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{{Taxobox| color = lightgrey| name = Bacteria| fossil_range = Archean or earlier - Recent] cells magnified 25,000 times| domain =
Bacteria| subdivision_ranks = Phyla| subdivision =Actinobacteria
Aquificae
Chlamydiae
Bacteroidetes (phylum)/
ChlorobiChloroflexiChrysiogenetes
CyanobacteriaDeferribacteraceaeDeinococcus-Thermus
Dictyoglomi
Fibrobacteres/Acidobacteria
Firmicutes
FusobacteriaGemmatimonadetesVerrucomicrobia
NitrospiraePlanctomycetes
ProteobacteriaSpirochaetes
ThermodesulfobacteriaThermomicrobia
Thermotogae
Verrucomicrobia-->
Bacteria (singular:
bacterium) are unicellular
microorganisms. Typically a few
micrometres in length, individual bacteria have a wide-range of shapes, ranging from spheres to rods to spirals. Bacteria are ubiquitous in every habitat (ecology) on Earth, growing in soil, hot springs, nuclear waste, seawater, and deep in the Crust (geology). There are typically 40 million bacterial
cell (biology) in a gram of soil and a million bacterial cells in a millilitre of fresh water; in all, there are approximately five
Names of large numbers#The "standard dictionary numbers" (5×1030) bacteria in the world. Bacteria are vital in recycling nutrients, and many important steps in nutrient cycles depend on bacteria, such as the nitrogen fixation from the Earth's atmosphere. However, most of these bacteria have not been characterised, and only about half of the
phylum of bacteria have species that can be microbiological culture in the laboratory. The study of bacteria is known as
bacteriology, a branch of
microbiology.
There are approximately 10 times as many bacterial cells as
human cells in the human body, with large numbers of bacteria on the
skin and in the
gastrointestinal tract. Although the vast majority of these bacteria are rendered harmless or beneficial by the protective effects of the
immune system, a few pathogenic bacteria cause
infectious diseases, including
cholera, syphilis, anthrax,
leprosy and
bubonic plague. The most common fatal bacterial diseases are respiratory infections, with
tuberculosis alone killing about 2 million people a year, mostly in sub-Saharan Africa. In developed country,
antibiotics are used to treat bacterial infections and in various agricultural processes, so antibiotic resistance is becoming common. In industry, bacteria are important in processes such as wastewater treatment, the production of cheese and
yoghurt, and the manufacture of antibiotics and other chemicals.
Bacteria are
prokaryotes. Unlike cells of animals and other
eukaryotes, bacterial cells do not contain a cell nucleus and rarely harbour
cell membrane organelles. Although the term
bacteria traditionally included all prokaryotes, the
scientific classification changed after the discovery in the 1990s that prokaryotic life consists of two very different groups of organisms that evolution independently from an ancient common ancestor. These domain (biology) are called Bacteria and
Archaea.
History of bacteriology
The existence of
microorganisms was hypothesized during the late
Middle Ages. In
The Canon of Medicine (1020),
Abū Alī ibn Sīnā (Avicenna) stated that bodily
secretions are contaminated by "foul foreign earthly bodies" before a person becomes infected, but he did not view these bodies as primary causes of
disease. When the Black Death bubonic plague reached
al-Andalus in the 14th century, Ibn Khatima and Ibn al-Khatib wrote of infectious diseases being caused by contagious entities that enter the human body.Ibrahim B. Syed, (2002). "Islamic Medicine: 1000 years ahead of its times",
Journal of the Islamic Medical Association 2, p. 2-9. These ideas about the contagious nature of some diseases became more popular in Europe during the Renaissance, particularly through the writing of Girolamo Fracastoro.
, the first person to observe bacteria using a microscope.
Bacteria were first observed by
Anton van Leeuwenhoek in 1676, using a single-lens microscope of his own design. He called them "animalcules" and published his observations in a series of letters to the
Royal Society. The name
bacterium was introduced much later, by
Christian Gottfried Ehrenberg in 1828, and is derived from the
List of Greek words with English derivatives βακτήριον -α ,
bacterion -a , meaning "small staff".
Louis Pasteur demonstrated in 1859 that the
fermentation (food) process is caused by the growth of microorganisms, and that this growth is not due to
spontaneous generation. (
Yeasts and molds, commonly associated with fermentation, are not bacteria, but rather fungus.) Along with his contemporary,
Robert Koch, Pasteur was an early advocate of the
germ theory of disease.Robert Koch was a pioneer in medical microbiology and worked on
cholera, anthrax and tuberculosis. In his research into tuberculosis, Koch finally proved the germ theory, for which he was awarded a Nobel Prize in Physiology or Medicine in 1905. In
Koch's postulates, he set out criteria to test if an organism is the cause of a
disease; these postulates are still used today.
Though it was known in the nineteenth century that bacteria are the cause of many diseases, no effective antiseptic treatments were available. In 1910,
Paul Ehrlich developed the first antibiotic, by changing dyes that selectively stained
Treponema pallidum—the spirochete that causes
syphilis—into compounds that selectively killed the pathogen. Ehrlich had been awarded a 1908 Nobel Prize for his work on immunology, and pioneered the use of stains to detect and identify bacteria, with his work being the basis of the
Gram stain and the Ziehl-Neelsen stain.
A major step forward in the study of bacteria was the recognition in 1977 by Carl Woese that
archaea have a separate line of evolutionary descent from bacteria. This new
phylogenetic taxonomy was based on the
sequencing of Svedberg ribosome
RNA, and divided prokaryotes into two evolutionary domains as part of the three-domain system.
Origin and early evolution
The ancestors of modern bacteria were single-celled microorganisms that were the Origin of life to develop on earth, about 1 E17 s. For about 3 billion years, all organisms were microscopic, and bacteria and archaea were the dominant forms of life. Although bacterial
fossils exist, such as stromatolites, their lack of distinctive morphology (biology) prevents them from being used to examine the past history of bacterial evolution, or to date the time of origin of a particular bacterial species. However, gene sequences can be used to reconstruct the bacterial phylogenetics, and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage. The most recent common ancestor of bacteria and archaea was probably a
thermophile that lived about 2.5 billion–3.2 billion years ago.
Bacteria were also involved in the second great evolutionary divergence, that of the archaea and eukaryotes. Here, eukaryotes resulted from ancient bacteria entering into
endosymbiont associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea. This involved the engulfment by proto-eukaryotic cells of alpha-proteobacterial symbionts to form either mitochondrion or
hydrogenosomes, which are still being found in all known Eukarya (sometimes in highly reduced form, e. g. in ancient "amitochondrial" protozoa). Later on, an independent second engulfment by some mitochondria-containing eukaryotes of cyanobacterial-like organisms led to the formation of
chloroplasts in algae and plants. There are even some algal groups known that clearly originated from subsequent events of endosymbiosis by heterotrophic eukaryotic hosts engulfing a eukaryotic algae that developed into "second-generation" plastids.
Morphology
and arrangements.
Bacteria display a wide diversity of shapes and sizes, called
morphology (biology). Bacterial cells are about 10 times smaller than eukaryotic cells and are typically 0.5–5.0 micrometres in length. However, a few species–for example
Thiomargarita namibiensis and
Epulopiscium fishelsoni–are up to half a
millimetre long and are visible to the unaided eye. Among the smallest bacteria are members of the genus
Mycoplasma, which measure only 0.3 micrometres, as small as the largest viruses.
Most bacterial species are either spherical, called coccus (
sing. coccus, from Greek
kókkos, grain, seed) or rod-shaped, called bacillus (
sing. bacillus, from Latin
baculus, stick). Some rod-shaped bacteria, called vibrio, are slightly curved or comma-shaped; others, can be spiral-shaped, called
spirillum, or tightly coiled, called spirochetes. A small number of species even have tetrahedral or cuboidal shapes. This wide variety of shapes is determined by the bacterial
cell wall and
cytoskeleton, and is important because it can influence the ability of bacteria to acquire nutrients, attach to surfaces, swim through liquids and escape
predation.
Many bacterial species exist simply as single cells, others associate in characteristic patterns:
Neisseria form diploids (pairs),
Streptococcus form chains, and
Staphylococcus group together in "bunch of grapes" clusters. Bacteria can also be elongated to form filaments, for example the
Actinobacteria. Filamentous bacteria are often surrounded by a sheath that contains many individual cells; certain types, such as species of the genus
Nocardia, even form complex, branched filaments, similar in appearance to fungal
mycelia.
s, relative to those of other organisms and
biomolecules
Bacteria often attach to surfaces and form dense aggregations called
biofilms or microbial mats. These films can range from a few micrometers in thickness to up to half a meter in depth, and may contain multiple species of bacteria,
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. In natural environments, such as soil or the surfaces of plants, the majority of bacteria are bound to surfaces in biofilms. Biofilms are also important for chronic bacterial infections and infections of implant (medicine) medical devices, as bacteria protected within these structures are much harder to kill than individual bacteria.
Even more complex morphological changes are sometimes possible. For example, when starved of amino acids, Myxobacteria detect surrounding cells in a process known as quorum sensing, migrate towards each other, and aggregate to form fruiting bodies up to 500 micrometres long and containing approximately 100,000 bacterial cells. In these fruiting bodies, the bacteria perform separate tasks; this type of cooperation is a simple type of multicellular organism organisation. For example, about one in 10 cells migrate to the top of these fruiting bodies and cellular differentiation into a specialised dormant state called myxospores, which are more resistant to desiccation and other adverse environmental conditions than are ordinary cells.
Cellular structure
Intracellular structures
The bacterial cell is surrounded by a
lipid membrane, or
cell membrane, which encompasses the contents of the cell and acts as a barrier to hold nutrients, proteins and other essential components of the cytoplasm within the cell. As they are
prokaryotes, bacteria do not have membrane-bound
organelles in their cytoplasm and thus contain few intracellular structures. They consequently lack a cell nucleus,
mitochondrion,
chloroplasts and the other organelles present in eukaryotic cells, such as the
Golgi apparatus and endoplasmic reticulum.
Many important
biochemistry reactions, such as
Energy#Biology generation, occur due to
diffusions across membranes, creating a potential difference analogous to a battery (electricity). The absence of internal membranes in bacteria means these reactions, such as electron transport chain, occur across the cell membrane, between the cytoplasm and the
periplasmic space. Additionally, while some transporter proteins consume chemical energy, others harness concentration gradients to import nutrients across the cell membrane or to expel undesired molecules from the cytoplasm.
Bacteria do not have a membrane-bound nucleus, and their
genetic material is typically a single circular chromosome located in the cytoplasm in an irregularly shaped body called the nucleoid. The nucleoid contains the chromosome with associated proteins and RNA. Like all living organisms, bacteria contain
ribosomes for the production of proteins, but the structure of the bacterial ribosome is different from those of eukaryotes and
Archaea. The order Planctomycetes are an exception to the general absence of internal membranes in bacteria, because they have a membrane around their nucleoid and contain other membrane-bound cellular structures.
Some bacteria produce intracellular nutrient storage granules, such as glycogen, polyphosphate, sulfur or
polyhydroxyalkanoates. These granules enable bacteria to store compounds for later use. Certain bacterial species, such as the Photosynthesis#Bacterial variations Cyanobacteria, produce internal gas vesicles, which they use to regulate their buoyancy - allowing them to move up or down into water layers with different light intensities and nutrient levels.
Extracellular structures
Around the outside of the cell membrane is the bacterial
cell wall. Bacterial cell walls are made of peptidoglycan (called murein in older sources), which is made from
polysaccharide chains cross-linked by unusual
peptides containing D-
amino acids. Bacterial cell walls are different from the cell walls of
plants and fungus, which are made of cellulose and chitin, respectively. The cell wall of bacteria is also distinct from that of Archaea, which do not contain peptidoglycan. The cell wall is essential to the survival of many bacteria, and the antibiotic
penicillin is able to kill bacteria by inhibiting a step in the synthesis of peptidoglycan.
There are broadly speaking two different types of cell wall in bacteria, called Gram-positive and
Gram-negative. The names originate from the reaction of cells to the
Gram stain, a test long-employed for the classification of bacterial species.
Gram-positive bacteria possess a thick cell wall containing many layers of peptidoglycan and teichoic acids. In contrast, Gram-negative bacteria have a relatively thin cell wall consisting of a few layers of peptidoglycan surrounded by a second lipid membrane containing lipopolysaccharides and lipoproteins. Most bacteria have the Gram-negative cell wall, and only the
Firmicutes and
Actinobacteria (previously known as the low G+C and high G+C Gram-positive bacteria, respectively) have the alternative Gram-positive arrangement. 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.
In many bacteria an S-layer of rigidly arrayed protein molecules covers the outside of the cell. This layer provides chemical and physical protection for the cell surface and can act as a
macromolecule diffusion barrier. S-layers have diverse but mostly poorly understood functions, but are known to act as virulence factors in
Campylobacter and contain surface
enzymes in
Bacillus stearothermophilus.
electron micrograph, showing multiple flagella on the cell surface
Flagellum are rigid protein structures, about 20 metres 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.
Fimbriae are fine filaments of protein, just 2–10 nanometres in diameter and up to several micrometers in length. They are distributed over the surface of the cell, and resemble fine hairs when seen under the electron microscope. Fimbriae are believed to be involved in attachment to solid surfaces or to other cells and are essential for the virulence of some bacterial pathogens.
Pilus (
sing. pilus) are cellular appendages, slightly larger than fimbriae, that can transfer genetic material between bacterial cells in a process called bacterial conjugation (see bacterial genetics, below).
Capsules or slime layers are produced by many bacteria to surround their cells, and vary in structural complexity: ranging from a disorganised slime layer of extra-cellular
polymer, to a highly structured capsule (microbiology) or glycocalyx. These structures can protect cells from engulfment by eukaryotic cells, such as macrophages. They can also act as antigens and be involved in cell recognition, as well as aiding attachment to surfaces and the formation of biofilms.
The assembly of these extracellular structures is dependent on bacterial
secretion. 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.
Endospores
(stained purple) growing in cerebrospinal fluid
Certain genera of Gram-positive bacteria, such as
Bacillus,
Clostridium,
Sporohalobacter,
Anaerobacter and
Heliobacteria, can form highly resistant, dormant structures called endospores. In almost all cases, one endospore is formed and this is not a reproductive process, although
Anaerobacter can make up to seven endospores in a single cell. Endospores have a central core of cytoplasm containing
DNA and
ribosomes surrounded by a cortex layer and protected by an impermeable and rigid coat.
Endospores show no detectable metabolism and can survive extreme physical and chemical stresses, such as high levels of
ultraviolet, gamma ray, detergents,
disinfectants, heat, pressure and desiccation. In this dormant state, these organisms may remain viable for millions of years, and endospores even allow bacteria to survive exposure to the
Vacuum#Outer space and radiation in space. Endospore-forming bacteria can also cause disease: for example, anthrax can be contracted by the inhalation of
Bacillus anthracis endospores, and contamination of deep puncture wounds with
Clostridium tetani endospores causes tetanus.
Metabolism
cyanobacteria
In contrast to higher organisms, bacteria exhibit an extremely wide variety of metabolism types. 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. Bacterial metabolism is classified on the basis of three major criteria: the kind of Energy#Biology used for growth, the source of carbon, and the
electron donors used for growth. An additional criterion of respiratory microorganisms are the electron acceptors used for aerobic or anaerobic respiration.
Carbon metabolism in bacteria is either
heterotrophic, where
organic compound compounds are used as carbon sources, or
autotrophic, meaning that cellular carbon is obtained by Carbon fixation
carbon dioxide. Typical autotrophic bacteria are phototrophic cyanobacteria, green sulfur-bacteria and some purple bacteria, but also many chemolithotrophic species, e. g. nitrifying or sulfur-oxidising bacteria. Energy metabolism of bacteria is either based on
phototrophy, the use of light through
photosynthesis, or on
chemotrophy, the use of chemical substances for energy, which are mostly oxidised at the expense of oxygen or alternative electron acceptors (aerobic/anaerobic respiration).
Finally, bacteria are further divided into lithotrophs that use inorganic electron donors and organotrophs that use organic compounds as electron donors. Chemotrophic organisms use the respective electron donors for energy conservation (by aerobic/anaerobic respiration or fermentation) and biosynthetic reactions (e.g. carbon dioxide fixation), whereas phototrophic organisms use them only for biosynthetic purposes. Respiratory organisms use chemical compounds as a source of energy by taking electrons from the
redox substrate and transferring them to a terminal electron acceptor in a redox. This reaction releases energy that can be used to synthesise
adenosine triphosphate and drive metabolism. In aerobic organisms,
oxygen is used as the electron acceptor. In anaerobic organisms other inorganic compounds, such as
nitrate,
sulfate or carbon dioxide are used as electron acceptors. This leads to the ecologically important processes of denitrification, sulfate reduction and acetogenesis, respectively.
Another way of life of chemotrophs in the absence of possible electron acceptors is fermentation, where the electrons taken from the reduced substrates are transferred to oxidised intermediates to generate reduced fermentation products (e. g.
lactic acid,
ethanol,
hydrogen,
butyrate). Fermentation is possible, because the energy content of the substrates is higher than that of the products, which allows the organisms to synthesise ATP and drive their metabolism.
These processes are also important in biological responses to
pollution; for example, sulfate-reducing bacteria are largely responsible for the production of the highly toxic forms of
mercury (element) (
methylmercury and dimethylmercury) in the environment. Non-respiratory anaerobes use fermentation (biochemistry) 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.
Lithotrophic bacteria can use inorganic compounds as a source of energy. Common inorganic electron donors are hydrogen,
carbon monoxide,
ammonia (leading to
nitrification), ferrous iron and other reduced metal ions, and several reduced
sulfur compounds. Unusually, the gas
methane can be used by methanotrophic bacteria as both a source of electrons and a substrate for carbon anabolism. In both aerobic phototrophy and chemolithotrophy, oxygen is used as a terminal electron acceptor, while under anaerobic conditions inorganic compounds are used instead. Most lithotrophic organisms are autotrophic, whereas organotrophic organisms are heterotrophic.
In addition to fixing carbon dioxide in photosynthesis, some bacteria also fix nitrogen gas (nitrogen fixation) using the enzyme nitrogenase. This environmentally important trait can be found in bacteria of nearly all the metabolic types listed above, but is not universal.
Growth and reproduction
Unlike multicellular organisms, increases in the size of bacteria (
cell growth) and their reproduction by cell division are tightly linked in unicellular organisms. Bacteria grow to a fixed size and then reproduce through binary fission, a form of asexual reproduction. Under optimal conditions, bacteria can grow and divide extremely rapidly, and bacterial populations can double as quickly as every 9.8 minutes. In cell division, two identical
clone (genetics) daughter cells are produced. Some bacteria, while still reproducing asexually, form more complex reproductive structures that facilitate the dispersal of the newly formed daughter cells. Examples include fruiting body formation by
Myxobacteria and arial hyphae formation by
Streptomyces, or budding. Budding involves a cell forming a protrusion that breaks away and produces a daughter cell.
cells.
In the laboratory, bacteria are usually grown using solid or liquid media. Solid growth media such as agar plates are used to isolate pure cultures of a bacterial strain. However, liquid growth media are used when measurement of growth or large volumes of cells are required. Growth in stirred liquid media occurs as an even cell suspension, making the cultures easy to divide and transfer, although isolating single bacteria from liquid media is difficult. The use of selective media (media with specific nutrients added or deficient, or with antibiotics added) can help identify specific organisms.
Most laboratory techniques for growing bacteria use high levels of nutrients to produce large amounts of cells cheaply and quickly. However, in natural environments nutrients are limited, meaning that bacteria cannot continue to reproduce indefinitely. This nutrient limitation has led the evolution of different growth strategies (see r/K selection theory). Some organisms can grow extremely rapidly when nutrients become available, such as the formation of
algal bloom (and cyanobacterial) blooms that often occur in lakes during the summer. Other organisms have adaptations to harsh environments, such as the production of multiple
antibiotics by
Streptomyces that inhibit the growth of competing microorganisms. In nature, many organisms live in communities (e.g.
biofilms) which may allow for increased supply of nutrients and protection from environmental stresses. These relationships can be essential for growth of a particular organism or group of organisms (
syntrophy).
Bacterial growth follows three phases. When a population of bacteria first enter a high-nutrient environment that allows growth, the cells need to adapt to their new environment. The first phase of growth is the lag time, a period of slow growth when the cells are adapting to fast growth. The lag phase has high biosynthesis rates, as enzymes and active transporters are produced. The second phase of growth is the
logarithmic (log phase), also known as the exponential phase. The log phase is marked by rapid exponential growth. The rate at which cells grow during this phase is known as the
growth rate (
k), and the time it takes the cells to double is known as the
generation time (
g). During log phase, nutrients are metabolised at maximum speed until one of the nutrients is depleted and starts limiting growth. The final phase of growth is the
stationary phase and is caused by depleted nutrients. The cells reduce their metabolic activity and consume non-essential cellular proteins. The stationary phase is a transition from rapid growth to a stress response state and there is increased expression of genes involved in DNA repair,
antioxidant and
active transport.
Genetics
Most bacteria have a single circular
chromosome that can range in size from only 160,000 base pairs in the
endosymbiont bacteria
Candidatus Carsonella ruddii, to 12,200,000 base pairs in the soil-dwelling bacteria
Sorangium cellulosum.
Spirochaetes of the
genus Borrelia are a notable exception to this arrangement, with bacteria such as
Borrelia burgdorferi, the cause of
Lyme disease, containing a single linear chromosome. Bacteria may also contain
plasmids, which are small extra-chromosomal DNAs that may contain genes for
antibiotic resistance or virulence. Another type of bacterial DNA are
lysogeny viruses (
bacteriophages). Many types of bacteriophage exist, some simply infect and
lytic cycle their host (biology) bacteria, while others insert into the bacterial chromosome. A bacteriophage can contain genes that contribute to its host's phenotype: for example, in the evolution of Escherichia coli O157:H7 and
Clostridium botulinum, the
toxin genes in an integrated phage converted a harmless ancestral bacteria into a lethal pathogen.
Bacteria, as asexual organisms, inherit identical copies of their parent's genes (i.e., they are clone (genetics)). However, all bacteria can evolve by selection on changes to their genetic material
DNA caused by
genetic recombination or mutations. Mutations come from errors made during the replication of DNA or from exposure to
mutagens. Mutation rates vary widely among different species of bacteria and even among different clones of a single species of bacteria. Genetic changes in bacterial genomes come from either random mutation during replication or "stress-directed mutation", where genes involved in a particular growth-limiting process have an increased mutation rate.
Some bacteria also transfer genetic material between cells. This can occur in three main ways. Firstly, bacteria can take up exogenous DNA from their environment, in a process called transformation (genetics). Genes can also be transferred by the process of transduction (genetics), when the integration of a bacteriophage introduces foreign DNA into the chromosome. The third method of gene transfer is
bacterial conjugation, where DNA is transferred through direct cell contact. This gene acquisition from other bacteria or the environment is called horizontal gene transfer and may be common under natural conditions. Gene transfer is particularly important in
antibiotic resistance as it allows the rapid transfer of resistance genes between different pathogens.
Movement
]
Motile bacteria can move using flagellum, bacterial gliding, twitching motility or changes of buoyancy. In twitching motility, bacterial use their type IV
pilus as a grappling hook, repeatedly extending it, anchoring it and then retracting it with remarkable force (>80 p
Newton).
Bacterial species differ in the number and arrangement of flagella on their surface; some have a single flagellum (monotrichous), a flagellum at each end (amphitrichous), clusters of flagella at the poles of the cell (
lophotrichous), while others have flagella distributed over the entire surface of the cell (
peritrichous). The bacterial flagella is the best-understood motility structure in any organism and is made of about 20 proteins, with approximately another 30 proteins required for its regulation and assembly. The flagellum is a rotating structure driven by a motor at the base that uses the electrochemical gradient across the membrane for power. This motor drives the motion of the filament, which acts as a propeller. Many bacteria (such as
Escherichia coli) have two distinct modes of movement: forward movement (swimming) and tumbling. The tumbling allows them to reorient and makes their movement a three-dimensional
random walk. (See external links below for link to videos.) The flagella of a unique group of bacteria, the
spirochaetes, are found between two membranes in the periplasmic space. They have a distinctive
helix body that twists about as it moves.
Motile bacteria are attracted or repelled by certain stimulus (physiology) in behaviors called
taxes: these include
chemotaxis,
phototaxis and
magnetotaxis. In one peculiar group, the
myxobacteria, individual bacteria move together to form waves of cells that then differentiate to form fruiting bodies containing spores. The
myxobacteria move only when on solid surfaces, unlike
E. coli which is
motile in liquid or solid media.
Several
Listeria and
Shigella species move inside host cells by usurping the cytoskeleton, which is normally used to move organelles inside the cell. By promoting actin
biopolymer at one pole of their cells, they can form a kind of tail that pushes them through the host cell's cytoplasm.
Classification and identification
Scientific Classification seeks to describe the diversity of bacterial species by naming and grouping organisms based on similarities. Bacteria can be classified on the basis of cell structure, cellular metabolism or on differences in cell components such as DNA,
fatty acids, pigments,
antigens and quinones. While these schemes allowed the identification and classification of bacterial strains, it was unclear whether these differences represented variation between distinct species or between strains of the same species. This uncertainty was due to the lack of distinctive structures in most bacteria, as well as
lateral gene transfer between unrelated species. Due to lateral gene transfer, some closely related bacteria can have very different morphologies and metabolisms. To overcome this uncertainty, modern bacterial classification emphasizes
molecular systematics, using genetic techniques such as guanine
cytosine GC-content determination, genome-genome hybridization, as well as DNA sequencing genes that have not undergone extensive lateral gene transfer, such as the ribosomal DNA. Classification of bacteria is determined by publication in the International Journal of Systematic Bacteriology,http://ijs.sgmjournals.org/ and Bergey's Manual of Systematic Bacteriology.http://www.bergeys.org/
The term "bacteria" was traditionally applied to all microscopic, single-celled prokaryotes. However, molecular systematics showed prokaryotic life to consist of two separate
domain (biology)s, originally called
Eubacteria and
Archaebacteria, but now called
Bacteria and
Archaea that evolved independently from an ancient common ancestor. These two domains, along with Eukarya, are the basis of the
three-domain system, which is currently the most widely used classification system in bacteriology. However, due to the relatively recent introduction of molecular systematics and the analysis of genome sequences, bacterial classification remains a changing and expanding field. For example, a few biologists argue that Archaea evolved from Gram-positive bacteria.
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. showing the incredible diversity of bacteria, compared to other organisms.
Eukaryotes are colored red,
archaea green and bacteria blue.The
Gram stain, developed in 1884 by Hans Christian Gram, characterises bacteria based on the structural characteristics of their cell walls. The thick layers of peptidoglycan in the "Gram-positive" cell wall stain purple, while the thin "Gram-negative" cell wall appears pink. By combining morphology and Gram-staining, most bacteria can be classified as belonging to one of four groups (Gram-positive cocci, Gram-positive bacilli, Gram-negative cocci and Gram-negative bacilli). Some organisms are best identified by stains other than the Gram stain, particularly mycobacteria or
Nocardia, which show acid-fastness on Ziehl-Neelsen stain or similar stains. Other organisms may need to be identified by their growth in special media, or by other techniques, such as
serology.
Microbiological culture techniques are designed to promote the growth and identify particular bacteria, while restricting the growth of the other bacteria in the sample. Often these techniques are designed for specific specimens; for example, a
sputum sample will be treated to identify organisms that cause pneumonia, while feces specimens are cultured on
selective media to identify organisms that cause
diarrhea, while preventing growth of non-pathogenic bacteria. Specimens that are normally sterile, such as
blood,
urine or cerebrospinal fluid, are cultured under conditions designed to grow all possible organisms. Once a pathogenic organism has been isolated, it can be further characterised by its morphology, growth patterns such as (aerobic organism or anaerobic organism growth,
hemolysis (microbiology)) and staining.
As with bacterial classification, identification of bacteria is increasingly using molecular methods. Diagnostics using such DNA-based tools, such as polymerase chain reaction, are increasingly popular due to their specificity and speed, compared to culture-based methods. These methods also allow the detection and identification of "viable but nonculturable" cells that are metabolically active but non-dividing. However, even using these improved methods, the total number of bacterial species is not known and cannot even be estimated with any certainty. Attempts to quantify bacterial diversity have ranged from 107 to 109 total species, but even these diverse estimates may be out by many orders of magnitude.
Interactions with other organisms
Despite their apparent simplicity, bacteria can form complex associations with other organisms. These symbiosis associations can be divided into parasitism,
mutualism and
commensalism. Due to their small size, commensal bacteria are ubiquitous and grow on animals and plants exactly as they will grow on any other surface. However, their growth can be increased by warmth and
sweating, and large populations of these organisms in humans are the cause of body odor.
Mutualists
Certain bacteria form close spatial associations that are essential for their survival. One such mutualistic association, called interspecies hydrogen transfer, occurs between clusters of
anaerobic bacteria that consume organic acids such as
butyric acid or
propionic acid and produce
hydrogen, and
methanogenic Archaea that consume hydrogen. The bacteria in this association are unable to consume the organic acids as this reaction produces hydrogen that accumulates in their surroundings. Only the intimate association with the hydrogen-consuming Archaea keeps the hydrogen concentration low enough to allow the bacteria to grow.
In soil, microorganisms which reside in the rhizosphere (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. This serves to provide an easily absorbable form of nitrogen for many plants, which cannot fix nitrogen themselves. Many other bacteria are found as symbionts
Bacteria in the human body 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
Milk#Physical and chemical structure to lactic acid (see
Lactobacillus), as well as fermenting complex undigestible carbohydrates. The presence of this gut flora also inhibits the growth of potentially pathogenic bacteria (usually through competitive exclusion) and these beneficial bacteria are consequently sold as probiotic
dietary supplements.
Pathogens
(red) invading cultured human cells
If bacteria form a parasitic association with other organisms, they are classed as
pathogens. Pathogenic bacteria are a major cause of human death and disease and cause infections such as
tetanus,
typhoid fever, diphtheria, syphilis,
cholera, food-borne illness,
leprosy and
tuberculosis. A pathogenic cause for a known medical disease may only be discovered many years after, as was the case with
Helicobacter pylori and Timeline of peptic ulcer disease and Helicobacter pylori. Bacterial diseases are also important in agriculture, with bacteria causing leaf spot,
fireblight and
wilting in plants, as well as
Johne's disease, mastitis,
salmonella and
anthrax in farm animals.
Each species of pathogen has a characteristic spectrum of interactions with its human host (biology). Some organisms, such as
Staphylococcus or
Streptococcus, can cause skin infections,
pneumonia, meningitis and even overwhelming
sepsis, a systemic inflammatory response producing shock (medical), massive vasodilator and death. Yet these organisms are also part of the normal human flora and usually exist on the skin or in the nose without causing any disease at all. Other organisms invariably cause disease in humans, such as the
Rickettsia, which are obligate intracellular parasites able to grow and reproduce only within the cells of other organisms. One species of Rickettsia causes
typhus, while another causes Rocky Mountain spotted fever. Chlamydia, another phylum of obligate intracellular parasites, contains species that can cause pneumonia, or
urinary tract infection and may be involved in coronary heart disease. Finally, some species such as
Pseudomonas aeruginosa,
Burkholderia cenocepacia, and
Mycobacterium avium complex are
opportunistic infection and cause disease mainly in people suffering from
immunosuppression or cystic fibrosis. PMID 14980298
Bacterial infections may be treated with antibiotics, which are classified as
bacteriocide if they kill bacteria, or bacteriostatic if they just prevent bacterial growth. There are many types of antibiotics and each class
enzyme inhibitor 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. 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
{{Taxobox| color = lightgrey| name = Bacteria| fossil_range =
Archean or earlier - Recent] cells magnified 25,000 times| domain =
Bacteria| subdivision_ranks = Phyla| subdivision =
ActinobacteriaAquificaeChlamydiae
Bacteroidetes (phylum)/Chlorobi
ChloroflexiChrysiogenetesCyanobacteriaDeferribacteraceaeDeinococcus-ThermusDictyoglomiFibrobacteres/Acidobacteria
Firmicutes
FusobacteriaGemmatimonadetesVerrucomicrobiaNitrospiraePlanctomycetesProteobacteriaSpirochaetes
Thermodesulfobacteria
Thermomicrobia
Thermotogae
Verrucomicrobia-->
Bacteria (singular:
bacterium) are unicellular
microorganisms. Typically a few
micrometres in length, individual bacteria have a wide-range of shapes, ranging from
spheres to rods to spirals. Bacteria are ubiquitous in every habitat (ecology) on Earth, growing in soil, hot springs,
nuclear waste, seawater, and deep in the Crust (geology). There are typically 40 million bacterial
cell (biology) in a gram of soil and a million bacterial cells in a millilitre of fresh water; in all, there are approximately five Names of large numbers#The "standard dictionary numbers" (5×1030) bacteria in the world. Bacteria are vital in recycling nutrients, and many important steps in nutrient cycles depend on bacteria, such as the nitrogen fixation from the Earth's atmosphere. However, most of these bacteria have not been characterised, and only about half of the phylum of bacteria have species that can be microbiological culture in the
laboratory. The study of bacteria is known as bacteriology, a branch of microbiology.
There are approximately 10 times as many bacterial cells as human cells in the human body, with large numbers of bacteria on the
skin and in the
gastrointestinal tract. Although the vast majority of these bacteria are rendered harmless or beneficial by the protective effects of the immune system, a few pathogenic bacteria cause infectious diseases, including cholera, syphilis,
anthrax, leprosy and bubonic plague. The most common fatal bacterial diseases are respiratory infections, with
tuberculosis alone killing about 2 million people a year, mostly in
sub-Saharan Africa. In
developed country, antibiotics are used to treat bacterial infections and in various agricultural processes, so antibiotic resistance is becoming common. In industry, bacteria are important in processes such as
wastewater treatment, the production of
cheese and
yoghurt, and the manufacture of antibiotics and other chemicals.
Bacteria are prokaryotes. Unlike cells of animals and other eukaryotes, bacterial cells do not contain a cell nucleus and rarely harbour
cell membrane organelles. Although the term
bacteria traditionally included all prokaryotes, the scientific classification changed after the discovery in the 1990s that prokaryotic life consists of two very different groups of organisms that
evolution independently from an ancient common ancestor. These domain (biology) are called Bacteria and Archaea.
History of bacteriology
The existence of microorganisms was hypothesized during the late Middle Ages. In
The Canon of Medicine (1020),
Abū Alī ibn Sīnā (Avicenna) stated that bodily secretions are contaminated by "foul foreign earthly bodies" before a person becomes infected, but he did not view these bodies as primary causes of disease. When the Black Death bubonic plague reached al-Andalus in the 14th century, Ibn Khatima and Ibn al-Khatib wrote of
infectious diseases being caused by contagious entities that enter the human body.Ibrahim B. Syed, (2002). "Islamic Medicine: 1000 years ahead of its times",
Journal of the Islamic Medical Association 2, p. 2-9. These ideas about the contagious nature of some diseases became more popular in Europe during the Renaissance, particularly through the writing of
Girolamo Fracastoro.
, the first person to observe bacteria using a microscope.
Bacteria were first observed by
Anton van Leeuwenhoek in 1676, using a single-lens
microscope of his own design. He called them "animalcules" and published his observations in a series of letters to the Royal Society. The name
bacterium was introduced much later, by
Christian Gottfried Ehrenberg in 1828, and is derived from the List of Greek words with English derivatives βακτήριον -α ,
bacterion -a , meaning "small staff".
Louis Pasteur demonstrated in 1859 that the
fermentation (food) process is caused by the growth of microorganisms, and that this growth is not due to spontaneous generation. (Yeasts and molds, commonly associated with fermentation, are not bacteria, but rather
fungus.) Along with his contemporary,
Robert Koch, Pasteur was an early advocate of the
germ theory of disease.Robert Koch was a pioneer in medical microbiology and worked on
cholera, anthrax and
tuberculosis. In his research into tuberculosis, Koch finally proved the germ theory, for which he was awarded a
Nobel Prize in Physiology or Medicine in 1905. In
Koch's postulates, he set out criteria to test if an organism is the cause of a
disease; these postulates are still used today.
Though it was known in the nineteenth century that bacteria are the cause of many diseases, no effective
antiseptic treatments were available. In 1910,
Paul Ehrlich developed the first antibiotic, by changing dyes that selectively stained
Treponema pallidum—the spirochete that causes syphilis—into compounds that selectively killed the pathogen. Ehrlich had been awarded a 1908 Nobel Prize for his work on immunology, and pioneered the use of stains to detect and identify bacteria, with his work being the basis of the
Gram stain and the Ziehl-Neelsen stain.
A major step forward in the study of bacteria was the recognition in 1977 by Carl Woese that
archaea have a separate line of evolutionary descent from bacteria. This new
phylogenetic taxonomy was based on the
sequencing of Svedberg
ribosome RNA, and divided prokaryotes into two evolutionary domains as part of the
three-domain system.
Origin and early evolution
The ancestors of modern bacteria were single-celled microorganisms that were the
Origin of life to develop on earth, about
1 E17 s. For about 3 billion years, all organisms were microscopic, and bacteria and archaea were the dominant forms of life. Although bacterial fossils exist, such as stromatolites, their lack of distinctive morphology (biology) prevents them from being used to examine the past history of bacterial evolution, or to date the time of origin of a particular bacterial species. However, gene sequences can be used to reconstruct the bacterial phylogenetics, and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage. The
most recent common ancestor of bacteria and archaea was probably a
thermophile that lived about 2.5 billion–3.2 billion years ago.
Bacteria were also involved in the second great evolutionary divergence, that of the archaea and eukaryotes. Here, eukaryotes resulted from ancient bacteria entering into
endosymbiont associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea. This involved the engulfment by proto-eukaryotic cells of alpha-proteobacterial symbionts to form either
mitochondrion or
hydrogenosomes, which are still being found in all known Eukarya (sometimes in highly reduced form, e. g. in ancient "amitochondrial" protozoa). Later on, an independent second engulfment by some mitochondria-containing eukaryotes of cyanobacterial-like organisms led to the formation of
chloroplasts in algae and plants. There are even some algal groups known that clearly originated from subsequent events of endosymbiosis by heterotrophic eukaryotic hosts engulfing a eukaryotic algae that developed into "second-generation" plastids.
Morphology
and arrangements.
Bacteria display a wide diversity of shapes and sizes, called
morphology (biology). Bacterial cells are about 10 times smaller than eukaryotic cells and are typically 0.5–5.0
micrometres in length. However, a few species–for example
Thiomargarita namibiensis and
Epulopiscium fishelsoni–are up to half a
millimetre long and are visible to the unaided eye. Among the smallest bacteria are members of the genus
Mycoplasma, which measure only 0.3 micrometres, as small as the largest viruses.
Most bacterial species are either spherical, called coccus (
sing. coccus, from Greek
kókkos, grain, seed) or rod-shaped, called
bacillus (
sing. bacillus, from Latin
baculus, stick). Some rod-shaped bacteria, called vibrio, are slightly curved or comma-shaped; others, can be spiral-shaped, called
spirillum, or tightly coiled, called spirochetes. A small number of species even have tetrahedral or cuboidal shapes. This wide variety of shapes is determined by the bacterial cell wall and cytoskeleton, and is important because it can influence the ability of bacteria to acquire nutrients, attach to surfaces, swim through liquids and escape
predation.
Many bacterial species exist simply as single cells, others associate in characteristic patterns:
Neisseria form diploids (pairs),
Streptococcus form chains, and
Staphylococcus group together in "bunch of grapes" clusters. Bacteria can also be elongated to form filaments, for example the
Actinobacteria. Filamentous bacteria are often surrounded by a sheath that contains many individual cells; certain types, such as species of the genus
Nocardia, even form complex, branched filaments, similar in appearance to fungal mycelia.
s, relative to those of other organisms and biomolecules
Bacteria often attach to surfaces and form dense aggregations called biofilms or microbial mats. These films can range from a few micrometers in thickness to up to half a meter in depth, and may contain multiple species of bacteria,
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. In natural environments, such as soil or the surfaces of plants, the majority of bacteria are bound to surfaces in biofilms. Biofilms are also important for chronic bacterial infections and infections of implant (medicine) medical devices, as bacteria protected within these structures are much harder to kill than individual bacteria.
Even more complex morphological changes are sometimes possible. For example, when starved of amino acids, Myxobacteria detect surrounding cells in a process known as
quorum sensing, migrate towards each other, and aggregate to form fruiting bodies up to 500 micrometres long and containing approximately 100,000 bacterial cells. In these fruiting bodies, the bacteria perform separate tasks; this type of cooperation is a simple type of
multicellular organism organisation. For example, about one in 10 cells migrate to the top of these fruiting bodies and cellular differentiation into a specialised dormant state called myxospores, which are more resistant to desiccation and other adverse environmental conditions than are ordinary cells.
Cellular structure
Intracellular structures
The bacterial cell is surrounded by a
lipid membrane, or cell membrane, which encompasses the contents of the cell and acts as a barrier to hold nutrients, proteins and other essential components of the
cytoplasm within the cell. As they are prokaryotes, bacteria do not have membrane-bound organelles in their cytoplasm and thus contain few intracellular structures. They consequently lack a
cell nucleus, mitochondrion,
chloroplasts and the other organelles present in eukaryotic cells, such as the Golgi apparatus and
endoplasmic reticulum.
Many important biochemistry reactions, such as
Energy#Biology generation, occur due to diffusions across membranes, creating a potential difference analogous to a
battery (electricity). The absence of internal membranes in bacteria means these reactions, such as electron transport chain, occur across the cell membrane, between the cytoplasm and the periplasmic space. Additionally, while some transporter proteins consume chemical energy, others harness concentration gradients to import nutrients across the cell membrane or to expel undesired molecules from the cytoplasm.
Bacteria do not have a membrane-bound nucleus, and their
genetic material is typically a single circular
chromosome located in the cytoplasm in an irregularly shaped body called the nucleoid. The nucleoid contains the chromosome with associated proteins and
RNA. Like all living organisms, bacteria contain
ribosomes for the production of proteins, but the structure of the bacterial ribosome is different from those of eukaryotes and Archaea. The order Planctomycetes are an exception to the general absence of internal membranes in bacteria, because they have a membrane around their nucleoid and contain other membrane-bound cellular structures.
Some bacteria produce intracellular nutrient storage granules, such as glycogen, polyphosphate,
sulfur or
polyhydroxyalkanoates. These granules enable bacteria to store compounds for later use. Certain bacterial species, such as the Photosynthesis#Bacterial variations Cyanobacteria, produce internal gas vesicles, which they use to regulate their buoyancy - allowing them to move up or down into water layers with different light intensities and nutrient levels.
Extracellular structures
Around the outside of the cell membrane is the bacterial
cell wall. Bacterial cell walls are made of
peptidoglycan (called murein in older sources), which is made from polysaccharide chains cross-linked by unusual peptides containing D-
amino acids. Bacterial cell walls are different from the cell walls of plants and fungus, which are made of cellulose and chitin, respectively. The cell wall of bacteria is also distinct from that of Archaea, which do not contain peptidoglycan. The cell wall is essential to the survival of many bacteria, and the antibiotic
penicillin is able to kill bacteria by inhibiting a step in the synthesis of peptidoglycan.
There are broadly speaking two different types of cell wall in bacteria, called
Gram-positive and Gram-negative. The names originate from the reaction of cells to the Gram stain, a test long-employed for the classification of bacterial species.
Gram-positive bacteria possess a thick cell wall containing many layers of peptidoglycan and
teichoic acids. In contrast, Gram-negative bacteria have a relatively thin cell wall consisting of a few layers of peptidoglycan surrounded by a second lipid membrane containing
lipopolysaccharides and
lipoproteins. Most bacteria have the Gram-negative cell wall, and only the
Firmicutes and
Actinobacteria (previously known as the low G+C and high G+C Gram-positive bacteria, respectively) have the alternative Gram-positive arrangement. 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.
In many bacteria an S-layer of rigidly arrayed protein molecules covers the outside of the cell. This layer provides chemical and physical protection for the cell surface and can act as a
macromolecule diffusion barrier. S-layers have diverse but mostly poorly understood functions, but are known to act as virulence factors in
Campylobacter and contain surface enzymes in
Bacillus stearothermophilus.
electron micrograph, showing multiple flagella on the cell surface
Flagellum are rigid protein structures, about 20
metres 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.
Fimbriae are fine filaments of protein, just 2–10 nanometres in diameter and up to several micrometers in length. They are distributed over the surface of the cell, and resemble fine hairs when seen under the
electron microscope. Fimbriae are believed to be involved in attachment to solid surfaces or to other cells and are essential for the virulence of some bacterial pathogens. Pilus (
sing. pilus) are cellular appendages, slightly larger than fimbriae, that can transfer genetic material between bacterial cells in a process called
bacterial conjugation (see bacterial genetics, below).
Capsules or slime layers are produced by many bacteria to surround their cells, and vary in structural complexity: ranging from a disorganised slime layer of extra-cellular polymer, to a highly structured capsule (microbiology) or glycocalyx. These structures can protect cells from engulfment by eukaryotic cells, such as macrophages. They can also act as antigens and be involved in cell recognition, as well as aiding attachment to surfaces and the formation of biofilms.
The assembly of these extracellular structures is dependent on bacterial secretion. 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.
Endospores
(stained purple) growing in cerebrospinal fluid
Certain genera of Gram-positive bacteria, such as
Bacillus,
Clostridium,
Sporohalobacter,
Anaerobacter and
Heliobacteria, can form highly resistant, dormant structures called
endospores. In almost all cases, one endospore is formed and this is not a reproductive process, although
Anaerobacter can make up to seven endospores in a single cell. Endospores have a central core of
cytoplasm containing
DNA and ribosomes surrounded by a cortex layer and protected by an impermeable and rigid coat.
Endospores show no detectable
metabolism and can survive extreme physical and chemical stresses, such as high levels of
ultraviolet,
gamma ray, detergents, disinfectants, heat, pressure and
desiccation. In this dormant state, these organisms may remain viable for millions of years, and endospores even allow bacteria to survive exposure to the
Vacuum#Outer space and radiation in space. Endospore-forming bacteria can also cause disease: for example, anthrax can be contracted by the inhalation of
Bacillus anthracis endospores, and contamination of deep puncture wounds with
Clostridium tetani endospores causes
tetanus.
Metabolism
cyanobacteria
In contrast to higher organisms, bacteria exhibit an extremely wide variety of metabolism types. 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. Bacterial metabolism is classified on the basis of three major criteria: the kind of
Energy#Biology used for growth, the source of
carbon, and the
electron donors used for growth. An additional criterion of respiratory microorganisms are the
electron acceptors used for aerobic or anaerobic respiration.
Carbon metabolism in bacteria is either heterotrophic, where
organic compound compounds are used as carbon sources, or
autotrophic, meaning that cellular carbon is obtained by Carbon fixation
carbon dioxide. Typical autotrophic bacteria are phototrophic
cyanobacteria, green sulfur-bacteria and some
purple bacteria, but also many chemolithotrophic species, e. g. nitrifying or sulfur-oxidising bacteria. Energy metabolism of bacteria is either based on
phototrophy, the use of light through photosynthesis, or on chemotrophy, the use of chemical substances for energy, which are mostly oxidised at the expense of oxygen or alternative electron acceptors (aerobic/anaerobic respiration).
Finally, bacteria are further divided into lithotrophs that use inorganic electron donors and
organotrophs that use organic compounds as electron donors. Chemotrophic organisms use the respective electron donors for energy conservation (by aerobic/anaerobic respiration or fermentation) and biosynthetic reactions (e.g. carbon dioxide fixation), whereas phototrophic organisms use them only for biosynthetic purposes. Respiratory organisms use chemical compounds as a source of energy by taking electrons from the
redox substrate and transferring them to a terminal electron acceptor in a
redox. This reaction releases energy that can be used to synthesise adenosine triphosphate and drive metabolism. In
aerobic organisms,
oxygen is used as the electron acceptor. In
anaerobic organisms other inorganic compounds, such as nitrate, sulfate or carbon dioxide are used as electron acceptors. This leads to the ecologically important processes of
denitrification, sulfate reduction and
acetogenesis, respectively.
Another way of life of chemotrophs in the absence of possible electron acceptors is fermentation, where the electrons taken from the reduced substrates are transferred to oxidised intermediates to generate reduced fermentation products (e. g.
lactic acid,
ethanol, hydrogen, butyrate). Fermentation is possible, because the energy content of the substrates is higher than that of the products, which allows the organisms to synthesise ATP and drive their metabolism.
These processes are also important in biological responses to pollution; for example,
sulfate-reducing bacteria are largely responsible for the production of the highly toxic forms of mercury (element) (methylmercury and dimethylmercury) in the environment. Non-respiratory anaerobes use
fermentation (biochemistry) 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.
Lithotrophic bacteria can use inorganic compounds as a source of energy. Common inorganic electron donors are hydrogen,
carbon monoxide, ammonia (leading to nitrification), ferrous iron and other reduced metal ions, and several reduced
sulfur compounds. Unusually, the gas
methane can be used by
methanotrophic bacteria as both a source of electrons and a substrate for carbon anabolism. In both aerobic phototrophy and
chemolithotrophy, oxygen is used as a terminal electron acceptor, while under anaerobic conditions inorganic compounds are used instead. Most lithotrophic organisms are autotrophic, whereas organotrophic organisms are heterotrophic.
In addition to fixing carbon dioxide in photosynthesis, some bacteria also fix nitrogen gas (nitrogen fixation) using the enzyme nitrogenase. This environmentally important trait can be found in bacteria of nearly all the metabolic types listed above, but is not universal.
Growth and reproduction
Unlike multicellular organisms, increases in the size of bacteria (cell growth) and their reproduction by cell division are tightly linked in unicellular organisms. Bacteria grow to a fixed size and then reproduce through
binary fission, a form of asexual reproduction. Under optimal conditions, bacteria can grow and divide extremely rapidly, and bacterial populations can double as quickly as every 9.8 minutes. In cell division, two identical
clone (genetics) daughter cells are produced. Some bacteria, while still reproducing asexually, form more complex reproductive structures that facilitate the dispersal of the newly formed daughter cells. Examples include fruiting body formation by
Myxobacteria and arial hyphae formation by
Streptomyces, or budding. Budding involves a cell forming a protrusion that breaks away and produces a daughter cell.
cells.
In the laboratory, bacteria are usually grown using solid or liquid media. Solid growth media such as agar plates are used to isolate pure cultures of a bacterial strain. However, liquid growth media are used when measurement of growth or large volumes of cells are required. Growth in stirred liquid media occurs as an even cell suspension, making the cultures easy to divide and transfer, although isolating single bacteria from liquid media is difficult. The use of selective media (media with specific nutrients added or deficient, or with antibiotics added) can help identify specific organisms.
Most laboratory techniques for growing bacteria use high levels of nutrients to produce large amounts of cells cheaply and quickly. However, in natural environments nutrients are limited, meaning that bacteria cannot continue to reproduce indefinitely. This nutrient limitation has led the evolution of different growth strategies (see r/K selection theory). Some organisms can grow extremely rapidly when nutrients become available, such as the formation of algal bloom (and cyanobacterial) blooms that often occur in lakes during the summer. Other organisms have adaptations to harsh environments, such as the production of multiple antibiotics by
Streptomyces that inhibit the growth of competing microorganisms. In nature, many organisms live in communities (e.g. biofilms) which may allow for increased supply of nutrients and protection from environmental stresses. These relationships can be essential for growth of a particular organism or group of organisms (
syntrophy).
Bacterial growth follows three phases. When a population of bacteria first enter a high-nutrient environment that allows growth, the cells need to adapt to their new environment. The first phase of growth is the
lag time, a period of slow growth when the cells are adapting to fast growth. The lag phase has high biosynthesis rates, as enzymes and
active transporters are produced. The second phase of growth is the
logarithmic (log phase), also known as the exponential phase. The log phase is marked by rapid exponential growth. The rate at which cells grow during this phase is known as the
growth rate (
k), and the time it takes the cells to double is known as the
generation time (
g). During log phase, nutrients are metabolised at maximum speed until one of the nutrients is depleted and starts limiting growth. The final phase of growth is the stationary phase and is caused by depleted nutrients. The cells reduce their metabolic activity and consume non-essential cellular proteins. The stationary phase is a transition from rapid growth to a stress response state and there is increased expression of genes involved in DNA repair,
antioxidant and active transport.
Genetics
Most bacteria have a single circular
chromosome that can range in size from only 160,000 base pairs in the endosymbiont bacteria
Candidatus Carsonella ruddii, to 12,200,000 base pairs in the soil-dwelling bacteria
Sorangium cellulosum.
Spirochaetes of the genus
Borrelia are a notable exception to this arrangement, with bacteria such as
Borrelia burgdorferi, the cause of Lyme disease, containing a single linear chromosome. Bacteria may also contain
plasmids, which are small extra-chromosomal DNAs that may contain genes for antibiotic resistance or
virulence. Another type of bacterial DNA are lysogeny viruses (bacteriophages). Many types of bacteriophage exist, some simply infect and
lytic cycle their host (biology) bacteria, while others insert into the bacterial chromosome. A bacteriophage can contain genes that contribute to its host's
phenotype: for example, in the evolution of
Escherichia coli O157:H7 and
Clostridium botulinum, the
toxin genes in an integrated phage converted a harmless ancestral bacteria into a lethal pathogen.
Bacteria, as asexual organisms, inherit identical copies of their parent's genes (i.e., they are clone (genetics)). However, all bacteria can evolve by selection on changes to their genetic material
DNA caused by genetic recombination or
mutations. Mutations come from errors made during the replication of DNA or from exposure to
mutagens. Mutation rates vary widely among different species of bacteria and even among different clones of a single species of bacteria. Genetic changes in bacterial genomes come from either random mutation during replication or "stress-directed mutation", where genes involved in a particular growth-limiting process have an increased mutation rate.
Some bacteria also transfer genetic material between cells. This can occur in three main ways. Firstly, bacteria can take up exogenous DNA from their environment, in a process called
transformation (genetics). Genes can also be transferred by the process of transduction (genetics), when the integration of a bacteriophage introduces foreign DNA into the chromosome. The third method of gene transfer is
bacterial conjugation, where DNA is transferred through direct cell contact. This gene acquisition from other bacteria or the environment is called
horizontal gene transfer and may be common under natural conditions. Gene transfer is particularly important in
antibiotic resistance as it allows the rapid transfer of resistance genes between different pathogens.
Movement
]
Motile bacteria can move using
flagellum,
bacterial gliding, twitching motility or changes of buoyancy. In twitching motility, bacterial use their type IV pilus as a grappling hook, repeatedly extending it, anchoring it and then retracting it with remarkable force (>80 pNewton).
Bacterial species differ in the number and arrangement of flagella on their surface; some have a single flagellum (monotrichous), a flagellum at each end (
amphitrichous), clusters of flagella at the poles of the cell (
lophotrichous), while others have flagella distributed over the entire surface of the cell (peritrichous). The bacterial flagella is the best-understood motility structure in any organism and is made of about 20 proteins, with approximately another 30 proteins required for its regulation and assembly. The flagellum is a rotating structure driven by a motor at the base that uses the
electrochemical gradient across the membrane for power. This motor drives the motion of the filament, which acts as a propeller. Many bacteria (such as
Escherichia coli) have two distinct modes of movement: forward movement (swimming) and tumbling. The tumbling allows them to reorient and makes their movement a three-dimensional random walk. (See external links below for link to videos.) The flagella of a unique group of bacteria, the
spirochaetes, are found between two membranes in the periplasmic space. They have a distinctive
helix body that twists about as it moves.
Motile bacteria are attracted or repelled by certain stimulus (physiology) in behaviors called
taxes: these include chemotaxis, phototaxis and
magnetotaxis. In one peculiar group, the
myxobacteria, individual bacteria move together to form waves of cells that then differentiate to form fruiting bodies containing spores. The myxobacteria move only when on solid surfaces, unlike
E. coli which is
motile in liquid or solid media.
Several
Listeria and
Shigella species move inside host cells by usurping the cytoskeleton, which is normally used to move
organelles inside the cell. By promoting actin
biopolymer at one pole of their cells, they can form a kind of tail that pushes them through the host cell's cytoplasm.
Classification and identification
Scientific Classification seeks to describe the diversity of bacterial species by naming and grouping organisms based on similarities. Bacteria can be classified on the basis of cell structure, cellular metabolism or on differences in cell components such as
DNA,
fatty acids, pigments,
antigens and
quinones. While these schemes allowed the identification and classification of bacterial strains, it was unclear whether these differences represented variation between distinct species or between strains of the same species. This uncertainty was due to the lack of distinctive structures in most bacteria, as well as
lateral gene transfer between unrelated species. Due to lateral gene transfer, some closely related bacteria can have very different morphologies and metabolisms. To overcome this uncertainty, modern bacterial classification emphasizes molecular systematics, using genetic techniques such as
guanine cytosine GC-content determination, genome-genome hybridization, as well as
DNA sequencing genes that have not undergone extensive lateral gene transfer, such as the
ribosomal DNA. Classification of bacteria is determined by publication in the International Journal of Systematic Bacteriology,http://ijs.sgmjournals.org/ and Bergey's Manual of Systematic Bacteriology.http://www.bergeys.org/
The term "bacteria" was traditionally applied to all microscopic, single-celled prokaryotes. However, molecular systematics showed prokaryotic life to consist of two separate domain (biology)s, originally called
Eubacteria and
Archaebacteria, but now called
Bacteria and
Archaea that evolved independently from an ancient common ancestor. These two domains, along with Eukarya, are the basis of the three-domain system, which is currently the most widely used classification system in bacteriology. However, due to the relatively recent introduction of molecular systematics and the analysis of genome sequences, bacterial classification remains a changing and expanding field. For example, a few biologists argue that Archaea evolved from Gram-positive bacteria.
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. showing the incredible diversity of bacteria, compared to other organisms. Eukaryotes are colored red, archaea green and bacteria blue.The
Gram stain, developed in 1884 by
Hans Christian Gram, characterises bacteria based on the structural characteristics of their cell walls. The thick layers of peptidoglycan in the "Gram-positive" cell wall stain purple, while the thin "Gram-negative" cell wall appears pink. By combining morphology and Gram-staining, most bacteria can be classified as belonging to one of four groups (Gram-positive cocci, Gram-positive bacilli, Gram-negative cocci and Gram-negative bacilli). Some organisms are best identified by stains other than the Gram stain, particularly mycobacteria or
Nocardia, which show
acid-fastness on Ziehl-Neelsen stain or similar stains. Other organisms may need to be identified by their growth in special media, or by other techniques, such as
serology.
Microbiological culture techniques are designed to promote the growth and identify particular bacteria, while restricting the growth of the other bacteria in the sample. Often these techniques are designed for specific specimens; for example, a
sputum sample will be treated to identify organisms that cause pneumonia, while feces specimens are cultured on
selective media to identify organisms that cause diarrhea, while preventing growth of non-pathogenic bacteria. Specimens that are normally sterile, such as
blood,
urine or
cerebrospinal fluid, are cultured under conditions designed to grow all possible organisms. Once a pathogenic organism has been isolated, it can be further characterised by its morphology, growth patterns such as (aerobic organism or anaerobic organism growth, hemolysis (microbiology)) and staining.
As with bacterial classification, identification of bacteria is increasingly using molecular methods. Diagnostics using such DNA-based tools, such as polymerase chain reaction, are increasingly popular due to their specificity and speed, compared to culture-based methods. These methods also allow the detection and identification of "viable but nonculturable" cells that are metabolically active but non-dividing. However, even using these improved methods, the total number of bacterial species is not known and cannot even be estimated with any certainty. Attempts to quantify bacterial diversity have ranged from 107 to 109 total species, but even these diverse estimates may be out by many orders of magnitude.
Interactions with other organisms
Despite their apparent simplicity, bacteria can form complex associations with other organisms. These
symbiosis associations can be divided into
parasitism,
mutualism and
commensalism. Due to their small size, commensal bacteria are ubiquitous and grow on animals and plants exactly as they will grow on any other surface. However, their growth can be increased by warmth and sweating, and large populations of these organisms in humans are the cause of
body odor.
Mutualists
Certain bacteria form close spatial associations that are essential for their survival. One such mutualistic association, called interspecies hydrogen transfer, occurs between clusters of anaerobic bacteria that consume organic acids such as butyric acid or propionic acid and produce
hydrogen, and
methanogenic Archaea that consume hydrogen. The bacteria in this association are unable to consume the organic acids as this reaction produces hydrogen that accumulates in their surroundings. Only the intimate association with the hydrogen-consuming Archaea keeps the hydrogen concentration low enough to allow the bacteria to grow.
In soil, microorganisms which reside in the
rhizosphere (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. This serves to provide an easily absorbable form of nitrogen for many plants, which cannot fix nitrogen themselves. Many other bacteria are found as symbionts Bacteria in the human body 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 Milk#Physical and chemical structure to lactic acid (see
Lactobacillus), as well as fermenting complex undigestible
carbohydrates. The presence of this gut flora also inhibits the growth of potentially pathogenic bacteria (usually through
competitive exclusion) and these beneficial bacteria are consequently sold as
probiotic dietary supplements.
Pathogens
(red) invading cultured human cells
If bacteria form a parasitic association with other organisms, they are classed as pathogens. Pathogenic bacteria are a major cause of human death and disease and cause infections such as tetanus, typhoid fever,
diphtheria, syphilis,
cholera,
food-borne illness,
leprosy and
tuberculosis. A pathogenic cause for a known medical disease may only be discovered many years after, as was the case with Helicobacter pylori and
Timeline of peptic ulcer disease and Helicobacter pylori. Bacterial diseases are also important in agriculture, with bacteria causing
leaf spot, fireblight and wilting in plants, as well as
Johne's disease,
mastitis,
salmonella and anthrax in farm animals.
Each species of pathogen has a characteristic spectrum of interactions with its human host (biology). Some organisms, such as
Staphylococcus or
Streptococcus, can cause skin infections, pneumonia,
meningitis and even overwhelming
sepsis, a systemic inflammatory response producing
shock (medical), massive vasodilator and death. Yet these organisms are also part of the normal human flora and usually exist on the skin or in the
nose without causing any disease at all. Other organisms invariably cause disease in humans, such as the Rickettsia, which are obligate intracellular parasites able to grow and reproduce only within the cells of other organisms. One species of Rickettsia causes typhus, while another causes
Rocky Mountain spotted fever.
Chlamydia, another phylum of obligate intracellular parasites, contains species that can cause pneumonia, or urinary tract infection and may be involved in coronary heart disease. Finally, some species such as
Pseudomonas aeruginosa,
Burkholderia cenocepacia, and
Mycobacterium avium complex are opportunistic infection and cause disease mainly in people suffering from immunosuppression or
cystic fibrosis. PMID 14980298
Bacterial infections may be treated with antibiotics, which are classified as bacteriocide if they kill bacteria, or bacteriostatic if they just prevent bacterial growth. There are many types of antibiotics and each class
enzyme inhibitor 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. 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
Medical Glossary - NHS Direct
They are produced by the immune system to fight against bacteria, viruses and disease. Audiometry Audiometry is any testing that checks hearing.
Bacteria
Bacteria are generally simple structures. The bacterial cell lacks a membrane-bound nucleus. Because of this, bacteria are described as prokaryotes.
Definition: bacteria from Online Medical Dictionary
The Online Medical Dictionary is a searchable dictionary of definitions from medicine, science and technology.
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Bacteria - Wikipedia, the free encyclopedia
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