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Bacteria

2007 Schools Wikipedia Selection. Related subjects: Organisms

                    iBacterium
   Escherichia coli cells magnified 25,000 times
   Escherichia coli cells magnified 25,000 times
             Scientific classification

   Domain: Bacteria

                                    Phyla

   Actinobacteria
   Aquificae
   Chlamydiae
   Bacteroidetes/ Chlorobi
   Chloroflexi
   Chrysiogenetes
   Cyanobacteria
   Deferribacteres
   Deinococcus-Thermus
   Dictyoglomi
   Fibrobacteres/ Acidobacteria
   Firmicutes
   Fusobacteria
   Gemmatimonadetes
   Lentisphaerae
   Nitrospirae
   Planctomycetes
   Proteobacteria
   Spirochaetes
   Thermodesulfobacteria
   Thermomicrobia
   Thermotogae
   Verrucomicrobia

   Bacteria (singular: bacterium) are unicellular microorganisms. Bacteria
   are prokaryotes and, unlike animals and other eukaryotes, bacterial
   cells do not contain cell nuclei or other membrane-bound organelles.
   Although the term bacteria has traditionally been generally applied to
   all prokaryotes, the scientific nomenclature changed after the
   discovery that prokaryotic life consists of two very different groups
   of organisms that evolved independently. These evolutionary domains are
   called Bacteria and Archaea. Bacteria are a few micrometres long and
   have many different shapes including spheres, rods or spirals. The
   study of bacteria is bacteriology, a branch of microbiology.

   Bacteria are ubiquitous, living in every possible habitat on the planet
   including soil, underwater, deep in the earth's crust, and even such
   environments as acidic hot springs, and radioactive waste. There are
   typically forty million bacterial cells in a gram of soil, and one
   million bacterial cells in a millilitre of fresh water: in all, there
   are around five million trillion trillion (5 × 10^30) bacteria in the
   world. These vast numbers of bacteria are vital in recycling nutrients,
   and many important steps in nutrient cycles depend on bacteria, such as
   the fixation of nitrogen from the atmosphere. However, most of these
   bacteria have not been characterised, since only about half of the
   phyla of bacteria have species that can be cultured in the laboratory.

   There are ten times more bacterial cells than human cells in the human
   body, with large numbers of bacteria on the skin and in the digestive
   tract. Although the vast majority of these bacteria are harmless or
   beneficial, a few pathogenic bacteria cause infectious diseases,
   including cholera, syphilis, anthrax, leprosy and bubonic plague. The
   most common bacterial disease is tuberculosis, which kills about 2
   million people every year, mostly in sub-Saharan Africa. In developed
   countries, antibiotics are used to treat bacterial infections, and as a
   result antibiotic resistance is becoming increasingly common. In
   industry, bacteria are important in processes such as wastewater
   treatment, the production of cheese and yoghurt and the industrial
   production of antibiotics and other chemicals.

History of bacteriology

   Anton van Leeuwenhoek, the first person to observe bacteria using a
   microscope.
   Enlarge
   Anton van Leeuwenhoek, the first person to observe bacteria using a
   microscope.

   The first bacteria were observed by Anton van Leeuwenhoek in 1674 using
   a single-lens microscope of his own design. His observations were
   published in a long 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 Greek word βακτηριον meaning "small
   stick".

   Louis Pasteur demonstrated in 1859 that the fermentation process is
   caused by the growth of microorganisms, and that this growth is not due
   to spontaneous generation. He was also an early advocate of the germ
   theory of disease, together with his contemporary, Robert Koch. Robert
   Koch was a pioneer in medical microbiology and worked on cholera,
   anthrax and tuberculosis. In his work on tuberculosis, Koch finally
   proved the germ theory, for which he was awarded a Nobel Prize 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.

   Although it was known in the 19th century that bacteria are the cause
   of many diseases, no effective antibacterial treatments were available.
   The first antibiotic was developed by Paul Ehrlich in 1910, by changing
   dyes that selectively-stained Treponema pallidum, the spirochete that
   caused syphilis, into compounds that selectively killed the pathogen.
   Ehrlich was also awarded a 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 forwards in the study of bacteria was the recognition in
   1977 by Carl Woese that archaea were a separate line of evolutionary
   descent from bacteria. This new phylogenetic taxonomy was based on
   sequencing of 16S ribosomal 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 first forms of life to develop on earth, approximately 4
   billion years ago. For approximately 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 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 phylogeny and these studies indicate that
   bacteria diverged first from the archaeal/eukaryotic lineage. The last
   universal common ancestor of bacteria and archaea was probably a
   hyperthermophile that lived approximately 2.5 to 3.2 billion years ago.

   Bacteria were also involved in the second great evolutionary
   divergence, that of the archaea and eukaryotes. The eukaryotes arose
   when ancient bacteria entered into endosymbiotic associations with the
   ancestors of eukaryotic cells. This involved the engulfment of
   alpha-proteobacteria to form mitochondria and cyanobacterial-like
   organisms to form chloroplasts.

Morphology

   Bacteria display a large diversity of cell morphologies and
   arrangements
   Enlarge
   Bacteria display a large diversity of cell morphologies and
   arrangements

   Bacteria display a wide diversity of shapes and sizes, called
   morphologies. Bacterial cells are about ten times smaller than
   eukaryotic cells and are typically 0.5-5  micrometres in length.
   However a few species, for example Thiomargarita namibiensis and
   Epulopiscium fishelsoni, are up to half a millimetre long and 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 (pl. cocci,
   from Greek kókkos, grain, seed) or rod-shaped, called bacillus (pl.
   bacilli, from Latin baculus, stick). Some rod-shaped bacteria, called
   vibrio, are slightly curved or comma-shaped, while others, called
   spirilla, form twisted spirals. This wide variety of shapes are
   determined by the bacterial cell wall and cytoskeleton. These different
   shapes are important as they can influence the ability of bacteria to
   acquire nutrients, attach to surfaces, swim through liquids or escape
   predation.

   Many bacterial species exist simply as single cells, while others tend
   to associate in diploids (pairs), characteristic for example Neisseria,
   or chains, such as Streptococcus, while members of the genus
   Staphylococcus, form characteristic "bunch of grapes" clusters.
   Bacteria can also be elongated to form filaments, for example the
   Actinobacteria. Filamentous bacteria are often surrounded by a sheath
   which contains many individual cells, and certain species, such as the
   genus Nocardia, form complex, branched filaments, similar in appearance
   to fungal mycelia.
   The sizes of prokaryotes relative to other organisms and biomolecules.
   Enlarge
   The sizes of prokaryotes relative to 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 thick to up to half a metre in depth and may contain only a
   single bacterial species, or 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 implanted 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 and this type of
   co-operation is a simple type of multicellular organisation. For
   example, about one in ten cells migrates to the top of these fruiting
   bodies and differentiates into a specialised dormant state called
   myxospores, which are more resistant to desiccation and other adverse
   environmental conditions than ordinary cells.

Cellular structure

   Diagram of the cellular structure of a typical bacterial cell
   Enlarge
   Diagram of the cellular structure of a typical bacterial cell

Intracellular structures

   The bacterial cell is surrounded by a lipid membrane, or cell membrane,
   which encompasses the contents of the cell, or cytoplasm, and acts as a
   barrier to hold nutrients, proteins and other essential molecules
   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 mitochondria,
   chloroplasts and the other organelles present in eukaryotic cells, such
   as the golgi apparatus and endoplasmic reticulum.

   Many important biochemical reactions, such as energy generation, occur
   due to concentration gradients across membranes creating a potential
   difference, analogous to a battery. The absence of internal membranes
   in bacteria means these reactions, such as electron transport, occur
   across the plasma membrane, between the cytoplasm and the periplasmic
   space.

   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, as
   they have a membrane around their nucleoid and contain other
   membrane-bound cellular structures.

   Some bacteria also 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 photosynthetic Cyanobacteria, produce
   internal gas vesicles which they use to regulate their buoyancy to
   regulate the optimal light intensity or 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 fungi 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 an outer 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 only kill Gram positive
   bacteria and is ineffective against 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 macromolecular
   diffusion barrier. S-layers have diverse but mostly poorly-understood
   functions, but are known to act as virulence factors in Campylobacter
   and contain surface enzymes in Bacillus stearothermophilus.

   Flagella are rigid protein structures, about 20  nanometres in diameter
   and up to 20 micrometres in length, that are used for motility.
   Flagella are driven by the energy released by the transfer of ions down
   an electrochemical gradient across the cell membrane.

   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. Pili (sing. pilus) are
   cellular appendages, slightly larger than fimbriae, that enable the
   transfer of genetic material between bacterial cells, called
   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 or glycocalyx. These structures can protect cells
   from engulfment by eukaryotic cells such as macrophages, they can act
   as antigens and be involved in cell recognition, as well as aiding
   attachment to surfaces and biofilm formation.
   Bacillus anthracis (stained purple) growing in cerebrospinal fluid.
   Enlarge
   Bacillus anthracis (stained purple) growing in cerebrospinal fluid.

Spores

   Certain genera of gram-positive bacteria, such as Bacillus,
   Clostridium, Sporohalobacter, Anaerobacter, and Heliobacterium, 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 spores 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 spore coat.

   Endospores show no detectable metabolism and can survive extreme
   physical and chemical stresses, such as high levels of UV light, gamma
   radiation, detergents, disinfectants, heat, 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 and radiation in space. Spores can also be a cause of disease:
   for example, inhalation of Bacillus anthracis spores causes anthrax,
   and contamination of deep puncture wounds with Clostridium tetani
   spores causes tetanus.

Metabolism

   Fillaments of photosynthetic cyanobacteria
   Enlarge
   Fillaments of photosynthetic cyanobacteria

   In contrast to higher organisms, bacteria exhibit an extremely wide
   variety of metabolic 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 can be divided broadly on the
   basis of the kind of energy used for growth, electron donors and
   electron acceptors and by the source of carbon used.

   Carbon metabolism in bacteria is usually heterotrophic: where organic
   carbon compounds are used as both carbon and energy sources. As an
   alternative to heterotrophy some bacteria such as cyanobacteria and
   purple bacteria are autotrophic, meaning that they obtain cellular
   carbon by fixing carbon dioxide.

   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. Chemotrophs are divided into lithotrophs that
   use inorganic electron donors for respiration and organotrophs that use
   organic compounds as electron donors. To use chemical compounds as a
   source of energy, electrons are taken from the reduced substrate and
   transferred to a terminal electron acceptor in a redox reaction. This
   reaction releases energy that can be used to 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
   environmentally important processes of denitrification, sulfate
   reduction and acetogenesis, respectively. Non-respiratory anaerobes use
   fermentation to generate energy and reducing power, secreting metabolic
   by-products (such as ethanol in brewing) as waste. Facultative
   anaerobes can switch between fermentation and different terminal
   electron acceptors depending on the environmental conditions in which
   they find themselves.

   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, in unicellular organisms increases in
   the size of bacteria ( cell growth) and their reproduction by cell
   division are tightly linked. 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 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 is resulted of a 'bud' of a cell growing from another cell, and
   then finally breaking away.
   Solid agar plate with bacterial colonies
   Enlarge
   Solid agar plate with bacterial colonies

   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 extremely 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 (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 phase, a period of slow growth when the cells are adapting to
   fast growth. The lag phase has high biosynthesis rates, as enzymes and
   nutrient transporters are produced. The second phase of growth is the
   logarithmic phase (log phase), also known as the exponential phase. The
   log phase is marked by rapid exponential growth. The rate at which
   cells grow during this phase is known as the growth rate (k) and the
   time it takes the cells to double is known as the generation time (g).
   During log phase, nutrients are metabolised at maximum speed until one
   of the nutrients is depleted and starts limiting growth. The final
   phase of growth is the stationary phase and is caused by depleted
   nutrients. The cells reduce their metabolic activity, and consume
   non-essential cellular proteins. The stationary phase is a transition
   from rapid growth to a stress response state and there is increased
   expression of genes involved in DNA repair, antioxidant metabolism and
   nutrient transport.

Genetics

   Most bacteria have a single circular chromosome that can range in size
   from only 580,000 base pairs in the human pathogen Mycoplasma
   genitalium, to 12,200,000 base pairs in the soil-dwelling bacteria
   Sorangium cellulosum. Spirochaetes 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 factors. Another
   type of bacterial DNA are integrated viruses ( bacteriophages). Many
   types of bacteriophage exist, some simply infect their host bacteria
   and lyse the cell, while others insert into the bacterial chromosome.
   Bacteriophages can contain genes that contribute to its host's
   phenotype, for example in Escherichia coli and Clostridium botulinum an
   integrated phage can convert a harmless bacteria into a lethal pathogen
   by producing toxins.

   Bacteria, as asexual organisms, inherit identical copies of their
   parent's genes (i.e., they are clonal). However, all bacteria can
   evolve by selection on changes to their genetic material DNA caused by
   genetic recombination or mutations. Mutations come from errors made
   during the replication of DNA or from exposure to mutagens. Mutation
   rates vary widely among different species of bacteria and even among
   different clones of a single species of bacteria. 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. Often, the
   genes transferred are not from within the main bacterial chromosome,
   but are carried on a small circular piece of DNA called a plasmid.
   Genes can also be transferred by the process of transduction, when the
   integration of a bacteriophage introduces foreign DNA into the
   chromosome. The third method of gene transfer is bacterial conjugation,
   where DNA is transferred through direct cell contact. This gene
   acquisition from other bacteria or the environment is called horizontal
   gene transfer and may be common under natural conditions. Gene transfer
   is particularly important in antibiotic resistance as it allows the
   rapid transfer of resistance genes between different pathogens.

Movement

   The different arrangements of bacterial flagella: A-Monotrichous;
   B-Lophotrichous; C-Amphitrichous; D-Peritrichous;
   Enlarge
   The different arrangements of bacterial flagella: A-Monotrichous;
   B-Lophotrichous; C-Amphitrichous; D-Peritrichous;

   Motile bacteria can move using flagella, bacterial gliding, or changes
   of buoyancy. A unique group of bacteria, the spirochaetes, have
   structures similar to flagella, called axial filaments that are found
   between two membranes in the periplasmic space. They have a distinctive
   helical body that twists about as it moves.

   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
   proton-motive force for power. This motor drives the motion of the
   filament, which acts as a propeller. Many bacteria (such as E. coli)
   have two distinct modes of movement: forward movement (swimming) and
   tumbling. The tumbling allows them to reorient and makes their movement
   a three-dimensional random walk. (See external links below for link to
   videos.)

   Motile bacteria are attracted or repelled by certain stimuli 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.

Groups and identification

   When bacteria were originally studied by botanists, they were
   classified in the same way as plants, that is, mainly by shape.
   Classification solely on the basis of morphology, though, was largely
   unsuccessful. The first formal classification scheme arose after the
   Gram stain was developed by Hans Christian Gram. This staining
   technique identifies bacteria based on the structural characteristics
   of their cell walls. If the bacteria species is "Gram-positive", it
   will stain purple. If the bacteria species is "Gram-negative" it would
   appear pink. This scheme included:
     * Gracilicutes - Gram negative staining bacteria with a second cell
       membrane
     * Firmicutes - Gram positive staining bacteria with a thick
       peptidoglycan wall
     * Mollicutes - Gram negative staining bacteria with no cell wall or
       second membrane
     * Mendosicutes - atypically staining strains now known to belong to
       the Archaea

   By combining morphology and gram-staining, the preponderance of
   isolates of interest can be characterized 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 mycobacterial
   organisms or Nocardia, which show acid-fastness on Ziehl – Neelsen or
   similar stains. Other organisms may need to be identified by their
   growth in special media, or by other techniques, such as serology.

   Morphological classifications alone are not successful in
   distinguishing pathogens from non-pathogens. Consequently, the need to
   identify human pathogens was a major impetus for the development of
   techniques to identify bacteria. Medical bacteriological techniques are
   designed to selectively grow and identify pathogens rather than normal
   flora (as far as possible) and are designed for specific specimens.
   Thus, a sputum sample will be treated in such a way as to identify any
   organisms that might cause pneumonia, while stool specimens are
   cultured on selective media to identify organisms that might cause
   diarrhoea, while preventing growth of non-pathogenic bacteria.
   Specimens that are normally sterile, such as blood, urine or spinal
   fluid, are handled in such a way as to grow all possible organisms.
   Once a pathogenic organism has been isolated, it can be further
   characterized through its morphology, growth patterns ( aerobic vs.
   anaerobic, patterns of hemolysis), and staining characteristics.

   Bacteria can also be classified on the basis of differences in cellular
   metabolism as determined by a wide variety of specific tests, or based
   on differences in their constituent cellular chemical compounds such as
   fatty acids, pigments, antigens and quinones. The term "bacteria" was
   traditionally applied to all microscopic, single-celled prokaryotes but
   prokaryotic life is nowadays divided into two evolutionary domains that
   were originally called Eubacteria and Archaebacteria, but are now
   called Bacteria and Archaea. It should be noted, however, that due to
   our current poor understanding of microbial diversity, bacterial
   taxonomy remains a changing and expanding field.

Interactions with other organisms

   Despite their apparent simplicity, bacteria can form complex
   associations with other organisms. These symbiotic associations can be
   divided into parasitism, mutualism and commensalism. Due to their small
   size, commensal bacteria are ubiquitous and grow on animals and plants
   exactly as they will grow on any other surface. However, their growth
   can be increased by warmth and sweat and large populations of these
   organisms in humans are the cause of body odour.

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 and produce hydrogen, and methanogenic Archaea
   that consume hydrogen. These bacteria are unable to consume the organic
   acids and grow when hydrogen accumulates in their surroundings, and
   only the intimate association with the hydrogen-consuming Archaea can
   keep the hydrogen concentration low enough to allow them 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 in humans and other organisms.
   For example, the presence of over 1,000 bacterial species in the normal
   human gut flora of the intestines can contribute to gut immunity,
   synthesise vitamins such as folic acid, vitamin K and biotin, and
   ferment complex undigestable carbohydrates. Bacteria that offer some
   benefit to human hosts include Lactobacillus species, which convert
   milk protein to lactic acid in the gut. The presence of such bacterial
   colonies also inhibits the growth of potentially pathogenic bacteria
   (usually through competitive exclusion) and these beneficial bacteria
   are consequently sold as probiotic dietary supplements.

Pathogens

   Color-enhanced scanning electron micrograph showing Salmonella
   typhimurium (red) invading cultured human cells.
   Enlarge
   Colour-enhanced scanning electron micrograph showing Salmonella
   typhimurium (red) invading cultured human cells.

   If bacteria form a parasitic association with other organisms, they are
   classed as pathogens. Pathogenic bacteria are an important cause of
   human death and disease and cause infections such as tetanus, typhoid
   fever, diphtheria, syphilis, cholera, food-borne illness, leprosy, and
   tuberculosis. Bacterial diseases are also important in agriculture,
   with bacteria causing leaf spot, fireblight, and wilts in plants, and
   Johne's disease, mastitis, salmonella and anthrax in farm animals.

   Each species of pathogen has a characteristic spectrum of interactions
   with its human hosts. Some organisms, such as Staphylococcus or
   Streptococcus, can cause skin infections, pneumonia, meningitis, and
   even overwhelming sepsis, a systemic inflammatory response producing
   shock, massive vasodilation, and death. 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 Mycobacterium
   avium, are opportunistic pathogens, and cause disease mainly in
   immunosuppressed people.

   Bacterial infections may be treated with antibiotics, which are
   classified as bacteriocidal if they kill bacteria, or bacteriostatic if
   they just prevent bacterial growth. There are many types of antibiotics
   and each class inhibits a process that is different in the pathogen
   from that found in the host. An example of how antibiotics produce
   selective toxicity are chloramphenicol and puromycin, which inhibit the
   bacterial ribosome, but not the structurally-different eukaryotic
   ribosome. Antibiotics are used both in treating human disease and in
   intensive farming to promote animal growth, where they may be
   contributing to the rapid development of antibiotic resistance in
   bacterial populations. Infections can be prevented by antiseptic
   measures such as sterilizating the skin prior to piercing it with the
   needle of a syringe, and by proper care of indwelling catheters.
   Surgical and dental instruments are also sterilized to prevent
   contamination and infection by bacteria. Sanitizers and disinfectants
   are used to kill bacteria or other pathogens on surfaces to prevent
   contamination and further reduce the risk of infection.

Uses in technology and industry

   Bacteria, often Lactobacillus in combination with yeasts and molds,
   have been used for thousands of years in the preparation of fermented
   foods such as cheese, pickles, soy sauce, sauerkraut, vinegar, wine,
   and yogurt.

   The ability of bacteria to degrade a variety of organic compounds is
   remarkable and has been used in waste processing, and bioremediation.
   Bacteria capable of digesting the hydrocarbons in petroleum are often
   used to clean up oil spills. Fertilizer was added to some of the
   beaches in Prince William Sound in an attempt to promote the growth of
   these naturally occurring bacteria after the infamous 1989 Exxon Valdez
   oil spill. These efforts were effective on beaches that were not too
   thickly covered in oil. Bacteria are also used for the bioremediation
   of industrial toxic wastes. In the chemical industry, bacteria are most
   important in the production of enantiomerically pure chemicals for use
   as pharmaceuticals or agrochemicals.

   Bacteria can also be used in the place of pesticides in the biological
   pest control. This commonly uses Bacillus thuringiensis (also called
   BT), a Gram-positive, soil dwelling bacterium. This bacteria is used as
   a Lepidopteran-specific insecticide under trade names such as Dipel and
   Thuricide. Because of their specificity, these pesticides are regarded
   as Environmentally friendly, with little or no effect on humans,
   wildlife, pollinators, and most other beneficial insects.

   Because of their ability to quickly grow, and the relative ease with
   which they can be manipulated, bacteria are the workhorses for the
   fields of molecular biology, genetics and biochemistry. By making
   mutations in bacterial DNA and examining the resulting phenotypes,
   scientists hcan determine the function of many different genes, enzymes
   and metabolic pathways. Lessons learned from bacteria are then be
   applied to more complex organisms. This aim of understanding the
   biochemistry of a cell reaches its most complex expression in the
   synthesis of huge amounts of enzyme kinetic and gene expression data
   into mathematical models of entire organisms. This is achievable in
   some well-studied bacteria, with models of Escherichia coli metabolism
   now being produced and tested. This understanding of bacterial
   metabolism and genetics allows the use of biotechnology to bioengineer
   bacteria for the production of therapeutic proteins, such as insulin,
   growth factors or antibodies.

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