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{{two other uses|the microorganisms|the genus|Bacillus}}
{{featured article}}
{{Taxobox
| color = lightgrey
| name = Bacteria
| fossil_range = [[Archean]] or earlier - Recent
| image = EscherichiaColi NIAID.jpg
| image_width = 210px
| image_caption = Scanning electron micrograph of ''[[Escherichia coli]]'' bacilli
| domain = '''Bacteria'''
| subdivision_ranks = Phyla<ref>{{cite web |url=http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock |title=Bacteria (eubacteria) |accessdate=2008-09-10 |work=Taxonomy Browser |publisher=NCBI |date= }}</ref>
| subdivision =
*'''[[gram positive]]/no [[Bacterial outer membrane|outer membrane]]'''
[[Actinobacteria]] (high-[[GC-content|G+C]])<br />
[[Firmicutes]] (low-[[GC-content|G+C]])<br />
[[Tenericutes]] (no [[Cell wall|wall]])<br />
*'''[[gram negative]]/[[Bacterial outer membrane|outer membrane]] present'''
[[Aquificae]]<br />
[[Bacteroidetes]]/[[Chlorobi]]<br />
[[Chlamydiae]]/[[Verrucomicrobia]]<br />
[[Deinococcus-Thermus]]<br />
[[Fusobacteria]]<br />
[[Gemmatimonadetes]]<br />
[[Nitrospirae]]<br />
[[Proteobacteria]]<br />
[[Spirochaete]]s<br />
[[Synergistetes]]<br />
*'''unknown/ungrouped'''
[[Acidobacteria]]<br />
[[Chloroflexi]]<br />
[[Chrysiogenetes]]<br />
[[Cyanobacteria]]<br />
[[Deferribacteraceae|Deferribacteres]]<br />
[[Dictyoglomi]]<br />
[[Fibrobacteres]]<br />
[[Planctomycetes]]<br />
[[Thermodesulfobacteria]]<br />
[[Thermotogae]]
}}

The '''bacteria''' ({{Audio-IPA|en-us-bacteria.ogg|[bækˈtɪəriə]}}; ''singular'': '''bacterium'''){{Ref_label|A|α|none}} are a large group of unicellular, [[prokaryote]], [[microorganism]]s. Typically a few [[micrometre]]s in length, bacteria have a wide range of shapes, ranging from [[sphere]]s to rods and spirals. Bacteria are ubiquitous in every [[habitat]] on [[Earth]], growing in soil, [[Hot spring|acidic hot springs]], [[radioactive waste]],<ref>{{cite journal |author=Fredrickson JK, Zachara JM, Balkwill DL, ''et al.'' |title=Geomicrobiology of high-level nuclear waste-contaminated vadose sediments at the Hanford site, Washington state |journal=Applied and Environmental Microbiology |volume=70 |issue=7 |pages=4230–41 |year=2004 |month=July |pmid=15240306 |pmc=444790 |doi=10.1128/AEM.70.7.4230-4241.2004}}</ref> water, and deep in the [[Crust (geology)|Earth's crust]], as well as in organic matter and the live bodies of plants and animals. 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 name=pmid9618454>{{cite journal |author=Whitman WB, Coleman DC, Wiebe WJ |title=Prokaryotes: the unseen majority |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=95 |issue=12 |pages=6578–83 |year=1998 |month=June |pmid=9618454 |pmc=33863 |doi=10.1073/pnas.95.12.6578}}</ref> forming much of the world's [[biomass (ecology)|biomass]].<ref name=pmid9618454/> Bacteria are vital in recycling nutrients, with many steps in [[nutrient cycle]]s depending on these organisms, such as the [[nitrogen fixation|fixation of nitrogen]] from the [[Earth's atmosphere|atmosphere]] and [[putrefaction]]. However, most bacteria have not been characterized, and only about half of the [[phylum|phyla]] of bacteria have species that can be [[microbiological culture|grown]] in the laboratory.<ref name=Rappe>{{cite journal |author=Rappé MS, Giovannoni SJ |title=The uncultured microbial majority |journal=Annual Review of Microbiology |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 in the [[human flora]] of bacteria as there are human cells in the body, with large numbers of bacteria on the [[skin]] and as [[gut flora]].<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 |month=October |pmid=16701579 |doi=10.1016/j.anaerobe.2005.05.001}}</ref> The vast majority of the bacteria in the body are rendered harmless by the protective effects of the [[immune system]], and a few are [[probiotic|beneficial]]. However, a few species of bacteria are [[pathogenic bacteria|pathogenic]] 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 [[Infection|bacterial infections]] and in agriculture, so [[antibiotic resistance]] is becoming common. In industry, bacteria are important in [[sewage treatment]], the production of [[cheese]] and [[yoghurt]] through [[fermentation (biochemistry)|fermentation]], as well as in [[biotechnology]], and the manufacture of antibiotics and other chemicals.<ref>{{cite journal |author=Ishige T, Honda K, Shimizu S |title=Whole organism biocatalysis |journal=Current Opinion in Chemical Biology |volume=9 |issue=2 |pages=174–80 |year=2005 |month=April |pmid=15811802 |doi=10.1016/j.cbpa.2005.02.001}}</ref>

Once regarded as plants constituting the class Schizomycetes, bacteria are now classified as [[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 prokaryotes consist 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 name=autogenerated2>{{cite journal |author=Woese CR, Kandler O, Wheelis ML |title=Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=87 |issue=12 |pages=4576–9 |year=1990 |month=June |pmid=2112744 |pmc=54159 |doi=10.1073/pnas.87.12.4576}}</ref>

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

[[Image:Antoni van Leeuwenhoek.png|thumb|240px|right|[[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=260–9 |year=1976 |month=June |pmid=786250 |pmc=413956 |url=http://mmbr.asm.org/cgi/pmidlookup?view=long&pmid=786250}}</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 |doi=10.1098/rstl.1702.0042}}</ref> The name ''bacterium'' was introduced much later, by [[Christian Gottfried Ehrenberg]] in 1838.<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 |doi=10.1016/S0952-7915(96)80075-6}}</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 |doi=10.1046/j.1440-1622.2000.01983.x}}</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|pmid = 15014180 |doi=10.1056/NEJMp048021}}</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 USA |volume=74 |issue=11 |pages=5088–5090 |year=1977|pmid = 270744 |doi=10.1073/pnas.74.11.5088 |pmc=432104}}</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 CR, Kandler O, Wheelis ML |title=Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=87 |issue=12 |pages=4576–9 |year=1990 |month=June |pmid=2112744 |doi=10.1073/pnas.87.12.4576 |pmc=54159}}</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 |journal=Proc Natl Acad Sci USA |volume=91 |issue=15 |pages=6735–42 |year=1994 |pmid=8041691 |pmc=44277 |doi=10.1073/pnas.91.15.6735}}</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|pmid = 12116647 |doi=10.1080/106351501750435040}}</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 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=Microbiology and Molecular Biology Reviews |volume=61 |issue=4 |pages=456–502 |year=1997 |month=December |pmid=9409149 |pmc=232621 |url=http://mmbr.asm.org/cgi/pmidlookup?view=long&pmid=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 |doi=10.1007/s00239-003-2522-6}}</ref><ref>{{cite journal |author=Battistuzzi FU, Feijao A, Hedges SB |title=A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land |journal=BMC Evolutionary Biology |volume=4 |issue= |pages=44 |year=2004 |month=November |pmid=15535883 |pmc=533871 |doi=10.1186/1471-2148-4-44}}</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 |doi=10.1002/bies.20516}}</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 |doi=10.1126/science.1094884}}</ref> This involved the engulfment by proto-eukaryotic cells of alpha-proteobacterial symbionts to form either [[mitochondrion|mitochondria]] or [[hydrogenosome]]s, which are still found in all known Eukarya (sometimes in highly [[reduced form]], e.g. in ancient "amitochondrial" protozoa). Later on, some eukaryotes that already contained mitochondria also engulfed cyanobacterial-like organisms. This led to the formation of [[chloroplast]]s 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.<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= 1999|pmid=10690412 |doi=10.1146/annurev.genet.33.1.351}}</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 |doi=10.1016/S1369-5266(99)00025-4}}</ref> This is known as [[Endosymbiotic theory#Secondary endosymbiosis|secondary endosymbiosis]].

==Morphology==
{{see|Bacterial cellular morphologies}}

[[Image:Bacterial morphology diagram.svg|right|thumb|360px|Bacteria display many 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=2001|pmid=11544351 |doi=10.1146/annurev.micro.55.1.105}}</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 |pmc=235991}}</ref> Some bacteria may be even smaller, but these [[ultramicrobacteria]] are not well-studied.<ref name=Velimirov2001>{{cite journal | author = Velimirov, B.
| year = 2001 | title = Nanobacteria, Ultramicrobacteria and Starvation Forms: A Search for the Smallest Metabolizing Bacterium | journal = Microbes and Environments | volume = 16 | issue = 2 | pages = 67–77 | url = http://www.jstage.jst.go.jp/article/jsme2/16/2/67/_pdf | accessdate = 2008-06-23 | doi = 10.1264/jsme2.2001.67}}</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). Elongation is associated with swimming.<ref>Dusenbery, David B. (2009). ''Living at Micro Scale'', pp.20-25. Harvard University Press, Cambridge, Mass. ISBN 978-0-674-03116-6.</ref> 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|pmid = 15143003 |doi=10.1099/ijs.0.02746-0}}</ref> More recently, bacteria were discovered deep under the Earth's crust that grow as long rods 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.<ref>{{cite journal |author=Wanger Onstott Southam |title=Stars of the terrestrial deep subsurface: A novel `star-shaped' bacterial morphotype from a South African platinum mine |journal=Geobiology |volume=6 |issue=3 |pages=325–330 |year=2008 |doi=10.1111/j.1472-4669.2008.00163.x |pmid=18498531 |last1=Wanger |first1=G |last2=Onstott |first2=TC |last3=Southam |first3=G}}</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 |doi=10.1038/nrmicro1205}}</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 |doi=10.1128/MMBR.00001-06 |pmc=1594593}}</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 |doi=10.1067/mjd.2003.302}}</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 |pmc=2732559}}</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 |doi=10.1016/j.tim.2004.11.006}}</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|pmid = 11104821 |doi=10.1128/MMBR.64.4.847-867.2000 |pmc=99016}}</ref> Biofilms are also important in medicine, as these structures are often present during chronic bacterial infections or in infections of [[implant (medicine)|implanted]] [[medical device]]s, and bacteria protected within biofilms are much harder to kill than individual isolated 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 |doi=10.1128/CMR.15.2.167-193.2002 |pmc=118068}}</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 =1999|pmid = 10547700 |doi=10.1146/annurev.micro.53.1.525}}</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 drying and other adverse environmental conditions than are ordinary cells.<ref name=autogenerated1>{{cite journal |author=Kaiser D |title=Signaling in myxobacteria |journal=Annu Rev Microbiol |volume=58 |issue=|pages=75–98 |year=2004|pmid=15487930 |doi=10.1146/annurev.micro.58.030603.123620}}</ref>

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

[[Image:Average prokaryote cell- en.svg|thumb|280px|right|Structure and contents of a typical [[Gram positive]] bacterial cell]]

===Intracellular structures===
The bacterial cell is surrounded by a [[lipid]] membrane, or [[cell membrane]], which encloses the contents of the cell and acts as a barrier to hold nutrients, [[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 large 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 | publisher = WH Freeman | year = 2002 | isbn = 0-7167-4955-6}}</ref> Bacteria were once seen as simple bags of cytoplasm, but elements such as [[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 |doi=10.1016/j.cell.2005.02.026}}</ref><ref>{{cite journal |author=Shih YL, Rothfield L |title=The bacterial cytoskeleton |journal=Microbiology and Molecular Biology Reviews |volume=70 |issue=3 |pages=729–54 |year=2006 |month=September |pmid=16959967 |pmc=1594594 |doi=10.1128/MMBR.00017-06}}</ref> and the localization of proteins to specific locations within the cytoplasm<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 |month=March |pmid=15766522 |doi=10.1016/j.cell.2005.02.026}}</ref> have been found to show levels of complexity. These subcellular compartments have been called "bacterial hyperstructures".<ref>{{cite journal |author=Norris V, den Blaauwen T, Cabin-Flaman A, ''et al.'' |title=Functional taxonomy of bacterial hyperstructures |journal=Microbiol. Mol. Biol. Rev. |volume=71 |issue=1 |pages=230–53 |year=2007 |month=March |pmid=17347523 |pmc=1847379 |doi=10.1128/MMBR.00035-06 |url=http://mmbr.asm.org/cgi/pmidlookup?view=long&pmid=17347523 |last12=Saier M |first12=Jr |last13=Skarstad |first13=K}}</ref>

[[Bacterial microcompartment|Micro-compartments]] such as [[carboxysome]]<ref>{{cite journal |author=Kerfeld CA, Sawaya MR, Tanaka S, ''et al.'' |title=Protein structures forming the shell of primitive bacterial organelles |journal=Science (journal) |volume=309 |issue=5736 |pages=936–8 |year=2005 |month=August |pmid=16081736 |doi=10.1126/science.1113397}}</ref> provides a further level of organization, which are compartments within bacteria that are surrounded by [[polyhedron|polyhedral]] protein shells, rather than by lipid membranes.<ref name=Bobik2007>{{cite journal | author = Bobik, T. A. | title = Bacterial Microcompartments | year = 2007 | journal = Microbe | volume = 2 | pages = 25–31 | url = http://www.asm.org/ASM/files/ccLibraryFiles/Filename/000000002765/znw00107000025.pdf | publisher = Am Soc Microbiol|format=PDF}}</ref> These "polyhedral organelles" localize and compartmentalize bacterial metabolism, a function performed by the membrane-bound organelles in eukaryotes.<ref name=Bobik2006>{{cite journal | author = Bobik, T. A. | year = 2006 | title = Polyhedral organelles compartmenting bacterial metabolic processes | journal = Applied Microbiology and Biotechnology | volume = 70 | issue = 5 | pages = 517–525 | doi = 10.1007/s00253-005-0295-0 | url = http://www.springerlink.com/index/EM21R3556222521H.pdf|format=PDF | pmid = 16525780 | last1 = Bobik | first1 = TA}}</ref><ref>{{cite journal |author=Yeates TO, Kerfeld CA, Heinhorst S, Cannon GC, Shively JM |title=Protein-based organelles in bacteria: carboxysomes and related microcompartments |journal=Nat. Rev. Microbiol. |volume=6 |pages=681–691 |year=2008 |month=August |pmid=18679172 |doi=10.1038/nrmicro1913 |issue=9}}</ref>

Many important [[biochemistry|biochemical]] reactions, such as [[Energy#Biology|energy]] generation, occur by [[diffusion|concentration gradient]]s across membranes, a potential difference also found in a [[battery (electricity)|battery]]. The general lack of internal membranes in bacteria means 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 FM |title=Conservation and transformation of energy by bacterial membranes |journal=Bacteriological Reviews |volume=36 |issue=2 |pages=172–230 |year=1972 |month=June |pmid=4261111 |pmc=408323 |url=http://mmbr.asm.org/cgi/pmidlookup?view=long&pmid=4261111}}</ref> However, in many photosynthetic bacteria the plasma membrane is highly folded and fills most of the cell with layers of light-gathering membrane.<ref name=bryantfrigaard>{{cite journal |author=Bryant DA, Frigaard NU
|year=2006 |title=Prokaryotic photosynthesis and phototrophy illuminated |journal=Trends Microbiol. |volume=14 |issue=11 |pages=488 |doi=10.1016/j.tim.2006.09.001 |pmid=16997562 |last1=Bryant |first1=DA |last2=Frigaard |first2=NU }}</ref> These light-gathering complexs may even form lipid-enclosed structures called [[chlorosome]]s in [[green sulfur bacteria]].<ref>{{cite journal |author=Psencík J, Ikonen TP, Laurinmäki P, ''et al.'' |title=Lamellar organization of pigments in chlorosomes, the light harvesting complexes of green photosynthetic bacteria |journal=Biophys. J. |volume=87 |issue=2 |pages=1165–72 |year=2004 |month=August |pmid=15298919 |pmc=1304455 |doi=10.1529/biophysj.104.040956 |url=http://www.biophysj.org/cgi/pmidlookup?view=long&pmid=15298919}}</ref> Other proteins import nutrients across the cell membrane, or to expel undesired molecules from the cytoplasm.

[[Image:Carboxysome 3 images.png|thumb|left|450px|[[Carboxysome]]s are protein-enclosed bacterial organelles. Top left is an [[electron microscope]] image of carboxysomes in ''[[Halothiobacillus|Halothiobacillus neapolitanus]]'', below is an image of purified carboxysomes. On the right is a model of their structure. Scale bars are 100&nbsp;nm.<ref>{{cite journal |author=Tanaka S, Kerfeld CA, Sawaya MR, ''et al.'' |title=Atomic-level models of the bacterial carboxysome shell |journal=Science (journal) |volume=319 |issue=5866 |pages=1083–6 |year=2008 |month=February |pmid=18292340 |doi=10.1126/science.1151458}}</ref>]]
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 |doi=10.1002/jcb.20519}}</ref> The nucleoid contains the chromosome with associated proteins and [[RNA]]. The order [[Planctomycetes]] are an exception to the general absence of internal membranes in bacteria, because they have a membrane 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 |doi=10.1146/annurev.micro.59.030804.121258}}</ref> Like all [[Organism|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|pmid = 16261170 |doi=10.1038/nrmicro1265}}</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 |doi=10.1099/mic.0.27428-0}}</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 |journal=Archives of Microbiology |volume=163 |issue=6 |pages=391–9 |year=1995 |month=June |pmid=7575095 |doi=10.1007/BF00272127}}</ref> or [[polyhydroxyalkanoates]].<ref>{{cite journal |author=Kadouri D, Jurkevitch E, Okon Y, Castro-Sowinski S |title=Ecological and agricultural significance of bacterial polyhydroxyalkanoates |journal=Critical Reviews in Microbiology |volume=31 |issue=2 |pages=55–67 |year=2005 |pmid=15986831 |doi=10.1080/10408410590899228}}</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 AE |title=Gas vesicles |journal=Microbiological Reviews |volume=58 |issue=1 |pages=94–144 |year=1994 |month=March |pmid=8177173 |pmc=372955 |url=http://mmbr.asm.org/cgi/pmidlookup?view=long&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 |doi=10.1093/glycob/11.3.25R}}</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|pmid = 14557293 |doi=10.1128/CMR.16.4.673-687.2003 |pmc=207114}}</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 bilayer|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 |journal=Genome Biology |volume=3 |issue=2 |pages=REVIEWS0003 |year=2002 |pmid=11864374 |pmc=139013 |url=http://genomebiology.com/1465-6906/3/REVIEWS0003 |doi=10.1186/gb-2002-3-2-reviews0003}}</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 |doi=10.1016/j.mib.2004.08.007}}</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|pmid = 10049812 |doi=10.1006/jsbi.1998.4070}}</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 |last12=Morelli |first12=L |last13=Callegari |first13=ML |last14=Nomellini |first14=JF |last15=Bingle |first15=WH |last16=Smit |first16=J |last17=Leibovitz |first17=E |last18=Lemaire |first18=M |last19=Miras |first19=I |last20=Salamitou |first20=S |last21=Béguin |first21=P |last22=Ohayon |first22=H |last23=Gounon |first23=P |last24=Matuschek |first24=M |last25=Koval |first25=SF}}</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=2004|pmid=15037363 |doi=10.1016/S0074-7696(04)33003-2}}</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|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 |doi=10.1046/j.1365-2958.1997.2411604.x}}</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 |doi=10.1128/IAI.72.10.5676-5686.2004 |pmc=517526}}</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 |doi=10.1054/tuld.1998.0200}}</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 BB, Falkow S |title=Common themes in microbial pathogenicity revisited |journal=Microbiology and Molecular Biology Reviews |volume=61 |issue=2 |pages=136–69 |year=1997 |month=June |pmid=9184008 |pmc=232605 |url=http://mmbr.asm.org/cgi/pmidlookup?view=long&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 WL, Munakata N, Horneck G, Melosh HJ, Setlow P |title=Resistance of Bacillus endospores to extreme terrestrial and extraterrestrial environments |journal=Microbiology and Molecular Biology Reviews |volume=64 |issue=3 |pages=548–72 |year=2000 |month=September |pmid=10974126 |pmc=99004 |url=http://mmbr.asm.org/cgi/pmidlookup?view=long&pmid=10974126 |doi=10.1128/MMBR.64.3.548-572.2000}}</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 =1999|pmid = 10425769|format=PDF}}</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 |doi=10.1023/A:1020561122764}}</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 |doi=10.1038/35038060}}</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 |doi=10.1126/science.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|pmid = 15748651 |doi=10.1016/j.mrfmmm.2004.10.012}}</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 CL |title=Toxigenic clostridia |journal=Clinical Microbiology Reviews |volume=3 |issue=1 |pages=66–98 |year=1990 |month=January |pmid=2404569 |pmc=358141 |url=http://cmr.asm.org/cgi/pmidlookup?view=long&pmid=2404569}}</ref>

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

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 |doi=10.1023/A:1006515817767}}</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|pmid = 16689892 |doi=10.1111/j.1365-294X.2006.02882.x}}</ref> Bacterial metabolism is classified into [[primary nutritional groups|nutritional groups]] 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 |doi=10.1016/S0959-437X(05)80206-0}}</ref>

{|class="wikitable" style="margin-left: auto; margin-right: auto;"
|+ Nutritional types in bacterial metabolism
|-
!Nutritional type
!Source of energy
!Source of carbon
!Examples
|-
|&nbsp;[[Phototroph]]s&nbsp;
|align="center" |Sunlight
|align="center" |&nbsp;Organic compounds (photoheterotrophs) or carbon fixation (photoautotrophs)
|&nbsp;[[Cyanobacteria]], [[Green sulfur bacteria]], [[Chloroflexi]], or [[Purple bacteria]]&nbsp;
|-
|&nbsp;[[Lithotroph]]s
|align="center" |Inorganic compounds
|align="center" |&nbsp;Organic compounds (lithoheterotrophs) or carbon fixation (lithoautotrophs)
|&nbsp;[[Thermodesulfobacteria]], ''[[Hydrogenophilaceae]]'', or [[Nitrospirae]]&nbsp;
|-
|&nbsp;[[Organotroph]]s
|align="center" |Organic compounds
|align="center" |&nbsp;Organic compounds (chemoheterotrophs) or carbon fixation (chemoautotrophs) &nbsp;
|&nbsp;''[[Bacillus]]'', ''[[Clostridium]]'' or ''[[Enterobacteriaceae]]''&nbsp;
|}

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]]. 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.<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|pmid = 7832590 |doi=10.1007/BF00872217}}</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).

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

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 compound]]s 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 compound]]s, 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 |date=1 December 1997|pmid=9409151 |pmc=232623 }}</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 |doi=10.1002/biof.5520060103}}</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 = 543–566 |doi=10.1146/annurev.ecolsys.29.1.543}}</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 |doi=10.1098/rstb.2005.1657 |pmc=1569495}}</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 |doi=10.1046/j.1462-2920.2003.00451.x}}</ref>

==Growth and reproduction==
[[Image:Binary fission anim.gif|thumb|right|175px|Many bacteria reproduce through ''[[binary fission]]'']]
{{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 |doi=10.1080/1040-840291046696}}</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 RG |title=Pseudomonas natriegens, a marine bacterium with a generation time of less than 10 minutes |journal=Journal of Bacteriology |volume=83 |issue= 4|pages=736–7 |year=1962 |month=April |pmid=13888946 |pmc=279347 |url=http://jb.asm.org/cgi/pmidlookup?view=long&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 aerial [[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 |doi=10.1371/journal.pbio.0030045|pmc=546039}}</ref>]]

In the laboratory, bacteria are usually grown using solid or liquid media. Solid [[Growth medium|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=Infectious Disease Clinics of North America |volume=15 |issue=4 |pages=1047–71 |year=2001 |pmid=11780267 |doi=10.1016/S0891-5520(05)70186-0}}</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=2001|pmid=12805693 |doi=10.1100/tsw.2001.16}}</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 USA |volume=100 Suppl 2 |issue=|pages=14555&ndash;61 |year=2003|pmid=12970466 |doi=10.1073/pnas.1934677100 |pmc=304118}}</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 |doi=10.1017/S1464793102006127}}</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|pmid = 16524598 |doi=10.1016/j.jtbi.2006.01.029}}</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=2001|pmid=11407115 |doi=10.1016/S0065-2911(01)44011-2}}</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 |doi=10.1126/science.1134196}}</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 |doi=10.1007/s00203-002-0479-2}}</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|pmid = 7934868 |doi=10.1111/j.1365-2958.1993.tb00963.x}}</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 |date=1 July 1995|pmid=7608058 |url=http://jb.asm.org/cgi/pmidlookup?view=long&pmid=7608058 |pmc=177115 }}</ref>

Bacteria may also contain [[plasmid]]s, which are small extra-chromosomal DNAs that may contain genes for [[antibiotic resistance]] or [[virulence|virulence factors]].

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 |doi=10.1111/j.1365-2958.2006.05150.x}}</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 |doi=10.1111/j.1365-2958.2004.04012.x}}</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|pmid = 10489325 |doi=10.1006/plas.1999.1421}}</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 |doi=10.1016/j.tim.2004.07.003}}</ref>

=== Bacteriophages ===

[[Bacteriophage]]s are viruses that change the bacterial DNA. 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 WD |title=Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion |journal=Microbiology and Molecular Biology Reviews |volume=68 |issue=3 |pages=560–602 |year=2004 |month=September |pmid=15353570 |pmc=515249 |doi=10.1128/MMBR.68.3.560-602.2004}}</ref> Bacteria resist phage infection through [[restriction modification system]]s that degrade foreign DNA,<ref>{{cite journal |author=Bickle TA, Krüger DH |title=Biology of DNA restriction |journal=Microbiol. Rev. |volume=57 |issue=2 |pages=434–50 |date=1 June 1993|pmid=8336674 |pmc=372918 |url=http://mmbr.asm.org/cgi/pmidlookup?view=long&pmid=8336674 }}</ref> 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]].<ref>{{cite journal |author=Barrangou R, Fremaux C, Deveau H, ''et al.'' |title=CRISPR provides acquired resistance against viruses in prokaryotes |journal=Science (journal) |volume=315 |issue=5819 |pages=1709–12 |year=2007 |month=March |pmid=17379808 |doi=10.1126/science.1138140}}</ref><ref>{{cite journal |author=Brouns SJ, Jore MM, Lundgren M, ''et al.'' |title=Small CRISPR RNAs guide antiviral defense in prokaryotes |journal=Science (journal) |volume=321 |issue=5891 |pages=960–4 |year=2008 |month=August |pmid=18703739 |doi=10.1126/science.1159689}}</ref> This CRISPR system provides bacteria with [[immunity (medical)|acquired immunity]] to infection.

==Behavior==
===Secretion===
Bacteria frequently secrete chemicals into their environment in order to modify it favorably. The [[secretion]]s are often proteins and may act as enzymes that digest some form of food in the environment.

===Bioluminescence===
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.<ref>Dusenbery, David B. (1996). ''Life at Small Scale''. Scientific American Library. ISBN 0-7167-5060-0.</ref>

===Multicellularity===

(''See also:'' [[Prokaryote#Sociality]])

Bacteria often function as multicellular aggregates known as [[biofilms]], exchanging a variety of molecular signals for [[Cell signaling|inter-cell communication]], and engaging in coordinated multicellular behavior.<ref name=shapiro1>{{cite journal |author=Shapiro JA |title=Thinking about bacterial populations as multicellular organisms |journal=Annu. Rev. Microbiol. |volume=52 |issue= |pages=81–104 |year=1998 |pmid=9891794 |doi=10.1146/annurev.micro.52.1.81 |url=http://www.sci.uidaho.edu/newton/math501/Sp05/Shapiro.pdf}}</ref><ref name=costerton1>{{cite journal |author=Costerton JW, Lewandowski Z, Caldwell DE, Korber DR, Lappin-Scott HM |title=Microbial biofilms |journal=Annu. Rev. Microbiol. |volume=49 |issue= |pages=711–45 |year=1995 |pmid=8561477 |doi=10.1146/annurev.mi.49.100195.003431 |url=http://www.ncbi.nlm.nih.gov/pubmed/8561477}}</ref>

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.<ref name=shapiro1/> For example, bacteria in biofilms can have more than 500 times increased resistance to [[Bactericide|antibacterial]] agents than individual "planktonic" bacteria of the same species.<ref name=costerton1/>

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.

It is thought that bacteria are too small to use [[pheromone]]s to attract other individuals, as is common among animals.<ref>Dusenbery, David B. (2009). ''Living at Micro Scale'', Chapter 19. Harvard University Press, Cambridge, Mass. ISBN 978-0-674-03116-6.</ref>

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

Many bacteria can move using a variety of mechanisms: [[Flagellum|flagella]] are used for swimming through water; [[bacterial gliding]] and twitching motility move bacteria across surfaces; and changes of buoyancy allow vertical motion.<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|pmid = 12624192 |doi=10.1099/mic.0.25948-0}}</ref>

[[Image:Flagellum base diagram en.svg|thumb|right|350px|Flagellum of Gram-negative Bacteria. The base drives the rotation of the hook and filament.]]

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.<ref>Dusenbery, David B. (2009). ''Living at Micro Scale'', p. 136. Harvard University Press, Cambridge, Mass. ISBN 978-0-674-03116-6.</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 [[Newton (unit)|pN]]).<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 |doi=10.1038/35024105}}</ref>

[[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 that the flat, paddle-like, forms appropriate at human size scale.<ref>Dusenbery, David B. (2009). ''Living at Micro Scale'', Chapter 13. Harvard University Press, Cambridge, Mass. ISBN 978-0-674-03116-6.</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 reversible motor at the base that uses the [[electrochemical gradient]] across the membrane for power.<ref>{{cite journal |author=Macnab RM |title=The bacterial flagellum: reversible rotary propellor and type III export apparatus |journal=J. Bacteriol. |volume=181 |issue=23 |pages=7149–53 |date=1 December 1999|pmid=10572114 |pmc=103673 |url=http://jb.asm.org/cgi/pmidlookup?view=long&pmid=10572114 }}</ref> 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 |doi=10.1128/AEM.00158-06 |pmc=1489374}}</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 |doi=10.1177/154411130401500404}}</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 |doi=10.1016/S0006-3495(97)78132-3 |pmc=1180996}}</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 name=autogenerated1 /> 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 |doi=10.1128/MMBR.65.4.595-626.2001 |pmc=99042 }}</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, [[Cell metabolism|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 |journal=Annu Rev Genet |volume=37 |pages=283–328|year = 2003|pmid=14616063 |doi=10.1146/annurev.genet.37.050503.084247 |url=http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.genet.37.050503.084247}}</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 GJ, Woese CR, Overbeek R |title=The winds of (evolutionary) change: breathing new life into microbiology |journal=Journal of Bacteriology |volume=176 |issue=1 |pages=1–6 |year=1994 |month=January |pmid=8282683 |pmc=205007 |url=http://jb.asm.org/cgi/pmidlookup?view=long&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 [[International Committee on Systematic Bacteriology]] (ICSB) maintains international rules for the naming of bacteria and taxonomic categories and for the ranking of them in the [[International Code of Nomenclature of Bacteria]].

The term "bacteria" was traditionally applied to all microscopic, single-celled prokaryotes. However, molecular systematics showed prokaryotic life to consist of two separate [[domain (biology)|domain]]s, originally called ''Eubacteria'' and ''Archaebacteria'', but now called ''Bacteria'' and ''[[Archaea]]'' that evolved independently from an ancient common ancestor.<ref name=autogenerated2 /> 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 |doi=10.1080/10408410091154219}}</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 |doi=10.1016/j.sbi.2005.04.001}}</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.
{{PhylomapA|size=400px|align=left|caption=[[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 |doi=10.1126/science.1123061}}</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 GL, Walker DH |title=Detection of infection or infectious agents by use of cytologic and histologic stains |journal=Clinical Microbiology Reviews |volume=9 |issue=3 |pages=382–404 |year=1996 |month=July |pmid=8809467 |pmc=172900 |url=http://cmr.asm.org/cgi/pmidlookup?view=long&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 name=Thomson/><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|pmid = 8181237}}</ref> 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 |date=8 August 2000|pmid=10951731 |pmc=80298 }}</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= 2005|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. Following present classification, there are fewer than 9,000 known species of bacteria (including cyanobacteria)<ref>[http://www.environment.gov.au/biodiversity/abrs/publications/other/species-numbers/02-exec-summary.html#allspecies ABRS - Numbers of living species in Australia and the World Report - Excutive Summary<!-- Bot generated title -->]</ref>, but attempts to estimate the true level of bacterial diversity have ranged from 10<sup>7</sup> to 10<sup>9</sup> total species - and even these diverse estimates may be off by many orders of magnitude.<ref>{{cite journal |author=Curtis TP, Sloan WT, Scannell JW |title=Estimating prokaryotic diversity and its limits |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=99 |issue=16 |pages=10494–9 |year=2002 |month=August |pmid=12097644 |pmc=124953 |doi=10.1073/pnas.142680199}}</ref><ref>{{cite journal |author=Schloss PD, Handelsman J |title=Status of the microbial census |journal=Microbiology and Molecular Biology Reviews |volume=68 |issue=4 |pages=686–91 |year=2004 |month=December |pmid=15590780 |pmc=539005 |doi=10.1128/MMBR.68.4.686-691.2004}}</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 (biology)|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]].

===Predators===
Some species of bacteria kill and then consume other microorganisms, these species called ''predatory bacteria''.<ref>{{cite journal |author=Martin MO |title=Predatory prokaryotes: an emerging research opportunity |journal=J. Mol. Microbiol. Biotechnol. |volume=4 |issue=5 |pages=467–77 |year=2002 |month=September |pmid=12432957}}</ref> These include organisms such as ''[[Myxococcus xanthus]]'', which forms swarms of cells that kill and digest any bacteria they encounter.<ref>{{cite journal |author=Velicer GJ, Stredwick KL |title=Experimental social evolution with Myxococcus xanthus |journal=Antonie Van Leeuwenhoek |volume=81 |issue=1-4 |pages=155–64 |year=2002 |month=August |pmid=12448714 |doi=10.1023/A:1020546130033}}</ref> Other bacterial predators either attach to their prey in order to digest them and absorb nutrients, such as ''[[Vampirococcus]]'', or invade another cell and multiply inside the cytosol, such as ''Daptobacter''.<ref>{{cite journal |author=Guerrero R, Pedros-Alio C, Esteve I, Mas J, Chase D, Margulis L |title=Predatory prokaryotes: predation and primary consumption evolved in bacteria |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=83 |issue= |pages=2138–42 |year=1986 |month=April |pmid=11542073 |pmc=323246 |doi= 10.1073/pnas.83.7.2138|url=http://www.pnas.org/cgi/pmidlookup?view=long&pmid=11542073}}</ref> These predatory bacteria are thought to have evolved from [[Detritivore|saprophages]] that consumed dead microorganisms, through adaptations that allowed them to entrap and kill other organisms.<ref>{{cite journal |author=Velicer GJ, Mendes-Soares H |title=Bacterial predators |journal=Current Biology |volume=19 |issue=2 |pages=R55–R56 |year=2009 |month=January|doi=10.1016/j.cub.2008.10.043 |pmid=19174136 |last1=Velicer |first1=GJ |last2=Mendes-Soares |first2=H}}</ref>

===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 acid]]s 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 |doi=10.1111/j.1462-2920.2006.00989.x}}</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 |doi=10.1093/jxb/eri197}}</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 |doi=10.1038/sj.embor.7400731 |pmc=1500832}}</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 |doi=10.1111/j.1365-2958.2006.05056.x}}</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|pmid = 2109988 |doi=10.3109/07853899009147239}}</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 |date=1 May 2005|pmid=15867327 }}</ref>

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

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 [[Inflammation|inflammatory response]] producing [[shock (circulatory)|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=2002|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 parasite]]s 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|pmid = 14706098 |doi=10.1046/j.1462-5822.2003.00352.x}}</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 ER |title=Diseases associated with immunosuppression |journal=Environmental Health Perspectives |volume=43 |issue= |pages=9–19 |year=1982 |month=February |pmid=7037390 |pmc=1568899 |doi=10.2307/3429162}}</ref><ref name="Saiman">{{cite journal |author=Saiman L |title=Microbiology of early CF lung disease |journal=Paediatric Respiratory Reviews |volume=5 Suppl A |issue= |pages=S367–9 |year=2004 |pmid=14980298}}</ref>

[[File:Bacterial infections and involved species.png|thumb|left|380px|Overview of bacterial infections and main species involved.<ref name=Microbiology33> {{cite book |author=Fisher, Bruce; Harvey, Richard P.; Champe, Pamela C. |title=Lippincott's Illustrated Reviews: Microbiology (Lippincott's Illustrated Reviews Series) |publisher=Lippincott Williams & Wilkins |location=Hagerstwon, MD |year= 2007|pages=Chapter 33, pages 367–392 |isbn=0-7817-8215-5 |oclc= |doi=}}</ref><ref>[http://www.lef.org/protocols/infections/bacterial_infection_01.htm LEF.org > Bacterial Infections] Updated: 01/19/2006. Retrieved on April 11, 2009</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 |doi=10.1146/annurev.micro.58.030603.123822}}</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 GG |title=Agricultural use of antibiotics and the evolution and transfer of antibiotic-resistant bacteria |journal=CMAJ |volume=159 |issue=9 |pages=1129–36 |year=1998 |month=November |pmid=9835883 |pmc=1229782 |url=http://www.cmaj.ca/cgi/pmidlookup?view=reprint&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 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 [[lactic acid bacteria]] such as ''[[Lactobacillus]]'' and ''[[Lactococcus]]'', 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 |doi=10.1007/s10123-002-0089-5}}</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=10.1385/ABAB:129:1:130}}</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 |doi=10.1016/S0958-1669(99)00040-3}}</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=10.1111/j.1574-6968.2001.tb10489.x}}</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 |doi=10.1002/ps.1221}}</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 |doi=10.1080/10408410490270712}}</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 MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M |title=A functional update of the Escherichia coli K-12 genome |journal=Genome Biology |volume=2 |issue=9 |pages=RESEARCH0035 |year=2001 |pmid=11574054 |pmc=56896 |url=http://genomebiology.com/1465-6906/2/RESEARCH0035 |doi=10.1186/gb-2001-2-9-research0035}}</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 model]]s 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 |doi=10.1038/nature02289}}</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 |pmc=193654}}</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 |doi=10.1007/s00253-004-1809-x}}</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 |doi=10.1002/biot.200500051}}</ref>

==See also==
*[[Biotechnology]]
*[[Extremophile]]s
*[[List of bacterial orders]]
*[[Transgenic bacteria]]
*[[Psychrotrophic bacteria]]
*[[Microorganism]]
*[[International Code of Nomenclature of Bacteria]]

==Notes==
'''α.''' {{Note_label|A|α|none}} The word ''bacteria'' derives from the [[Greek language|Greek]] βακτήριον, ''baktērion'', meaning "small staff".

==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 |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 |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 | date=15 September 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 | pmc=107498 }}
* {{cite book |author=Funke BR, Tortora GJ, Case CL |title=Microbiology: an introduction |edition = 8th |publisher=Benjamin Cummings |location=San Francisco |year=2004 |pages= |isbn=0-8053-7614-3}}
* {{cite book |author=Shively, Jessup M. |title=Complex Intracellular Structures in Prokaryotes (Microbiology Monographs) |publisher=Springer |location=Berlin |year=2006 |isbn=3-540-32524-7}}
* {{cite journal | author=Witzany G, | title=Bio-Communication of Bacteria and their Evolutionary Roots in Natural Genome Editing Competences of Viruses | journal=Open Evol J | year=2008 | volume=2 |pages=44–54 | doi=10.2174/1874404400802010044}}

==External links==
{{Wikispecies}}
{{Sisterlinks}}
* [http://microbewiki.kenyon.edu/index.php/MicrobeWiki MicrobeWiki], an extensive [[wiki]] about [http://microbewiki.kenyon.edu/index.php/Microbial_Biorealm bacteria] and [http://microbewiki.kenyon.edu/index.php/Viral_Biorealm viruses]
* [http://www.ncppb.com Bacteria which affect crops and other plants]
* [http://www.dsmz.de/bactnom/bactname.htm Bacterial Nomenclature Up-To-Date from DSMZ]
* [http://www.bacterio.cict.fr/eubacteria.html Genera of the domain Bacteria] - list of Prokaryotic names with Standing in Nomenclature
* [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.]
* [http://www.newscientist.com/channel/life/dn14094-bacteria-make-major-evolutionary-shift-in-the-lab.html Bacteria Make Major Evolutionary Shift in the Lab]
* [http://ascb.org/ibioseminars/Bassler/Bassler1.cfm Cell-Cell Communication in Bacteria] on-line lecture by [[Bonnie Bassler]], and [http://www.ted.com/index.php/talks/bonnie_bassler_on_how_bacteria_communicate.html TED: Discovering bacteria's amazing communication system ]
* [http://esciencenews.com/articles/2009/02/19/online.collaboration.identifies.bacteria Online collaboration for bacterial taxonomy.]
* [http://www.smartymaps.com/map.php?s=prokaryote Parts of a bacterial cell]
* [http://wormweb.org/bacteriachemo Bacterial Chemotaxis Interactive Simulator] - A web-app that uses several simple algorithms to simulate bacterial chemotaxis.

{{Bacteria classification}}
{{Bacteria}}

[[Category:Bacteria|*]]
[[Category:Bacteriology]]
[[Category:Microbiology]]

{{Link FA|ca}}
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{{Link FA|eu}}
{{Link FA|hu}}
{{Link FA|no}}
{{Link FA|pl}}
{{Link FA|uk}}

[[ace:Bakteri]]
[[af:Bakterie]]
[[ar:بكتيريا]]
[[an:Eubacteria]]
[[ay:Jisk'a laq'u]]
[[az:Bakteriyalar]]
[[bn:ব্যাক্টেরিয়া]]
[[zh-min-nan:Sè-khún]]
[[be-x-old:Бактэрыі]]
[[bs:Bakterije]]
[[br:Bakteri]]
[[bg:Бактерии]]
[[ca:Eubacteri]]
[[cs:Bakterie]]
[[cy:Bacteria]]
[[da:Bakterie]]
[[de:Bakterien]]
[[dv:ބެކްޓީރިޔާ]]
[[et:Bakterid]]
[[el:Βακτήριο]]
[[es:Bacteria]]
[[eo:Bakterioj]]
[[eu:Bakterio]]
[[fa:باکتری]]
[[fo:Bakteria]]
[[fr:Bacteria]]
[[ga:Baictéar]]
[[gl:Bacteria]]
[[ko:세균]]
[[hi:जीवाणु]]
[[hsb:Bakterije]]
[[hr:Bakterije]]
[[io:Bakterio]]
[[ilo:Bacteria]]
[[id:Bakteri]]
[[ia:Bacterio]]
[[is:Gerlar]]
[[it:Bacteria]]
[[he:חיידקים]]
[[kn:ಬ್ಯಾಕ್ಟೀರಿಯ]]
[[ka:ბაქტერიები]]
[[kk:Бактериялар]]
[[sw:Bakteria]]
[[ht:Bakteri]]
[[ku:Bakterî]]
[[la:Bacterium]]
[[lv:Baktērija]]
[[lb:Bakterien]]
[[lt:Bakterijos]]
[[lij:Bacteria]]
[[hu:Baktériumok]]
[[mk:Бактерија]]
[[ml:ബാക്റ്റീരിയ]]
[[mr:जीवाणू]]
[[ms:Bakteria]]
[[mn:Нян]]
[[my:ဗက်တီးရီးယား]]
[[nah:Nemiltōpīllōtl]]
[[nl:Bacteriën]]
[[ja:真正細菌]]
[[no:Bakterier]]
[[nn:Bakterie]]
[[nrm:Bactéthie]]
[[oc:Bactèri]]
[[ps:باکټريا]]
[[nds:Bakterien]]
[[pl:Bakterie]]
[[pt:Bactéria]]
[[kaa:Bakteriya]]
[[ro:Bacterie]]
[[qu:Añaki]]
[[ru:Бактерии]]
[[sah:Бактериялар]]
[[sq:Bakteriologjia]]
[[simple:Bacteria]]
[[sk:Baktérie]]
[[sl:Bakterije]]
[[sr:Бактерија]]
[[sh:Bakterija]]
[[su:Baktéri]]
[[fi:Bakteerit]]
[[sv:Bakterier]]
[[tl:Bakterya]]
[[ta:பாக்டீரியா]]
[[te:బాక్టీరియా]]
[[th:แบคทีเรีย]]
[[tg:Бактерия]]
[[tr:Bakteri]]
[[uk:Бактерії]]
[[vi:Vi khuẩn]]
[[fiu-vro:Pisiläne]]
[[wa:Bactereye]]
[[war:Bakterya]]
[[yi:באקטעריע]]
[[yo:Baktéríà]]
[[bat-smg:Bakterėjės]]
[[zh:细菌]]

Revision as of 08:12, 21 May 2010

BOO! :P

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