Once regarded asplants constituting the classSchizomycetes ("fission fungi"), bacteria are now classified asprokaryotes. Unlike cells of animals and othereukaryotes, bacterial cells contain circular chromosomes, do not contain anucleus and rarely harbourmembrane-boundorganelles. Although the termbacteria traditionally included all prokaryotes, thescientific classification changed after the discovery in the 1990s that prokaryotes consist of two very different groups of organisms thatevolved from anancient common ancestor. Theseevolutionary domains are called Bacteria andArchaea.[5] UnlikeArchaea, bacteria contain ester-linked lipids in the cell membrane, are resistant to diphtheria toxin, use formylmethionine in protein synthesis initiation, and have numerous genetic differences, including a different 16S rRNA.
Although an estimated 43,000 species of bacteria have been named, most of them have never been studied.[10] In fact, just 10 bacterial species account for half of all publications, whereas nearly 75% of all named bacteria don’t have a single paper devoted to them.[10] The best-studied species,Escherichia coli, has more than 300,000 studies published on it,[10] but many of these papers likely use it only as acloning 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, mostlypathogenic bacteria relevant to human health.[10][11]
WhileE. coli is probably the best-studied bacterium, a quarter of its 4000 genes are poorly studied or remain uncharacterized. Some bacteria withminimal genomes (< 600 genes, e.g.Mycoplasma) usually have a large fraction of their genes functionally characterized, given that most of them areessential and conserved in many other species.[12]
The ancestors of bacteria were unicellular microorganisms that were thefirst forms of life to appear on Earth, about 4 billion years ago.[14] For about 3 billion years, most organisms were microscopic, and bacteria and archaea were the dominant forms of life.[15][16][17] Although bacterialfossils exist, such asstromatolites, their lack of distinctivemorphology 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 bacterialphylogeny, and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage.[18] Themost recent common ancestor (MRCA) of bacteria and archaea was probably ahyperthermophile that lived about 2.5 billion–3.2 billion years ago.[19][20][21] The earliest life on land may have been bacteria some 3.22 billion years ago.[22]
Bacteria were also involved in the second great evolutionary divergence, that of the archaea and eukaryotes.[23][24] Here, eukaryotes resulted from the entering of ancient bacteria intoendosymbiotic associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea.[25][26] This involved the engulfment by proto-eukaryotic cells ofalphaproteobacterialsymbionts to form eithermitochondria orhydrogenosomes, which are still found in all known Eukarya (sometimes in highlyreduced form, e.g. in ancient "amitochondrial" protozoa). Later, some eukaryotes that already contained mitochondria also engulfedcyanobacteria-like organisms, leading to the formation ofchloroplasts in algae and plants. This is known asprimary endosymbiosis.[27]
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.[28][29] There are thought to be approximately 2×1030 bacteria on Earth,[30] forming abiomass that is only exceeded by plants.[31] They are abundant in lakes and oceans, in arctic ice, andgeothermal springs[32] where they provide the nutrients needed to sustain life by converting dissolved compounds, such ashydrogen sulphide andmethane, to energy.[33] They live on and in plants and animals. Most do not cause diseases, are beneficial to their environments, and are essential for life.[4][34] 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 x 1026 bacteria which provide up to 50% of the oxygen humans breathe.[35] Only around 2% of bacterial species have been fully studied.[36]
Size. 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,[40]Epulopiscium fishelsoni reaches 0.7 mm,[41] andThiomargarita magnifica can reach even 2 cm in length, which is 50 times larger than other known bacteria.[42][43] Among the smallest bacteria are members of the genusMycoplasma, which measure only 0.3 micrometres, as small as the largestviruses.[44] Some bacteria may be even smaller, but theseultramicrobacteria are not well-studied.[45]
Shape. Most bacterial species are either spherical, calledcocci (singular coccus, from Greekkókkos, grain, seed), or rod-shaped, calledbacilli (sing. bacillus, fromLatinbaculus, stick).[46] Some bacteria, calledvibrio, are shaped like slightly curved rods or comma-shaped; others can be spiral-shaped, calledspirilla, or tightly coiled, calledspirochaetes. A small number of other unusual shapes have been described, such as star-shaped bacteria.[47] This wide variety of shapes is determined by the bacterialcell wall andcytoskeleton and is important because it can influence the ability of bacteria to acquire nutrients, attach to surfaces, swim through liquids and escapepredators.[48][49]
Multicellularity. Most bacterial species exist as single cells; others associate in characteristic patterns:Neisseria forms diploids (pairs),streptococci form chains, andstaphylococci group together in "bunch of grapes" clusters. Bacteria can also group to form larger multicellular structures, such as the elongatedfilaments ofActinomycetota species, the aggregates ofMyxobacteria species, and the complex hyphae ofStreptomyces species.[51] 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 asquorum sensing, migrate towards each other, and aggregate to form fruiting bodies up to 500 micrometres long and containing approximately 100,000 bacterial cells.[52] 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.[53]
Biofilms. Bacteria often attach to surfaces and form dense aggregations calledbiofilms[54] and larger formations known asmicrobial mats.[55] 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 asmicrocolonies, through which there are networks of channels to enable better diffusion of nutrients.[56][57] In natural environments, such as soil or the surfaces of plants, the majority of bacteria are bound to surfaces in biofilms.[58] Biofilms are also important in medicine, as these structures are often present during chronic bacterial infections or in infections ofimplantedmedical devices, and bacteria protected within biofilms are much harder to kill than individual isolated bacteria.[59]
Structure and contents of a typicalGram-positive bacterial cell (seen by the fact that onlyone cell membrane is present)
Intracellular structures
The bacterial cell is surrounded by acell membrane, which is made primarily ofphospholipids. This membrane encloses the contents of the cell and acts as a barrier to hold nutrients,proteins and other essential components of thecytoplasm within the cell.[60] Unlikeeukaryotic cells, bacteria usually lack large membrane-bound structures in their cytoplasm such as anucleus,mitochondria,chloroplasts and the other organelles present in eukaryotic cells.[61] However, some bacteria have protein-bound organelles in the cytoplasm whichcompartmentalise aspects of bacterial metabolism,[62][63] such as thecarboxysome.[64] Additionally, bacteria have a multi-componentcytoskeleton to control the localisation of proteins and nucleic acids within the cell, and to manage the process ofcell division.[65][66][67]
Many importantbiochemical reactions, such as energy generation, occur due toconcentration gradients across membranes, creating apotential difference analogous to a battery. The general lack of internal membranes in bacteria means these reactions, such aselectron transport, occur across the cell membrane between the cytoplasm and the outside of the cell orperiplasm.[68] However, in many photosynthetic bacteria, the plasma membrane is highly folded and fills most of the cell with layers of light-gathering membrane.[69] These light-gathering complexes may even form lipid-enclosed structures calledchlorosomes ingreen sulfur bacteria.[70]
Bacteria do not have a membrane-bound nucleus, and theirgenetic material is typically a singlecircular bacterial chromosome ofDNA located in the cytoplasm in an irregularly shaped body called thenucleoid.[71] The nucleoid contains thechromosome with its associated proteins andRNA. Like all otherorganisms, bacteria containribosomes for the production of proteins, but the structure of the bacterial ribosome is different from that ofeukaryotes and archaea.[72]
Around the outside of the cell membrane is thecell wall. Bacterial cell walls are made ofpeptidoglycan (also called murein), which is made frompolysaccharide chains cross-linked bypeptides containing D-amino acids.[78] Bacterial cell walls are different from the cell walls ofplants andfungi, which are made ofcellulose andchitin, respectively.[79] The cell wall of bacteria is also distinct from that of achaea, which do not contain peptidoglycan. The cell wall is essential to the survival of many bacteria, and the antibioticpenicillin (produced by a fungus calledPenicillium) is able to kill bacteria by inhibiting a step in the synthesis of peptidoglycan.[79]
There are broadly speaking two different types of cell wall in bacteria, that classify bacteria intoGram-positive bacteria andGram-negative bacteria. The names originate from the reaction of cells to theGram stain, a long-standing test for the classification of bacterial species.[80]
Gram-positive bacteria possess a thick cell wall containing many layers of peptidoglycan andteichoic acids. In contrast, Gram-negative bacteria have a relatively thin cell wall consisting of a few layers of peptidoglycan surrounded by a secondlipid membrane containinglipopolysaccharides andlipoproteins. Most bacteria have the Gram-negative cell wall, and only members of theBacillota group andactinomycetota (previously known as the low G+C and high G+C Gram-positive bacteria, respectively) have the alternative Gram-positive arrangement.[81] These differences in structure can produce differences in antibiotic susceptibility; for instance,vancomycin can kill only Gram-positive bacteria and is ineffective against Gram-negativepathogens, such asHaemophilus influenzae orPseudomonas aeruginosa.[82] Some bacteria have cell wall structures that are neither classically Gram-positive or Gram-negative. This includes clinically important bacteria such asmycobacteria which have a thick peptidoglycan cell wall like a Gram-positive bacterium, but also a second outer layer of lipids.[83]
Flagella are rigid protein structures, about 20 nanometres in diameter and up to 20 micrometres in length, that are used formotility. Flagella are driven by the energy released by the transfer ofions down anelectrochemical gradient across the cell membrane.[87]
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 theelectron microscope.[88] 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.[89]Pili (sing. pilus) are cellular appendages, slightly larger than fimbriae, that can transfergenetic material between bacterial cells in a process calledconjugation where they are calledconjugation pili or sex pili (see bacterial genetics, below).[90] They can also generate movement where they are calledtype IV pili.[91]
Glycocalyx is produced by many bacteria to surround their cells,[92] and varies in structural complexity: ranging from a disorganisedslime layer ofextracellular polymeric substances to a highly structuredcapsule. These structures can protect cells from engulfment by eukaryotic cells such asmacrophages (part of the humanimmune system).[93] They can also act asantigens and be involved in cell recognition, as well as aiding attachment to surfaces and the formation of biofilms.[94]
The assembly of these extracellular structures is dependent onbacterial 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 thevirulence of pathogens, so are intensively studied.[94]
Somegenera of Gram-positive bacteria, such asBacillus,Clostridium,Sporohalobacter,Anaerobacter, andHeliobacterium, can form highly resistant, dormant structures calledendospores.[96] Endospores develop within the cytoplasm of the cell; generally, a single endospore develops in each cell.[97] Each endospore contains a core ofDNA andribosomes surrounded by a cortex layer and protected by a multilayer rigid coat composed of peptidoglycan and a variety of proteins.[97]
Endospore-forming bacteria can cause disease; for example,anthrax can be contracted by the inhalation ofBacillus anthracis endospores, and contamination of deep puncture wounds withClostridium tetani endospores causestetanus, which, likebotulism, is caused by a toxin released by the bacteria that grow from the spores.[104]Clostridioides difficile infection, a common problem in healthcare settings, is caused by spore-forming bacteria.[105]
Bacteria exhibit an extremely wide variety ofmetabolic types.[106] The distribution of metabolic traits within a group of bacteria has traditionally been used to define theirtaxonomy, but these traits often do not correspond with modern genetic classifications.[107] Bacterial metabolism is classified intonutritional groups on the basis of three major criteria: the source ofenergy, theelectron donors used, and the source ofcarbon used for growth.[108]
Unlike in multicellular organisms, increases in cell size (cell growth) and reproduction bycell division are tightly linked in unicellular organisms. Bacteria grow to a fixed size and then reproduce throughbinary fission, a form ofasexual reproduction.[117] Under optimal conditions, bacteria can grow and divide extremely rapidly, and some bacterial populations can double as quickly as every 17 minutes.[118] In cell division, two identicalclone 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 bymyxobacteria and aerialhyphae formation byStreptomyces species, or budding. Budding involves a cell forming a protrusion that breaks away and produces a daughter cell.[119]
In the laboratory, bacteria are usually grown using solid or liquid media.[120] Solidgrowth media, such asagar plates, are used toisolate 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.[121]
Most laboratory techniques for growing bacteria use high levels of nutrients to produce large amounts of cells cheaply and quickly.[120] 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 (seer/K selection theory). Some organisms can grow extremely rapidly when nutrients become available, such as the formation ofalgal andcyanobacterial blooms that often occur in lakes during the summer.[122] Other organisms have adaptations to harsh environments, such as the production of multipleantibiotics by Streptomyces that inhibit the growth of competing microorganisms.[123] In nature, many organisms live in communities (e.g.,biofilms) that may allow for increased supply of nutrients and protection from environmental stresses.[58] These relationships can be essential for growth of a particular organism or group of organisms (syntrophy).[124]
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 thelag 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.[125][126] The second phase of growth is thelogarithmic phase, also known as the exponential phase. The log phase is marked by rapidexponential growth. The rate at which cells grow during this phase is known as thegrowth rate (k), and the time it takes the cells to double is known as thegeneration 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 thestationary 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 increasedexpression of genes involved inDNA repair,antioxidant metabolism andnutrient transport.[127] The final phase is thedeath phase where the bacteria run out of nutrients and die.[128]
Helium ion microscopy image showingT4 phage infectingE. 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 wide[129]
Whether they have a single chromosome or more than one, almost all bacteria have ahaploidgenome. This means that they have only one copy of each gene encoding proteins. This is in contrast toeukaryotes, 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 aprotein if thegene 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 aninactivating mutation.[137]
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 ofintrons do exist in bacteria, these are much rarer than in eukaryotes.[138]
Bacteria, as asexual organisms, inherit an identical copy of the parent's genome and areclonal. However, all bacteria can evolve by selection on changes to their genetic materialDNA caused bygenetic recombination ormutations. Mutations arise from errors made during the replication of DNA or from exposure tomutagens. Mutation rates vary widely among different species of bacteria and even among different clones of a single species of bacteria.[139] 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.[140]
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 calledtransformation.[141] Many bacteria cannaturally take up DNA from the environment, while others must be chemically altered in order to induce them to take up DNA.[142] 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.[143] Second,bacteriophages can integrate into the bacterial chromosome, introducing foreign DNA in a process known astransduction. Many types of bacteriophage exist; some infect andlyse theirhost bacteria, while others insert into the bacterial chromosome.[144] Bacteria resist phage infection throughrestriction modification systems that degrade foreign DNA[145] and a system that usesCRISPR 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 ofRNA interference.[146][147] Third, bacteria can transfer genetic material through direct cell contact viaconjugation.[148]
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.[149][150] In such cases, gene acquisition from other bacteria or the environment is calledhorizontal gene transfer and may be common under natural conditions.[151]
Transmission electron micrograph ofDesulfovibrio vulgaris showing a single flagellum at one end of the cell. Scale bar is 0.5 micrometres long
Many bacteria aremotile (able to move themselves) and do so using a variety of mechanisms. The best studied of these areflagella, long filaments that are turned by a motor at the base to generate propeller-like movement.[152] The bacterial flagellum is made of about 20 proteins, with approximately another 30 proteins required for its regulation and assembly.[152] The flagellum is a rotating structure driven by a reversible motor at the base that uses theelectrochemical gradient across the membrane for power.[153]
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 asE. coli) have two distinct modes of movement: forward movement (swimming) andtumbling. The tumbling allows them toreorient and makes their movement a three-dimensionalrandom walk.[154] Bacterial species differ in the number and arrangement of flagella on their surface; some have a singleflagellum (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, thespirochaetes, are found between two membranes in the periplasmic space. They have a distinctivehelical body that twists about as it moves.[152]
Two other types of bacterial motion are calledtwitching motility that relies on a structure called thetype IV pilus,[155] andgliding 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.[156]
Motile bacteria are attracted or repelled by certainstimuli in behaviours calledtaxes: these includechemotaxis,phototaxis,energy taxis, andmagnetotaxis.[157][158][159] In one peculiar group, the myxobacteria, individual bacteria move together to form waves of cells that then differentiate to form fruiting bodies containing spores.[53] The myxobacteria move only when on solid surfaces, unlikeE. coli, which is motile in liquid or solid media.[160]
SeveralListeria andShigella species move inside host cells by usurping thecytoskeleton, which is normally used to moveorganelles inside the cell. By promotingactinpolymerisation at one pole of their cells, they can form a kind of tail that pushes them through the host cell's cytoplasm.[161]
A few bacteria have chemical systems that generate light. Thisbioluminescence often occurs in bacteria that live in association with fish, and the light probably serves to attract fish or other large animals.[162]
Bacteria often function as multicellular aggregates known asbiofilms, exchanging a variety of molecular signals forintercell communication and engaging in coordinated multicellular behaviour.[163][164]
The communal benefits of multicellular cooperation include a cellulardivision 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.[163] For example, bacteria in biofilms can have more than five hundred times increased resistance toantibacterial agents than individual "planktonic" bacteria of the same species.[164]
One type of intercellular communication by amolecular signal is calledquorum sensing, which serves the purpose of determining whether the local population density is sufficient to support investment in processes that are only successful if large numbers of similar organisms behave similarly, such as excretingdigestive enzymes or emitting light.[165][166] Quorum sensing enables bacteria to coordinategene expression and to produce, release, and detectautoinducers orpheromones that accumulate with the growth in cell population.[167]
Streptococcus mutans visualised with a Gram stainPhylogenetic tree showing the diversity of bacteria, compared to other organisms. Here bacteria are represented by three main supergroups: theCPRultramicrobacterias,Terrabacteria andGracilicutes according to 2019 genomic analyses[168]
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 asDNA,fatty acids, pigments,antigens andquinones.[121] 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 aslateral gene transfer between unrelated species.[169] Due to lateral gene transfer, some closely related bacteria can have very different morphologies and metabolisms. To overcome this uncertainty, modern bacterial classification emphasisesmolecular systematics, using genetic techniques such asguaninecytosineratio determination, genome-genome hybridisation, as well assequencing genes that have not undergone extensive lateral gene transfer, such as therRNA gene.[170] Classification of bacteria is determined by publication in the International Journal of Systematic Bacteriology,[171] and Bergey's Manual of Systematic Bacteriology.[172] TheInternational Committee on Systematic Bacteriology (ICSB) maintains international rules for the naming of bacteria and taxonomic categories and for the ranking of them in theInternational Code of Nomenclature of Bacteria.[173]
Historically, bacteria were considered a part of thePlantae, the plant kingdom, and were called "Schizomycetes" (fission-fungi).[174] For this reason, collective bacteria and other microorganisms in a host are often called "flora".[175]The term "bacteria" was traditionally applied to all microscopic, single-cell prokaryotes. However, molecular systematics showed prokaryotic life to consist of two separatedomains, originally called Eubacteria and Archaebacteria, but now called Bacteria and Archaea that evolved independently from an ancient common ancestor.[5] 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 thethree-domain system, which is currently the most widely used classification system in microbiology.[176] 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.[177][178] For example,Cavalier-Smith argued that the Archaea and Eukaryotes evolved from Gram-positive bacteria.[179]
The identification of bacteria in the laboratory is particularly relevant inmedicine, 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.[180] Once a pathogenic organism has been isolated, it can be further characterised by its morphology, growth patterns (such asaerobic oranaerobic growth),patterns of hemolysis, and staining.[181]
Classification by staining
TheGram stain, developed in 1884 byHans Christian Gram, characterises bacteria based on the structural characteristics of their cell walls.[182][80] The thick layers of peptidoglycan in the "Gram-positive" cell wall stain purple, while the thin "Gram-negative" cell wall appears pink.[182] 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 orNocardia, which showacid fastness onZiehl–Neelsen or similar stains.[183]
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.[184] Often these techniques are designed for specific specimens; for example, asputum sample will be treated to identify organisms that causepneumonia, whilestool specimens are cultured onselective media to identify organisms that causediarrhea while preventing growth of non-pathogenic bacteria. Specimens that are normally sterile, such asblood,urine orspinal fluid, are cultured under conditions designed to grow all possible organisms.[121][185] Other organisms may need to be identified by their growth in special media, or by other techniques, such asserology.[186]
Molecular classification
As with bacterial classification, identification of bacteria is increasingly using molecular methods,[187] andmass spectroscopy.[188] Most bacteria have not been characterised and there are many species that cannot begrown in the laboratory.[189] Diagnostics using DNA-based tools, such aspolymerase chain reaction, are increasingly popular due to their specificity and speed, compared to culture-based methods.[190] These methods also allow the detection and identification of "viable but nonculturable" cells that are metabolically active but non-dividing.[191] 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,[10] 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.[192][193]
Overview of bacterial infections and main species involved[199]
Despite their apparent simplicity, bacteria can form complex associations with other organisms. Thesesymbiotic associations can be divided intoparasitism,mutualism andcommensalism.[200]
Commensals
The word "commensalism" is derived from the word "commensal", meaning "eating at the same table"[201] and all plants and animals are colonised by commensal bacteria. In humans and other animals, millions of them live on the skin, the airways, the gut and other orifices.[202][203]Referred to as "normal flora",[204] or "commensals",[205] these bacteria usually cause no harm but may occasionally invade other sites of the body and cause infection.Escherichia coli is a commensal in the human gut but can cause urinary tract infections.[206] Similarly, streptococci, which are part of the normal flora of the human mouth, can causeheart disease.[207]
Predators
Some species of bacteria kill and then consume other microorganisms; these species are calledpredatory bacteria.[208] These include organisms such asMyxococcus xanthus, which formsswarms of cells that kill and digest any bacteria they encounter.[209] 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.[210] These predatory bacteria are thought to have evolved fromsaprophages that consumed dead microorganisms, through adaptations that allowed them to entrap and kill other organisms.[211]
Mutualists
Certain bacteria form close spatial associations that are essential for their survival. One such mutualistic association, called interspecies hydrogen transfer, occurs between clusters ofanaerobic bacteria that consumeorganic acids, such asbutyric acid orpropionic acid, and producehydrogen, andmethanogenic archaea that consume hydrogen.[212] 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.[213]
Mutualistic relationship between plants and nitrogen fixing bacteria found in the rhisozphere
In soil, microorganisms that reside in therhizosphere (a zone that includes theroot surface and the soil that adheres to the root after gentle shaking) carry outnitrogen fixation, converting nitrogen gas to nitrogenous compounds.[214] This serves to provide an easily absorbable form of nitrogen for many plants, which cannot fix nitrogen themselves. Many other bacteria are found assymbiontsin humans and other organisms. For example, the presence of over 1,000 bacterial species in the normal humangut flora of theintestines can contribute to gut immunity, synthesisevitamins, such asfolic acid,vitamin K andbiotin, convertsugars tolactic acid (seeLactobacillus), as well as fermenting complex undigestiblecarbohydrates.[215][216][217] The presence of this gut flora also inhibits the growth of potentially pathogenic bacteria (usually throughcompetitive exclusion) and these beneficial bacteria are consequently sold asprobioticdietary supplements.[218]
The body is continually exposed to many species of bacteria, including beneficial commensals, which grow on the skin andmucous membranes, andsaprophytes, which grow mainly in the soil and indecaying 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 naturalimmunity orinnate resistance against manymicroorganisms.[220] Unlike someviruses, bacteria evolve relatively slowly so many bacterial diseases also occur in other animals.[221]
Bacterial infections may be treated withantibiotics, which are classified asbacteriocidal if they kill bacteria orbacteriostatic if they just prevent bacterial growth. There are many types of antibiotics, and each classinhibits a process that is different in the pathogen from that found in the host. An example of how antibiotics produce selective toxicity arechloramphenicol andpuromycin, which inhibit the bacterialribosome, but not the structurally different eukaryotic ribosome.[233] Antibiotics are used both in treating human disease and inintensive farming to promote animal growth, where they may be contributing to the rapid development ofantibiotic resistance in bacterial populations.[234] Infections can be prevented byantiseptic 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 alsosterilised to prevent contamination by bacteria.Disinfectants such asbleach are used to kill bacteria or other pathogens on surfaces to prevent contamination and further reduce the risk of infection.[235]
Because of their ability to quickly grow and the relative ease with which they can be manipulated, bacteria are the workhorses for the fields ofmolecular biology,genetics, andbiochemistry. By making mutations in bacterial DNA and examining the resulting phenotypes, scientists can determine the function of genes,enzymes, andmetabolic pathways in bacteria, then apply this knowledge to more complex organisms.[244] This aim of understanding the biochemistry of a cell reaches its most complex expression in the synthesis of huge amounts ofenzyme kinetic andgene expression data intomathematical models of entire organisms. This is achievable in some well-studied bacteria, with models ofEscherichia coli metabolism now being produced and tested.[245][246] This understanding of bacterial metabolism and genetics allows the use of biotechnology tobioengineer bacteria for the production of therapeutic proteins, such asinsulin,growth factors, orantibodies.[247][248]
Because of their importance for research in general, samples of bacterial strains are isolated and preserved inBiological Resource Centres. This ensures the availability of the strain to scientists worldwide.[249]
Bacteria were first observed by the Dutch microscopistAntonie van Leeuwenhoek in 1676, using a single-lensmicroscope 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, asanimalcules. He published his observations in a series of letters to theRoyal Society of London.[250] 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.[251] His observations also included protozoans, and his findings were looked at again in the light of the more recent findings ofcell theory.[252]
Christian Gottfried Ehrenberg introduced the word "bacterium" in 1828.[253] In fact, hisBacterium was a genus that contained non-spore-forming rod-shaped bacteria,[254] as opposed toBacillus, a genus of spore-forming rod-shaped bacteria defined by Ehrenberg in 1835.[255]
Louis Pasteur demonstrated in 1859 that the growth of microorganisms causes thefermentation process and that this growth is not due tospontaneous generation (yeasts andmolds, commonly associated with fermentation, are not bacteria, but ratherfungi). Along with his contemporaryRobert Koch, Pasteur was an early advocate of thegerm theory of disease.[256] Before them,Ignaz Semmelweis andJoseph 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.[257]
Robert Koch, a pioneer in medical microbiology, worked oncholera,anthrax andtuberculosis. In his research into tuberculosis, Koch finally proved the germ theory, for which he received aNobel Prize in 1905.[258] InKoch's postulates, he set out criteria to test if an organism is the cause of adisease, and these postulates are still used today.[259]
Ferdinand Cohn is said to be a founder ofbacteriology, studying bacteria from 1870. Cohn was the first to classify bacteria based on their morphology.[260][261]
Though it was known in the nineteenth century that bacteria are the cause of many diseases, no effectiveantibacterial treatments were available.[262] In 1910,Paul Ehrlich developed the first antibiotic, by changing dyes that selectively stainedTreponema pallidum—thespirochaete that causessyphilis—into compounds that selectively killed the pathogen.[263] Ehrlich, who had been awarded a 1908 Nobel Prize for his work onimmunology, pioneered the use of stains to detect and identify bacteria, with his work being the basis of theGram stain and theZiehl–Neelsen stain.[264]
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