Certain [[Genus|genera]] of Gram-positive bacteria, such as ''[[Bacillus]]'', ''[[Clostridium]]'', ''[[Sporohalobacter]]'', ''[[Anaerobacter]]'' and ''[[Heliobacteria|Heliobacterium]]'', can form highly resistant, dormant structures called [[endospore]]s.<ref>{{cite journal |author=Nicholson W, Munakata N, Horneck G, Melosh H, Setlow P |title=Resistance of Bacillus endospores to extreme terrestrial and extraterrestrial environments | url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=10974126 |journal=Microbiol Mol Biol Rev |volume=64 |issue=3 |pages=548&ndash;72 |year=2000 |pmid=10974126}}</ref> 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.<ref>{{cite journal |author=Siunov A, Nikitin D, Suzina N, Dmitriev V, Kuzmin N, Duda V |title=Phylogenetic status of Anaerobacter polyendosporus, an anaerobic, polysporogenic bacterium | url=http://ijs.sgmjournals.org/cgi/reprint/49/3/1119.pdf |journal=Int J Syst Bacteriol |volume=49 Pt 3 |issue=|pages=1119&ndash;24 | year =|id = PMID 10425769}}</ref> Endospores have a central core of [[cytoplasm]] containing [[DNA]] and [[ribosome]]s surrounded by a cortex layer and protected by an impermeable and rigid coat.

Endospores show no detectable [[metabolism]] and can survive extreme physical and chemical stresses, such as high levels of [[ultraviolet|UV light]], [[gamma ray|gamma radiation]], [[detergent]]s, [[disinfectant]]s, heat, pressure and [[desiccation]].<ref>{{cite journal |author=Nicholson W, Fajardo-Cavazos P, Rebeil R, Slieman T, Riesenman P, Law J, Xue Y |title=Bacterial endospores and their significance in stress resistance |journal=Antonie Van Leeuwenhoek |volume=81 |issue=1&ndash;4 |pages=27&ndash;32 |year=2002 |pmid=12448702}}</ref> In this dormant state, these organisms may remain viable for millions of years,<ref>{{cite journal |author=Vreeland R, Rosenzweig W, Powers D |title=Isolation of a 250 million-year-old halotolerant bacterium from a primary salt crystal |journal=Nature |volume=407 |issue=6806 |pages=897&ndash;900 |year=2000 |pmid=11057666}}</ref><ref>{{cite journal |author=Cano R, Borucki M |title=Revival and identification of bacterial spores in 25- to 40-million-year-old Dominican amber |journal=Science |volume=268 |issue=5213 |pages=1060&ndash;4 |year=1995 |pmid=7538699}}</ref> and endospores even allow bacteria to survive exposure to the [[Vacuum#Outer space|vacuum]] and radiation in space.<ref>{{cite journal |author=Nicholson W, Schuerger A, Setlow P |title=The solar UV environment and bacterial spore UV resistance: considerations for Earth-to-Mars transport by natural processes and human spaceflight |journal=Mutat Res |volume=571 |issue=1&ndash;2 |pages=249&ndash;64 |year=2005|id = PMID 15748651}}</ref> 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]].<ref>{{cite journal |author=Hatheway C |title=Toxigenic clostridia | url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=2404569 |journal=Clin Microbiol Rev |volume=3 |issue=1 |pages=66&ndash;98 |year=1990 |pmid=2404569}}</ref>

==Metabolism==
{{further|[[Microbial metabolism]]}}

[[Image:Bluegreen algae.jpg|thumb|200px|right|Filaments of [[Photosynthesis|photosynthetic]] [[cyanobacteria]]]]

In contrast to higher organisms, bacteria exhibit an extremely wide variety of [[metabolism|metabolic]] types.<ref>{{cite journal |author=Nealson K |title=Post-Viking microbiology: new approaches, new data, new insights |journal=Orig Life Evol Biosph |volume=29 |issue=1 |pages=73–93 |year=1999 |pmid=11536899}}</ref> 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.<ref>{{cite journal |author=Xu J |title=Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances |journal=Mol Ecol |volume=15 |issue=7 |pages=1713–31 |year=2006|id = PMID 16689892}}</ref> Bacterial metabolism is classified on the basis of three major criteria: the kind of [[Energy#Biology|energy]] used for growth, the source of [[carbon]], and the [[electron donor]]s used for growth. An additional criterion of respiratory microorganisms are the [[electron acceptor]]s used for aerobic or anaerobic respiration.<ref>{{cite journal |author=Zillig W |title=Comparative biochemistry of Archaea and Bacteria |journal=Curr Opin Genet Dev |volume=1 |issue=4 |pages=544-51 |year=1991 |pmid=1822288}}</ref>

Carbon metabolism in bacteria is either [[heterotroph]]ic, where [[organic compound|organic carbon]] compounds are used as carbon sources, or [[autotroph]]ic, meaning that cellular carbon is obtained by [[Carbon fixation|fixing]] [[carbon dioxide]]. 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.<ref>{{cite journal |author=Hellingwerf K, Crielaard W, Hoff W, Matthijs H, Mur L, van Rotterdam B |title=Photobiology of bacteria |journal=Antonie Van Leeuwenhoek |volume=65 |issue=4 |pages=331&ndash;47 |year=1994|id = PMID 7832590}}</ref> Energy metabolism of bacteria is either based on [[phototroph]]y, the use of light through [[photosynthesis]], or on [[chemotroph]]y, 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 [[lithotroph]]s that use inorganic electron donors and [[organotroph]]s 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 [[redox|reduced]] substrate and transferring them to a [[terminal electron acceptor]] in a [[redox|redox reaction]]. This reaction releases energy that can be used to synthesise [[adenosine triphosphate|ATP]] and drive metabolism. In [[aerobic organism]]s, [[oxygen]] is used as the electron acceptor. In [[anaerobic organism]]s 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. [[lactic acid|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.<ref>{{cite journal |author=Zumft W |title=Cell biology and molecular basis of denitrification | url=http://mmbr.asm.org/cgi/reprint/61/4/533?view=long&pmid=9409151 |journal=Microbiol Mol Biol Rev |volume=61 |issue=4 |pages=533&ndash;616 |year=1997 |pmid=9409151}}</ref><ref>{{cite journal |author=Drake H, Daniel S, Küsel K, Matthies C, Kuhner C, Braus-Stromeyer S |title=Acetogenic bacteria: what are the in situ consequences of their diverse metabolic versatilities? |journal=Biofactors |volume=6 |issue=1 |pages=13&ndash;24 |year=1997 |pmid=9233536}}</ref>

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 (element)|mercury]] ([[methylmercury|methyl-]] and [[dimethylmercury]]) in the environment.<ref>{{cite journal | last = Morel | first = FMM | coauthors = Kraepiel AML, Amyot M |year=1998 |title=The chemical cycle and bioaccumulation of mercury |journal=Annual Review of Ecological Systems |volume=29|pages = 543&mdash;566}}</ref> Non-respiratory anaerobes use [[fermentation (biochemistry)|fermentation]] to generate energy and reducing power, secreting metabolic by-products (such as [[ethanol]] in brewing) as waste. [[Facultative anaerobe]]s can switch between fermentation and different [[terminal electron acceptor]]s 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 [[methanotroph]]ic bacteria as both a source of [[electron]]s and a substrate for carbon anabolism.<ref>{{cite journal |author=Dalton H |title=The Leeuwenhoek Lecture 2000 the natural and unnatural history of methane-oxidizing bacteria| url=http://www.journals.royalsoc.ac.uk/content/yl6umjthf30e4a59/ |journal=Philos Trans R Soc Lond B Biol Sci |volume=360 |issue=1458 |pages=1207&ndash;22 |year=2005 |pmid=16147517}}</ref> In both aerobic phototrophy and [[chemolithotroph]]y, 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.<ref>{{cite journal |author=Zehr J, Jenkins B, Short S, Steward G |title=Nitrogenase gene diversity and microbial community structure: a cross-system comparison |journal=Environ Microbiol |volume=5 |issue=7 |pages=539&ndash;54 |year=2003 |pmid=12823187}}</ref>

==Growth and reproduction==
{{further|[[Bacterial growth]]}}
Unlike multicellular organisms, increases in the size of bacteria ([[cell growth]]) and their reproduction by [[cell division]] are tightly linked in unicellular organisms. Bacteria grow to a fixed size and then reproduce through [[binary fission]], a form of [[asexual reproduction]].<ref>{{cite journal |author=Koch A |title=Control of the bacterial cell cycle by cytoplasmic growth |journal=Crit Rev Microbiol |volume=28 |issue=1 |pages=61&ndash;77 |year=2002 |pmid=12003041}}</ref> Under optimal conditions, bacteria can grow and divide extremely rapidly, and bacterial populations can double as quickly as every 9.8&nbsp;minutes.<ref>{{cite journal |author=Eagon R |title=Pseudomonas natriegens, a marine bacterium with a generation time of less than 10 minutes | url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=13888946 |journal=J Bacteriol |volume=83 |issue=|pages=736&ndash;7 | year =|id = PMID 13888946}}</ref> In cell division, two identical [[clone (genetics)|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 arial [[hypha]]e formation by ''[[Streptomyces]]'', or budding. Budding involves a cell forming a protrusion that breaks away and produces a daughter cell.

[[Image:Growing colony of E. coli.jpg|thumb|left|300px|A growing colony of ''[[Escherichia coli]]'' cells<ref>{{cite journal |author=Stewart EJ, Madden R, Paul G, Taddei F |title=Aging and death in an organism that reproduces by morphologically symmetric division |journal=PLoS Biol. |volume=3 |issue=2 |pages=e45 |year=2005 |pmid=15685293}}</ref>]]

In the laboratory, bacteria are usually grown using solid or liquid media. Solid growth media such as [[agar plate]]s 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.<ref name=Thomson>{{cite journal |author=Thomson R, Bertram H |title=Laboratory diagnosis of central nervous system infections |journal=Infect Dis Clin North Am |volume=15 |issue=4 |pages=1047&ndash;71 |year=2001 |pmid=11780267}}</ref>

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 [[r/K selection theory]]). Some organisms can grow extremely rapidly when nutrients become available, such as the formation of [[algal bloom|algal]] (and cyanobacterial) blooms that often occur in lakes during the summer.<ref>{{cite journal |author=Paerl H, Fulton R, Moisander P, Dyble J |title=Harmful freshwater algal blooms, with an emphasis on cyanobacteria |journal=ScientificWorldJournal |volume=1 |issue=|pages=76&ndash;113 |year=|pmid=12805693}}</ref> Other organisms have adaptations to harsh environments, such as the production of multiple [[antibiotic]]s by ''[[Streptomyces]]'' that inhibit the growth of competing microorganisms.<ref>{{cite journal |author=Challis G, Hopwood D |title=Synergy and contingency as driving forces for the evolution of multiple secondary metabolite production by Streptomyces species | url=http://www.pnas.org/cgi/content/full/100/suppl_2/14555 |journal=Proc Natl Acad Sci U S A |volume=100 Suppl 2 |issue=|pages=14555&ndash;61 |year=|pmid=12970466}}</ref> In nature, many organisms live in communities (e.g. [[biofilm]]s) which may allow for increased supply of nutrients and protection from environmental stresses.<ref name=Davey/> These relationships can be essential for growth of a particular organism or group of organisms ([[syntrophy]]).<ref>{{cite journal |author=Kooijman S, Auger P, Poggiale J, Kooi B |title=Quantitative steps in symbiogenesis and the evolution of homeostasis |journal=Biol Rev Camb Philos Soc |volume=78 |issue=3 |pages=435&ndash;63 |year=2003 |pmid=14558592}}</ref>

[[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 time|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.<ref>{{cite journal |author=Prats C, López D, Giró A, Ferrer J, Valls J |title=Individual-based modelling of bacterial cultures to study the microscopic causes of the lag phase |journal=J Theor Biol |volume=241 |issue=4 |pages=939&ndash;53 |year=2006|id = PMID 16524598}}</ref> The second phase of growth is the [[logarithm]]ic 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|antioxidant metabolism]] and [[active transport|nutrient transport]].<ref>{{cite journal |author=Hecker M, Völker U |title=General stress response of Bacillus subtilis and other bacteria |journal=Adv Microb Physiol |volume=44 |issue=|pages=35&ndash;91 |year=|pmid=11407115}}</ref>

==Genetics==
{{further|[[Plasmid]], [[Genome]]}}
Most bacteria have a single circular [[chromosome]] that can range in size from only 160,000 [[base pair]]s in the [[endosymbiont|endosymbiotic]] bacteria ''[[Candidatus Carsonella ruddii]]'',<ref>{{cite journal |author=Nakabachi A, Yamashita A, Toh H, Ishikawa H, Dunbar H, Moran N, Hattori M |title=The 160-kilobase genome of the bacterial endosymbiont Carsonella |journal=Science |volume=314 |issue=5797 |pages=267 |year=2006 |pmid=17038615}}</ref> to 12,200,000 base pairs in the soil-dwelling bacteria ''[[Sorangium cellulosum]]''.<ref>{{cite journal |author=Pradella S, Hans A, Spröer C, Reichenbach H, Gerth K, Beyer S |title=Characterisation, genome size and genetic manipulation of the myxobacterium Sorangium cellulosum So ce56 |journal=Arch Microbiol |volume=178 |issue=6 |pages=484-92 |year=2002 |pmid=12420170}}</ref> [[Spirochaete]]s 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.<ref>{{cite journal |author=Hinnebusch J, Tilly K |title=Linear plasmids and chromosomes in bacteria |journal=Mol Microbiol |volume=10 |issue=5 |pages=917-22 |year=1993|id = PMID 7934868}}</ref> The genes in bacterial genomes are usually a single continuous stretch of DNA and although several different types of [[intron]]s do exist in bacteria, these are much more rare than in eukaryotes.<ref>{{cite journal |author=Belfort M, Reaban ME, Coetzee T, Dalgaard JZ |title=Prokaryotic introns and inteins: a panoply of form and function |journal=J. Bacteriol. |volume=177 |issue=14 |pages=3897–903 |year=1995 |pmid=7608058 |url=http://jb.asm.org/cgi/pmidlookup?view=long&pmid=7608058}}</ref>

Bacteria may also contain [[plasmid]]s, which are small extra-chromosomal DNAs that may contain genes for [[antibiotic resistance]] or [[virulence|virulence factors]]. Another type of bacterial DNA are [[lysogeny|integrated]] viruses ([[bacteriophage]]s). Many types of bacteriophage exist, some simply infect and [[lytic cycle|lyse]] their [[host (biology)|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|''Escherichia coli'' O157:H7]] and ''[[Clostridium botulinum]]'', the [[toxin]] genes in an integrated phage converted a harmless ancestral bacteria into a lethal pathogen.<ref>{{cite journal |author=Brüssow H, Canchaya C, Hardt W |title=Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion | url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15353570 |journal=Microbiol Mol Biol Rev |volume=68 |issue=3 |pages=560–602 |year=2004 |pmid=15353570}}</ref>

Bacteria, as asexual organisms, inherit identical copies of their parent's genes (i.e., they are [[clone (genetics)|clonal]]). However, all bacteria can evolve by selection on changes to their genetic material [[DNA]] caused by [[genetic recombination]] or [[mutation]]s. Mutations come from errors made during the replication of DNA or from exposure to [[mutagen]]s. Mutation rates vary widely among different species of bacteria and even among different clones of a single species of bacteria.<ref>{{cite journal |author=Denamur E, Matic I |title=Evolution of mutation rates in bacteria |journal=Mol Microbiol |volume=60 |issue=4 |pages=820&ndash;7 |year=2006 |pmid=16677295}}</ref> 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.<ref>{{cite journal |author=Wright B |title=Stress-directed adaptive mutations and evolution |journal=Mol Microbiol |volume=52 |issue=3 |pages=643&ndash;50 |year=2004 |pmid=15101972}}</ref>

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 (genetics)|transformation]]. Genes can also be transferred by the process of [[transduction (genetics)|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.<ref>{{cite journal |author=Davison J |title=Genetic exchange between bacteria in the environment |journal=Plasmid |volume=42 |issue=2 |pages=73&ndash;91 |year=1999|id = PMID 10489325}}</ref> Gene transfer is particularly important in [[antibiotic resistance]] as it allows the rapid transfer of resistance genes between different pathogens.<ref>{{cite journal |author=Hastings P, Rosenberg S, Slack A |title=Antibiotic-induced lateral transfer of antibiotic resistance |journal=Trends Microbiol |volume=12 |issue=9 |pages=401&ndash;4 |year=2004 |pmid=15337159}}</ref>

==Movement==
{{further|[[Chemotaxis]], [[Flagella]], [[Pilus]]}}

[[Image:flagella.png|thumb|250px|left|The different arrangements of bacterial flagella:
A-Monotrichous;
B-Lophotrichous;
C-Amphitrichous and
D-Peritrichous]]

Motile bacteria can move using [[flagellum|flagella]], [[bacterial gliding]], twitching motility or changes of buoyancy.<ref name=Bardy>{{cite journal |author=Bardy S, Ng S, Jarrell K |title=Prokaryotic motility structures | url=http://mic.sgmjournals.org/cgi/content/full/149/2/295?view=long&pmid=12624192 |journal=Microbiology |volume=149 |issue=Pt 2 |pages=295&ndash;304 |year=2003|id = PMID 12624192}}</ref>  In twitching motility, bacterial use their type IV [[pilus|pili]] as a grappling hook, repeatedly extending it, anchoring it and then retracting it with remarkable force (>80 p[[Newton|N]]).<ref>{{cite journal |author=Merz A, So M, Sheetz M |title=Pilus retraction powers bacterial twitching motility |journal=Nature |volume=407 |issue=6800 |pages=98–102 |year=2000 |pmid=10993081}}</ref>

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.<ref name=Bardy/> The flagellum is a rotating structure driven by a motor at the base that uses the [[electrochemical gradient]] across the membrane for power. This motor drives the motion of the filament, which acts as a propeller. Many bacteria (such as ''[[Escherichia coli|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]].<ref>{{cite journal |author=Wu M, Roberts J, Kim S, Koch D, DeLisa M |title=Collective bacterial dynamics revealed using a three-dimensional population-scale defocused particle tracking technique | url=http://aem.asm.org/cgi/content/full/72/7/4987?view=long&pmid=16820497 |journal=Appl Environ Microbiol |volume=72 |issue=7 |pages=4987&ndash;94 |year=2006 |pmid=16820497}}</ref> (See external links below for link to videos.) The flagella of a unique group of bacteria, the [[spirochaete]]s, are found between two membranes in the periplasmic space. They have a distinctive [[helix|helical]] body that twists about as it moves.<ref name=Bardy/>

Motile bacteria are attracted or repelled by certain [[stimulus (physiology)|stimuli]] in behaviors called ''taxes'': these include [[chemotaxis]], [[phototaxis]] and [[magnetotaxis]].<ref>{{cite journal |author=Lux R, Shi W |title=Chemotaxis-guided movements in bacteria |journal=Crit Rev Oral Biol Med |volume=15 |issue=4 |pages=207-20 |year=2004 |pmid=15284186}}</ref><ref>{{cite journal |author=Frankel R, Bazylinski D, Johnson M, Taylor B |title=Magneto-aerotaxis in marine coccoid bacteria |journal=Biophys J |volume=73 |issue=2 |pages=994&ndash;1000 |year=1997 |pmid=9251816}}</ref> In one peculiar group, the [[myxobacteria]], individual bacteria move together to form waves of cells that then differentiate to form fruiting bodies containing spores.<ref>{{cite journal |author=Kaiser D |title=Signaling in myxobacteria |journal=Annu Rev Microbiol |volume=58 |issue=|pages=75–98 | year =|id = PMID 15487930}}</ref> The [[myxobacteria]] move only when on solid surfaces, unlike ''E. coli'' which is [[Motility|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 [[organelle]]s inside the cell. By promoting [[actin]] [[biopolymer|polymerization]] at one pole of their cells, they can form a kind of tail that pushes them through the host cell's cytoplasm.<ref>{{cite journal |author=Goldberg MB |title=Actin-based motility of intracellular microbial pathogens |journal=Microbiol Mol Biol Rev |volume=65 |issue=4 |pages=595–626 |year=2001 |pmid=11729265 }}</ref>

==Classification and identification==
[[Image:Streptococcus mutans Gram.jpg|right|thumb|200px|''Streptococcus mutans'' visualized with a Gram stain]]
{{further|[[Scientific classification]], [[Systematics]] and [[Clinical pathology]]}}

[[Scientific classification|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 acid]]s, pigments, [[antigen]]s and [[quinone]]s.<ref name=Thomson/> 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.<ref>{{cite journal |author=Boucher Y, Douady CJ, Papke RT, Walsh DA, Boudreau ME, Nesbo CL, Case RJ, Doolittle WF |title=Lateral gene transfer and the origins of prokaryotic groups. | http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.genet.37.050503.084247 |journal=Annu Rev Genet |volume=37 |pages=283–328|year = 2003|pmid=14616063}}</ref> 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]] [[GC-content|ratio]] determination, genome-genome hybridization, as well as [[DNA sequencing|sequencing]] genes that have not undergone extensive lateral gene transfer, such as the [[ribosomal DNA|rRNA gene]].<ref>{{cite journal |author=Olsen G, Woese C, Overbeek R |title=The winds of (evolutionary) change: breathing new life into microbiology | url=http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=205007&blobtype=pdf |journal=J Bacteriol |volume=176 |issue=1 |pages=1&ndash;6 |year=1994 |pmid=8282683}}</ref>  Classification of bacteria is determined by publication in the International Journal of Systematic Bacteriology,<ref>[http://ijs.sgmjournals.org/ IJSEM - Home<!-- Bot generated title -->]</ref> and Bergey's Manual of Systematic Bacteriology.<ref>[http://www.bergeys.org/ Bergey's Manual Trust<!-- Bot generated title -->]</ref>

The term "bacteria" was traditionally applied to all microscopic, single-celled prokaryotes. However, molecular systematics showed prokaryotic life to consist of two separate [[domain (biology)|domain]]s, originally called ''Eubacteria'' and ''Archaebacteria'', but now called ''Bacteria'' and ''[[Archaea]]'' that evolved independently from an ancient common ancestor.<ref>{{cite journal |author=Woese C, Kandler O, Wheelis M |title=Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya |url=http://www.pnas.org/cgi/reprint/87/12/4576 |journal=Proc Natl Acad Sci U S A |volume=87 |issue=12 |pages=4576&ndash;9 |year=1990 |pmid=2112744}}</ref> 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.<ref name=Gupta>{{cite journal |author=Gupta R |title=The natural evolutionary relationships among prokaryotes. |journal=Crit Rev Microbiol |volume=26 |issue=2 |pages=111-31 |year=2000 |pmid=10890353}}</ref> 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.<ref name=Rappe/><ref>{{cite journal |author=Doolittle RF |title=Evolutionary aspects of whole-genome biology |journal=Curr Opin Struct Biol |volume=15 |issue=3 |pages=248–253 |year=2005 |pmid=11837318}}</ref> For example, a few biologists argue that the Archaea and Eukaryotes evolved from Gram-positive bacteria.<ref name=Cavalier-Smith2002>{{cite journal |author=Cavalier-Smith T |title=The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. |journal=Int J Syst Evol Microbiol |volume=52 |issue=Pt 1 |pages=7–76 |year=2002 |pmid=11837318}}</ref>

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.
[[Image:Collapsed tree labels simplified.png|thumb|400px|left|[[Phylogenetic tree]] showing the diversity of bacteria, compared to other organisms.<ref>{{cite journal |author=Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P |title=Toward automatic reconstruction of a highly resolved tree of life |journal=Science |volume=311 |issue=5765 |pages=1283-7 |year=2006 |pmid=16513982}}</ref> [[Eukaryote]]s are colored red, [[archaea]] green and bacteria blue.]]
The [[Gram stain]], developed in 1884 by [[Hans Christian Gram]], characterises bacteria based on the structural characteristics of their cell walls.<ref name=Gram/> 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-fast]]ness on [[Ziehl-Neelsen stain|Ziehl–Neelsen]] or similar stains.<ref>{{cite journal |author=Woods G, Walker D |title=Detection of infection or infectious agents by use of cytologic and histologic stains | url=http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=172900&blobtype=pdf |journal=Clin Microbiol Rev |volume=9 |issue=3 |pages=382&ndash;404 |year=1996|id = PMID 8809467}}</ref> Other organisms may need to be identified by their growth in special media, or by other techniques, such as [[serology]].

[[Microbiological culture|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 [[feces|stool]] specimens are cultured on [[selective media]] to identify organisms that cause [[diarrhea|diarrhoea]], while preventing growth of non-pathogenic bacteria. Specimens that are normally sterile, such as [[blood]], [[urine]] or [[cerebrospinal fluid|spinal fluid]], are cultured under conditions designed to grow all possible organisms.<ref>{{cite journal |author=Weinstein M |title=Clinical importance of blood cultures |journal=Clin Lab Med |volume=14 |issue=1 |pages=9&ndash;16 |year=1994|id = PMID 8181237}}</ref><ref name=Thomson/> Once a pathogenic organism has been isolated, it can be further characterised by its morphology, growth patterns such as ([[aerobic organism|aerobic]] or [[anaerobic organism|anaerobic]] growth, [[hemolysis (microbiology)|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.<ref>{{cite journal |author=Louie M, Louie L, Simor AE |title=The role of DNA amplification technology in the diagnosis of infectious diseases |journal=CMAJ | url=http://www.cmaj.ca/cgi/content/full/163/3/301 |volume=163 |issue=3 |pages=301–309 |year=2000 |pmid=10951731}}</ref> These methods also allow the detection and identification of "viable but nonculturable" cells that are metabolically active but non-dividing.<ref>{{cite journal |author=Oliver J |title=The viable but nonculturable state in bacteria | url=http://www.msk.or.kr/jsp/view_old_journalD.jsp?paperSeq=2134 |journal=J Microbiol |volume=43 Spec No |issue= |pages=93–100 |year= |id=PMID 15765062}}</ref> However, even using these improved methods, the total number of bacterial species is not known and cannot even be estimated with any certainty. Attempts to quantify bacterial diversity have ranged from 10<sup>7</sup> to 10<sup>9</sup> total species, but even these diverse estimates may be out by many orders of magnitude.<ref>{{cite journal |author=Curtis T, Sloan W, Scannell J |title=Estimating prokaryotic diversity and its limits |url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12097644 |journal=Proc Natl Acad Sci U S A |volume=99 |issue=16 |pages=10494-9 |year=2002 |pmid=12097644}}</ref><ref>{{cite journal |author=Schloss P, Handelsman J |title=Status of the microbial census |url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15590780#r6 |journal=Microbiol Mol Biol Rev |volume=68 |issue=4 |pages=686-91 |year=2004 |pmid=15590780}}</ref>

==Interactions with other organisms==
Despite their apparent simplicity, bacteria can form complex associations with other organisms. These [[symbiosis|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 [[Perspiration|sweat]], and large populations of these organisms in humans are the cause of [[body odor]].

===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 [[methanogen]]ic Archaea that consume hydrogen.<ref>{{cite journal |author=Stams A, de Bok F, Plugge C, van Eekert M, Dolfing J, Schraa G |title=Exocellular electron transfer in anaerobic microbial communities |journal=Environ Microbiol |volume=8 |issue=3 |pages=371&ndash;82 |year=2006 |pmid=16478444}}</ref> 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.

In soil, microorganisms which reside in the [[Rhizosphere (ecology)|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.<ref>{{cite journal |author=Barea J, Pozo M, Azcón R, Azcón-Aguilar C |title=Microbial co-operation in the rhizosphere | url=http://jxb.oxfordjournals.org/cgi/content/full/56/417/1761 |journal=J Exp Bot |volume=56 |issue=417 |pages=1761&ndash;78 |year=2005 |pmid=15911555}}</ref> This serves to provide an easily absorbable form of nitrogen for many plants, which cannot fix nitrogen themselves. Many other bacteria are found as [[symbiont]]s [[Bacteria in the human body|in humans]] and other organisms. For example, the presence of over 1,000 bacterial species in the normal human [[gut flora]] of the [[intestine]]s can contribute to gut immunity, synthesise [[vitamin]]s such as [[folic acid]], [[vitamin K]] and [[biotin]], convert [[Milk#Physical and chemical structure|milk protein]] to [[lactic acid]] (see ''[[Lactobacillus]]''), as well as fermenting complex undigestible [[carbohydrate]]s.<ref>{{cite journal |author=O'Hara A, Shanahan F |title=The gut flora as a forgotten organ |journal=EMBO Rep |volume=7 |issue=7 |pages=688&ndash;93 |year=2006 |pmid=16819463}}</ref><ref>{{cite journal |author=Zoetendal E, Vaughan E, de Vos W |title=A microbial world within us |journal=Mol Microbiol |volume=59 |issue=6 |pages=1639&ndash;50 |year=2006 |pmid=16553872}}</ref><ref>{{cite journal |author=Gorbach S |title=Lactic acid bacteria and human health |journal=Ann Med |volume=22 |issue=1 |pages=37&ndash;41 |year=1990|id = PMID 2109988}}</ref> 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 supplement]]s.<ref>{{cite journal |author=Salminen S, Gueimonde M, Isolauri E |title=Probiotics that modify disease risk | url=http://jn.nutrition.org/cgi/content/full/135/5/1294 |journal=J Nutr |volume=135 |issue=5 |pages=1294&ndash;8 |year=2005 |pmid=15867327}}</ref>

===Pathogens===
{{Main|Pathogenic bacteria}}

[[Image:SalmonellaNIAID.jpg|thumb|250px|right|Color-enhanced scanning electron micrograph showing ''[[Salmonella typhimurium]]'' (red) invading cultured human cells]]

If bacteria form a parasitic association with other organisms, they are classed as [[pathogen]]s. 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 [[Timeline of peptic ulcer disease and Helicobacter pylori|peptic ulcer disease]]. Bacterial diseases are also important in [[agriculture]], with bacteria causing [[leaf spot]], [[fire blight]] and [[Wilting|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 interactions with its human [[host (biology)|hosts]]. Some organisms, such as ''[[Staphylococcus]]'' or ''[[Streptococcus]]'', can cause skin infections, [[pneumonia]], [[meningitis]] and even overwhelming [[sepsis]], a systemic inflammatory response producing [[shock (medical)|shock]], massive [[vasodilator|vasodilation]] and death.<ref>{{cite journal |author=Fish D |title=Optimal antimicrobial therapy for sepsis |journal=Am J Health Syst Pharm |volume=59 Suppl 1 |issue=|pages=S13&ndash;9 |year=|pmid=11885408}}</ref> 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 (bacterium)|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]].<ref>{{cite journal |author=Belland R, Ouellette S, Gieffers J, Byrne G |title=Chlamydia pneumoniae and atherosclerosis |journal=Cell Microbiol |volume=6 |issue=2 |pages=117&ndash;27 |year=2004|id = PMID 14706098}}</ref> Finally, some species such as ''[[Pseudomonas aeruginosa]]'', ''[[Burkholderia cenocepacia]]'', and ''[[Mycobacterium avium complex|Mycobacterium avium]]'' are [[opportunistic infection|opportunistic pathogens]] and cause disease mainly in people suffering from [[immunosuppression]] or [[cystic fibrosis]].<ref>{{cite journal |author=Heise E |title=Diseases associated with immunosuppression | url=http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1568899&blobtype=pdf |journal=Environ Health Perspect |volume=43 |issue=|pages=9&ndash;19 |year=|pmid=7037390}}</ref><ref name="Saiman">{{cite journal | last = Saiman | first = L |yar = 2004 |title=Microbiology of early CF lung disease |journal=Paediatr Respir Rev.volume=5 Suppl A |pages=S367&ndash;369}} PMID 14980298</ref>

Bacterial infections may be treated with [[antibiotic]]s, which are classified as [[Bactericide|bacteriocidal]] if they kill bacteria, or [[bacteriostatic]] if they just prevent bacterial growth. There are many types of antibiotics and each class [[enzyme inhibitor|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.<ref>{{cite journal |author=Yonath A, Bashan A |title=Ribosomal crystallography: initiation, peptide bond formation, and amino acid polymerization are hampered by antibiotics |journal=Annu Rev Microbiol |volume=58 |pages=233&ndash;51 |year=2004 |pmid=15487937}}</ref> 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.<ref>{{cite journal |author=Khachatourians G |title=Agricultural use of antibiotics and the evolution and transfer of antibiotic-resistant bacteria | url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9835883 |journal=CMAJ |volume=159 |issue=9 |pages=1129–36 |year=1998|id = PMID 9835883}}</ref> 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 [[sterilization (microbiology)|sterilized]] to prevent contamination and infection by bacteria. [[Disinfectant]]s 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|[[Economic importance of bacteria]]}}
Bacteria, often ''[[Lactobacillus]]'' in combination with [[yeast]]s and [[mold]]s, have been used for thousands of years in the preparation of [[fermentation (food)|fermented]] foods such as [[cheese]], [[Pickling|pickle]]s, [[soy sauce]], [[sauerkraut]], [[vinegar]], [[wine]] and [[yoghurt]].<ref>{{cite journal |author=Johnson M, Lucey J |title=Major technological advances and trends in cheese |journal=J Dairy Sci |volume=89 |issue=4 |pages=1174–8 |year=2006 |pmid=16537950}}</ref><ref>{{cite journal |author=Hagedorn S, Kaphammer B |title=Microbial biocatalysis in the generation of flavor and fragrance chemicals |journal=Annu. Rev. Microbiol. |volume=48 |issue= |pages=773-800 |year=1994 |pmid=7826026 |doi=10.1146/annurev.mi.48.100194.004013}}</ref>

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 [[hydrocarbon]]s in [[petroleum]] are often used to clean up [[oil spill]]s.<ref>{{cite journal |author=Cohen Y |title=Bioremediation of oil by marine microbial mats |journal=Int Microbiol |volume=5 |issue=4 |pages=189&ndash;93 |year=2002 |pmid=12497184}}</ref> 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|''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 waste]]s.<ref>{{cite journal |author=Neves LC, Miyamura TT, Moraes DA, Penna TC, Converti A |title=Biofiltration methods for the removal of phenolic residues |journal=Appl. Biochem. Biotechnol. |volume=129-132 |issue= |pages=130-52 |year=2006 |pmid=16915636 |doi=}}</ref> In the chemical industry, bacteria are most important in the production of [[enantiomer]]ically pure chemicals for use as [[pharmaceutical company|pharmaceuticals]] or [[agrichemical]]s.<ref>{{cite journal |author=Liese A, Filho M |title=Production of fine chemicals using biocatalysis |journal=Curr Opin Biotechnol |volume=10 |issue=6 |pages=595&ndash;603 |year=1999 |pmid=10600695}}</ref>

Bacteria can also be used in the place of [[pesticide]]s 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 [[Lepidoptera]]n-specific [[insecticide]]s under trade names such as Dipel and Thuricide.<ref>{{cite journal |author=Aronson AI, Shai Y |title=Why Bacillus thuringiensis insecticidal toxins are so effective: unique features of their mode of action |journal=FEMS Microbiol. Lett. |volume=195 |issue=1 |pages=1-8 |year=2001 |pmid=11166987 |doi=}}</ref> Because of their specificity, these pesticides are regarded as [[environmentally friendly]], with little or no effect on humans, [[wildlife]], [[pollinator]]s and most other [[beneficial insect]]s.<ref>{{cite journal |author=Bozsik A |title=Susceptibility of adult Coccinella septempunctata (Coleoptera: Coccinellidae) to insecticides with different modes of action |journal=Pest Manag Sci |volume=62 |issue=7 |pages=651–4 |year=2006 |pmid=16649191}}</ref><ref>{{cite journal |author=Chattopadhyay A, Bhatnagar N, Bhatnagar R |title=Bacterial insecticidal toxins |journal=Crit Rev Microbiol |volume=30 |issue=1 |pages=33–54 |year=2004 |pmid=15116762}}</ref>

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, [[enzyme]]s and [[metabolic pathway]]s in bacteria, then apply this knowledge to more complex organisms.<ref>{{cite journal |author=Serres M, Gopal S, Nahum L, Liang P, Gaasterland T, Riley M |title=A functional update of the Escherichia coli K-12 genome | url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=11574054 |journal=Genome Biol |volume=2 |issue=9 |pages=RESEARCH0035 |year=2001 |pmid=11574054}}</ref> This aim of understanding the biochemistry of a cell reaches its most complex expression in the synthesis of huge amounts of [[enzyme kinetics|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.<ref>{{cite journal |author=Almaas E, Kovács B, Vicsek T, Oltvai Z, Barabási A |title=Global organization of metabolic fluxes in the bacterium Escherichia coli |journal=Nature |volume=427 |issue=6977 |pages=839–43 |year=2004 |pmid=14985762}}</ref><ref>{{cite journal |author=Reed JL, Vo TD, Schilling CH, Palsson BO |title=An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) |journal=Genome Biol. |volume=4 |issue=9 |pages=R54 |year=2003 |pmid=12952533 |doi=10.1186/gb-2003-4-9-r54}}</ref> This understanding of bacterial metabolism and genetics allows the use of [[biotechnology]] to [[bioengineering|bioengineer]] bacteria for the production of therapeutic proteins, such as [[insulin]], [[growth factor]]s, or [[antibody|antibodies]].<ref>{{cite journal |author=Walsh G |title=Therapeutic insulins and their large-scale manufacture |journal=Appl Microbiol Biotechnol |volume=67 |issue=2 |pages=151&ndash;9 |year=2005 |pmid=15580495}}</ref><ref>{{cite journal |author=Graumann K, Premstaller A |title=Manufacturing of recombinant therapeutic proteins in microbial systems |journal=Biotechnol J |volume=1 |issue=2 |pages=164&ndash;86 |year=2006 |pmid=16892246}}</ref>

==See also==
*[[Human flora]]
*[[Bioaerosol]]
*[[Biotechnology]]
*[[Contamination control]]
*[[Denitrification]]
*''[[Desulforudis audaxviator]]''
*[[Extremophile]]s
*[[Transgenic bacteria]]
*[[Microorganism]]

==References==
{{reflist|2}}

==Further reading==
* {{cite book |author=Alcamo IE |title=Fundamentals of microbiology |publisher=Jones and Bartlett |location=Boston |year=2001 |pages= |isbn=0-7637-1067-9}}
* {{cite book |author=Atlas RM |title=Principles of microbiology |publisher=Mosby |location=St. Louis |year=1995 |pages= |isbn=0-8016-7790-4}}
* {{cite book |author=Martinko JM, Madigan MT |title=Brock Biology of Microorganisms | edition = 11th ed. |publisher=Prentice Hall |location=Englewood Cliffs, N.J |year=2005 |pages= |isbn=0-13-144329-1}}
* {{cite book |author=Holt JC, Bergey DH |title=Bergey's manual of determinative bacteriology |edition = 9th ed. |publisher=Williams & Wilkins |location=Baltimore |year=1994 |pages= |isbn=0-683-00603-7}}
* {{cite journal | author=Hugenholtz P, Goebel BM, Pace NR | title=Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity | journal=J Bacteriol | year=1998 | pages=4765&ndash;74 | volume=180 | issue=18 | pmid = 9733676 | url=http://jb.asm.org/cgi/content/full/180/18/4765?view=full&pmid=9733676}}
* {{cite book |author=Funke BR, Tortora GJ, Case CL |title=Microbiology: an introduction |edition = 8th ed, |publisher=Benjamin Cummings |location=San Francisco |year=2004 |pages= |isbn=0-8053-7614-3}}

==External links==
* [http://www.dsmz.de/bactnom/bactname.htm Bacterial Nomenclature Up-To-Date from DSMZ]
* [http://www.sciencenews.org/pages/sn_arc99/4_17_99/fob5.htm The largest bacteria]
* [http://tolweb.org/tree?group=Eubacteria&contgroup=Life_on_Earth Tree of Life: Eubacteria]
* [http://www.rowland.harvard.edu/labs/bacteria/index_movies.html Videos] of bacteria swimming and tumbling, use of optical tweezers and other videos.
* [http://www.stephenjaygould.org/library/gould_bacteria.html Planet of the Bacteria] by [[Stephen Jay Gould]]
* [http://www.textbookofbacteriology.net/ On-line text book on bacteriology]
* [http://www.blackwellpublishing.com/trun/artwork/Animations/Overview/overview.html Animated guide to bacterial cell structure.]

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