Bacteria constitute a large domain
of prokaryotic microorganisms.
Typically a few micrometres
in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals. Bacteria were among the first life
forms to appear on Earth,
and are present in most habitats
on the planet, growing in soil, acidic
hot springs, radioactive
waste,[2] water, and deep in the Earth's
crust, as well as in organic matter and
the live bodies of plants and animals, providing outstanding examples of mutualism
in the digestive tracts of humans, termites and cockroaches.
There are typically
40 million bacterial cells in a gram of soil and a million bacterial cells in a
millilitre of fresh water;
in all, there are approximately five nonillion
(5×1030) bacteria on Earth,[3] forming a biomass
that exceeds that of all plants and animals.[4] Bacteria are vital in recycling nutrients, with many steps
in nutrient cycles
depending on these organisms, such as the fixation
of nitrogen from the atmosphere
and putrefaction.
In the biological communities surrounding hydrothermal vents
and cold
seeps, bacteria provide the nutrients
needed to sustain life by converting dissolved compounds such as hydrogen
sulphide and methane. Most bacteria have not been characterised, and only about
half of the phyla of bacteria have species that can be grown
in the laboratory.[5] The study of bacteria is known as bacteriology, a branch of microbiology.
There are approximately ten times as
many bacterial cells in the human
flora as there are human cells in the
body, with large numbers of bacteria on the skin and as gut
flora.[6] The vast majority of the bacteria in the body are rendered
harmless by the protective effects of the immune
system, and a few are beneficial. However, a few species of bacteria are pathogenic
and cause infectious diseases,
including cholera, syphilis,
anthrax, leprosy,
and bubonic plague.
The most common fatal bacterial diseases are respiratory infections, with tuberculosis alone killing about 2 million people a year, mostly in sub-Saharan Africa.[7] In developed
countries, antibiotics are used to treat bacterial
infections and in agriculture, so antibiotic resistance is becoming common. In industry, bacteria are important in sewage
treatment and the breakdown of oil
spills, the production of cheese and yogurt
through fermentation, the recovery of gold, palladium, copper and other metals
in the mining sector,[8] as well as in biotechnology, and the manufacture of antibiotics and other chemicals.[9]
Once regarded as plants constituting the class Schizomycetes, bacteria are
now classified as prokaryotes.
Unlike cells of animals and other eukaryotes, bacterial cells do not contain a nucleus and rarely harbour membrane-bound organelles.
Although the term bacteria traditionally included all prokaryotes, the scientific classification changed after the discovery in the 1990s that prokaryotes
consist of two very different groups of organisms that evolved independently from an ancient common ancestor. These evolutionary domains are called Bacteria and Archaea.[10]
Etymology
The word bacteria is the
plural of the New Latin
bacterium, which is the latinisation of the Greek βακτήριον (baktērion),[11] the diminutive of βακτηρία (baktēria), meaning
"staff, cane",[12] because the first ones to be discovered were rod-shaped.[13]
History
of bacteriology
For the history of microbiology, see
Microbiology. For the history of bacterial classification, see Bacterial taxonomy.
For the natural history of Bacteria, see Last universal ancestor.
 |
| Anthony Van Leuwenhoek |
Antonie van Leeuwenhoek, the first microbiologist and the first person to observe bacteria using a microscope.
Bacteria were first observed by Antonie van Leeuwenhoek in 1676, using a single-lens microscope of his own design.[14] He called them "animalcules" and published his
observations in a series of letters to the Royal
Society.[15][16][17] The name Bacterium was introduced much later, by Christian Gottfried Ehrenberg in 1828.[18] In fact, Bacterium
was a genus that contained non-spore-forming rod-shaped bacteria,[19]
as opposed to Bacillus, a genus of spore-forming rod-shaped bacteria
defined by Ehrenberg in 1835.[20]
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. (Yeasts
and molds, commonly associated with fermentation, are not bacteria,
but rather fungi.) Along with his contemporary Robert
Koch, Pasteur was an early advocate of
the germ theory of disease.[21] 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 1905.[22] In Koch's postulates, he set out criteria to test if an organism is the cause of
a disease, and these postulates are still used today.[23]
Though it was known in the
nineteenth century that bacteria are the cause of many diseases, no effective antibacterial treatments were available.[24] In 1910, Paul
Ehrlich developed the first antibiotic, by
changing dyes that selectively stained Treponema pallidum — the spirochaete that causes syphilis — into compounds that selectively killed the pathogen.[25] 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.[26]
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.[27] This new phylogenetic taxonomy
was based on the sequencing
of 16S ribosomal RNA,
and divided prokaryotes into two evolutionary domains, as part of the three-domain system.[28]
Origin
and early evolution
Further information: Timeline of evolution
The ancestors of modern bacteria
were single-celled microorganisms that were the first
forms of life to appear on Earth, about 4 billion
years ago. For about 3 billion years, all organisms were microscopic, and
bacteria and archaea were the dominant forms of life.[29][30] Although bacterial fossils exist, such as stromatolites, their lack of distinctive morphology
prevents them from being used to examine the history of bacterial evolution, or
to date the time of origin of a particular bacterial species. However, gene
sequences can be used to reconstruct the bacterial phylogeny, and these studies indicate that bacteria diverged first
from the archaeal/eukaryotic lineage.[31]
Bacteria were also involved in the
second great evolutionary divergence, that of the archaea and eukaryotes. Here,
eukaryotes resulted from ancient bacteria entering into endosymbiotic associations with the ancestors of eukaryotic cells, which
were themselves possibly related to the Archaea.[32][33] This involved the engulfment by proto-eukaryotic cells of
alpha-proteobacterial symbionts to form either mitochondria or hydrogenosomes, which are still found in all known Eukarya (sometimes in
highly reduced form,
e.g. in ancient "amitochondrial" protozoa). Later on, some eukaryotes
that already contained mitochondria also engulfed cyanobacterial-like
organisms. This led to the formation of chloroplasts in algae and plants. There are also some algae that
originated from even later endosymbiotic events. Here, eukaryotes engulfed a
eukaryotic algae that developed into a "second-generation" plastid.[34][35] This is known as secondary endosymbiosis.
Morphology
 |
| Bacteria Morphologies |
Bacteria display a wide diversity of
shapes and sizes, called morphologies.
Bacterial cells are about one tenth the size of eukaryotic cells and are
typically 0.5–5.0 micrometres
in length. However, a few species — for example, Thiomargarita namibiensis and Epulopiscium fishelsoni — are up to half a millimetre long and are visible to
the unaided eye;[36] E. fishelsoni reaches 0.7 mm.[37] Among the smallest bacteria are members of the genus Mycoplasma, which measure only 0.3 micrometres, as small as the
largest viruses.[38] Some bacteria may be even smaller, but these ultramicrobacteria
are not well-studied.[39]
Most bacterial species are either
spherical, called cocci
(sing. coccus, from Greek κόκκος-kókkos, grain, seed), or
rod-shaped, called bacilli
(sing. bacillus, from Latin
baculus, stick). Elongation is associated with swimming.[40] Some rod-shaped bacteria, called vibrio, are slightly curved or comma-shaped; others, can be
spiral-shaped, called spirilla,
or tightly coiled, called spirochaetes. A small number of species even have tetrahedral or
cuboidal shapes.[41] More recently, bacteria were discovered deep under the
Earth's crust that grow as long rods with a star-shaped cross-section. The
large surface area to volume ratio of this morphology may give these bacteria
an advantage in nutrient-poor environments.[42] This wide variety of shapes is determined by the bacterial cell
wall and cytoskeleton, and is important because it can influence the ability of
bacteria to acquire nutrients, attach to surfaces, swim through liquids and
escape predators.[43][44]
 |
| Thermopiles Extreme |
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.[45]
 |
| Range of Sizes |
Bacteria often attach to surfaces
and form dense aggregations called biofilms or bacterial
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.[46][47] In natural environments, such as soil or the surfaces of
plants, the majority of bacteria are bound to surfaces in biofilms.[48] Biofilms are also important in medicine, as these
structures are often present during chronic bacterial infections or in
infections of implanted
medical devices,
and bacteria protected within biofilms are much harder to kill than individual
isolated bacteria.[49]
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.[50] In these fruiting bodies, the bacteria perform separate
tasks; this type of cooperation is a simple type of multicellular
organisation. For example, about one in 10 cells migrate to the top of these
fruiting bodies and differentiate into a specialised dormant state called myxospores, which
are more resistant to drying and other adverse environmental conditions than
are ordinary cells.[51]
Cellular
structure
Further information: Bacterial cell structure
 |
| Bacteria Anatomy and Structure |
Intracellular
structures
The bacterial cell is surrounded by
a lipid membrane, or cell
membrane, which encloses the contents of the
cell and acts as a barrier to hold nutrients, proteins and other essential components of the cytoplasm within the cell. As they are prokaryotes, bacteria do not tend to have membrane-bound organelles in their cytoplasm and thus contain few large intracellular
structures. They consequently lack a true nucleus, mitochondria,
chloroplasts and the other organelles present in eukaryotic cells, such
as the Golgi apparatus
and endoplasmic reticulum.[52] Bacteria were once seen as simple bags of cytoplasm, but
elements such as prokaryotic cytoskeleton,[53][54] and the localization of proteins to specific locations
within the cytoplasm[53] have been found to show levels of complexity. These
subcellular compartments have been called "bacterial
hyperstructures".[55]
Micro-compartments such as carboxysomes[56] provides a further level of organization, which are
compartments within bacteria that are surrounded by polyhedral protein shells, rather than by lipid membranes.[57] These "polyhedral organelles" localize and
compartmentalize bacterial metabolism, a function performed by the
membrane-bound organelles in eukaryotes.[58][59]
Many important biochemical reactions, such as energy
generation, occur by concentration gradients across membranes. The general lack of internal membranes in
bacteria means reactions such as electron transport occur across the cell membrane between the cytoplasm and
the periplasmic space.[60] However, in many photosynthetic bacteria the plasma membrane
is highly folded and fills most of the cell with layers of light-gathering
membrane.[61] These light-gathering complexes may even form
lipid-enclosed structures called chlorosomes in green sulfur bacteria.[62] Other proteins import nutrients across the cell membrane,
or to expel undesired molecules from the cytoplasm.
 |
| Caryboxysomes |
Carboxysomes are protein-enclosed bacterial organelles. Top left is an electron microscope
image of carboxysomes in Halothiobacillus
neapolitanus, below is an image of purified
carboxysomes. On the right is a model of their structure. Scale bars are
100 nm.[63]
Most 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.[64] The nucleoid contains the chromosome with associated
proteins and RNA. The order Planctomycetes are an exception to the general absence of internal
membranes in bacteria, because they have a double membrane around their nucleoids
and contain other membrane-bound cellular structures.[65] 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.[66]
Some bacteria produce intracellular
nutrient storage granules, such as glycogen,[67] polyphosphate,[68] sulfur[69] or polyhydroxyalkanoates.[70] 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 –
allowing them to move up or down into water layers with different light
intensities and nutrient levels.[71]
Extracellular
structures
Further information: Cell
envelope
In most bacteria a cell
wall is present on the outside of the
cytoplasmic membrane. A common bacterial cell wall material is peptidoglycan (called murein in older sources), which is made from polysaccharide chains cross-linked by peptides containing D-amino
acids.[72] Bacterial cell walls are different from the cell walls of plants and fungi,
which are made of cellulose
and chitin, respectively.[73] 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.[73]
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.[74]
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.[75] 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.[76]
In many bacteria an S-layer of rigidly arrayed protein molecules covers the outside of
the cell.[77] 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.[78]
 |
| Heliobacter pylori |
Helicobacter pylori electron micrograph, showing multiple flagella on the cell
surface
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.[79]
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.[80] Pili
(sing. pilus) are cellular appendages, slightly larger than fimbriae,
that can transfer genetic material
between bacterial cells in a process called conjugation
(see bacterial genetics, below).[81]
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.[82] They can also act as antigens and be involved in cell
recognition, as well as aiding attachment to surfaces and the formation of
biofilms.[83]
The assembly of these extracellular
structures is dependent on bacterial secretion
systems. These transfer proteins from the
cytoplasm into the periplasm or into the environment around the cell. Many
types of secretion systems are known and these structures are often essential
for the virulence
of pathogens, so are intensively studied.[84]
Endospores
 |
| Bacillus Anthracis |
Certain genera of Gram-positive bacteria, such as Bacillus, Clostridium,
Sporohalobacter,
Anaerobacter and Heliobacterium, can form highly resistant, dormant structures called endospores.[85] 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.[86] 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 UV light,
gamma
radiation, detergents, disinfectants,
heat, freezing, pressure and desiccation.[87] In this dormant state, these organisms may remain viable
for millions of years,[88][89] and endospores even allow bacteria to survive exposure to
the vacuum
and radiation in space.[90] According to scientist Dr. Steinn Sigurdsson, "There
are viable bacterial spores that have been found that are 40 million years old
on Earth — and we know they're very hardened to radiation."[91] 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.[92]
Metabolism
Further information: Microbial metabolism
Bacteria exhibit an extremely wide
variety of metabolic
types.[93] 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.[94] Bacterial metabolism is classified into nutritional groups on the basis of three major criteria: the kind of energy 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.[95]
Nutritional
types in bacterial metabolism
|
|||
Nutritional
type
|
Source
of energy
|
Source
of carbon
|
Examples
|
Sunlight
|
Organic
compounds (photoheterotrophs) or carbon fixation (photoautotrophs)
|
||
Inorganic
compounds
|
Organic
compounds (lithoheterotrophs) or carbon fixation (lithoautotrophs)
|
||
Organic
compounds
|
Organic
compounds (chemoheterotrophs) or carbon fixation (chemoautotrophs)
|
||
Carbon metabolism in bacteria is
either heterotrophic,
where organic carbon
compounds are used as carbon sources, or autotrophic, meaning that cellular carbon is obtained by fixing carbon dioxide.
Heterotrophic bacteria include parasitic types. Typical autotrophic bacteria
are phototrophic cyanobacteria,
green sulfur-bacteria and some purple
bacteria, but also many chemolithotrophic
species, such as nitrifying or sulfur-oxidising bacteria.[96] Energy metabolism of bacteria is either based on phototrophy, the use of light through photosynthesis, or based 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).
 |
| Cyanobacteri |
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 reduced
substrate and transferring them to a terminal electron acceptor in a redox reaction.
This reaction releases energy that can be used to synthesise ATP
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. lactate, ethanol,
hydrogen, butyric acid).
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.[97][98]
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
(methyl-
and dimethylmercury)
in the environment.[99] 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.[100] 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.[101]
Regardless of the type of metabolic
process they employ, the majority of bacteria are only able to take in raw
materials in the form of relatively small molecules, which enter the cell by
diffusion or through molecular channels in cell membranes. The Planctomycetes
are the exception (as they are in possessing membranes around their nuclear
material). It has recently been shown that Gemmata obscuriglobus is able
to take in large molecules via a process that in some ways resembles endocytosis, the process used by eukaryotic cells to engulf external
items.[37][102]
Growth
and reproduction
Many bacteria reproduce through binary
fission
Further information: Bacterial
growth
Unlike in multicellular organisms,
increases in cell size (cell
growth and reproduction by cell
division) are tightly linked in unicellular
organisms. Bacteria grow to a fixed size and then reproduce through binary
fission, a form of asexual reproduction.[103] Under optimal conditions, bacteria can grow and divide
extremely rapidly, and bacterial populations can double as quickly as every
9.8 minutes.[104] In cell division, two identical clone
daughter cells are produced. Some bacteria, while still reproducing asexually,
form more complex reproductive structures that help disperse the newly formed
daughter cells. Examples include fruiting body formation by Myxobacteria and aerial hyphae formation by Streptomyces, or budding. Budding involves a cell forming a protrusion
that breaks away and produces a daughter cell.
 |
| A colony of Escherichia coli |
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.[106]
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.[107] Other organisms have adaptations to harsh environments,
such as the production of multiple antibiotics by Streptomyces that inhibit the growth of competing microorganisms.[108] In nature, many organisms live in communities (e.g., biofilms) that may allow for increased supply of nutrients and
protection from environmental stresses.[48] These relationships can be essential for growth of a
particular organism or group of organisms (syntrophy).[109]
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 the high-nutrient environment and preparing for fast
growth. The lag phase has high biosynthesis rates, as proteins necessary for
rapid growth are produced.[110] 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.[111]
Genetics
Most bacteria have a single circular
chromosome that can range in size from only 160,000 base
pairs in the endosymbiotic bacteria Candidatus
Carsonella ruddii,[112] to 12,200,000 base pairs in the soil-dwelling bacteria Sorangium cellulosum.[113] 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.[114] The genes in bacterial genomes are usually a single
continuous stretch of DNA and although several different types of introns do exist in bacteria, these are much more rare than in
eukaryotes.[115]
Bacteria may also contain plasmids, which are small extra-chromosomal DNAs that may contain
genes for antibiotic resistance or virulence factors.
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.[116] 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.[117]
Some bacteria also transfer genetic
material between cells. This can occur in three main ways. First, bacteria can
take up exogenous DNA from their environment, in a process called transformation. 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.[118] Gene transfer is particularly important in antibiotic resistance as it allows the rapid transfer of resistance genes between
different pathogens.[119]
Bacteriophages
Main article: Bacteriophage
Bacteriophages
are viruses that infect bacteria. Many types of bacteriophage exist, some simply
infect and lyse
their host
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 bacterium into a
lethal pathogen.[120] Bacteria resist phage infection through restriction
modification systems that degrade foreign DNA,[121] and a system that uses CRISPR sequences to retain fragments of the genomes of phage that
the bacteria have come into contact with in the past, which allows them to
block virus replication through a form of RNA
interference.[122][123] This CRISPR system provides bacteria with acquired immunity
to infection.
Behavior
Secretion
Bacteria frequently secrete
chemicals into their environment in order to modify it favorably. The secretions are often proteins and may act as enzymes that digest some
form of food in the environment.
Bioluminescence
A few bacteria have chemical systems
that generate light. This bioluminescence often occurs in bacteria that live in association with
fish, and the light probably serves to attract fish or other large animals.[124] – see Milky
seas effect
Multicellularity
Bacteria often function as
multicellular aggregates known as biofilms, exchanging a variety of molecular signals for inter-cell
communication, and engaging in coordinated
multicellular behavior.[125][126]
The communal benefits of
multicellular cooperation include a cellular division of labor, accessing
resources that cannot effectively be utilized by single cells, collectively
defending against antagonists, and optimizing population survival by
differentiating into distinct cell types.[125] For example, bacteria in biofilms can have more than 500
times increased resistance to antibacterial agents than individual "planktonic" bacteria of
the same species.[126]
One type of inter-cellular
communication by a molecular signal is called quorum
sensing, which serves the purpose of
determining whether there is a local population density that is sufficiently
high that it is productive to invest in processes that are only successful if
large numbers of similar organisms behave similarly, as in excreting digestive
enzymes or emitting light.
Quorum sensing allows bacteria to
coordinate gene expression, and enables them to produce, release and detect autoinducers or pheromones
which accumulate with the growth in cell population.[127]
Movement
Many bacteria can move using a
variety of mechanisms: flagella
are used for swimming through water; bacterial
gliding and twitching motility move
bacteria across surfaces; and changes of buoyancy allow vertical motion.[128]
The base drives the rotation of the hook and filament.
 |
| Flagellum of Gram-negative Bacteria. |
Swimming bacteria frequently move
near 10 body lengths per second and a few as fast as 100. This makes them at
least as fast as fish, on a relative scale.[129]
In twitching motility, bacterial use
their type IV pili as a grappling hook, repeatedly extending it, anchoring it
and then retracting it with remarkable force (>80 pN).[130]
Flagella
are semi-rigid cylindrical structures that are rotated and function much like
the propeller on a ship. Objects as small as bacteria operate a low Reynolds
number and cylindrical forms are more
efficient than the flat, paddle-like, forms appropriate at human size scale.[131]
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.[128] The flagellum is a rotating structure driven by a
reversible motor at the base that uses the electrochemical gradient across the membrane for power.[132] 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.[133] (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 helical
body that twists about as it moves.[128]
Motile bacteria are attracted or
repelled by certain stimuli
in behaviors called taxes: these include chemotaxis, phototaxis,
energy
taxis and magnetotaxis.[134][135][136] In one peculiar group, the myxobacteria, individual bacteria move together to form waves of cells that
then differentiate to form fruiting bodies containing spores.[51] 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 polymerization
at one pole of their cells, they can form a kind of tail that pushes them
through the host cell's cytoplasm.[137]
Classification
and identification
Main article: Bacterial taxonomy
 |
Streptococcus mutans visualized with a Gram stain
|
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.[106] 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.[138] 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
ratio determination, genome-genome hybridization, as well as sequencing genes that have not undergone extensive lateral gene transfer,
such as the rRNA gene.[139] Classification of bacteria is determined by publication in
the International Journal of Systematic Bacteriology,[140]
and Bergey's Manual of Systematic Bacteriology.[141] The International
Committee on Systematic Bacteriology
(ICSB) maintains international rules for the naming of bacteria and taxonomic
categories and for the ranking of them in the International Code
of Nomenclature of Bacteria.
The term "bacteria" was
traditionally applied to all microscopic, single-cell prokaryotes. However,
molecular systematics showed prokaryotic life to consist of two separate domains,
originally called Eubacteria and Archaebacteria, but now called Bacteria
and Archaea that evolved independently from an ancient common ancestor.[10] The archaea and eukaryotes are more closely related to each
other than either is to the bacteria. These two domains, along with Eukarya,
are the basis of the three-domain system,
which is currently the most widely used classification system in
microbiolology.[142] However, due to the relatively recent introduction of
molecular systematics and a rapid increase in the number of genome sequences
that are available, bacterial classification remains a changing and expanding
field.[5][143] For example, a few biologists argue that the Archaea and
Eukaryotes evolved from Gram-positive bacteria.[144]
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.
 |
Phylogenetic tree
showing the diversity of bacteria, compared to other organisms.[145] 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.[74] The thick layers of peptidoglycan in the
"Gram-positive" cell wall stain purple, while the thin
"Gram-negative" cell wall appears pink. By combining morphology and
Gram-staining, most bacteria can be classified as belonging to one of four
groups (Gram-positive cocci, Gram-positive bacilli, Gram-negative cocci and
Gram-negative bacilli). Some organisms are best identified by stains other than
the Gram stain, particularly mycobacteria or Nocardia, which show acid-fastness on Ziehl–Neelsen
or similar stains.[146] Other organisms may need to be identified by their growth
in special media, or by other techniques, such as serology.
Culture
techniques are designed to promote the growth and identify particular bacteria,
while restricting the growth of the other bacteria in the sample. Often these
techniques are designed for specific specimens; for example, a sputum sample will be treated to identify organisms that cause pneumonia, while stool
specimens are cultured on selective
media to identify organisms that cause diarrhoea, while preventing growth of non-pathogenic bacteria.
Specimens that are normally sterile, such as blood, urine
or spinal fluid,
are cultured under conditions designed to grow all possible organisms.[106][147] Once a pathogenic organism has been isolated, it can be
further characterised by its morphology, growth patterns such as (aerobic or anaerobic
growth, patterns of hemolysis) and staining.
As with bacterial classification,
identification of bacteria is increasingly using molecular methods. Diagnostics
using such DNA-based tools, such as polymerase chain reaction, are increasingly popular due to their specificity and
speed, compared to culture-based methods.[148] These methods also allow the detection and identification
of "viable but nonculturable" cells that are metabolically active but non-dividing.[149] However, even using these improved methods, the total
number of bacterial species is not known and cannot even be estimated with any
certainty. Following present classification, there are a little less than 9,300
known species of prokaryotes, which includes bacteria and archaea.[150] but attempts to estimate the true level of bacterial
diversity have ranged from 107 to 109 total
species – and even these diverse estimates may be off by many orders of
magnitude.[151][152]
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 odor.
Predators
Some species of bacteria kill and
then consume other microorganisms, these species called predatory bacteria.[153] These include organisms such as Myxococcus xanthus, which forms swarms of cells that kill and digest any
bacteria they encounter.[154] Other bacterial predators either attach to their prey in
order to digest them and absorb nutrients, such as Vampirococcus, or invade another cell and multiply inside the cytosol, such
as Daptobacter.[155] These predatory bacteria are thought to have evolved from saprophages that consumed dead microorganisms, through adaptations that
allowed them to entrap and kill other organisms.[156]
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.[157] The bacteria in this association are unable to consume the
organic acids as this reaction produces hydrogen that accumulates in their
surroundings. Only the intimate association with the hydrogen-consuming Archaea
keeps the hydrogen concentration low enough to allow the bacteria to grow.
In soil, microorganisms that reside
in the rhizosphere
(a zone that includes the root
surface and the soil that adheres to the root after gentle shaking) carry out nitrogen
fixation, converting nitrogen gas to
nitrogenous compounds.[158] This serves to provide an easily absorbable form of
nitrogen for many plants, which cannot fix nitrogen themselves. Many other
bacteria are found as symbionts
in humans and other organisms. For example, the presence of over
1,000 bacterial species in the normal human gut
flora of the intestines can contribute to gut immunity, synthesise vitamins such as folic
acid, vitamin
K and biotin, convert sugars to lactic acid
(see Lactobacillus),
as well as fermenting complex undigestible carbohydrates.[159][160][161] 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.[162]
 |
Color-enhanced scanning electron
micrograph showing Salmonella typhimurium (red) invading cultured human cells
|
Pathogens
Main article: Pathogenic bacteria
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, foodborne
illness, leprosy and tuberculosis. A pathogenic cause for a known medical disease may only be
discovered many years after, as was the case with Helicobacter pylori and peptic
ulcer disease. Bacterial diseases are also
important in agriculture,
with bacteria causing leaf spot,
fire
blight and wilts in plants, as well as Johne's
disease, mastitis, salmonella
and anthrax in farm animals.
Each species of pathogen has a
characteristic spectrum of interactions with its human hosts. Some organisms, such as Staphylococcus or Streptococcus, can cause skin infections, pneumonia, meningitis
and even overwhelming sepsis,
a systemic inflammatory response producing shock,
massive vasodilation
and death.[163] 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.[164] Finally, some species such as Pseudomonas aeruginosa, Burkholderia cenocepacia, and Mycobacterium avium are opportunistic pathogens and cause disease mainly in people suffering from immunosuppression or cystic
fibrosis.[165][166]
 |
| Overview of bacterial infections and main species involved. |
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.[169] 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.[170] Infections can be prevented by antiseptic measures such as sterilizing 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 by bacteria. Disinfectants such as bleach
are used to kill bacteria or other pathogens on surfaces to prevent
contamination and further reduce the risk of infection.
Significance
in technology and industry
Further information: Economic importance
of bacteria
Bacteria, often lactic acid bacteria such as Lactobacillus and Lactococcus, 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.[171][172]
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.[173] 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 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.[174] In the chemical
industry, bacteria are most important in the
production of enantiomerically
pure chemicals for use as pharmaceuticals
or agrichemicals.[175]
Bacteria can also be used in the
place of pesticides
in the biological pest control. This commonly involves Bacillus thuringiensis (also called BT), a Gram-positive, soil dwelling bacterium.
Subspecies of this bacteria are used as a Lepidopteran-specific insecticides under trade names such as Dipel and Thuricide.[176] 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.[177][178]
Because of their ability to quickly
grow and the relative ease with which they can be manipulated, bacteria are the
workhorses for the fields of molecular
biology, genetics and biochemistry. By making mutations in bacterial DNA and examining the
resulting phenotypes, scientists can determine the function of genes, enzymes and metabolic
pathways in bacteria, then apply this
knowledge to more complex organisms.[179] 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.[180][181] 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.[182][183]
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