Introduction of bacteria

The bacteria are a large group of single-celled, prokaryote microorganisms. Typically a

few micrometers in length, bacteria have a wide range of shapes, ranging from spheres to
rods and spirals. Bacteria are ubiquitous in every habitat on Earth, growing in soil, acidic
hot springs, radioactive waste, water, and deep in the Earth's crust, as well as in organic
matter and the live bodies of plants and animals. There are typically 40 million bacterial
cells in a gram of soil and a million bacterial cells in a milliliter of fresh water; in all,
there are approximately five nonillion (5×1030) bacteria on Earth, forming much of the
world's biomass. 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. However, most bacteria have not been characterized, and
only about half of the phyla of bacteria have species that can be grown in the laboratory.
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. 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. 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, the production of cheese and yogurt through fermentation, as well as in
biotechnology, and the manufacture of antibiotics and other chemicals.

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 harbor 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.

History of bacteriology
Bacteria were first observed by Antonie 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 1838.

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

2
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 1905. 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.

Though it was known in the nineteenth century that bacteria are the cause of many
diseases, no effective antibacterial treatments were available. 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. 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 has a separate line of evolutionary descent from bacteria. 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.

Cellular 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 nucleus, mitochondria, chloroplasts and
the other organelles present in eukaryotic cells, such as the Golgi apparatus and
endoplasmic reticulum. Bacteria were once seen as simple bags of cytoplasm, but
elements such as prokaryotic cytoskeleton and the localization of proteins to specific
locations within the cytoplasm have been found to show levels of complexity. These sub
cellular compartments have been called "bacterial hyper structures".

Micro-compartments such as carboxysome provide a further level of organization, which

are compartments within bacteria that are surrounded by polyhedral protein shells, rather
than by lipid membranes. These "polyhedral organelles" localize and compartmentalize
bacterial metabolism, a function performed by the membrane-bound organelles in
eukaryotes.

Many important biochemical reactions, such as energy generation, occur by concentration

gradients across membranes, a potential difference also found in a battery. 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. However, in
many photosynthetic bacteria the plasma membrane is highly folded and fills most of the
cell with layers of light-gathering membrane. These light-gathering complexes may even

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form lipid-enclosed structures called chlorosomes in green sulfur bacteria. Other proteins
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.
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. 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.

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 photosynthetic Cyan
bacteria, 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.

Extra cellular 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.

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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 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 nanometers 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 can transfer genetic material between bacterial cells in a process called
conjugation (see bacterial genetics, below).

5
Metabolism
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 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.

Nutritional types in bacterial metabolism

Nutritional Source of
Source of carbon Examples
type energy
Organic compounds
Cyanobacteria, Green sulfur
(photoheterotrophs) or
Phototrophs Sunlight bacteria, Chloroflexi, or Purple
carbon fixation
bacteria
(photoautotroph)
Organic compounds Thermodesulfobacteria,
Inorganic
Lithotrophs (lithoheterotrophs) or carbon Hydrogenophilaceae, or
compounds
fixation (lithoautotrophs) Nitrospirae
Organic compounds
Organic (chemoheterotrophs) or Bacillus, Clostridium or
Organotrophs
compounds carbon fixation Enterobacteriaceae
(chemoautotrophs)

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 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.

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.

6
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 . 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).

Introduction of virus
A virus is a small infectious agent that can replicate only inside the living cells of
organisms. Most viruses are too small to be seen directly with a light microscope. Viruses
infect all types of organisms, from animals and plants to bacteria and archaea. Since the
initial discovery of tobacco mosaic virus by Martinus Beijerinck in 1898, about 5,000
viruses have been described in detail, although there are millions of different types.
Viruses are found in almost every ecosystem on Earth and are the most abundant type of
biological entity. The study of viruses is known as virology, a sub-specialty of
microbiology.

Virus particles (known as virions) consist of two or three parts: the genetic material made
from either DNA or RNA, long molecules that carry genetic information; a protein coat
that protects these genes; and in some cases an envelope of lipids that surrounds the
protein coat when they are outside a cell. The shapes of viruses range from simple helical
and icosahedral forms to more complex structures. The average virus is about one one-
hundredth the size of the average bacterium.

The origins of viruses in the evolutionary history of life are unclear: some may have
evolved from plasmids — pieces of DNA that can move between cells — while others
may have evolved from bacteria. In evolution, viruses are an important means of
horizontal gene transfer, which increases genetic diversity.

Viruses spread in many ways; plant viruses are often transmitted from plant to plant by
insects that feed on sap, such as aphids, while animal viruses can be carried by blood-
sucking insects. These disease-bearing organisms are known as vectors. Influenza viruses
are spread by coughing and sneezing. The norovirus and rotavirus, common causes of
viral gastroenteritis, are transmitted by the faecal-oral route and are passed from person to
person by contact, entering the body in food or water. HIV is one of several viruses
transmitted through sexual contact and by exposure to infected blood. Viruses can infect
only a limited range of host cells called the "host range". This can be narrow or, as when
a virus is capable of infecting many species, broad.

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Etymology
The word is from the Latin virus referring to poison and other noxious substances, first
used in English in 1392. Virulent, from Latin virulentus (poisonous), dates to 1400. A
meaning of "agent that causes infectious disease" is first recorded in 1728, before the
discovery of viruses by Dmitry Ivanovsky in 1892. The plural is viruses. The adjective
viral dates to 1948. The term virion is also used to refer to a single infective viral particle.

History
Louis Pasteur was unable to find a causative agent for rabies and speculated about a
pathogen too small to be detected by optical microscope. ] In 1884, the French
microbiologist Charles Chamber land invented a filter (known today as the Chamber land
filter or Chamber land-Pasteur filter) with pores smaller than bacteria. Thus, he could
pass a solution containing bacteria through the filter and completely remove them from
the solution. In 1892, the Russian biologist Dmitry Ivanovsky used this filter to study
what is now known as the tobacco mosaic virus. His experiments showed that crushed
leaf extracts from infected tobacco plants remain infectious after filtration. Ivanovsky
suggested the infection might be caused by a toxin produced by bacteria, but did not
pursue the idea. At the time it was thought that all infectious agents could be retained by
filters and grown on a nutrient medium—this was part of the germ theory of disease. In
1898, the Dutch microbiologist Martinus Beijerinck repeated the experiments and
became convinced that the filtered solution contained a new form of infectious agent. He
observed that the agent multiplied only in cells that were dividing, but as his experiments
did not show that it was made of particles, he called it a contagium vivum fluidum
(soluble living germ) and re-introduced the word virus. Beijerinck maintained that viruses
were liquid in nature, a theory later discredited by Wendell Stanley, who proved they
were particulate. In the same year, 1899, Friedrich Loeffler and Frosch passed the agent
of foot-and-mouth disease (aphthovirus) through a similar filter and ruled out the
possibility of a toxin because of the reduced concentration; they concluded that the agent
could replicate.

In the early 20th century, the English bacteriologist Frederick Twort discovered a group
of viruses that infect bacteria, now called bacteriophages (or commonly phages), and the
French-Canadian microbiologist Félix d'Herelle described viruses that, when added to
bacteria on agar, would produce areas of dead bacteria. He accurately diluted a
suspension of these viruses and discovered that the highest dilutions (lowest virus
concentrations), rather than killing all the bacteria, formed discrete areas of dead
organisms. Counting these areas and multiplying by the dilution factor allowed him to
calculate the number of viruses in the original suspension. Phages were heralded as a
potential treatment for diseases such as typhoid and cholera, but their promise was
forgotten with the development of penicillin. The study of phages provided insights into
the switching on and off of genes, and a useful mechanism for introducing foreign genes
into bacteria.

8
By the end of the 19th century, viruses were defined in terms of their infectivity, their
ability to be filtered, and their requirement for living hosts. Viruses had been grown only
in plants and animals. In 1906, Ross Granville Harrison invented a method for growing
tissue in lymph, and, in 1913, E. Steinhardt, C. Israeli, and R. A. Lambert used this
method to grow vaccinia virus in fragments of guinea pig corneal tissue. In 1928, H. B.
Maitland and M. C. Maitland grew vaccinia virus in suspensions of minced hens'
kidneys. Their method was not widely adopted until the 1950s, when poliovirus was
grown on a large scale for vaccine production.

Another breakthrough came in 1931, when the American pathologist Ernest William
Good pasture grew influenza and several other viruses in fertilized chickens' eggs. In
1949, John F. Enders, Thomas Weller, and Frederick Robbins grew polio virus in
cultured human embryo cells, the first virus to be grown without using solid animal tissue
or eggs. This work enabled Jonas Salk to make an effective polio vaccine.

The first images of viruses were obtained upon the invention of electron microscopy in
1931 by the German engineers Ernst Ruska and Max Knoll In 1935, American
biochemist and virologist Wendell Meredith Stanley examined the tobacco mosaic virus
and found it was mostly made of protein. A short time later, this virus was separated into
protein and RNA parts. The tobacco mosaic virus was the first to be crystallized and its
structure could therefore be elucidated in detail. The first X-ray diffraction pictures of the
crystallized virus were obtained by Bernal and Fankuchen in 1941. On the basis of her
pictures, Rosalind Franklin discovered the full DNA structure of the virus in 1955. In the
same year, Heinz Fraenkel-Conrat and Robley Williams showed that purified tobacco
mosaic virus RNA and its coat protein can assemble by themselves to form functional
viruses, suggesting that this simple mechanism was probably the means through which
viruses were created within their host cells.

The second half of the 20th century was the golden age of virus discovery and most of
the 2,000 recognized species of animal, plant, and bacterial viruses were discovered
during these years. In 1957, equine arterivirus and the cause of Bovine virus diarrhea (a
pestivirus) were discovered. In 1963, the hepatitis B virus was discovered by Baruch
Blumberg, and in 1965, Howard Temin described the first retrovirus. Reverse
transcriptase, the key enzyme that retroviruses use to translate their RNA into DNA, was
first described in 1970, independently by Howard Martin Temin and David Baltimore. In
1983 Luc Montagnier's team at the Pasteur Institute in France, first isolated the retrovirus
now called HIV.

Origins
Viruses are found wherever there is life and have probably existed since living cells first
evolved. The origin of viruses is unclear because they do not form fossils, so molecular
techniques have been the most useful means of investigating how they arose. These
techniques rely on the availability of ancient viral DNA or RNA, but, unfortunately, most
of the viruses that have been preserved and stored in laboratories are less than 90 years
old. There are three main hypotheses that try to explain the origins of viruses:

9
Regressive hypothesis
Viruses may have once been small cells that parasitized larger cells. Over time,
genes not required by their parasitism were lost. The bacteria rickettsia and
Chlamydia are living cells that, like viruses, can reproduce only inside host cells.
They lend support to this hypothesis, as their dependence on parasitism is likely to
have caused the loss of genes that enabled them to survive outside a cell. This is
also called the degeneracy hypothesis.
Cellular origin hypothesis
Some viruses may have evolved from bits of DNA or RNA that "escaped" from
the genes of a larger organism. The escaped DNA could have come from plasmids
(pieces of naked DNA that can move between cells) or transposons (molecules of
DNA that replicate and move around to different positions within the genes of the
cell). Once called "jumping genes", transposons are examples of mobile genetic
elements and could be the origin of some viruses. They were discovered in maize
by Barbara McClintock in 1950. This is sometimes called the vagrancy
hypothesis.
Coevolution hypothesis
Viruses may have evolved from complex molecules of protein and nucleic acid at
the same time as cells first appeared on earth and would have been dependent on
cellular life for billions of years. Viroids are molecules of RNA that are not
classified as viruses because they lack a protein coat. However, they have
characteristics that are common to several viruses and are often called sub viral
agents. Viroids are important pathogens of plants. They do not code for proteins
but interact with the host cell and use the host machinery for their replication. The
hepatitis delta virus of humans has an RNA genome similar to viroids but has
protein coat derived from hepatitis B virus and cannot produce one of its own. It
is therefore a defective virus and cannot replicate without the help of hepatitis B
virus. Similarly, the virophage 'sputnik' is dependent on Mimi virus, which infects
the protozoan Acanthamoeba castellanii. These viruses that are dependent on the
presence of other virus species in the host cell are called satellites and may
represent evolutionary intermediates of viroids and viruses.

Prions are infectious protein molecules that do not contain DNA or RNA. They cause an
infection in sheep called scrapie and cattle bovine spongiform encephalopathy ("mad
cow" disease). In humans they cause kuru and Creutzfeldt-Jakob disease. They are able to
replicate because some proteins can exist in two different shapes and the prion changes
the normal shape of a host protein into the prion shape. This starts a chain reaction where
each prion protein converts many host proteins into more prions, and these new prions
then go on to convert even more protein into prions. Although they are fundamentally
different from viruses and viroids, their discovery gives credence to the idea that viruses
could have evolved from self-replicating molecules.

Computer analysis of viral and host DNA sequences is giving a better understanding of
the evolutionary relationships between different viruses and may help identify the
ancestors of modern viruses. To date, such analyses have not helped to decide on which
of these hypotheses are correct. However, it seems unlikely that all currently known

10
viruses have a common ancestor and viruses have probably arisen numerous times in the
past by one or more mechanisms.

Structure

Viruses display a wide diversity of shapes and sizes, called morphologies. Generally
viruses are much smaller than bacteria. Most viruses that have been studied have a
diameter between 10 and 300 nanometers. Some filoviruses have a total length of up to
1400 nm; their diameters are only about 80 nm. Most viruses cannot be seen with a light
microscope so scanning and transmission electron microscopes are used to visualise
virions. To increase the contrast between viruses and the background, electron-dense
"stains" are used. These are solutions of salts of heavy metals, such as tungsten, that
scatter the electrons from regions covered with the stain. When virions are coated with
stain (positive staining), fine detail is obscured. Negative staining overcomes this
problem by staining the background only.

A complete virus particle, known as a virion, consists of nucleic acid surrounded by a

protective coat of protein called a capsid. These are formed from identical protein
subunits called capsomers. Viruses can have a lipid "envelope" derived from the host cell
membrane. The capsid is made from proteins encoded by the viral genome and its shape
serves as the basis for morphological distinction. Virally coded protein subunits will self-
assemble to form a capsid, generally requiring the presence of the virus genome.
Complex viruses code for proteins that assist in the construction of their capsid. Proteins
associated with nucleic acid are known as nucleoproteins, and the association of viral
capsid proteins with viral nucleic acid is called a nucleocapsid. The capsid and entire
virus structure can be mechanically (physically) probed through atomic force
microscopy. In general, there are four main morphological virus types:

Helical

These viruses are composed of a single type of capsomer stacked around a central
axis to form a helical structure, which may have a central cavity, or hollow tube.
This arrangement results in rod-shaped or filamentous virions: these can be short
and highly rigid, or long and very flexible. The genetic material, generally single-
stranded RNA, but ssDNA in some cases, is bound into the protein helix by
interactions between the negatively charged nucleic acid and positive charges on

11
 the protein. Overall, the length of a helical capsid is related to the length of the
nucleic acid contained within it and the diameter is dependent on the size and
arrangement of capsomers. The well-studied Tobacco mosaic virus is an example
of a helical virus.

Icosahedral

Most animal viruses are icosahedral or near-spherical with icosahedral symmetry.

A regular icosahedron is the optimum way of forming a closed shell from
identical sub-units. The minimum number of identical capsomers required is
twelve, each composed of five identical sub-units. Many viruses, such as
rotavirus, have more than twelve capsomers and appear spherical but they retain
this symmetry. Capsomers at the apices are surrounded by five other capsomers
and are called pentons. Capsomers on the triangular faces are surrounded by six
others and are call hexons.

Envelope

Some species of virus envelop themselves in a modified form of one of the cell
membranes, either the outer membrane surrounding an infected host cell, or
internal membranes such as nuclear membrane or endoplasmic reticulum, thus
gaining an outer lipid bilayer known as a viral envelope. This membrane is
studded with proteins coded for by the viral genome and host genome; the lipid
membrane itself and any carbohydrates present originate entirely from the host.
The influenza virus and HIV use this strategy. Most enveloped viruses are
dependent on the envelope for their infectivity.

Complex

These viruses possess a capsid that is neither purely helical, nor purely
icosahedral, and that may possess extra structures such as protein tails or a
complex outer wall. Some bacteriophages, such as Enterobacteria phage T4 have
a complex structure consisting of an icosahedral head bound to a helical tail,
which may have a hexagonal base plate with protruding protein tail fibres. This
tail structure acts like a molecular syringe, attaching to the bacterial host and then
injecting the viral genome into the cell.

The poxviruses are large, complex viruses that have an unusual morphology. The viral
genome is associated with proteins within a central disk structure known as a nucleoid.
The nucleoid is surrounded by a membrane and two lateral bodies of unknown function.
The virus has an outer envelope with a thick layer of protein studded over its surface. The
whole virion is slightly pleiomorphic, ranging from ovoid to brick shape. Mimivirus is
the largest known virus, with a capsid diameter of 400 nm. Protein filaments measuring
100 nm project from the surface. The capsid appears hexagonal under an electron
microscope, therefore the capsid is probably icosahedral.

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Some viruses that infect Archaea have complex structures that are unrelated to any other
form of virus, with a wide variety of unusual shapes, ranging from spindle-shaped
structures, to viruses that resemble hooked rods, teardrops or even bottles. Other archaeal
viruses resemble the tailed bacteriophages, and can have multiple tail structures

Introduction of Lichen

Lichens are composite organisms consisting of a symbiotic association of a fungus (the

mycobiont) with a photosynthetic partner (the photobiont or phycobiont), usually either a
green alga (commonly Trebouxia) or cyanobacterium (commonly Nostoc). The
morphology, physiology and biochemistry of lichens are very different from those of the
isolated fungus and alga in culture. Lichens occur in some of the most extreme
environments on Earth—arctic tundra, hot deserts, rocky coasts and toxic slag heaps.
However, they are also abundant as epiphytes on leaves and branches in rain forests and
temperate woodland, on bare rock, including walls and gravestones and on exposed soil
surfaces (e.g. Collema) in otherwise mesic habitats. Lichens are widespread and may be
long-lived; however, many species are also vulnerable to environmental disturbance, and
may be useful to scientists in assessing the effects of air pollution, ozone depletion, and
metal contamination. Lichens have also been used in making dyes and perfumes, as well
as in traditional medicines.

History
Although lichens had been recognized as organisms for quite some time, it was not until
1867, when Swiss botanist Simon Schwendener proposed his dual theory of lichens that
the true nature of the lichen association began to emerge. Schwendener's hypothesis,
which at the time lacked experimental evidence, arose from his extensive analysis of the
anatomy and development in lichens, algae, and fungi using a light microscope. Many of
the leading lichenologists at the time, such as James Crombie and Nylander, rejected
Schwendener's hypothesis because the common consensus was that all living organisms

13
were autonomous. Other prominent biologists, such as Heinrich Anton de Bary, Albert
Bernhard Frank, and Hermann Hellriegel were not so quick to reject Schwendener's ideas
and the concept soon spread into other areas of study, such as microbial, plant, animal
and human pathogens. When the complex relationships between pathogenic
microorganisms and their hosts were finally identified—refuting the idea of holistic
organisms—Schwendener's hypothesis began to gain popularity. Further experimental
proof of the dual nature of lichens was obtained when Eugene Thomas published his
results in 1939 on the first successful re-synthesis experiment.

Morphology and structure

Some lichens have the aspect of leaves (foliose lichens); others cover the substrate like a
crust (crustose lichens) (illustration, right), others such as the genus Ramalina adopt
shrubby forms (fruticose lichens), and there are gelatinous lichens such as the genus
Collema.

Although the form of lichen is determined by the genetic material of the fungal partner,
association with a photobiont is required for the development of that form. When grown
in the laboratory in the absence of its photobiont, a lichen fungus develops as an
undifferentiated mass of hyphae. If combined with its photobiont under appropriate
conditions, its characteristic form emerges, in the process called morphogenesis (Brodo,
Sharnoff & Sharnoff, 2001). In a few remarkable cases, a single lichen fungus can
develop into two very different lichen forms when associating with either a green algal or
a cyanobacterial symbiont. Quite naturally, these alternative forms were at first
considered to be different species, until they were first found growing in a conjoined
manner.

There is evidence to suggest that the lichen symbiosis is parasitic or commensalistic,

rather than mutualistic (Ahmadjian 1993). However, this now needs to be re-examined in
light of Coxon's work. The photosynthetic partner can exist in nature independently of
the fungal partner, but not vice versa. Furthermore, photobiont cells are routinely
destroyed in the course of nutrient exchange. The association is able to continue because
reproduction of the photobiont cells matches the rate at which they are destroyed. (ibid.)

Under magnification, a section through a typical foliose lichen thallus reveals four layers
of interlaced fungal filaments. The uppermost layer is formed by densely agglutinated
fungal hyphae building a protective outer layer called the cortex, which can reach several
hundred μm in thickness. This cortex may be further topped by an epicortex 0.6-1μm
thick in some Parmeliaceae, which may be with or without pores, and is secreted by cells
—it is not itself cellular. In lichens that include both green algal and cyanobacterial
symbionts, the cyanobacteria may be held on the upper or lower surface in small pustules
called cephalodia. Beneath the upper cortex is an algal layer composed of algal cells
embedded in rather densely interwoven fungal hyphae. Each cell or group of cells of the
photobiont is usually individually wrapped by hyphae, and in some cases penetrated by
an haustorium. Beneath this algal layer is a third layer of loosely interwoven fungal
hyphae without algal cells. This layer is called the medulla. Beneath the medulla, the

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bottom surface resembles the upper surface and is called the lower cortex, again
consisting of densely packed fungal hyphae. The lower cortex often bears root like fungal
structures known as rhizines, which serve to attach the thallus to the substrate on which it
grows. Lichens also sometimes contain structures made from fungal metabolites, for
example crustose lichens sometimes have a polysaccharide layer in the cortex. Although
each lichen thallus generally appears homogeneous, some evidence seems to suggest that
the fungal component may consist of more than one genetic individual of that species.
This seems to also be true of the photobiont species involved.

Growth form
Lichens are informally classified by growth form into:

• crustose (paint-like, flat), e.g., Caloplaca flavescens

• filamentous (hair-like), e.g., Ephebe lanata
• foliose (leafy), e.g., Hypogymnia physodes
• fruticose (branched), e.g., Cladonia evansii, C. subtenuis, and Usnea australis
• leprose (powdery), e.g., Lepraria incana
• squamulose (consisting of small scale-like structures, lacking a lower cortex),
e.g., Normandina pulchella
• gelatinous lichens, in which the cyanobacteria produce a polysaccharide that
absorbs and retains water.

Taxonomy and classification

Lichens are named based on the fungal component, which plays the primary role in
determining the lichen's form. The fungus typically comprises the majority of lichen’s
bulk, though in filamentous and gelatinous lichens this is not always the case. The lichen
fungus is typically a member of the Ascomycota—rarely a member of the
Basidiomycota, and then termed basidiolichens to differentiate them from the more
common ascolichens. Formerly, some lichen taxonomists placed lichens in their own

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division, the Mycophycophyta, but this practice is no longer accepted because the
components belong to separate lineages. Neither the ascolichens nor the basidiolichens
form monophyletic lineages in their respective fungal phyla, but they do form several
major solely or primarily lichen-forming groups within each phylum. Even more unusual
than basidiolichens is the fungus Geosiphon pyriforme, a member of the Glomeromycota
that is unique in that it encloses a cyanobacterial symbiont inside its cells. Geosiphon is
not usually considered to be lichen, and its peculiar symbiosis was not recognized for
many years. The genus is more closely allied to endomycorrhizal genera.

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