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{{about|the microorganisms|the genus|Bacterium (genus)|other uses}}{{pp-semi-indef}}{{pp-move-indef}}{{short description|A domain of prokaryotes – single celled organisms without a nucleus}}{{Use dmy dates|date=March 2014}}{{featured article}}{{Use British English|date=September 2016}}{{Automatic taxobox| name = Bacteria!Nutritional type!Source of energy!Source of carbon!Examples| Phototrophs | Lithotrophs| Organotrophs
3800Archean or earlier â€“ present}}| image = EscherichiaColi NIAID.jpgScanning electron microscope>Scanning electron micrograph of Escherichia coli rods| taxon = BacteriaCarl Woese>Woese, Otto Kandler & Mark Wheelis>Wheelis, 1990| subdivision_ranks = Phyla }}Bacteria ({{IPAc-en|audio=en-us-bacteria.ogg|b|æ|k|ˈ|t|ɪər|i|É™}}; common noun bacteria, singular bacterium) are a type of biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a number of shapes, ranging from spheres to rods and spirals. Bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste,JOURNAL, Fredrickson JK, Zachara JM, Balkwill DL, Kennedy D, Li SM, Kostandarithes HM, Daly MJ, Romine MF, Brockman FJ, Geomicrobiology of high-level nuclear waste-contaminated vadose sediments at the Hanford site, Washington state, Applied and Environmental Microbiology, 70, 7, 4230–41, July 2004, 15240306, 444790, 10.1128/AEM.70.7.4230-4241.2004, and the deep portions of Earth's crust. Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, and only about 27 percent of the bacterial phyla have species that can be grown in the laboratory (specifically unculturable phyla, known as candidate phyla, make up 103 out of approximately 142 known phyla).JOURNAL, Dudek NK, Sun CL, Burstein D, Novel Microbial Diversity and Functional Potential in the Marine Mammal Oral Microbiome, Current Biology, 27, 3752–3762, 2017, 10.1016/j.cub.2017.10.040, The study of bacteria is known as bacteriology, a branch of microbiology.There are typically 40 million bacterial cells in a gram of soil and a million bacterial cells in a millilitre of fresh water. There are approximately 5×1030 bacteria on Earth,JOURNAL, Whitman WB, Coleman DC, Wiebe WJ, Prokaryotes: the unseen majority, Proceedings of the National Academy of Sciences of the United States of America, 95, 12, 6578–83, June 1998, 9618454, 33863, 10.1073/pnas.95.12.6578, 1998PNAS...95.6578W, forming a biomass which exceeds that of all plants and animals.C.Michael Hogan. 2010. Bacteria. Encyclopedia of Earth. eds. Sidney Draggan and C.J.Cleveland, National Council for Science and the Environment, Washington, DC {{webarchive|url=https://web.archive.org/web/20110511132823weblink |date=11 May 2011 }} Bacteria are vital in many stages of the nutrient cycle by recycling nutrients such as the fixation of nitrogen from the atmosphere. The nutrient cycle includes the decomposition of dead bodies; bacteria are responsible for the putrefaction stage in this process.BOOK, Forbes SL, Tibbett M, Carter DO, Soil Analysis in Forensic Taphonomy, CRC Press, 2008, 203–223, Decomposition Chemistry in a Burial Environment, 978-1-4200-6991-4, In the biological communities surrounding hydrothermal vents and cold seeps, extremophile bacteria provide the nutrients needed to sustain life by converting dissolved compounds, such as hydrogen sulphide and methane, to energy. Data reported by researchers in October 2012 and published in March 2013 suggested that bacteria thrive in the Mariana Trench, which, with a depth of up to 11 kilometres, is the deepest known part of the oceans.WEB, Choi, Charles Q, vanc, Microbes Thrive in Deepest Spot on Earth,weblink 17 March 2013, LiveScience, 17 March 2013, no,weblink" title="web.archive.org/web/20130402234623weblink">weblink 2 April 2013, dmy-all, JOURNAL, Glud R, Wenzhöfer F, Middelboe M, Oguri K, Turnewitsch R, Canfield DE, Kitazato H, High rates of microbial carbon turnover in sediments in the deepest oceanic trench on Earth, Nature Geoscience, 2013, 6, 4, 284–88,weblink 10.1038/ngeo1773, 2013NatGe...6..284G, Other researchers reported related studies that microbes thrive inside rocks up to 580 metres below the sea floor under 2.6 kilometres of ocean off the coast of the northwestern United States.WEB, Oskin, Becky, vanc, Intraterrestrials: Life Thrives in Ocean Floor,weblink 14 March 2013, LiveScience, 17 March 2013, no,weblink" title="web.archive.org/web/20130402235647weblink">weblink 2 April 2013, dmy-all, According to one of the researchers, "You can find microbes everywhere—they're extremely adaptable to conditions, and survive wherever they are."The famous notion that bacterial cells in the human body outnumber human cells by a factor of 10:1 has been debunked. There are approximately 39 trillion bacterial cells in the human microbiota as personified by a "reference" 70 kg male 170 cm tall, whereas there are 30 trillion human cells in the body. This means that although they do have the upper hand in actual numbers, it is only by 30%, and not 900%.BIORXIV, Sender R, Fuchs S, Milo R, Revised estimates for the number of human and bacteria cells in the body, 2016, 036103, The largest number exist in the gut flora, and a large number on the skin.JOURNAL, Sears CL, A dynamic partnership: celebrating our gut flora, Anaerobe, 11, 5, 247–51, October 2005, 16701579, 10.1016/j.anaerobe.2005.05.001, The vast majority of the bacteria in the body are rendered harmless by the protective effects of the immune system, though many are beneficial, particularly in the gut flora. However several species of bacteria are pathogenic and cause infectious diseases, including cholera, syphilis, anthrax, leprosy, and bubonic plague. The most common fatal bacterial diseases are respiratory infections, with tuberculosis alone killing about 2 million people per year, mostly in sub-Saharan Africa.WEB,weblink 2002 WHO mortality data, 20 January 2007, no,weblink" title="web.archive.org/web/20131023060502weblink">weblink 23 October 2013, dmy-all, In developed countries, antibiotics are used to treat bacterial infections and are also used in farming, making antibiotic resistance a growing problem. In industry, bacteria are important in sewage treatment and the breakdown of oil spills, the production of cheese and yogurt through fermentation, the recovery of gold, palladium, copper and other metals in the mining sector,NEWS, Metal-Mining Bacteria Are Green Chemists,weblink Science Daily, 2 September 2010, no,weblink 31 August 2017, dmy-all, as well as in biotechnology, and the manufacture of antibiotics and other chemicals.JOURNAL, Ishige T, Honda K, Shimizu S, Whole organism biocatalysis, Current Opinion in Chemical Biology, 9, 2, 174–80, April 2005, 15811802, 10.1016/j.cbpa.2005.02.001, Once regarded as plants constituting the class Schizomycetes, bacteria are now classified as prokaryotes. Unlike cells of animals and other eukaryotes, bacterial cells do not contain a nucleus and rarely harbour membrane-bound organelles. Although the term bacteria traditionally included all prokaryotes, the scientific classification changed after the discovery in the 1990s that prokaryotes consist of two very different groups of organisms that evolved from an ancient common ancestor. These evolutionary domains are called Bacteria and Archaea.JOURNAL, Woese CR, Kandler O, Wheelis ML, Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya, Proceedings of the National Academy of Sciences of the United States of America, 87, 12, 4576–79, June 1990, 2112744, 54159, 10.1073/pnas.87.12.4576, 1990PNAS...87.4576W,

Etymology

{{Life timeline}}The word bacteria is the plural of the New Latin , which is the latinisation of the Greek (bakterion),{{LSJ|bakth/rion|βακτήριον|ref}}. the diminutive of (wikt:βακτηρία|βακτηρία) (bakteria), meaning "staff, cane",{{LSJ|bakthri/a|βακτηρία|shortref}}. because the first ones to be discovered were rod-shaped.bacterium {{webarchive|url=https://web.archive.org/web/20110127131124weblink |date=27 January 2011 }}, on Oxford Dictionaries.{{OEtymD|bacteria}}

Origin and early evolution

{{further|Timeline of evolution|Evolutionary history of life}}The ancestors of modern bacteria were unicellular microorganisms that were the first forms of life to appear on Earth, about 4 billion years ago. For about 3 billion years, most organisms were microscopic, and bacteria and archaea were the dominant forms of life.JOURNAL, Schopf JW, Disparate rates, differing fates: tempo and mode of evolution changed from the Precambrian to the Phanerozoic, Proceedings of the National Academy of Sciences of the United States of America, 91, 15, 6735–42, July 1994, 8041691, 44277, 10.1073/pnas.91.15.6735, 1994PNAS...91.6735S, JOURNAL, DeLong EF, Pace NR, Environmental diversity of bacteria and archaea, Systematic Biology, 50, 4, 470–78, August 2001, 12116647, 10.1080/106351501750435040, 10.1.1.321.8828, Although bacterial fossils exist, such as stromatolites, their lack of distinctive morphology prevents them from being used to examine the history of bacterial evolution, or to date the time of origin of a particular bacterial species. However, gene sequences can be used to reconstruct the bacterial phylogeny, and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage.JOURNAL, Brown JR, Doolittle WF, Archaea and the prokaryote-to-eukaryote transition, Microbiology and Molecular Biology Reviews, 61, 4, 456–502, December 1997, 9409149, 232621, The most recent common ancestor of bacteria and archaea was probably a hyperthermophile that lived about 2.5 billion–3.2 billion years ago.JOURNAL, Di Giulio M, The universal ancestor and the ancestor of bacteria were hyperthermophiles, Journal of Molecular Evolution, 57, 6, 721–30, December 2003, 14745541, 10.1007/s00239-003-2522-6, 2003JMolE..57..721D, JOURNAL, Battistuzzi FU, Feijao A, Hedges SB, A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land, BMC Evolutionary Biology, 4, 44, November 2004, 15535883, 533871, 10.1186/1471-2148-4-44, Bacteria were also involved in the second great evolutionary divergence, that of the archaea and eukaryotes. Here, eukaryotes resulted from the entering of ancient bacteria into endosymbiotic associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea.JOURNAL, Poole AM, Penny D, Evaluating hypotheses for the origin of eukaryotes, BioEssays, 29, 1, 74–84, January 2007, 17187354, 10.1002/bies.20516, JOURNAL, Dyall SD, Brown MT, Johnson PJ, Ancient invasions: from endosymbionts to organelles, Science, 304, 5668, 253–7, April 2004, 15073369, 10.1126/science.1094884, 2004Sci...304..253D, This involved the engulfment by proto-eukaryotic cells of alphaproteobacterial symbionts to form either mitochondria or hydrogenosomes, which are still found in all known Eukarya (sometimes in highly reduced form, e.g. in ancient "amitochondrial" protozoa). Later, some eukaryotes that already contained mitochondria also engulfed cyanobacteria-like organisms, leading to the formation of chloroplasts in algae and plants.JOURNAL, Lang BF, Gray MW, Burger G, Mitochondrial genome evolution and the origin of eukaryotes, Annual Review of Genetics, 33, 351–97, 1999, 10690412, 10.1146/annurev.genet.33.1.351, JOURNAL, McFadden GI, Endosymbiosis and evolution of the plant cell, Current Opinion in Plant Biology, 2, 6, 513–19, December 1999, 10607659, 10.1016/S1369-5266(99)00025-4, This is known as primary endosymbiosis.

Morphology

{{further|Bacterial cell structure#Cell morphology}}File:Bacterial morphology diagram.svg|left|thumb|upright=1.6|alt=a diagram showing bacteria morphology|Bacteria display many cell morphologies and arrangements]]Bacteria display a wide diversity of shapes and sizes, called morphologies. Bacterial cells are about one-tenth the size of eukaryotic cells and are typically 0.5–5.0 micrometres in length. However, a few species are visible to the unaided eye—for example, Thiomargarita namibiensis is up to half a millimetre longJOURNAL, Schulz HN, Jorgensen BB, Big bacteria, Annual Review of Microbiology, 55, 105–37, 2001, 11544351, 10.1146/annurev.micro.55.1.105, and Epulopiscium fishelsoni reaches 0.7 mm.JOURNAL, Williams, Caroline, vanc, 2011, Who are you calling simple?, New Scientist, 211, 2821, 38–41, 10.1016/S0262-4079(11)61709-0, Among the smallest bacteria are members of the genus Mycoplasma, which measure only 0.3 micrometres, as small as the largest viruses.JOURNAL, Robertson J, Gomersall M, Gill P, Mycoplasma hominis: growth, reproduction, and isolation of small viable cells, Journal of Bacteriology, 124, 2, 1007–18, November 1975, 1102522, 235991, Some bacteria may be even smaller, but these ultramicrobacteria are not well-studied.JOURNAL, Velimirov B, 2001, Nanobacteria, Ultramicrobacteria and Starvation Forms: A Search for the Smallest Metabolizing Bacterium, Microbes and Environments, 16, 2, 67–77, 10.1264/jsme2.2001.67, Most bacterial species are either spherical, called cocci (sing. coccus, from Greek kókkos, grain, seed), or rod-shaped, called bacilli (sing. bacillus, from Latin baculus, stick).Dusenbery, David B (2009). Living at Micro Scale, pp. 20–25. Harvard University Press, Cambridge, Massachusetts {{ISBN|978-0-674-03116-6}}. Some bacteria, called vibrio, are shaped like slightly curved rods or comma-shaped; others can be spiral-shaped, called spirilla, or tightly coiled, called spirochaetes. A small number of other unusual shapes have been described, such as star-shaped bacteria.JOURNAL, Yang DC, Blair KM, Salama NR, Staying in Shape: the Impact of Cell Shape on Bacterial Survival in Diverse Environments, Microbiology and Molecular Biology Reviews, 80, 1, 187–203, March 2016, 26864431, 4771367, 10.1128/MMBR.00031-15, This wide variety of shapes is determined by the bacterial cell wall and cytoskeleton, and is important because it can influence the ability of bacteria to acquire nutrients, attach to surfaces, swim through liquids and escape predators.JOURNAL, Cabeen MT, Jacobs-Wagner C, Bacterial cell shape, Nature Reviews. Microbiology, 3, 8, 601–10, August 2005, 16012516, 10.1038/nrmicro1205, JOURNAL, Young KD, The selective value of bacterial shape, Microbiology and Molecular Biology Reviews, 70, 3, 660–703, September 2006, 16959965, 1594593, 10.1128/MMBR.00001-06, File:Relative scale.svg|thumb|The range of sizes shown by prokaryotes, relative to those of other organisms and biomoleculebiomoleculeMany 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 group to form larger multicellular structures, such as the elongated filaments of Actinobacteria, the aggregates of Myxobacteria, and the complex hyphae of Streptomyces.JOURNAL, Claessen D, Rozen DE, Kuipers OP, Søgaard-Andersen L, van Wezel GP, Bacterial solutions to multicellularity: a tale of biofilms, filaments and fruiting bodies, Nature Reviews. Microbiology, 12, 2, 115–24, February 2014, 24384602, 10.1038/nrmicro3178, These multicellular structures are often only seen in certain conditions. For example, when starved of amino acids, Myxobacteria detect surrounding cells in a process known as quorum sensing, migrate towards each other, and aggregate to form fruiting bodies up to 500 micrometres long and containing approximately 100,000 bacterial cells.JOURNAL, Shimkets LJ, Intercellular signaling during fruiting-body development of Myxococcus xanthus, Annual Review of Microbiology, 53, 525–49, 1999, 10547700, 10.1146/annurev.micro.53.1.525, In these fruiting bodies, the bacteria perform separate tasks; for example, about one in ten cells migrate to the top of a fruiting body and differentiate into a specialised dormant state called a myxospore, which is more resistant to drying and other adverse environmental conditions.JOURNAL, Kaiser D, Signaling in myxobacteria, Annual Review of Microbiology, 58, 75–98, 2004, 15487930, 10.1146/annurev.micro.58.030603.123620, Bacteria often attach to surfaces and form dense aggregations called biofilms, and larger formations known as microbial mats. These biofilms and mats can range from a few micrometres in thickness to up to half a metre in depth, and may contain multiple species of bacteria, protists and archaea. Bacteria living in biofilms display a complex arrangement of cells and extracellular components, forming secondary structures, such as microcolonies, through which there are networks of channels to enable better diffusion of nutrients.JOURNAL, Donlan RM, Biofilms: microbial life on surfaces, Emerging Infectious Diseases, 8, 9, 881–90, September 2002, 12194761, 2732559, 10.3201/eid0809.020063, JOURNAL, Branda SS, Vik S, Friedman L, Kolter R, Biofilms: the matrix revisited, Trends in Microbiology, 13, 1, 20–26, January 2005, 15639628, 10.1016/j.tim.2004.11.006, In natural environments, such as soil or the surfaces of plants, the majority of bacteria are bound to surfaces in biofilms.JOURNAL, Davey ME, O'toole GA, Microbial biofilms: from ecology to molecular genetics, Microbiology and Molecular Biology Reviews, 64, 4, 847–67, December 2000, 11104821, 99016, 10.1128/MMBR.64.4.847-867.2000, Biofilms are also important in medicine, as these structures are often present during chronic bacterial infections or in infections of implanted medical devices, and bacteria protected within biofilms are much harder to kill than individual isolated bacteria.JOURNAL, Donlan RM, Costerton JW, Biofilms: survival mechanisms of clinically relevant microorganisms, Clinical Microbiology Reviews, 15, 2, 167–93, April 2002, 11932229, 118068, 10.1128/CMR.15.2.167-193.2002,

Cellular structure

{{further|Bacterial cell structure}}File:Prokaryote cell.svg|thumb|right|alt=Prokaryote cell with structure and parts|Structure and contents of a typical gram-positivegram-positive

Intracellular structures

The bacterial cell is surrounded by a cell membrane which is made primarily of phospholipids. This membrane encloses the contents of the cell and acts as a barrier to hold nutrients, proteins and other essential components of the cytoplasm within the cell.BOOK, Slonczewski JL, Foster JW, Microbiology : an Evolving Science, 2013, W W Norton, New York, 978-0393123678, Third, 82, Unlike eukaryotic cells, bacteria usually lack large membrane-bound structures in their cytoplasm such as a nucleus, mitochondria, chloroplasts and the other organelles present in eukaryotic cells.BOOK, Lodish H, Berk A, Kaiser CA, Krieger M, Bretscher A, Ploegh H, Amon A, Scott MP, Molecular Cell Biology, 7th, WH Freeman, 2013, 978-1429234139, 13, However, some bacteria have protein-bound organelles in the cytoplasm which compartmentalize aspects of bacterial metabolism,JOURNAL, Bobik TA, Polyhedral organelles compartmenting bacterial metabolic processes, Applied Microbiology and Biotechnology, 70, 5, 517–25, May 2006, 16525780, 10.1007/s00253-005-0295-0, JOURNAL, Yeates TO, Kerfeld CA, Heinhorst S, Cannon GC, Shively JM, Protein-based organelles in bacteria: carboxysomes and related microcompartments, Nature Reviews. Microbiology, 6, 9, 681–91, September 2008, 18679172, 10.1038/nrmicro1913, such as the carboxysome.JOURNAL, Kerfeld CA, Sawaya MR, Tanaka S, Nguyen CV, Phillips M, Beeby M, Yeates TO, Protein structures forming the shell of primitive bacterial organelles, Science, 309, 5736, 936–38, August 2005, 16081736, 10.1126/science.1113397, 2005Sci...309..936K, 10.1.1.1026.896, Additionally, bacteria have a multi-component cytoskeleton to control the localisation of proteins and nucleic acids within the cell, and to manage the process of cell division.JOURNAL, Gitai Z, The new bacterial cell biology: moving parts and subcellular architecture, Cell, 120, 5, 577–86, March 2005, 15766522, 10.1016/j.cell.2005.02.026, JOURNAL, Shih YL, Rothfield L, The bacterial cytoskeleton, Microbiology and Molecular Biology Reviews, 70, 3, 729–54, September 2006, 16959967, 1594594, 10.1128/MMBR.00017-06, JOURNAL, Norris V, den Blaauwen T, Cabin-Flaman A, Doi RH, Harshey R, Janniere L, Jimenez-Sanchez A, Jin DJ, Levin PA, Mileykovskaya E, Minsky A, Saier M, Skarstad K, Functional taxonomy of bacterial hyperstructures, Microbiology and Molecular Biology Reviews, 71, 1, 230–53, March 2007, 17347523, 1847379, 10.1128/MMBR.00035-06, Many important biochemical reactions, such as energy generation, occur due to concentration gradients across membranes, creating a potential difference analogous to a battery. The general lack of internal membranes in bacteria means these reactions, such as electron transport, occur across the cell membrane between the cytoplasm and the outside of the cell or periplasm.JOURNAL, Harold FM, Conservation and transformation of energy by bacterial membranes, Bacteriological Reviews, 36, 2, 172–230, June 1972, 4261111, 408323, However, in many photosynthetic bacteria the plasma membrane is highly folded and fills most of the cell with layers of light-gathering membrane.JOURNAL, Bryant DA, Frigaard NU, Prokaryotic photosynthesis and phototrophy illuminated, Trends in Microbiology, 14, 11, 488–96, November 2006, 16997562, 10.1016/j.tim.2006.09.001, These light-gathering complexes may even form lipid-enclosed structures called chlorosomes in green sulfur bacteria.JOURNAL, Psencík J, Ikonen TP, Laurinmäki P, Merckel MC, Butcher SJ, Serimaa RE, Tuma R, Lamellar organization of pigments in chlorosomes, the light harvesting complexes of green photosynthetic bacteria, Biophysical Journal, 87, 2, 1165–72, August 2004, 15298919, 1304455, 10.1529/biophysj.104.040956, 2004BpJ....87.1165P, File:Carboxysomes EM ptA.jpg|thumb|An electron micrograph of Halothiobacillus neapolitanusHalothiobacillus neapolitanusBacteria do not have a membrane-bound nucleus, and their genetic material is typically a single circular bacterial chromosome of DNA located in the cytoplasm in an irregularly shaped body called the nucleoid.JOURNAL, Thanbichler M, Wang SC, Shapiro L, The bacterial nucleoid: a highly organized and dynamic structure, Journal of Cellular Biochemistry, 96, 3, 506–21, October 2005, 15988757, 10.1002/jcb.20519, The nucleoid contains the chromosome with its associated proteins and RNA. Like all other organisms, bacteria contain ribosomes for the production of proteins, but the structure of the bacterial ribosome is different from that of eukaryotes and Archaea.JOURNAL, Poehlsgaard J, Douthwaite S, The bacterial ribosome as a target for antibiotics, Nature Reviews. Microbiology, 3, 11, 870–81, November 2005, 16261170, 10.1038/nrmicro1265, Some bacteria produce intracellular nutrient storage granules, such as glycogen,JOURNAL, Yeo M, Chater K, The interplay of glycogen metabolism and differentiation provides an insight into the developmental biology of Streptomyces coelicolor, Microbiology, 151, Pt 3, 855–61, March 2005, 15758231, 10.1099/mic.0.27428-0,weblink no,weblink" title="web.archive.org/web/20070929092242weblink">weblink 29 September 2007, dmy-all, polyphosphate,JOURNAL, Shiba T, Tsutsumi K, Ishige K, Noguchi T, Inorganic polyphosphate and polyphosphate kinase: their novel biological functions and applications, Biochemistry. Biokhimiia, 65, 3, 315–23, March 2000, 10739474,weblink no,weblink" title="web.archive.org/web/20060925070012weblink">weblink 25 September 2006, dmy-all, sulfurJOURNAL, Brune DC, Isolation and characterization of sulfur globule proteins from Chromatium vinosum and Thiocapsa roseopersicina, Archives of Microbiology, 163, 6, 391–99, June 1995, 7575095, 10.1007/BF00272127, or polyhydroxyalkanoates.JOURNAL, Kadouri D, Jurkevitch E, Okon Y, Castro-Sowinski S, Ecological and agricultural significance of bacterial polyhydroxyalkanoates, Critical Reviews in Microbiology, 31, 2, 55–67, 2005, 15986831, 10.1080/10408410590899228, Certain bacterial species, such as the photosynthetic Cyanobacteria, produce internal gas vacuoles which they use to regulate their buoyancy, allowing them to move up or down into water layers with different light intensities and nutrient levels.JOURNAL, Walsby AE, Gas vesicles, Microbiological Reviews, 58, 1, 94–144, March 1994, 8177173, 372955,

Extracellular structures

{{further|Cell envelope}}Around the outside of the cell membrane is the cell wall. Bacterial cell walls are made of peptidoglycan (also called murein), which is made from polysaccharide chains cross-linked by peptides containing D-amino acids.JOURNAL, van Heijenoort J, Formation of the glycan chains in the synthesis of bacterial peptidoglycan, Glycobiology, 11, 3, 25R–36R, March 2001, 11320055, 10.1093/glycob/11.3.25R, Bacterial cell walls are different from the cell walls of plants and fungi, which are made of cellulose and chitin, respectively.JOURNAL, Koch AL, Bacterial wall as target for attack: past, present, and future research, Clinical Microbiology Reviews, 16, 4, 673–87, October 2003, 14557293, 207114, 10.1128/CMR.16.4.673-687.2003, 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.There are broadly speaking two different types of cell wall in bacteria, that classify bacteria into gram-positive bacteria and gram-negative bacteria. The names originate from the reaction of cells to the Gram stain, a long-standing test for the classification of bacterial species.JOURNAL, Gram, HC, Hans Christian Gram, 1884, Ãœber die isolierte Färbung der Schizomyceten in Schnitt- und Trockenpräparaten, Fortschr. Med., 2, 185–89, Gram-positive bacteria possess a thick cell wall containing many layers of peptidoglycan and teichoic acids. In contrast, gram-negative bacteria have a relatively thin cell wall consisting of a few layers of peptidoglycan surrounded by a second lipid membrane containing lipopolysaccharides and lipoproteins. Most bacteria have the gram-negative cell wall, and only the Firmicutes and Actinobacteria (previously known as the low G+C and high G+C gram-positive bacteria, respectively) have the alternative gram-positive arrangement.JOURNAL, Hugenholtz P, Exploring prokaryotic diversity in the genomic era, Genome Biology, 3, 2, REVIEWS0003, 2002, 11864374, 139013, 10.1186/gb-2002-3-2-reviews0003, These differences in structure can produce differences in antibiotic susceptibility; for instance, vancomycin can kill only gram-positive bacteria and is ineffective against gram-negative pathogens, such as Haemophilus influenzae or Pseudomonas aeruginosa.JOURNAL, Walsh FM, Amyes SG, Microbiology and drug resistance mechanisms of fully resistant pathogens, Current Opinion in Microbiology, 7, 5, 439–44, October 2004, 15451497, 10.1016/j.mib.2004.08.007, Some bacteria have cell wall structures that are neither classically gram-positive or gram-negative. This includes clinically important bacteria such as Mycobacteria which have a thick peptidoglycan cell wall like a gram-positive bacterium, but also a second outer layer of lipids.JOURNAL, Alderwick LJ, Harrison J, Lloyd GS, Birch HL, The Mycobacterial Cell Wall – Peptidoglycan and Arabinogalactan, Cold Spring Harbor Perspectives in Medicine, 5, 8, a021113, March 2015, 25818664, 4526729, 10.1101/cshperspect.a021113, In many bacteria, an S-layer of rigidly arrayed protein molecules covers the outside of the cell.JOURNAL, Engelhardt H, Peters J, Structural research on surface layers: a focus on stability, surface layer homology domains, and surface layer-cell wall interactions, Journal of Structural Biology, 124, 2–3, 276–302, December 1998, 10049812, 10.1006/jsbi.1998.4070, This layer provides chemical and physical protection for the cell surface and can act as a macromolecular diffusion barrier. S-layers have diverse but mostly poorly understood functions, but are known to act as virulence factors in Campylobacter and contain surface enzymes in Bacillus stearothermophilus.JOURNAL, Beveridge TJ, Pouwels PH, Sára M, Kotiranta A, Lounatmaa K, Kari K, Kerosuo E, Haapasalo M, Egelseer EM, Schocher I, Sleytr UB, Morelli L, Callegari ML, Nomellini JF, Bingle WH, Smit J, Leibovitz E, Lemaire M, Miras I, Salamitou S, Béguin P, Ohayon H, Gounon P, Matuschek M, Koval SF, Functions of S-layers, FEMS Microbiology Reviews, 20, 1–2, 99–149, June 1997, 9276929, 10.1016/S0168-6445(97)00043-0, File:EMpylori.jpg|thumb|left|alt=Helicobacter pylori electron micrograph, showing multiple flagella on the cell surface|Helicobacter pyloriHelicobacter pyloriFlagella are rigid protein structures, about 20 nanometres in diameter and up to 20 micrometres in length, that are used for motility. Flagella are driven by the energy released by the transfer of ions down an electrochemical gradient across the cell membrane.BOOK, Kojima S, Blair DF, The bacterial flagellar motor: structure and function of a complex molecular machine, 233, 93–134, 2004, 15037363, 10.1016/S0074-7696(04)33003-2, 978-0-12-364637-8, International Review of Cytology, Fimbriae (sometimes called "attachment pili") are fine filaments of protein, usually 2–10 nanometres in diameter and up to several micrometres 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.JOURNAL, Beachey EH, Bacterial adherence: adhesin-receptor interactions mediating the attachment of bacteria to mucosal surface, The Journal of Infectious Diseases, 143, 3, 325–45, March 1981, 7014727, 10.1093/infdis/143.3.325, Pili (sing. pilus) are cellular appendages, slightly larger than fimbriae, that can transfer genetic material between bacterial cells in a process called conjugation where they are called conjugation pili or sex pili (see bacterial genetics, below).JOURNAL, Silverman PM, Towards a structural biology of bacterial conjugation, Molecular Microbiology, 23, 3, 423–29, February 1997, 9044277, 10.1046/j.1365-2958.1997.2411604.x, They can also generate movement where they are called type IV pili.JOURNAL, Costa TR, Felisberto-Rodrigues C, Meir A, Prevost MS, Redzej A, Trokter M, Waksman G, Secretion systems in Gram-negative bacteria: structural and mechanistic insights, Nature Reviews. Microbiology, 13, 6, 343–59, June 2015, 25978706, 10.1038/nrmicro3456, Glycocalyx is produced by many bacteria to surround their cells, and varies in structural complexity: ranging from a disorganised slime layer of extracellular polymeric substances to a highly structured capsule. These structures can protect cells from engulfment by eukaryotic cells such as macrophages (part of the human immune system).JOURNAL, Stokes RW, Norris-Jones R, Brooks DE, Beveridge TJ, Doxsee D, Thorson LM, 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, Infection and Immunity, 72, 10, 5676–86, October 2004, 15385466, 517526, 10.1128/IAI.72.10.5676-5686.2004, They can also act as antigens and be involved in cell recognition, as well as aiding attachment to surfaces and the formation of biofilms.JOURNAL, Daffé M, Etienne G, The capsule of Mycobacterium tuberculosis and its implications for pathogenicity, Tubercle and Lung Disease, 79, 3, 153–69, 1999, 10656114, 10.1054/tuld.1998.0200, The assembly of these extracellular structures is dependent on bacterial secretion systems. These transfer proteins from the cytoplasm into the periplasm or into the environment around the cell. Many types of secretion systems are known and these structures are often essential for the virulence of pathogens, so are intensively studied.JOURNAL, Finlay BB, Falkow S, Common themes in microbial pathogenicity revisited, Microbiology and Molecular Biology Reviews, 61, 2, 136–69, June 1997, 9184008, 232605,

Endospores

{{further|Endospore}}File:Gram Stain Anthrax.jpg|thumb|right|alt=Anthrax stained purple|Bacillus anthracis (stained purple) growing in cerebrospinal fluidcerebrospinal fluidCertain genera of gram-positive bacteria, such as Bacillus, Clostridium, Sporohalobacter, Anaerobacter, and Heliobacterium, can form highly resistant, dormant structures called endospores.JOURNAL, Nicholson WL, Munakata N, Horneck G, Melosh HJ, Setlow P, Resistance of Bacillus endospores to extreme terrestrial and extraterrestrial environments, Microbiology and Molecular Biology Reviews, 64, 3, 548–72, September 2000, 10974126, 99004, 10.1128/MMBR.64.3.548-572.2000, Endospores develop within the cytoplasm of the cell; generally a single endospore develops in each cell.JOURNAL, McKenney PT, Driks A, Eichenberger P, The Bacillus subtilis endospore: assembly and functions of the multilayered coat, Nature Reviews. Microbiology, 11, 1, 33–44, January 2013, 23202530, 10.1038/nrmicro2921, Each endospore contains a core of DNA and ribosomes surrounded by a cortex layer and protected by a multilayer rigid coat composed of peptidoglycan and a variety of proteins.Endospores show no detectable metabolism and can survive extreme physical and chemical stresses, such as high levels of UV light, gamma radiation, detergents, disinfectants, heat, freezing, pressure, and desiccation.JOURNAL, Nicholson WL, Fajardo-Cavazos P, Rebeil R, Slieman TA, Riesenman PJ, Law JF, Xue Y, Bacterial endospores and their significance in stress resistance, Antonie van Leeuwenhoek, 81, 1–4, 27–32, August 2002, 12448702, 10.1023/A:1020561122764, In this dormant state, these organisms may remain viable for millions of years,JOURNAL, Vreeland RH, Rosenzweig WD, Powers DW, Isolation of a 250 million-year-old halotolerant bacterium from a primary salt crystal, Nature, 407, 6806, 897–900, October 2000, 11057666, 10.1038/35038060, 2000Natur.407..897V, JOURNAL, Cano RJ, Borucki MK, Revival and identification of bacterial spores in 25- to 40-million-year-old Dominican amber, Science, 268, 5213, 1060–64, May 1995, 7538699, 10.1126/science.7538699, 1995Sci...268.1060C, and endospores even allow bacteria to survive exposure to the vacuum and radiation in space.JOURNAL, Nicholson WL, Schuerger AC, Setlow P, The solar UV environment and bacterial spore UV resistance: considerations for Earth-to-Mars transport by natural processes and human spaceflight, Mutation Research, 571, 1–2, 249–64, April 2005, 15748651, 10.1016/j.mrfmmm.2004.10.012, 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.JOURNAL, Hatheway CL, Toxigenic clostridia, Clinical Microbiology Reviews, 3, 1, 66–98, January 1990, 2404569, 358141, 10.1128/CMR.3.1.66,

Metabolism

{{further|Microbial metabolism}}Bacteria exhibit an extremely wide variety of metabolic types.JOURNAL, Nealson KH, Post-Viking microbiology: new approaches, new data, new insights, Origins of Life and Evolution of the Biosphere, 29, 1, 73–93, January 1999, 11536899, 10.1023/A:1006515817767, 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.JOURNAL, Xu J, Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances, Molecular Ecology, 15, 7, 1713–31, June 2006, 16689892, 10.1111/j.1365-294X.2006.02882.x, Bacterial metabolism is classified into nutritional groups on the basis of three major criteria: the source of energy, the electron donors used, and the source of carbon used for growth.JOURNAL, Zillig W, Comparative biochemistry of Archaea and Bacteria, Current Opinion in Genetics & Development, 1, 4, 544–51, December 1991, 1822288, 10.1016/S0959-437X(05)80206-0, Bacteria either derive energy from light using photosynthesis (called phototrophy), or by breaking down chemical compounds using oxidation (called chemotrophy).BOOK, Microbiology: An Evolving Science, Slonczewski JL, Foster JW, 3, WW Norton & Company, 491–44, Chemotrophs use chemical compounds as a source of energy by transferring electrons from a given electron donor to a terminal electron acceptor in a redox reaction. This reaction releases energy that can be used to drive metabolism. Chemotrophs are further divided by the types of compounds they use to transfer electrons. Bacteria that use inorganic compounds such as hydrogren, carbon monoxide, or ammonia as sources of electrons are called lithotrophs, while those that use organic compounds are called organotrophs. The compounds used to receive electrons are also used to classify bacteria: aerobic organisms use oxygen as the terminal electron acceptor, while anaerobic organisms use other compounds such as nitrate, sulfate, or carbon dioxide.Many bacteria get their carbon from other organic carbon, called heterotrophy. Others such as cyanobacteria and some purple bacteria are autotrophic, meaning that they obtain cellular carbon by fixing carbon dioxide.JOURNAL, Hellingwerf KJ, Crielaard W, Hoff WD, Matthijs HC, Mur LR, van Rotterdam BJ, Photobiology of bacteria, Antonie van Leeuwenhoek, 65, 4, 331–47, 1994, 7832590, 10.1007/BF00872217,weblink Submitted manuscript, In unusual circumstances, the gas methane can be used by methanotrophic bacteria as both a source of electrons and a substrate for carbon anabolism.JOURNAL, Dalton H, The Leeuwenhoek Lecture 2000 the natural and unnatural history of methane-oxidizing bacteria, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 360, 1458, 1207–22, June 2005, 16147517, 1569495, 10.1098/rstb.2005.1657, {|class="wikitable" style="margin-left: auto; margin-right: auto;"|+ Nutritional types in bacterial metabolism
Sunlight Organic compounds (photoheterotrophs) or carbon fixation (photoautotrophs)Cyanobacteria, Green sulfur bacteria, Chloroflexi (phylum)>Chloroflexi, or Purple bacteria 
Inorganic compounds Organic compounds (lithoheterotrophs) or carbon fixation (lithoautotrophs)| Thermodesulfobacteria, Hydrogenophilaceae, or Nitrospirae 
Organic compounds Organic compounds (chemoheterotrophs) or carbon fixation (chemoautotrophs)  | Bacillus, Clostridium or Enterobacteriaceae 
In many ways, bacterial metabolism provides traits that are useful for ecological stability and for human society. One example is that some bacteria have the ability to fix nitrogen gas using the enzyme nitrogenase. This environmentally important trait can be found in bacteria of most metabolic types listed above.JOURNAL, Zehr JP, Jenkins BD, Short SM, Steward GF, Nitrogenase gene diversity and microbial community structure: a cross-system comparison, Environmental Microbiology, 5, 7, 539–54, July 2003, 12823187, 10.1046/j.1462-2920.2003.00451.x, This leads to the ecologically important processes of denitrification, sulfate reduction, and acetogenesis, respectively.JOURNAL, Zumft WG, Cell biology and molecular basis of denitrification, Microbiology and Molecular Biology Reviews, 61, 4, 533–616, December 1997, 9409151, 232623, JOURNAL, Drake HL, Daniel SL, Küsel K, Matthies C, Kuhner C, Braus-Stromeyer S, Acetogenic bacteria: what are the in situ consequences of their diverse metabolic versatilities?, BioFactors, 6, 1, 13–24, 1997, 9233536, 10.1002/biof.5520060103, Bacterial metabolic processes are also important in biological responses to pollution; for example, sulfate-reducing bacteria are largely responsible for the production of the highly toxic forms of mercury (methyl- and dimethylmercury) in the environment.JOURNAL, Morel FM, Kraepiel AM, Amyot M, 1998, The chemical cycle and bioaccumulation of mercury, Annual Review of Ecology and Systematics, 29, 543–66, 10.1146/annurev.ecolsys.29.1.543, Non-respiratory anaerobes use fermentation to generate energy and reducing power, secreting metabolic by-products (such as ethanol in brewing) as waste. Facultative anaerobes can switch between fermentation and different terminal electron acceptors depending on the environmental conditions in which they find themselves.

Growth and reproduction

File:Three cell growth types.svg|thumb|upright=1.15|alt=drawing of showing the processes of binary fission, mitosis, and meiosis|Many bacteria reproduce through binary fission, which is compared to mitosis and meiosismeiosis{{further|Bacterial growth}}Unlike in multicellular organisms, increases in cell size (cell growth) and 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.JOURNAL, Koch AL, Control of the bacterial cell cycle by cytoplasmic growth, Critical Reviews in Microbiology, 28, 1, 61–77, 2002, 12003041, 10.1080/1040-840291046696, Under optimal conditions, bacteria can grow and divide extremely rapidly, and bacterial populations can double as quickly as every 9.8 minutes.JOURNAL, Eagon RG, Pseudomonas natriegens, a marine bacterium with a generation time of less than 10 minutes, Journal of Bacteriology, 83, 4, 736–37, April 1962, 13888946, 279347, In cell division, two identical clone daughter cells are produced. Some bacteria, while still reproducing asexually, form more complex reproductive structures that help disperse the newly formed daughter cells. Examples include fruiting body formation by Myxobacteria and aerial hyphae formation by Streptomyces, or budding. Budding involves a cell forming a protrusion that breaks away and produces a daughter cell.File:E.-coli-growth.gif|thumb|left|alt=E. coli colony |A colony of Escherichia coliEscherichia coliIn the laboratory, bacteria are usually grown using solid or liquid media. Solid growth media, such as agar plates, are used to isolate pure cultures of a bacterial strain. However, liquid growth media are used when measurement of growth or large volumes of cells are required. Growth in stirred liquid media occurs as an even cell suspension, making the cultures easy to divide and transfer, although isolating single bacteria from liquid media is difficult. The use of selective media (media with specific nutrients added or deficient, or with antibiotics added) can help identify specific organisms.JOURNAL, Thomson RB, Bertram H, Laboratory diagnosis of central nervous system infections, Infectious Disease Clinics of North America, 15, 4, 1047–71, December 2001, 11780267, 10.1016/S0891-5520(05)70186-0, 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 (and cyanobacterial) blooms that often occur in lakes during the summer.JOURNAL, Paerl HW, Fulton RS, Moisander PH, Dyble J, Harmful freshwater algal blooms, with an emphasis on cyanobacteria, TheScientificWorldJournal, 1, 76–113, April 2001, 12805693, 6083932, 10.1100/tsw.2001.16, Other organisms have adaptations to harsh environments, such as the production of multiple antibiotics by Streptomyces that inhibit the growth of competing microorganisms.JOURNAL, Challis GL, Hopwood DA, Synergy and contingency as driving forces for the evolution of multiple secondary metabolite production by Streptomyces species, Proceedings of the National Academy of Sciences of the United States of America, 100 Suppl 2, 90002, 14555–61, November 2003, 12970466, 304118, 10.1073/pnas.1934677100, 2003PNAS..10014555C, In nature, many organisms live in communities (e.g., biofilms) that may allow for increased supply of nutrients and protection from environmental stresses. These relationships can be essential for growth of a particular organism or group of organisms (syntrophy).JOURNAL, Kooijman SA, Auger P, Poggiale JC, Kooi BW, Quantitative steps in symbiogenesis and the evolution of homeostasis, Biological Reviews of the Cambridge Philosophical Society, 78, 3, 435–63, August 2003, 14558592, 10.1017/S1464793102006127, Bacterial growth follows four phases. When a population of bacteria first enter a high-nutrient environment that allows growth, the cells need to adapt to their new environment. The first phase of growth is the lag phase, a period of slow growth when the cells are adapting to the high-nutrient environment and preparing for fast growth. The lag phase has high biosynthesis rates, as proteins necessary for rapid growth are produced.JOURNAL, Prats C, López D, Giró A, Ferrer J, Valls J, Individual-based modelling of bacterial cultures to study the microscopic causes of the lag phase, Journal of Theoretical Biology, 241, 4, 939–53, August 2006, 16524598, 10.1016/j.jtbi.2006.01.029, The second phase of growth is the logarithmic 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 third phase of growth is the stationary phase and is caused by depleted nutrients. The cells reduce their metabolic activity and consume non-essential cellular proteins. The stationary phase is a transition from rapid growth to a stress response state and there is increased expression of genes involved in DNA repair, antioxidant metabolism and nutrient transport.BOOK, Hecker M, Völker U, General stress response of Bacillus subtilis and other bacteria, 44, 35–91, 2001, 11407115, 10.1016/S0065-2911(01)44011-2, 978-0-12-027744-5, Advances in Microbial Physiology, The final phase is the death phase where the bacteria run out of nutrients and die.BOOK, Microbiology: An Evolving Science, Slonczewski JL, Foster JW, 3, WW Norton & Company, 143,

Genetics

Most bacteria have a single circular chromosome that can range in size from only 160,000 base pairs in the endosymbiotic bacteria Carsonella ruddii,JOURNAL, Nakabachi A, Yamashita A, Toh H, Ishikawa H, Dunbar HE, Moran NA, Hattori M, The 160-kilobase genome of the bacterial endosymbiont Carsonella, Science, 314, 5797, 267, October 2006, 17038615, 10.1126/science.1134196, to 12,200,000 base pairs (12.2 Mbp) in the soil-dwelling bacteria Sorangium cellulosum.JOURNAL, Pradella S, Hans A, Spröer C, Reichenbach H, Gerth K, Beyer S, Characterisation, genome size and genetic manipulation of the myxobacterium Sorangium cellulosum So ce56, Archives of Microbiology, 178, 6, 484–92, December 2002, 12420170, 10.1007/s00203-002-0479-2, There are many exceptions to this, for example some Streptomyces and Borrelia species contain a single linear chromosome,JOURNAL, Hinnebusch J, Tilly K, Linear plasmids and chromosomes in bacteria, Molecular Microbiology, 10, 5, 917–22, December 1993, 7934868, 10.1111/j.1365-2958.1993.tb00963.x, JOURNAL, Lin YS, Kieser HM, Hopwood DA, Chen CW, The chromosomal DNA of Streptomyces lividans 66 is linear, Molecular Microbiology, 10, 5, 923–33, December 1993, 7934869, 10.1111/j.1365-2958.1993.tb00964.x, while some Vibrio species contain more than one chromosome.JOURNAL, Val ME, Soler-Bistué A, Bland MJ, Mazel D, Management of multipartite genomes: the Vibrio cholerae model, Current Opinion in Microbiology, 22, 120–26, December 2014, 25460805, 10.1016/j.mib.2014.10.003, Bacteria can also contain plasmids, small extra-chromosomal DNAs that may contain genes for various useful functions such as antibiotic resistance, metabolic capabilities, or various virulence factors.BOOK, Kado CI, Historical Events That Spawned the Field of Plasmid Biology, Microbiology Spectrum, 2, 5, 3, October 2014, 26104369, 10.1128/microbiolspec.PLAS-0019-2013, 9781555818975, Bacteria genomes usually encode a few hundred to a few thousand genes. The genes in bacterial genomes are usually a single continuous stretch of DNA and although several different types of introns do exist in bacteria, these are much rarer than in eukaryotes.JOURNAL, Belfort M, Reaban ME, Coetzee T, Dalgaard JZ, Prokaryotic introns and inteins: a panoply of form and function, Journal of Bacteriology, 177, 14, 3897–903, July 1995, 7608058, 177115, 10.1128/jb.177.14.3897-3903.1995, Bacteria, as asexual organisms, inherit an identical copy of the parent's genomes and are clonal. However, all bacteria can evolve by selection on changes to their genetic material DNA caused by genetic recombination or mutations. Mutations come from errors made during the replication of DNA or from exposure to mutagens. Mutation rates vary widely among different species of bacteria and even among different clones of a single species of bacteria.JOURNAL, Denamur E, Matic I, Evolution of mutation rates in bacteria, Molecular Microbiology, 60, 4, 820–27, May 2006, 16677295, 10.1111/j.1365-2958.2006.05150.x, 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.JOURNAL, Wright BE, Stress-directed adaptive mutations and evolution, Molecular Microbiology, 52, 3, 643–50, May 2004, 15101972, 10.1111/j.1365-2958.2004.04012.x, Some bacteria also transfer genetic material between cells. This can occur in three main ways. First, bacteria can take up exogenous DNA from their environment, in a process called transformation.JOURNAL, Chen I, Dubnau D, DNA uptake during bacterial transformation, Nature Reviews. Microbiology, 2, 3, 241–49, March 2004, 15083159, 10.1038/nrmicro844, Many bacteria can naturally take up DNA from the environment, while others must be chemically altered in order to induce them to take up DNA.JOURNAL, Johnsborg O, Eldholm V, Håvarstein LS, Natural genetic transformation: prevalence, mechanisms and function, Research in Microbiology, 158, 10, 767–78, December 2007, 17997281, 10.1016/j.resmic.2007.09.004, The development of competence in nature is usually associated with stressful environmental conditions, and seems to be an adaptation for facilitating repair of DNA damage in recipient cells.Bernstein H, Bernstein C, Michod RE (2012). "DNA repair as the primary adaptive function of sex in bacteria and eukaryotes". Chapter 1: pp. 1–49 in: DNA Repair: New Research, Sakura Kimura and Sora Shimizu (eds.). Nova Sci. Publ., Hauppauge, NY {{ISBN|978-1-62100-808-8}}. The second way bacteria transfer genetic material is by transduction, when the integration of a bacteriophage introduces foreign DNA into the chromosome. Many types of bacteriophage exist, some simply infect and lyse their host bacteria, while others insert into the bacterial chromosome.JOURNAL, Brüssow H, Canchaya C, Hardt WD, Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion, Microbiology and Molecular Biology Reviews, 68, 3, 560–602, table of contents, September 2004, 15353570, 515249, 10.1128/MMBR.68.3.560-602.2004, Bacteria resist phage infection through restriction modification systems that degrade foreign DNA,JOURNAL, Bickle TA, Krüger DH, Biology of DNA restriction, Microbiological Reviews, 57, 2, 434–50, June 1993, 8336674, 372918, 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.JOURNAL, Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P, CRISPR provides acquired resistance against viruses in prokaryotes, Science, 315, 5819, 1709–12, March 2007, 17379808, 10.1126/science.1138140, 2007Sci...315.1709B, JOURNAL, Brouns SJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJ, Snijders AP, Dickman MJ, Makarova KS, Koonin EV, van der Oost J, Small CRISPR RNAs guide antiviral defense in prokaryotes, Science, 321, 5891, 960–64, August 2008, 18703739, 5898235, 10.1126/science.1159689, 2008Sci...321..960B, The third method of gene transfer is conjugation, whereby DNA is transferred through direct cell contact. In ordinary circumstances, transduction, conjugation, and transformation involve transfer of DNA between individual bacteria of the same species, but occasionally transfer may occur between individuals of different bacterial species and this may have significant consequences, such as the transfer of antibiotic resistance.JOURNAL, Michod RE, Bernstein H, Nedelcu AM, Adaptive value of sex in microbial pathogens, Infection, Genetics and Evolution, 8, 3, 267–85, May 2008, 18295550, 10.1016/j.meegid.2008.01.002,weblink no,weblink" title="web.archive.org/web/20161230121043weblink">weblink 30 December 2016, dmy-all, JOURNAL, Hastings PJ, Rosenberg SM, Slack A, Antibiotic-induced lateral transfer of antibiotic resistance, Trends in Microbiology, 12, 9, 401–14, September 2004, 15337159, 10.1016/j.tim.2004.07.003, In such cases, gene acquisition from other bacteria or the environment is called horizontal gene transfer and may be common under natural conditions.JOURNAL, Davison J, Genetic exchange between bacteria in the environment, Plasmid, 42, 2, 73–91, September 1999, 10489325, 10.1006/plas.1999.1421,

Behaviour

Movement

{{further|Chemotaxis|Flagellum|Pilus}}File:Dvulgaris micrograph.JPG|thumb|Transmission electron micrograph of Desulfovibrio vulgarisDesulfovibrio vulgarisMany bacteria are motile and can move using a variety of mechanisms. The best studied of these are flagella, long filaments that are turned by a motor at the base to generate propeller-like movement.JOURNAL, Bardy SL, Ng SY, Jarrell KF, Prokaryotic motility structures, Microbiology, 149, Pt 2, 295–304, February 2003, 12624192, 10.1099/mic.0.25948-0, The bacterial flagellum is made of about 20 proteins, with approximately another 30 proteins required for its regulation and assembly. The flagellum is a rotating structure driven by a reversible motor at the base that uses the electrochemical gradient across the membrane for power.JOURNAL, Macnab RM, The bacterial flagellum: reversible rotary propellor and type III export apparatus, Journal of Bacteriology, 181, 23, 7149–53, December 1999, 10572114, 103673, (File:Flagella.png|thumb|The different arrangements of bacterial flagella: A-Monotrichous; B-Lophotrichous; C-Amphitrichous; D-Peritrichous)Bacteria can use flagella in different ways to generate different kinds of movement. Many bacteria (such as E. coli) have two distinct modes of movement: forward movement (swimming) and tumbling. The tumbling allows them to reorient and makes their movement a three-dimensional random walk.JOURNAL, Wu M, Roberts JW, Kim S, Koch DL, DeLisa MP, Collective bacterial dynamics revealed using a three-dimensional population-scale defocused particle tracking technique, Applied and Environmental Microbiology, 72, 7, 4987–94, July 2006, 16820497, 1489374, 10.1128/AEM.00158-06, 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 flagella of a unique group of bacteria, the spirochaetes, are found between two membranes in the periplasmic space. They have a distinctive helical body that twists about as it moves.Two other types of bacterial motion are called twitching motility that relies on a structure called the type IV pilus,JOURNAL, 10.1146/annurev.micro.56.012302.160938, 12142488, Type IV Pili and Twitching Motility, Annual Review of Microbiology, 56, 289–314, 2002, Mattick, John S, and gliding motility, that uses other mechanisms. In twitching motility, the rod-like pilus extends out from the cell, binds some substrate, and then retracts, pulling the cell forward.JOURNAL, Merz AJ, So M, Sheetz MP, Pilus retraction powers bacterial twitching motility, Nature, 407, 6800, 98–102, September 2000, 10993081, 10.1038/35024105, 2000Natur.407...98M, Motile bacteria are attracted or repelled by certain stimuli in behaviours called taxes: these include chemotaxis, phototaxis, energy taxis, and magnetotaxis.JOURNAL, Lux R, Shi W, Chemotaxis-guided movements in bacteria, Critical Reviews in Oral Biology and Medicine, 15, 4, 207–20, July 2004, 15284186, 10.1177/154411130401500404, JOURNAL, Schweinitzer T, Josenhans C, Bacterial energy taxis: a global strategy?, Archives of Microbiology, 192, 7, 507–20, July 2010, 20411245, 2886117, 10.1007/s00203-010-0575-7, JOURNAL, Frankel RB, Bazylinski DA, Johnson MS, Taylor BL, Magneto-aerotaxis in marine coccoid bacteria, Biophysical Journal, 73, 2, 994–1000, August 1997, 9251816, 1180996, 10.1016/S0006-3495(97)78132-3, 1997BpJ....73..994F, In one peculiar group, the myxobacteria, individual bacteria move together to form waves of cells that then differentiate to form fruiting bodies containing spores. The myxobacteria move only when on solid surfaces, unlike E. coli, which is motile in liquid or solid media.Several Listeria and Shigella species move inside host cells by usurping the cytoskeleton, which is normally used to move organelles inside the cell. By promoting actin polymerisation at one pole of their cells, they can form a kind of tail that pushes them through the host cell's cytoplasm.JOURNAL, Goldberg MB, Actin-based motility of intracellular microbial pathogens, Microbiology and Molecular Biology Reviews, 65, 4, 595–626, table of contents, December 2001, 11729265, 99042, 10.1128/MMBR.65.4.595-626.2001,

Communication

{{See also|Prokaryote#Sociality}}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.Dusenbery, David B (1996). Life at Small Scale. Scientific American Library. {{ISBN|0-7167-5060-0}}.Bacteria often function as multicellular aggregates known as biofilms, exchanging a variety of molecular signals for inter-cell communication, and engaging in coordinated multicellular behaviour.JOURNAL, Shapiro JA, Thinking about bacterial populations as multicellular organisms, Annual Review of Microbiology, 52, 81–104, 1998, 9891794, 10.1146/annurev.micro.52.1.81,weblinkweblink" title="web.archive.org/web/20110717183759weblink">weblink yes, 17 July 2011, JOURNAL, Costerton JW, Lewandowski Z, Caldwell DE, Korber DR, Lappin-Scott HM, Microbial biofilms, Annual Review of Microbiology, 49, 711–45, 1995, 8561477, 10.1146/annurev.mi.49.100195.003431, The communal benefits of multicellular cooperation include a cellular division of labour, accessing resources that cannot effectively be used by single cells, collectively defending against antagonists, and optimising population survival by differentiating into distinct cell types. For example, bacteria in biofilms can have more than 500 times increased resistance to antibacterial agents than individual "planktonic" bacteria of the same species.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.Quorum sensing allows bacteria to coordinate gene expression, and enables them to produce, release and detect autoinducers or pheromones which accumulate with the growth in cell population.JOURNAL, Miller MB, Bassler BL, Quorum sensing in bacteria, Annual Review of Microbiology, 55, 165–99, 2001, 11544353, 10.1146/annurev.micro.55.1.165,

Classification and identification

{{further|Scientific classification|Systematics|Bacterial phyla|Clinical pathology}}(File:Streptococcus mutans Gram.jpg|thumb|alt=blue stain of Streptococcus mutans|Streptococcus mutans visualised with a Gram stain){{PhylomapA|size=400px|align=right|caption=Phylogenetic tree showing the diversity of bacteria, compared to other organisms.JOURNAL, Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P, Toward automatic reconstruction of a highly resolved tree of life, Science, 311, 5765, 1283–87, March 2006, 16513982, 10.1126/science.1123061, 2006Sci...311.1283C, 10.1.1.381.9514, Eukaryotes are coloured red, archaea green and bacteria blue.}}Classification seeks to describe the diversity of bacterial species by naming and grouping organisms based on similarities. Bacteria can be classified on the basis of cell structure, cellular metabolism or on differences in cell components, such as DNA, fatty acids, pigments, antigens and quinones. 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.JOURNAL, Boucher Y, Douady CJ, Papke RT, Walsh DA, Boudreau ME, Nesbø CL, Case RJ, Doolittle WF, Lateral gene transfer and the origins of prokaryotic groups, Annual Review of Genetics, 37, 283–328, 2003, 14616063, 10.1146/annurev.genet.37.050503.084247, Due to lateral gene transfer, some closely related bacteria can have very different morphologies and metabolisms. To overcome this uncertainty, modern bacterial classification emphasises molecular systematics, using genetic techniques such as guanine cytosine ratio determination, genome-genome hybridisation, as well as sequencing genes that have not undergone extensive lateral gene transfer, such as the rRNA gene.JOURNAL, Olsen GJ, Woese CR, Overbeek R, The winds of (evolutionary) change: breathing new life into microbiology, Journal of Bacteriology, 176, 1, 1–6, January 1994, 8282683, 205007, 10.2172/205047, Classification of bacteria is determined by publication in the International Journal of Systematic Bacteriology,WEB,weblink IJSEM Home, Ijs.sgmjournals.org, 28 October 2011, 4 November 2011, no,weblink" title="web.archive.org/web/20111019160924weblink">weblink 19 October 2011, dmy-all, and Bergey's Manual of Systematic Bacteriology.WEB,weblink Bergey's Manual Trust, Bergeys.org, 4 November 2011, no,weblink" title="web.archive.org/web/20111107002356weblink">weblink 7 November 2011, dmy-all, The International Committee on Systematic Bacteriology (ICSB) maintains international rules for the naming of bacteria and taxonomic categories and for the ranking of them in the International Code of Nomenclature of Bacteria.The term "bacteria" was traditionally applied to all microscopic, single-cell prokaryotes. However, molecular systematics showed prokaryotic life to consist of two separate domains, originally called Eubacteria and Archaebacteria, but now called Bacteria and Archaea that evolved independently from an ancient common ancestor. 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 microbiology.JOURNAL, Gupta RS, The natural evolutionary relationships among prokaryotes, Critical Reviews in Microbiology, 26, 2, 111–31, 2000, 10890353, 10.1080/10408410091154219, 10.1.1.496.1356, 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.JOURNAL, Rappé MS, Giovannoni SJ, The uncultured microbial majority, Annual Review of Microbiology, 57, 369–94, 2003, 14527284, 10.1146/annurev.micro.57.030502.090759, JOURNAL, Doolittle RF, Evolutionary aspects of whole-genome biology, Current Opinion in Structural Biology, 15, 3, 248–53, June 2005, 15963888, 10.1016/j.sbi.2005.04.001, For example, a few biologists argue that the Archaea and Eukaryotes evolved from gram-positive bacteria.JOURNAL, Cavalier-Smith T, The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification, International Journal of Systematic and Evolutionary Microbiology, 52, Pt 1, 7–76, January 2002, 11837318, 10.1099/00207713-52-1-7, The identification of bacteria in the laboratory is particularly relevant in medicine, where the correct treatment is determined by the bacterial species causing an infection. Consequently, the need to identify human pathogens was a major impetus for the development of techniques to identify bacteria.The Gram stain, developed in 1884 by Hans Christian Gram, characterises bacteria based on the structural characteristics of their cell walls. The thick layers of peptidoglycan in the "gram-positive" cell wall stain purple, while the thin "gram-negative" cell wall appears pink. By combining morphology and Gram-staining, most bacteria can be classified as belonging to one of four groups (gram-positive cocci, gram-positive bacilli, gram-negative cocci and gram-negative bacilli). Some organisms are best identified by stains other than the Gram stain, particularly mycobacteria or Nocardia, which show acid-fastness on Ziehl–Neelsen or similar stains.JOURNAL, Woods GL, Walker DH, Detection of infection or infectious agents by use of cytologic and histologic stains, Clinical Microbiology Reviews, 9, 3, 382–404, July 1996, 8809467, 172900, 10.1128/CMR.9.3.382, Other organisms may need to be identified by their growth in special media, or by other techniques, such as serology.Culture techniques are designed to promote the growth and identify particular bacteria, while restricting the growth of the other bacteria in the sample. Often these techniques are designed for specific specimens; for example, a sputum sample will be treated to identify organisms that cause pneumonia, while stool specimens are cultured on selective media to identify organisms that cause diarrhoea, while preventing growth of non-pathogenic bacteria. Specimens that are normally sterile, such as blood, urine or spinal fluid, are cultured under conditions designed to grow all possible organisms.JOURNAL, Weinstein MP, Clinical importance of blood cultures, Clinics in Laboratory Medicine, 14, 1, 9–16, March 1994, 8181237, 10.1016/S0272-2712(18)30390-1, Once a pathogenic organism has been isolated, it can be further characterised by its morphology, growth patterns (such as aerobic or anaerobic growth), patterns of hemolysis, and staining.As with bacterial classification, identification of bacteria is increasingly using molecular methods. Diagnostics using DNA-based tools, such as polymerase chain reaction, are increasingly popular due to their specificity and speed, compared to culture-based methods.JOURNAL, Louie M, Louie L, Simor AE, The role of DNA amplification technology in the diagnosis of infectious diseases, CMAJ, 163, 3, 301–09, August 2000, 10951731, 80298,weblink no,weblink" title="web.archive.org/web/20060614185831weblink">weblink 14 June 2006, dmy-all, These methods also allow the detection and identification of "viable but nonculturable" cells that are metabolically active but non-dividing.JOURNAL, Oliver JD, The viable but nonculturable state in bacteria, Journal of Microbiology, 43 Spec No, 93–100, February 2005, 15765062,weblinkweblink" title="web.archive.org/web/20070928032546weblink">weblink yes, 28 September 2007, However, even using these improved methods, the total number of bacterial species is not known and cannot even be estimated with any certainty. Following present classification, there are a little less than 9,300 known species of prokaryotes, which includes bacteria and archaea;WEB, Euzéby JP, 8 December 2011,weblink Number of published names, List of Prokaryotic names with Standing in Nomenclature, 10 December 2011, yes,weblink" title="web.archive.org/web/20120119210136weblink">weblink 19 January 2012, but attempts to estimate the true number of bacterial diversity have ranged from 107 to 109 total species—and even these diverse estimates may be off by many orders of magnitude.JOURNAL, Curtis TP, Sloan WT, Scannell JW, Estimating prokaryotic diversity and its limits, Proceedings of the National Academy of Sciences of the United States of America, 99, 16, 10494–99, August 2002, 12097644, 124953, 10.1073/pnas.142680199, 2002PNAS...9910494C, JOURNAL, Schloss PD, Handelsman J, Status of the microbial census, Microbiology and Molecular Biology Reviews, 68, 4, 686–91, December 2004, 15590780, 539005, 10.1128/MMBR.68.4.686-691.2004,

Interactions with other organisms

(File:Bacterial infections and involved species.png|thumb|upright=1.35|alt=chart showing bacterial infections upon various parts of human body|Overview of bacterial infections and main species involved.BOOK, Fisher, Bruce, Harvey, Richard P, Champe, Pamela C, vanc, Lippincott's Illustrated Reviews: Microbiology (Lippincott's Illustrated Reviews Series), Lippincott Williams & Wilkins, Hagerstwon, MD, 2007, Chapter 33, 367–92, 978-0-7817-8215-9, LEF.org > Bacterial Infections Updated: 19 January 2006. Retrieved on 11 April 2009){{further|Microbes in human culture}}Despite their apparent simplicity, bacteria can form complex associations with other organisms. These symbiotic associations can be divided into parasitism, mutualism and commensalism. Due to their small size, commensal bacteria are ubiquitous and grow on animals and plants exactly as they will grow on any other surface. However, their growth can be increased by warmth and sweat, and large populations of these organisms in humans are the cause of body odour.

Predators

Some species of bacteria kill and then consume other microorganisms, these species are called predatory bacteria.JOURNAL, Martin MO, Predatory prokaryotes: an emerging research opportunity, Journal of Molecular Microbiology and Biotechnology, 4, 5, 467–77, September 2002, 12432957, These include organisms such as Myxococcus xanthus, which forms swarms of cells that kill and digest any bacteria they encounter.JOURNAL, Velicer GJ, Stredwick KL, Experimental social evolution with Myxococcus xanthus, Antonie van Leeuwenhoek, 81, 1–4, 155–64, August 2002, 12448714, 10.1023/A:1020546130033, Other bacterial predators either attach to their prey in order to digest them and absorb nutrients, such as Vampirovibrio chlorellavorus,JOURNAL, Gromov BV, 1972, Electron Microscope Study of Parasitism by Bdellovibrio Chorellavorus Bacteria on Cells of the Green Alga Chorella Vulgaris, Tsitologiya, 14, 2, 256–60, or invade another cell and multiply inside the cytosol, such as Daptobacter.JOURNAL, Guerrero R, Pedros-Alio C, Esteve I, Mas J, Chase D, Margulis L, Predatory prokaryotes: predation and primary consumption evolved in bacteria, Proceedings of the National Academy of Sciences of the United States of America, 83, 7, 2138–42, April 1986, 11542073, 323246, 10.1073/pnas.83.7.2138, 1986PNAS...83.2138G, These predatory bacteria are thought to have evolved from saprophages that consumed dead microorganisms, through adaptations that allowed them to entrap and kill other organisms.JOURNAL, Velicer GJ, Mendes-Soares H, Bacterial predators, Current Biology, 19, 2, R55–56, January 2009, 19174136, 10.1016/j.cub.2008.10.043,

Mutualists

Certain bacteria form close spatial associations that are essential for their survival. One such mutualistic association, called interspecies hydrogen transfer, occurs between clusters of anaerobic bacteria that consume organic acids, such as butyric acid or propionic acid, and produce hydrogen, and methanogenic Archaea that consume hydrogen.JOURNAL, Stams AJ, de Bok FA, Plugge CM, van Eekert MH, Dolfing J, Schraa G, Exocellular electron transfer in anaerobic microbial communities, Environmental Microbiology, 8, 3, 371–82, March 2006, 16478444, 10.1111/j.1462-2920.2006.00989.x, 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 that reside in the rhizosphere (a zone that includes the root surface and the soil that adheres to the root after gentle shaking) carry out nitrogen fixation, converting nitrogen gas to nitrogenous compounds.JOURNAL, Barea JM, Pozo MJ, Azcón R, Azcón-Aguilar C, Microbial co-operation in the rhizosphere, Journal of Experimental Botany, 56, 417, 1761–78, July 2005, 15911555, 10.1093/jxb/eri197, This serves to provide an easily absorbable form of nitrogen for many plants, which cannot fix nitrogen themselves. Many other bacteria are found as symbionts in humans and other organisms. For example, the presence of over 1,000 bacterial species in the normal human gut flora of the intestines can contribute to gut immunity, synthesise vitamins, such as folic acid, vitamin K and biotin, convert sugars to lactic acid (see Lactobacillus), as well as fermenting complex undigestible carbohydrates.JOURNAL, O'Hara AM, Shanahan F, The gut flora as a forgotten organ, EMBO Reports, 7, 7, 688–93, July 2006, 16819463, 1500832, 10.1038/sj.embor.7400731, JOURNAL, Zoetendal EG, Vaughan EE, de Vos WM, A microbial world within us, Molecular Microbiology, 59, 6, 1639–50, March 2006, 16553872, 10.1111/j.1365-2958.2006.05056.x, JOURNAL, Sherwood Gorbach, Gorbach SL, Lactic acid bacteria and human health, Annals of Medicine, 22, 1, 37–41, February 1990, 2109988, 10.3109/07853899009147239, The presence of this gut flora also inhibits the growth of potentially pathogenic bacteria (usually through competitive exclusion) and these beneficial bacteria are consequently sold as probiotic dietary supplements.JOURNAL, Salminen SJ, Gueimonde M, Isolauri E, Probiotics that modify disease risk, The Journal of Nutrition, 135, 5, 1294–98, May 2005, 15867327, 10.1093/jn/135.5.1294,

Pathogens

File:SalmonellaNIAID.jpg|thumb|alt=Color-enhanced scanning electron micrograph of red Salmonella typhimurium in yellow human cells|Colour-enhanced scanning electron micrograph showing Salmonella typhimuriumSalmonella typhimuriumIf bacteria form a parasitic association with other organisms, they are classed as pathogens. Pathogenic bacteria are a major cause of human death and disease and cause infections such as tetanus, typhoid fever, diphtheria, syphilis, cholera, foodborne illness, leprosy and tuberculosis. A pathogenic cause for a known medical disease may only be discovered many years after, as was the case with Helicobacter pylori and peptic ulcer disease. Bacterial diseases are also important in agriculture, with bacteria causing leaf spot, fire blight and wilts in plants, as well as Johne's disease, mastitis, salmonella and anthrax in farm animals.Each species of pathogen has a characteristic spectrum of interactions with its human hosts. Some organisms, such as Staphylococcus or Streptococcus, can cause skin infections, pneumonia, meningitis and even overwhelming sepsis, a systemic inflammatory response producing shock, massive vasodilation and death.JOURNAL, Fish DN, Optimal antimicrobial therapy for sepsis, American Journal of Health-System Pharmacy, 59 Suppl 1, S13–19, February 2002, 11885408, 10.1093/ajhp/59.suppl_1.S13, Yet these organisms are also part of the normal human flora and usually exist on the skin or in the nose without causing any disease at all. Other organisms invariably cause disease in humans, such as the Rickettsia, which are obligate intracellular parasites able to grow and reproduce only within the cells of other organisms. One species of Rickettsia causes typhus, while another causes Rocky Mountain spotted fever. Chlamydia, another phylum of obligate intracellular parasites, contains species that can cause pneumonia, or urinary tract infection and may be involved in coronary heart disease.JOURNAL, Belland RJ, Ouellette SP, Gieffers J, Byrne GI, Chlamydia pneumoniae and atherosclerosis, Cellular Microbiology, 6, 2, 117–27, February 2004, 14706098, 10.1046/j.1462-5822.2003.00352.x, Finally, some species, such as Pseudomonas aeruginosa, Burkholderia cenocepacia, and Mycobacterium avium, are opportunistic pathogens and cause disease mainly in people suffering from immunosuppression or cystic fibrosis.JOURNAL, Heise ER, Diseases associated with immunosuppression, Environmental Health Perspectives, 43, 9–19, February 1982, 7037390, 1568899, 10.2307/3429162, 3429162, JOURNAL, Saiman L, Microbiology of early CF lung disease, Paediatric Respiratory Reviews, 5 Suppl A, S367–69, 2004, 14980298, 10.1016/S1526-0542(04)90065-6, Bacterial infections may be treated with antibiotics, which are classified as bacteriocidal if they kill bacteria, or bacteriostatic if they just prevent bacterial growth. There are many types of antibiotics and each class inhibits a process that is different in the pathogen from that found in the host. An example of how antibiotics produce selective toxicity are chloramphenicol and puromycin, which inhibit the bacterial ribosome, but not the structurally different eukaryotic ribosome.JOURNAL, Yonath A, Bashan A, Ribosomal crystallography: initiation, peptide bond formation, and amino acid polymerization are hampered by antibiotics, Annual Review of Microbiology, 58, 233–51, 2004, 15487937, 10.1146/annurev.micro.58.030603.123822, 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.JOURNAL, Khachatourians GG, Agricultural use of antibiotics and the evolution and transfer of antibiotic-resistant bacteria, CMAJ, 159, 9, 1129–36, November 1998, 9835883, 1229782, Infections can be prevented by antiseptic measures such as sterilising 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 sterilised to prevent contamination by bacteria. Disinfectants such as bleach are used to kill bacteria or other pathogens on surfaces to prevent contamination and further reduce the risk of infection.

Significance in technology and industry

{{further|Economic importance of bacteria}}Bacteria, often lactic acid bacteria, such as Lactobacillus and Lactococcus, in combination with yeasts and moulds, have been used for thousands of years in the preparation of fermented foods, such as cheese, pickles, soy sauce, sauerkraut, vinegar, wine and yogurt.JOURNAL, Johnson ME, Lucey JA, Major technological advances and trends in cheese, Journal of Dairy Science, 89, 4, 1174–78, April 2006, 16537950, 10.3168/jds.S0022-0302(06)72186-5, JOURNAL, Hagedorn S, Kaphammer B, Microbial biocatalysis in the generation of flavor and fragrance chemicals, Annual Review of Microbiology, 48, 773–800, 1994, 7826026, 10.1146/annurev.mi.48.100194.004013, The ability of bacteria to degrade a variety of organic compounds is remarkable and has been used in waste processing and bioremediation. Bacteria capable of digesting the hydrocarbons in petroleum are often used to clean up oil spills.JOURNAL, Cohen Y, Bioremediation of oil by marine microbial mats, International Microbiology, 5, 4, 189–93, December 2002, 12497184, 10.1007/s10123-002-0089-5, Fertiliser was added to some of the beaches in Prince William Sound in an attempt to promote the growth of these naturally occurring bacteria after the 1989 Exxon Valdez oil spill. These efforts were effective on beaches that were not too thickly covered in oil. Bacteria are also used for the bioremediation of industrial toxic wastes.JOURNAL, Neves LC, Miyamura TT, Moraes DA, Penna TC, Converti A, Biofiltration methods for the removal of phenolic residues, Applied Biochemistry and Biotechnology, 129–132, 1–3, 130–52, 2006, 16915636, 10.1385/ABAB:129:1:130, In the chemical industry, bacteria are most important in the production of enantiomerically pure chemicals for use as pharmaceuticals or agrichemicals.JOURNAL, Liese A, Filho MV, Production of fine chemicals using biocatalysis, Current Opinion in Biotechnology, 10, 6, 595–603, December 1999, 10600695, 10.1016/S0958-1669(99)00040-3, Bacteria can also be used in the place of pesticides in the biological pest control. This commonly involves Bacillus thuringiensis (also called BT), a gram-positive, soil dwelling bacterium. Subspecies of this bacteria are used as a Lepidopteran-specific insecticides under trade names such as Dipel and Thuricide.JOURNAL, Aronson AI, Shai Y, Why Bacillus thuringiensis insecticidal toxins are so effective: unique features of their mode of action, FEMS Microbiology Letters, 195, 1, 1–8, February 2001, 11166987, 10.1111/j.1574-6968.2001.tb10489.x, Because of their specificity, these pesticides are regarded as environmentally friendly, with little or no effect on humans, wildlife, pollinators and most other beneficial insects.JOURNAL, Bozsik A, Susceptibility of adult Coccinella septempunctata (Coleoptera: Coccinellidae) to insecticides with different modes of action, Pest Management Science, 62, 7, 651–54, July 2006, 16649191, 10.1002/ps.1221, JOURNAL, Chattopadhyay A, Bhatnagar NB, Bhatnagar R, Bacterial insecticidal toxins, Critical Reviews in Microbiology, 30, 1, 33–54, 2004, 15116762, 10.1080/10408410490270712, Because of their ability to quickly grow and the relative ease with which they can be manipulated, bacteria are the workhorses for the fields of molecular biology, genetics and biochemistry. By making mutations in bacterial DNA and examining the resulting phenotypes, scientists can determine the function of genes, enzymes and metabolic pathways in bacteria, then apply this knowledge to more complex organisms.JOURNAL, Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M, A functional update of the Escherichia coli K-12 genome, Genome Biology, 2, 9, RESEARCH0035, 2001, 11574054, 56896, 10.1186/gb-2001-2-9-research0035, This aim of understanding the biochemistry of a cell reaches its most complex expression in the synthesis of huge amounts of enzyme kinetic and gene expression data into mathematical models of entire organisms. This is achievable in some well-studied bacteria, with models of Escherichia coli metabolism now being produced and tested.JOURNAL, Almaas E, Kovács B, Vicsek T, Oltvai ZN, Barabási AL, Global organization of metabolic fluxes in the bacterium Escherichia coli, Nature, 427, 6977, 839–43, February 2004, 14985762, 10.1038/nature02289, q-bio/0403001, 2004Natur.427..839A, JOURNAL, Reed JL, Vo TD, Schilling CH, Palsson BO, An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR), Genome Biology, 4, 9, R54, 2003, 12952533, 193654, 10.1186/gb-2003-4-9-r54, This understanding of bacterial metabolism and genetics allows the use of biotechnology to bioengineer bacteria for the production of therapeutic proteins, such as insulin, growth factors, or antibodies.JOURNAL, Walsh G, Therapeutic insulins and their large-scale manufacture, Applied Microbiology and Biotechnology, 67, 2, 151–59, April 2005, 15580495, 10.1007/s00253-004-1809-x, JOURNAL, Graumann K, Premstaller A, Manufacturing of recombinant therapeutic proteins in microbial systems, Biotechnology Journal, 1, 2, 164–86, February 2006, 16892246, 10.1002/biot.200500051, Because of their importance for research in general, samples of bacterial strains are isolated and preserved in Biological Resource Centers. This ensures the availability of the strain to scientists worldwide.

History of bacteriology

{{about||the history of microbiology|Microbiology|the history of bacterial classification|Bacterial taxonomy|the natural history of Bacteria|Last universal common ancestor}}File:Anthonie van Leeuwenhoek (1632-1723). Natuurkundige te Delft Rijksmuseum SK-A-957.jpeg|thumb|right|alt=painting of Antonie van Leeuwenhoek, in robe and frilled shirt, with ink pen and paper|Antonie van Leeuwenhoek, the first microbiologist and the first person to observe bacteria using a microscopemicroscopeBacteria were first observed by the Dutch microscopist Antonie van Leeuwenhoek in 1676, using a single-lens microscope of his own design.JOURNAL, Porter JR, Antony van Leeuwenhoek: tercentenary of his discovery of bacteria, Bacteriological Reviews, 40, 2, 260–69, June 1976, 786250, 413956, He then published his observations in a series of letters to the Royal Society of London.JOURNAL, 10.1098/rstl.1684.0030, van Leeuwenhoek A, 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, Philosophical Transactions, 14, 568–74, 1684, 155–166, JOURNAL, van Leeuwenhoek A, Part of a Letter from Mr Antony van Leeuwenhoek, concerning the Worms in Sheeps Livers, Gnats, and Animalcula in the Excrements of Frogs, Philosophical Transactions, 22, 509–18, 1700, 10.1098/rstl.1700.0013, 260–276, JOURNAL, van Leeuwenhoek A, Part of a Letter from Mr Antony van Leeuwenhoek, F.R.S. concerning Green Weeds Growing in Water, and Some Animalcula Found about Them, Philosophical Transactions, 23, 1304–11, 1702, 10.1098/rstl.1702.0042, 277–288, Bacteria were Leeuwenhoek's most remarkable microscopic discovery. They were just at the limit of what his simple lenses could make out and, in one of the most striking hiatuses in the history of science, no one else would see them again for over a century.BOOK, Asimov I, Isaac Asimov, 1982, Asimov's Biographical Encyclopedia of Science and Technology, 2nd, Garden City, NY, Doubleday and Company, 143, Asimov's Biographical Encyclopedia of Science and Technology, His observations had also included protozoans which he called animalcules, and his findings were looked at again in the light of the more recent findings of cell theory.Christian Gottfried Ehrenberg introduced the word "bacterium" in 1828.BOOK, Ehrenberg CG, Symbolae Physioe. Animalia evertebrata., Decas prima, Berlin, 1828, In fact, his Bacterium was a genus that contained non-spore-forming rod-shaped bacteria,JOURNAL, Breed RS, Conn HJ, The Status of the Generic Term Bacterium Ehrenberg 1828, Journal of Bacteriology, 31, 5, 517–18, May 1936, 16559906, 543738, as opposed to Bacillus, a genus of spore-forming rod-shaped bacteria defined by Ehrenberg in 1835.BOOK, Ehrenberg CG, Dritter Beitrag zur Erkenntniss grosser Organisation in der Richtung des kleinsten Raumes., Third contribution to the knowledge of great organization in the direction of the smallest space, German, Physikalische Abhandlungen der Koeniglichen Akademie der Wissenschaften, Berlin, 1835, 143–336, Louis Pasteur demonstrated in 1859 that the growth of microorganisms causes the fermentation process, and that this growth is not due to spontaneous generation. (Yeasts and moulds, commonly associated with fermentation, are not bacteria, but rather fungi.) Along with his contemporary Robert Koch, Pasteur was an early advocate of the germ theory of disease.WEB,weblink Pasteur's Papers on the Germ Theory, LSU Law Center's Medical and Public Health Law Site, Historic Public Health Articles, 23 November 2006,weblink" title="web.archive.org/web/20061218123426weblink">weblink 18 December 2006, no, Robert Koch, a pioneer in medical microbiology, worked on cholera, anthrax and tuberculosis. In his research into tuberculosis Koch finally proved the germ theory, for which he received a Nobel Prize in 1905.WEB,weblink The Nobel Prize in Physiology or Medicine 1905, Nobelprize.org, 22 November 2006,weblink" title="web.archive.org/web/20061210184150weblink">weblink 10 December 2006, no, In Koch's postulates, he set out criteria to test if an organism is the cause of a disease, and these postulates are still used today.JOURNAL, O'Brien SJ, Goedert JJ, HIV causes AIDS: Koch's postulates fulfilled, Current Opinion in Immunology, 8, 5, 613–18, October 1996, 8902385, 10.1016/S0952-7915(96)80075-6, Ferdinand Cohn is said to be a founder of bacteriology, studying bacteria from 1870. Cohn was the first to classify bacteria based on their morphology.WEB, Chung, King-Thom, vanc,weblink Ferdinand Julius Cohn (1828–1898): Pioneer of Bacteriology, Department of Microbiology and Molecular Cell Sciences, The University of Memphis, no,weblink" title="web.archive.org/web/20110727180844weblink">weblink 27 July 2011, dmy-all, JOURNAL, Drews, Gerhart, 1999,weblink Ferdinand Cohn, a founder of modern microbiology, ASM News, 65, 8, 547–52, yes,weblink" title="web.archive.org/web/20170713150622weblink">weblink 13 July 2017, dmy-all, Though it was known in the nineteenth century that bacteria are the cause of many diseases, no effective antibacterial treatments were available.JOURNAL, Thurston AJ, Of blood, inflammation and gunshot wounds: the history of the control of sepsis, The Australian and New Zealand Journal of Surgery, 70, 12, 855–61, December 2000, 11167573, 10.1046/j.1440-1622.2000.01983.x, 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.JOURNAL, Schwartz RS, Paul Ehrlich's magic bullets, The New England Journal of Medicine, 350, 11, 1079–80, March 2004, 15014180, 10.1056/NEJMp048021, 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.WEB,weblink Biography of Paul Ehrlich, Nobelprize.org, 26 November 2006,weblink" title="web.archive.org/web/20061128093700weblink">weblink 28 November 2006, no, A major step forward in the study of bacteria came in 1977 when Carl Woese recognised that archaea have a separate line of evolutionary descent from bacteria.JOURNAL, Woese CR, Fox GE, Phylogenetic structure of the prokaryotic domain: the primary kingdoms, Proceedings of the National Academy of Sciences of the United States of America, 74, 11, 5088–90, November 1977, 270744, 432104, 10.1073/pnas.74.11.5088, 1977PNAS...74.5088W, This new phylogenetic taxonomy depended on the sequencing of 16S ribosomal RNA, and divided prokaryotes into two evolutionary domains, as part of the three-domain system.

Computer-made form

In April 2019, scientists at ETH Zurich reported the creation of the world's first bacterial genome, named Caulobacter ethensis-2.0, made entirely by a computer, although a related viable form of C. ethensis-2.0 does not yet exist.NEWS, ETH Zurich, First bacterial genome created entirely with a computer,weblink 1 April 2019, EurekAlert!, 2 April 2019, JOURNAL, Venetz, Jonathan E., et al., Chemical synthesis rewriting of a bacterial genome to achieve design flexibility and biological functionality,weblink 1 April 2019, Proceedings of the National Academy of Sciences of the United States of America, 10.1073/pnas.1818259116, 2 April 2019,

See also

References

{{Reflist}}

Further reading

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  • BOOK, Alcamo IE, Fundamentals of microbiology, Jones and Bartlett, Boston, 2001, 978-0-7637-1067-5,
  • BOOK, Atlas RM, Principles of microbiology, Mosby, St. Louis, 1995, 978-0-8016-7790-8,
  • BOOK, Martinko JM, Madigan MT, Brock Biology of Microorganisms, 11th, Prentice Hall, Englewood Cliffs, N.J, 2005, 978-0-13-144329-7,
  • BOOK, Holt JC, Bergey DH, Bergey's manual of determinative bacteriology, 9th, Williams & Wilkins, Baltimore, 1994, 978-0-683-00603-2,
  • JOURNAL, Hugenholtz P, Goebel BM, Pace NR, Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity, Journal of Bacteriology, 180, 18, 4765–74, September 1998, 9733676, 107498,weblink
  • BOOK, Funke BR, Tortora GJ, Case CL, Microbiology: an introduction, 8th, Benjamin Cummings, San Francisco, 2004, 978-0-8053-7614-2,
  • BOOK, Ogunseitan OA, Microbial Diversity: Form and Function in Prokaryotes, Wiley-Blackwell, 2005, 978-1-4051-4448-3,
  • BOOK, Shively JM, Complex Intracellular Structures in Prokaryotes (Microbiology Monographs), Springer, Berlin, 2006, 978-3-540-32524-6,

External links

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