Bacteria are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryoticmicroorganisms. Typically a few micrometres in length, bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit the air, soil, water, acidic hot springs, radioactive waste, and the deep biosphere of Earth's crust. Bacteria play a vital role in many stages of the nutrient cycle by recycling nutrients and the fixation of nitrogen from the atmosphere. The nutrient cycle includes the decomposition of ; bacteria are responsible for the stage in this process. In the biological communities surrounding and , bacteria provide the nutrients needed to sustain life by converting dissolved compounds, such as and , to energy. Bacteria also live in , and relationships with plants and animals. Most bacteria have not been characterised and there are many species that cannot be in the laboratory. The study of bacteria is known as , a branch of .
Once regarded as plants constituting the class Schizomycetes ("fission fungi"), bacteria are now classified as prokaryotes. Unlike cells of animals and other eukaryotes, bacterial cells contain circular chromosomes, 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.10 Unlike Archaea, bacteria contain ester-linked lipids in the cell membrane,11 possess elongation factors that are resistant to ADP-ribosylation by diphtheria toxin,12 use formylmethionine in protein synthesis initiation,13 and have numerous genetic differences, including a different 16S rRNA.14
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Most bacterial species are either spherical, called cocci (singular coccus, from Greek kókkos, grain, seed), or rod-shaped, called bacilli (sing. bacillus, from Latin baculus, stick).
Most bacterial species are either spherical, called cocci (singular coccus, from Greek kókkos, grain, seed), or rod-shaped, called bacilli (sing. bacillus, from Latin baculus, stick).
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.
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.
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.
The cell wall is essential to the survival of many bacteria, and the antibiotic penicillin (produced by a fungus called Penicillium) is able to kill bacteria by inhibiting a step in the synthesis of peptidoglycan.
Some genera of Gram-positive bacteria, such as Bacillus, Clostridium, Sporohalobacter, Anaerobacter, and Heliobacterium, can form highly resistant, dormant structures called endospores.
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).
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).
Motile bacteria are attracted or repelled by certain stimuli in behaviours called taxes: these include chemotaxis, phototaxis, energy taxis, and magnetotaxis.
Terms the article defines in bold, quoted in context.
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Although an estimated 43,000 species of bacteria have been named, most of them have never been studied.20 In fact, just 10 bacterial species account for half of all publications, whereas nearly 75% of all named bacteria have no academic research devoted to them.20 The best-studied species, Escherichia coli, has more than 300,000 studies published on it,20 but many of these papers likely use it only as a cloning vehicle to study other species, without providing any insight into its own biology. 90% of scientific studies on bacteria focus on less than 1% of species, mostly pathogenic bacteria relevant to human health.2021
While E. coli is probably the best-studied bacterium, a quarter of its 4000 genes are poorly studied or remain uncharacterized. Some bacteria with minimal genomes (< 600 genes, e.g. Mycoplasma) usually have a large fraction of their genes functionally characterized, given that most of them are essential and conserved in many other species.22
The ancestors of bacteria were unicellular microorganisms that were the first forms of life to appear on Earth, about 4 billion years ago.24 For about 3 billion years, most organisms were microscopic, and bacteria and archaea were the dominant forms of life.2526 Although bacterial exist, such as , their lack of distinctive 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 , and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage. The (MRCA) of bacteria and archaea was probably a that lived about 2.5 billion–3.2 billion years ago. The earliest life on land may have been bacteria some 3.22 billion years ago.
Habitat
Bacteria are ubiquitous, living in every possible habitat on the planet including soil, underwater, deep in Earth's crust and even such extreme environments as acidic hot springs and radioactive waste.4041 There are thought to be approximately 2×1030 bacteria on Earth,42 forming a biomass that is only exceeded by plants.43 They are abundant in lakes and oceans, in arctic ice, and geothermal springs44 where they provide the nutrients needed to sustain life by converting dissolved compounds, such as hydrogen sulphide and methane, to energy.45 They live on and in plants and animals. Most do not cause diseases, are beneficial to their environments, and are essential for life.946 The soil is a rich source of bacteria and a few grams contain around a thousand million of them. They are all essential to soil ecology, breaking down toxic waste and recycling nutrients. They are even found in the atmosphere and one cubic metre of air holds around one hundred million bacterial cells. The oceans and seas harbour around 3 × 1026 bacteria which provide up to 50% of the oxygen humans breathe.47 Only around 2% of bacterial species have been fully studied.48
The range of sizes shown by prokaryotes (Bacteria), relative to those of other organisms and biomolecules52
Bacteria display a wide diversity of shapes and sizes. Bacterial cells are about one-tenth the size of eukaryotic cells and are typically 0.5–5.0 micrometres in length. However, a few species are visible to the unaided eye—for example, Thiomargarita namibiensis is up to half a millimetre long,53Epulopiscium fishelsoni reaches 0.7 mm,54 and Thiomargarita magnifica can reach even 2 cm in length, which is 50 times larger than other known giant bacteria.5556 Among the smallest bacteria are members of the genus , which measure only 0.3 micrometres, as small as the largest . Some bacteria may be even smaller, but these are not well-studied.
Structure and contents of a typical Gram-positive bacterial cell (seen by the fact that only one cell membrane is present)
Intracellular structures
The bacterial cell is surrounded by a 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 within the cell.72 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.73 However, some bacteria have protein-bound organelles in the cytoplasm which compartmentalise aspects of bacterial metabolism, such as the . Additionally, bacteria have a multi-component to control the localisation of proteins and nucleic acids within the cell, and to manage the process of .
Bacteria exhibit an extremely wide variety of metabolic types.119 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.120 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.121
Phototrophic bacteria derive energy from light using photosynthesis, while chemotrophic bacteria breaking down chemical compounds through oxidation.122 In both cases, metabolism can be driven by electron-transfer reactions in which electrons move from an electron donor to an electron acceptor. Chemotrophs are further divided by the types of compounds they use to transfer electrons. Bacteria that derive electrons from inorganic compounds such as hydrogen, , or are called , while those that use organic compounds are called . Still, more specifically, use as the terminal electron acceptor, while use other compounds such as , , or carbon dioxide.
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.130 Under optimal conditions, bacteria can grow and divide extremely rapidly, and some bacterial populations can double as quickly as every 17 minutes.131 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 and aerial formation by species, or budding. Budding involves a cell forming a protrusion that breaks away and produces a daughter cell.
Helium ion microscopy image showing T4 phage infecting E. coli. Some of the attached phage have contracted tails indicating that they have injected their DNA into the host. The bacterial cells are ~ 0.5 μm wide142
Most bacteria have a single circular chromosome that can range in size from only 160,000 base pairs in the endosymbiotic bacteria Carsonella ruddii,143 to 12,200,000 base pairs (12.2 Mbp) in the soil-dwelling bacteria Sorangium cellulosum,144 to 16.0 Mbp in another soil-dwelling bacteria, Minicystis rosea.145 There are many exceptions to this; for example, some Streptomyces and species contain a single linear chromosome, while some bacteria including species of contain more than one chromosome. Some bacteria contain , small extra-chromosomal molecules of DNA that may contain genes for various useful functions such as , metabolic capabilities, or various .
Transmission electron micrograph of Desulfovibrio vulgaris showing a single flagellum at one end of the cell. Scale bar is 0.5 micrometres long
Many bacteria are motile (able to move themselves) and do so 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.166 The bacterial flagellum is made of about 20 proteins, with approximately another 30 proteins required for its regulation and assembly.166 The flagellum is a rotating structure driven by a reversible motor at the base that uses the electrochemical gradient across the membrane for power.167
The different arrangements of bacterial flagella: A-Monotrichous; B-Lophotrichous; C-Amphitrichous; D-Peritrichous
Phylogenetic tree showing the diversity of bacteria, compared to other organisms. Here bacteria are represented by three main supergroups: the CPRultramicrobacterias, Bacillati and according to 2019 genomic analyses
Overview of bacterial infections and main species involved214
Despite their apparent simplicity, bacteria can form complex associations with other organisms. These symbiotic associations can be divided into parasitism, mutualism and commensalism.215
Commensals
The word "commensalism" is derived from the word "commensal", meaning "eating at the same table"216 and all plants and animals are colonised by commensal bacteria. In humans and other animals, trillions of them live on the skin, the airways, the gut and other orifices.217218 Referred to as "normal flora",219 or "commensals", these bacteria usually cause no harm but may occasionally invade other sites of the body and cause infection. is a commensal in the human gut but can cause urinary tract infections. Similarly, streptococci, which are part of the normal flora of the human mouth, can cause .
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.254 Fertiliser was added to some of the beaches in in an attempt to promote the growth of these naturally occurring bacteria after the 1989 . These efforts were effective on beaches that were not too thickly covered in oil. Bacteria are also used for the bioremediation of industrial . In the , bacteria are most important in the production of pure chemicals for use as or .
Bacteria were first observed by the Dutch microscopist Antonie van Leeuwenhoek in 1676, using a single-lens microscope of his own design. Leeuwenhoek did not recognize bacteria as a distinct category of microorganisms, referring to all microorganisms that he observed, including bacteria, protists, and microscopic animals, as . He published his observations in a series of letters to the . Bacteria were Leeuwenhoek's most remarkable microscopic discovery. Their size was just at the limit of what his simple lenses could resolve, and, in one of the most striking hiatuses in the history of science, no one else would see them again for over a century. His observations also included protozoans, and his findings were looked at again in the light of the more recent findings of .
Clark D (2010). Germs, Genes, & Civilization: how epidemics shaped who we are today. Upper Saddle River, N.J: FT Press. ISBN 978-0-13-701996-0. OCLC473120711.
Crawford D (2007). Deadly Companions: how microbes shaped our history. Oxford New York: Oxford University Press. ISBN 978-0-19-956144-5. OCLC183198723.
Hall B (2008). Strickberger's Evolution: the integration of genes, organisms and populations. Sudbury, Mass: Jones and Bartlett. ISBN 978-0-7637-0066-9. OCLC85814089.
Krasner R (2014). The Microbial Challenge: a public health perspective. Burlington, Mass: Jones & Bartlett Learning. ISBN 978-1-4496-7375-8. OCLC794228026.
Pommerville JC (2014). Fundamentals of Microbiology (10th ed.). Boston: Jones and Bartlett. ISBN 978-1-284-03968-9.
Wheelis M (2008). Principles of modern microbiology. Sudbury, Mass: Jones and Bartlett Publishers. . .
Bacteria were also involved in the second great evolutionary divergence, that of the archaea and eukaryotes.3334 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.3536 This involved the engulfment by proto-eukaryotic cells of alphaproteobacterialsymbionts to form either mitochondria or hydrogenosomes, which are still found in all known Eukarya (sometimes in highly reduced form, e.g. in species of amitochondrial protozoa).3738 Later, some eukaryotes that already contained mitochondria also engulfed cyanobacteria-like organisms, leading to the formation of chloroplasts in algae and plants. This is known as primary endosymbiosis.39
Bacteria display many cell morphologies and arrangements18
Most bacterial species are either spherical, called cocci (singular coccus, from Greek kókkos, grain, seed), or rod-shaped, called bacilli (sing. bacillus, from Latinbaculus, stick).59 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.60 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.6162
Multicellularity
Most bacterial species exist as single cells; others associate in characteristic patterns: Neisseria forms diploids (pairs), streptococci form chains, and staphylococci group together in "bunch of grapes" clusters. Bacteria can also group to form larger multicellular structures, such as the elongated filaments of Actinomycetota species, the aggregates of Myxobacteria species, and the complex hyphae of Streptomyces species.63 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.64 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.65
Biofilms
Bacteria often attach to surfaces and form dense aggregations called biofilms66 and larger formations known as microbial mats.67 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.6869 In natural environments, such as soil or the surfaces of plants, the majority of bacteria are bound to surfaces in biofilms.70 Biofilms are also important in medicine, as these structures are often present during chronic bacterial infections or in infections of implantedmedical devices, and bacteria protected within biofilms are much harder to kill than individual isolated bacteria.71
Many important biochemical reactions, such as energy generation, occur due to differences in concentration of molecules across membranes, creating a electrochemical potential 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.80 However, in many photosynthetic bacteria, the plasma membrane is highly folded and fills most of the cell with layers of light-gathering membrane.81 These light-gathering complexes may even form lipid-enclosed structures called chlorosomes in green sulfur bacteria.82
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.91 Bacterial cell walls are different from the cell walls of plants and fungi, which are made of cellulose and chitin, respectively.92 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 (produced by a fungus called Penicillium) is able to kill bacteria by inhibiting a step in the synthesis of peptidoglycan.92
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.93
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 members of the Bacillota group and actinomycetota (previously known as the low G+C and high G+C Gram-positive bacteria, respectively) have the alternative Gram-positive arrangement.94 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.95 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.96
In many bacteria, an S-layer of rigidly arrayed protein molecules covers the outside of the cell.97 This layer provides chemical and physical protection for the cell surface and can act as a macromoleculardiffusion barrier. S-layers have diverse functions and are known to act as virulence factors in Campylobacter species and contain surface enzymes in Bacillus stearothermophilus.9899
Flagella are rigid protein structures, about 20 nanometres in diameter and up to 20 micrometres in length, that are used for motility. Flagella are driven by the energy released by the transfer of ions down an electrochemical gradient across the cell membrane.100
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.101 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.102Pili (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).103 They can also generate movement where they are called type IV pili.104
Glycocalyx is produced by many bacteria to surround their cells,105 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).106 They can also act as antigens and be involved in cell recognition, as well as aiding attachment to surfaces and the formation of biofilms.107
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.107
Some genera of Gram-positive bacteria, such as Bacillus, Clostridium, Sporohalobacter, Anaerobacter, and Heliobacterium, can form highly resistant, dormant structures called endospores.109 Endospores develop within the cytoplasm of the cell; generally, a single endospore develops in each cell.110 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.110
Endospore-forming bacteria can 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, which, like botulism, is caused by a toxin released by the bacteria that grow from the spores.117Clostridioides difficile infection, a common problem in healthcare settings, is caused by spore-forming bacteria.118
Bacterial metabolic traits play important roles in maintaining ecological processes and supporting human activities. For example, diazotrophs have the ability to fix nitrogen gas using the enzyme nitrogenase.125 This trait, which can be found in bacteria of most metabolic types listed above,126 leads to the ecologically important processes of denitrification, sulfate reduction, and acetogenesis, respectively.127 Bacterial metabolic processes are important drivers 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.128 Nonrespiratory 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.129
In the laboratory, bacteria are usually grown using solid or liquid media.133 Solid growth media, such as agar plates, are used to isolate pure cultures of a bacterial strain. However, liquid growth media are used when the 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.134
Most laboratory techniques for growing bacteria use high levels of nutrients to produce large amounts of cells cheaply and quickly.133 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.135 Other organisms have adaptations to harsh environments, such as the production of multiple antibiotics by Streptomyces that inhibit the growth of competing microorganisms.136 In nature, many organisms live in communities (e.g., biofilms) that may allow for increased supply of nutrients and protection from environmental stresses.70 These relationships can be essential for growth of a particular organism or group of organisms (such as in syntrophy).137
Bacterial growth curve
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.138139 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.140 The final phase is the death phase where the bacteria run out of nutrients and die.141
Whether they have a single chromosome or more than one, almost all bacteria have a haploidgenome. This means that they have only one copy of each gene encoding proteins. This is in contrast to eukaryotes, which are diploid or polyploid, meaning they have two or more copies of each gene. This means that unlike humans, who may still be able to create a protein if the gene becomes mutated (since the human genome has an extra copy in each cell), a bacterium will be completely unable to create the protein if its gene incurs an inactivating mutation.151
Bacterial genomes usually encode a few hundred to a few thousand genes. The genes in bacterial genomes are usually a single continuous stretch of DNA. Although several different types of introns do exist in bacteria, these are much rarer than in eukaryotes.152
Bacteria, as asexual organisms, inherit an identical copy of the parent's genome and are clonal. However, all bacteria can evolve by selection on changes to their genetic material DNA caused by genetic recombination or mutations. Mutations arise 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.153 Genetic changes in bacterial genomes emerge from either random mutation during replication or "stress-directed mutation", where genes involved in a particular growth-limiting process have an increased mutation rate.154
Some bacteria 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.155 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.156 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.157 Second, bacteriophages can integrate into the bacterial chromosome, introducing foreign DNA in a process known as transduction. Many types of bacteriophage exist; some infect and lyse their host bacteria, while others insert into the bacterial chromosome.158 Bacteria resist phage infection through restriction modification systems that degrade foreign DNA159 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.160161 Third, bacteria can transfer genetic material through direct cell contact via conjugation.162
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.163164 In such cases, gene acquisition from other bacteria or the environment is called horizontal gene transfer and may be common under natural conditions.165
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-dimensionalrandom walk.168 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 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.166
Two other types of bacterial motion are called twitching motility that relies on a structure called the type IV pilus,169 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.170
Motile bacteria are attracted or repelled by certain stimuli in behaviours called taxes: these include chemotaxis, phototaxis, energy taxis, and magnetotaxis.171172173 In one peculiar group, the myxobacteria, individual bacteria move together to form waves of cells that then differentiate to form fruiting bodies containing spores.65 The myxobacteria move only when on solid surfaces, unlike E. coli, which is motile in liquid or solid media.174
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 actinpolymerisation at one pole of their cells, they can form a kind of tail that pushes them through the host cell's cytoplasm.175
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.176
Bacteria often function as multicellular aggregates known as biofilms, exchanging a variety of molecular signals for intercell communication and engaging in coordinated multicellular behaviour.177178
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.177 For example, bacteria in biofilms can have more than five hundred times the increased resistance to antibacterial agents than individual "planktonic" bacteria of the same species.178
One type of intercellular communication by a molecular signal is called quorum sensing.179180181 Quorum sensing determines whether the local population is dense enough to support investment in processes that are only successful if large numbers of similar organisms behave similarly, such as excreting digestive enzymes or emitting light.182183 Quorum sensing enables bacteria to coordinate gene expression and to produce, release, and detect autoinducers or pheromones that accumulate with the growth in cell population.184
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.134 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.186 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 guaninecytosineratio determination, genome-genome hybridisation, as well as sequencing genes that have not undergone extensive lateral gene transfer, such as the rRNA gene.187 Classification of bacteria is determined by publication in the International Journal of Systematic Bacteriology, and Bergey's Manual of Systematic Bacteriology.188 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.189
Historically, bacteria were considered a part of the Plantae, the plant kingdom, and were called "Schizomycetes" (fission-fungi).190 For this reason, collective bacteria and other microorganisms in a host are often called "flora".191 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.10 Archaea and eukaryotes are more closely related to each other than either group is to bacteria. This relationship forms the basis of the current widely-used three-domain system, which recognises Bacteria, Archaea, and Eukarya as the three primary domains of life.192 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.193194 For example, Cavalier-Smith argued that the Archaea and Eukaryotes evolved from Gram-positive bacteria.195
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.196 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.197
Classification by staining
The Gram stain, developed in 1884 by Hans Christian Gram, characterises bacteria based on the structural characteristics of their cell walls.19893 The thick layers of peptidoglycan in the "Gram-positive" cell wall stain purple, while the thin "Gram-negative" cell wall appears pink.198 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.199
Classification by culturing
Culture techniques are designed to promote the growth and identify particular bacteria while restricting the growth of the other bacteria in the sample.200 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.134201 Other organisms may need to be identified by their growth in special media, or by other techniques, such as serology.202
Molecular classification
As with bacterial classification, identification of bacteria is increasingly using molecular methods,203 and mass spectroscopy.204 Most bacteria have not been characterised and there are many species that cannot be grown in the laboratory.205 Diagnostics using DNA-based tools, such as polymerase chain reaction, are increasingly popular due to their specificity and speed, compared to culture-based methods.206 These methods also allow the detection and identification of "viable but nonculturable" cells that are metabolically active but non-dividing.207 The main way to characterize and classify these bacteria is to isolate their DNA from environmental samples and mass-sequence them. This approach has identified thousands, if not millions of candidate species. Based on some estimates, more than 43,000 species of bacteria have been described,20 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.208209
The following phyla have been proposed, but have not been validly published according to the Prokaryotic Code; phyla that do not belong to any kingdom are shown in bold:3213
Some species of bacteria kill and then consume other microorganisms; these species are called predatory bacteria.223 These include organisms such as Myxococcus xanthus, which forms swarms of cells that kill and digest any bacteria they encounter.224 Other bacterial predators either attach to their prey in order to digest them and absorb nutrients or invade another cell and multiply inside the cytosol.225 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.226
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.227 Without the archaea, the bacteria in this association would be unable to continuously consume the organic acids, as this reaction produces hydrogen that would accumulate in their surroundings. Only the intimate association with the hydrogen-consuming archaea keeps the hydrogen concentration low enough to allow the bacteria to grow.228
Mutualistic relationship between plants and nitrogen fixing bacteria found in the rhizosphere
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.229 This serves to provide an easily utilisable form of nitrogen for many plants, which cannot fix nitrogen themselves. Many other bacteria are found as symbiontsin 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.230231232 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 probioticdietary supplements.233
Colour-enhanced scanning electron micrograph showing Salmonella typhimurium (red) invading cultured human cells
The body is continually exposed to many species of bacteria, including beneficial commensals, which grow on the skin and mucous membranes, and saprophytes, which grow mainly in the soil and in decaying matter. The blood and tissue fluids contain nutrients sufficient to sustain the growth of many bacteria. The body has defence mechanisms that enable it to resist microbial invasion of its tissues and give it a natural immunity or innate resistance against many microorganisms.235 Unlike some viruses, bacteria evolve relatively slowly so many bacterial diseases also occur in other animals.236
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.249 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.250 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.251
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.260 The aim of understanding the biochemistry of a cell has led to the synthesis of large amounts of enzyme kinetics 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.261262 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.263264
Because of their importance for research in general, samples of bacterial strains are isolated and preserved in Biological Resource Centres. This ensures the availability of the strain to scientists worldwide.265
Christian Gottfried Ehrenberg introduced the word "bacterium" in 1828.19 In fact, his Bacterium was a genus that contained non-spore-forming rod-shaped bacteria,269 as opposed to Bacillus, a genus of spore-forming rod-shaped bacteria defined by Ehrenberg in 1835.270
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.271 Before them, Ignaz Semmelweis and Joseph Lister had realised the importance of sanitised hands in medical work. Semmelweis, who in the 1840s formulated his rules for handwashing in the hospital, prior to the advent of germ theory, attributed disease to "decomposing animal organic matter". His ideas were rejected and his book on the topic condemned by the medical community. After Lister, however, doctors started sanitising their hands in the 1870s.272
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 1905.273 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.274
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.275276
Though it was known in the nineteenth century that bacteria are the cause of many diseases, no effective antibacterial treatments were available.277 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.278 Ehrlich, who had been awarded a 1908 Nobel Prize for his work on immunology, 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.279
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.280 This new phylogenetictaxonomy depended on the sequencing of 16S ribosomal RNA and divided prokaryotes into two evolutionary domains, as part of the three-domain system.10
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Graham BeardsRestored revision 1376315104 by Grilledcheeseisgreat (talk): We don't write Van Beethoven, also see WP:ENGVAR as the article is written in British English−13diff
Unicellular organism lacking a membrane-bound nucleus
A prokaryote (from Ancient Greek πρό pró, meaning 'before'; and κάρυον káruon, meaning 'nut' or 'kernel'), less commonly spelled procaryote, is a cellular organism that lacks a distinct cell nucleus or other membrane-bound organelles.
The eukaryotes are cellular organisms of the domain Eukaryota or Eukarya, which have a distinct cell nucleus (formed by a nuclear membrane), membrane-bound organelles and organization supported by a cytoskeleton.
Decomposition is the process by which dead organic substances are broken down into simpler organic or inorganic matter such as carbon dioxide, water, simple sugars and mineral salts.
An oil spill is the release of a liquid petroleum hydrocarbon into the environment, especially the marine ecosystem, due to human activity, and is a form of pollution.
Resistance of microbes to drugs directed against them
Antimicrobial resistance (AMR or AR) occurs when microbes evolve mechanisms that protect them from antimicrobials, which are drugs used to treat infections in humans, animals, and plants.
Gut microbiota, gut microbiome, or gut flora are the microorganisms, including bacteria, archaea, fungi, and viruses, that live in the digestive tracts of animals.
Organism that thrives at relatively high temperatures
A thermophile is a type of extremophile that thrives at relatively high temperatures, between 41 and 122 °C (106 and 252 °F). Many thermophiles are archaea, though some of them are bacteria and fungi.
