Organism... Wikipedia

A microorganism (from the Greek : μικρός,
mikros , "small" and ὀργανισμός, organismós ,
"organism") is a microscopic living organism,
which may be single celled[1] or multicellular .
The study of microorganisms is called
microbiology , a subject that began with the
discovery of microorganisms in 1674 by
Antonie van Leeuwenhoek, using a microscope
of his own design.
Microorganisms are very diverse and include
all the bacteria and archaea and almost all the
protozoa . They also include some fungi , algae,
and certain animals, such as rotifers. Many
macroscopic animals and plants have
microscopic juvenile stages. Some
microbiologists also classify viruses (and
viroids) as microorganisms, but others
consider these as nonliving. [2][3]
Microorganisms live in every part of the
biosphere , including soil , hot springs , "seven
miles deep" in the ocean , "40 miles high" in the
atmosphere and inside rocks far down within
the Earth's crust (see also endolith ). [4]
Microorganisms, under certain test conditions,
have been observed to thrive in the vacuum of
outer space . [5][6] The total amount of soil and
subsurface bacterial carbon is estimated as 5
x 1017 g, or the "weight of the United
Kingdom". [4] The mass of prokaryote
microorganisms — which includes bacteria and
archaea, but not the nucleated eukaryote
microorganisms — may be as much as 0.8
trillion tons of carbon (of the total biosphere
mass of 4 trillion tons). [7] On 17 March 2013,
researchers reported data that suggested
microbial life forms thrive in the Mariana
Trench . the deepest spot in the Earth's
oceans. [8][9] Other researchers reported
related studies that microorganisms thrive
inside rocks up to 580 m (1,900 ft; 0.36 mi)
below the sea floor under 2,590 m (8,500 ft;
1.61 mi) of ocean off the coast of the
northwestern United States [8][10] as well as
2,400 m (7,900 ft; 1.5 mi) beneath the seabed
off Japan. [11] On 20 August 2014, scientists
confirmed the existence of microorganisms
living 800 m (2,600 ft; 0.50 mi) below the ice
of Antarctica. [12][13] According to one
researcher,"You can find microbes everywhere
— they're extremely adaptable to conditions,
and survive wherever they are." [8]
Microorganisms are crucial to nutrient
recycling in ecosystems as they act as
decomposers . As some microorganisms can fix
nitrogen , they are a vital part of the nitrogen
cycle , and recent studies indicate that airborne
microorganisms may play a role in
precipitation and weather. [14] Microorganisms
are also exploited in biotechnology , both in
traditional food and beverage preparation, and
in modern technologies based on genetic
engineering . A small proportion of
microorganisms are pathogenic and cause
disease and even death in plants and animals.
[15] Microorganisms are often referred to as
microbes , but this is usually used in reference
to pathogens.
Evolution
Further information: Timeline of evolution and
Experimental evolution
Single-celled microorganisms were the first
forms of life to develop on Earth,
approximately 3–4 billion years ago. [16][17]
[18] Further evolution was slow, [19] and for
about 3 billion years in the Precambrian eon,
all organisms were microscopic. [20] So, for
most of the history of life on Earth , the only
forms of life were microorganisms. [21]
Bacteria, algae and fungi have been identified
in amber that is 220 million years old, which
shows that the morphology of microorganisms
has changed little since the Triassic period. [22]
The newly discovered biological role played by
nickel, however — especially that engendered
by volcanic eruptions from the Siberian Traps
(site of the modern city of Norilsk ) — is
thought to have accelerated the evolution of
methanogens towards the end of the Permian–
Triassic extinction event. [23]
Microorganisms tend to have a relatively fast
rate of evolution. Most microorganisms can
reproduce rapidly, and bacteria are also able to
freely exchange genes through conjugation,
transformation and transduction, even between
widely divergent species. [24] This horizontal
gene transfer, coupled with a high mutation
rate and many other means of genetic
variation , allows microorganisms to swiftly
evolve (via natural selection ) to survive in new
environments and respond to environmental
stresses. This rapid evolution is important in
medicine, as it has led to the recent
development of "super-bugs ", pathogenic
bacteria that are resistant to modern
antibiotics . [25]
Pre-microbiology
The possibility that microorganisms exist was
discussed for many centuries before their
discovery in the 17th century. The existence of
unseen microbiological life was postulated by
Jainism , which is based on Mahavira's
teachings as early as 6th century BCE. [26]
Paul Dundas notes that Mahavira asserted the
existence of unseen microbiological creatures
living in earth, water, air and fire. [27] The Jain
scriptures also describe nigodas, which are
sub-microscopic creatures living in large
clusters and having a very short life, which are
said to pervade every part of the universe,
even the tissues of plants and animals. [28]
The earliest known idea to indicate the
possibility of diseases spreading by yet unseen
organisms was that of the Roman scholar
Marcus Terentius Varro in a 1st-century BC
book titled On Agriculture in which he warns
against locating a homestead near swamps:
In The Canon of Medicine (1020), Abū Alī ibn
Sīnā (Avicenna) hypothesized that tuberculosis
and other diseases might be contagious [30]
[31]
In 1546, Girolamo Fracastoro proposed that
epidemic diseases were caused by transferable
seedlike entities that could transmit infection
by direct or indirect contact, or even without
contact over long distances.
All these early claims about the existence of
microorganisms were speculative and while
grounded on indirect observations, they were
not based on direct observation of
microorganisms or systematized empirical
investigation, e.g. experimentation.
Microorganisms were neither proven, observed,
nor accurately described until the 17th
century. The reason for this was that all these
early studies lacked the microscope .
History of microorganisms'
discovery
See also: History of biology
Antonie van Leeuwenhoek, the
first microbiologist and the
first to observe
microorganisms using a
microscope
Lazzaro Spallanzani showed
that boiling a broth stopped it
from decaying
Louis Pasteur showed that
Spallanzani's findings held
even if air could enter through
a filter that kept particles out
Robert Koch showed that
microorganisms caused disease
Antonie Van Leeuwenhoek (1632–1723) was
one of the first people to observe
microorganisms, using microscopes of his own
design. [32] Robert Hooke, a contemporary of
Leeuwenhoek, also used microscopes to
observe microbial life; his 1665 book
Micrographia describes these observations and
coined the term cell.
Before Leeuwenhoek's discovery of
microorganisms in 1675, it had been a mystery
why grapes could be turned into wine , milk
into cheese , or why food would spoil.
Leeuwenhoek did not make the connection
between these processes and microorganisms,
but using a microscope, he did establish that
there were forms of life that were not visible
to the naked eye. [33][34] Leeuwenhoek's
discovery, along with subsequent observations
by Spallanzani and Pasteur, ended the long-
held belief that life spontaneously appeared
from non-living substances during the process
of spoilage.
Lazzaro Spallanzani (1729–1799) found that
boiling broth would sterilise it, killing any
microorganisms in it. He also found that new
microorganisms could only settle in a broth if
the broth was exposed to air.
Louis Pasteur (1822–1895) expanded upon
Spallanzani's findings by exposing boiled
broths to the air, in vessels that contained a
filter to prevent all particles from passing
through to the growth medium, and also in
vessels with no filter at all, with air being
admitted via a curved tube that would not
allow dust particles to come in contact with
the broth. By boiling the broth beforehand,
Pasteur ensured that no microorganisms
survived within the broths at the beginning of
his experiment. Nothing grew in the broths in
the course of Pasteur's experiment. This
meant that the living organisms that grew in
such broths came from outside, as spores on
dust, rather than spontaneously generated
within the broth. Thus, Pasteur dealt the death
blow to the theory of spontaneous generation
and supported germ theory.
In 1876, Robert Koch (1843–1910) established
that microorganisms can cause disease. He
found that the blood of cattle which were
infected with anthrax always had large
numbers of Bacillus anthracis . Koch found that
he could transmit anthrax from one animal to
another by taking a small sample of blood
from the infected animal and injecting it into a
healthy one, and this caused the healthy
animal to become sick. He also found that he
could grow the bacteria in a nutrient broth,
then inject it into a healthy animal, and cause
illness. Based on these experiments, he devised
criteria for establishing a causal link between a
microorganism and a disease and these are
now known as Koch's postulates . [35]
Although these postulates cannot be applied in
all cases, they do retain historical importance
to the development of scientific thought and
are still being used today. [36]
On 8 November 2013, scientists reported the
discovery of what may be the earliest signs of
life on Earth—the oldest complete fossils of a
microbial mat (associated with sandstone in
Western Australia ) estimated to be 3.48 billion
years old. [37][38]
Classification and structure
Evolutionary tree showing the common
ancestry of all three domains of life. [39]
Bacteria are colored blue, eukaryotes red, and
archaea green. Relative positions of some
phyla are shown around the tree.
Microorganisms can be found almost
anywhere in the taxonomic organization of life
on the planet. Bacteria and archaea are almost
always microscopic, while a number of
eukaryotes are also microscopic, including
most protists , some fungi , as well as some
animals and plants. Viruses are generally
regarded as not living and therefore not
considered as microorganisms, although the
field of microbiology also encompasses the
study of viruses.
Main article: Prokaryote
Prokaryotes are organisms that lack a cell
nucleus and the other membrane bound
organelles. They are almost always unicellular,
although some species such as myxobacteria
can aggregate into complex structures as part
of their life cycle .
Consisting of two domains, bacteria and
archaea , the prokaryotes are the most diverse
and abundant group of organisms on Earth
and inhabit practically all environments where
the temperature is below +140 °C. They are
found in water , soil , air , animals'
gastrointestinal tracts , hot springs and even
deep beneath the Earth's crust in rocks. [40]
Practically all surfaces that have not been
specially sterilized are covered by prokaryotes.
The number of prokaryotes on Earth is
estimated to be around five million trillion
trillion, or 5 × 10 30, accounting for at least
half the biomass on Earth. [41]
Main article: Bacteria
Staphylococcus aureus bacteria magnified
about 10,000x
Almost all bacteria are invisible to the naked
eye, with a few extremely rare exceptions, such
as Thiomargarita namibiensis . [42] They lack a
nucleus and other membrane-bound organelles,
and can function and reproduce as individual
cells, but often aggregate in multicellular
colonies. [43] Their genome is usually a single
loop of DNA , although they can also harbor
small pieces of DNA called plasmids. These
plasmids can be transferred between cells
through bacterial conjugation. Bacteria are
surrounded by a cell wall, which provides
strength and rigidity to their cells. They
reproduce by binary fission or sometimes by
budding , but do not undergo meiotic sexual
reproduction. However, many bacterial species
can transfer DNA between individual cells by a
process referred to as natural transformation.
[44][45] In nature, the development of
competence for transformation is usually
associated with stressful environmental
conditions, and seems to be an adaptation for
facilitating repair of DNA damage in recipient
cells. [46][47] Some species form
extraordinarily resilient spores , but for bacteria
this is a mechanism for survival, not
reproduction. Under optimal conditions bacteria
can grow extremely rapidly and can double as
quickly as every 20 minutes. [48]
Main article: Archaea
Archaea are also single-celled organisms that
lack nuclei . In the past, the differences
between bacteria and archaea were not
recognised and archaea were classified with
bacteria as part of the kingdom Monera.
However, in 1990 the microbiologist Carl
Woese proposed the three-domain system that
divided living things into bacteria, archaea and
eukaryotes. [49] Archaea differ from bacteria in
both their genetics and biochemistry. For
example, while bacterial cell membranes are
made from phosphoglycerides with ester
bonds, archaean membranes are made of ether
lipids . [50]
Archaea were originally described in extreme
environments, such as hot springs, but have
since been found in all types of habitats. [51]
Only now are scientists beginning to realize
how common archaea are in the environment,
with crenarchaeota being the most common
form of life in the ocean, dominating
ecosystems below 150 m in depth. [52][53]
These organisms are also common in soil and
play a vital role in ammonia oxidation. [54]
Main article: Eukaryote
Most living things that are visible to the naked
eye in their adult form are eukaryotes ,
including humans . However, a large number of
eukaryotes are also microorganisms. Unlike
bacteria and archaea , eukaryotes contain
organelles such as the cell nucleus , the Golgi
apparatus and mitochondria in their cells. The
nucleus is an organelle that houses the DNA
that makes up a cell's genome . DNA itself is
arranged in complex chromosomes . [55]
Mitochondria are organelles vital in metabolism
as they are the site of the citric acid cycle and
oxidative phosphorylation . They evolved from
symbiotic bacteria and retain a remnant
genome. [56] Like bacteria, plant cells have cell
walls , and contain organelles such as
chloroplasts in addition to the organelles in
other eukaryotes. Chloroplasts produce energy
from light by photosynthesis , and were also
originally symbiotic bacteria. [56]
Unicellular eukaryotes consist of a single cell
throughout their life cycle. This qualification is
significant since most multicellular eukaryotes
consist of a single cell called a zygote only at
the beginning of their life cycles. Microbial
eukaryotes can be either haploid or diploid,
and some organisms have multiple cell nuclei .
[57]
Unicellular eukaryotes usually reproduce
asexually by mitosis under favorable
conditions. However, under stressful
conditions such as nutrient limitations and
other conditions associated with DNA damage,
they tend to reproduce sexually by meiosis and
syngamy. [46][58]
Main article: Protista
Of eukaryotic groups, the protists are most
commonly unicellular and microscopic. This is
a highly diverse group of organisms that are
not easy to classify. [59][60] Several algae
species are multicellular protists, and slime
molds have unique life cycles that involve
switching between unicellular, colonial, and
multicellular forms. [61] The number of species
of protists is unknown since we may have
identified only a small portion. Studies from
2001-2004 have shown that a high degree of
protist diversity exists in oceans, deep sea-
vents, river sediment and an acidic river which
suggests that a large number of eukaryotic
microbial communities have yet to be
discovered. [62][63]
A microscopic mite Lorryia formosa
Main article: Micro-animals
Some micro animals are multicellular but at
least one animal group, Myxozoa, is unicellular
in its adult form. Microscopic arthropods
include dust mites and spider mites.
Microscopic crustaceans include copepods ,
some cladocera and water bears . Many
nematodes are also too small to be seen with
the naked eye. A common group of
microscopic animals are the rotifers, which are
filter feeders that are usually found in fresh
water. Some micro-animals reproduce both
sexually and asexually and may reach new
habitats by producing eggs which can survive
harsh environments that would kill the adult
animal. However, some simple animals, such
as rotifers, tardigrades and nematodes, can
dry out completely and remain dormant for
long periods of time. [64]
Main article: Fungus
The fungi have several unicellular species,
such as baker's yeast (Saccharomyces
cerevisiae ) and fission yeast
( Schizosaccharomyces pombe). Some fungi,
such as the pathogenic yeast Candida albicans ,
can undergo phenotypic switching and grow as
single cells in some environments, and
filamentous hyphae in others. [65] Fungi
reproduce both asexually, by budding or binary
fission, as well by producing spores, which are
called conidia when produced asexually, or
basidiospores when produced sexually.
Main article: Plant
The green algae are a large group of
photosynthetic eukaryotes that include many
microscopic organisms. Although some green
algae are classified as protists , others such as
charophyta are classified with embryophyte
plants, which are the most familiar group of
land plants. Algae can grow as single cells, or
in long chains of cells. The green algae include
unicellular and colonial flagellates, usually but
not always with two flagella per cell, as well
as various colonial, coccoid, and filamentous
forms. In the Charales, which are the algae
most closely related to higher plants, cells
differentiate into several distinct tissues within
the organism. There are about 6000 species of
green algae. [66]
Habitats and ecology
Microorganisms are found in almost every
habitat present in nature. Even in hostile
environments such as the poles , deserts ,
geysers , rocks, and the deep sea . Some types
of microorganisms have adapted to the
extreme conditions and sustained colonies;
these organisms are known as extremophiles .
Extremophiles have been isolated from rocks
as much as 7 kilometres below the Earth's
surface, [67] and it has been suggested that
the amount of living organisms below the
Earth's surface may be comparable with the
amount of life on or above the surface. [40]
Extremophiles have been known to survive for
a prolonged time in a vacuum, and can be
highly resistant to radiation , which may even
allow them to survive in space. [68] Many
types of microorganisms have intimate
symbiotic relationships with other larger
organisms; some of which are mutually
beneficial (mutualism ), while others can be
damaging to the host organism ( parasitism). If
microorganisms can cause disease in a host
they are known as pathogens and then they
are sometimes referred to as microbes.
Main article: Extremophile
Extremophiles are microorganisms that have
adapted so that they can survive and even
thrive in conditions that are normally fatal to
most life-forms. For example, some species
have been found in the following extreme
environments:
Temperature: as high as 130 °C (266 °F),
[69] as low as −17 °C (1 °F) [70]
Acidity/alkalinity: less than pH 0, [71] up to
pH 11.5 [72]
Salinity : up to saturation[73]
Pressure : up to 1,000-2,000 atm, down to 0
atm (e.g. vacuum of space ) [74]
Radiation : up to 5k Gy[75]
Extremophiles are significant in different ways.
They extend terrestrial life into much of the
Earth's hydrosphere , crust and atmosphere,
their specific evolutionary adaptation
mechanisms to their extreme environment can
be exploited in bio-technology , and their very
existence under such extreme conditions
increases the potential for extraterrestrial life.
[76]
The nitrogen cycle in soils depends on the
fixation of atmospheric nitrogen . One way this
can occur is in the nodules in the roots of
legumes that contain symbiotic bacteria of the
genera Rhizobium , Mesorhizobium, Sinorhizobium,
Bradyrhizobium , and Azorhizobium. [77]
Symbiotic microorganisms such as fungi and
algae form an association in lichen . Certain
fungi form mycorrhizal symbioses with trees
that increase the supply of nutrients to the
tree.
Importance
Microorganisms are vital to humans and the
environment, as they participate in the carbon
and nitrogen cycles , as well as fulfilling other
vital roles in virtually all ecosystems , such as
recycling other organisms' dead remains and
waste products through decomposition .
Microorganisms also have an important place
in most higher-order multicellular organisms
as symbionts . Many blame the failure of
Biosphere 2 on an improper balance of
microorganisms. [78]
Some forms of bacteria that live in animals'
stomachs help in their digestion. For example,
cows have a variety of different
microorganisms in their stomachs that are
essential in their digestion of grass and hay.
The gastrointestinal tract contains an
immensely complex ecology of
microorganisms. A typical person harbors
more than 500 distinct species of bacteria,
representing dozens of different lifestyles and
capabilities. The composition and distribution
of this menagerie varies with age, state of
health and diet.
The number and type of bacteria in the
gastrointestinal tract vary dramatically by
region. In healthy individuals the stomach and
proximal small intestine contain few
microorganisms, largely a result of the
bacteriocidal activity of gastric acid; those
that are present are aerobes and facultative
anaerobes. One interesting testimony to the
ability of gastric acid to suppress bacterial
populations is seen in patients with
achlorhydria, a genetic condition which
prevents secretion of gastric acid. Such
patients, which are otherwise healthy, may
have as many as 10,000 to 100,000,000
microorganisms per ml of stomach contents.
In sharp contrast to the stomach and small
intestine, the contents of the colon literally
teem with bacteria, predominantly strict
anaerobes (bacteria that survive only in
environments virtually devoid of oxygen).
Between these two extremes is a transitional
zone, usually in the ileum, where moderate
numbers of both aerobic and anaerobic
bacteria are found.
The gastrointestinal tract is sterile at birth, but
colonization typically begins within a few
hours of birth, starting in the small intestine
and progressing caudally over a period of
several days. In most circumstances, a
"mature" microbial flora is established by 3 to
4 weeks of age.
It is also clear that microbial populations exert
a profound effect on structure and function of
the digestive tract. For example:
The morphology of the intestine of germ-free
animals differs considerably from normal
animals - villi of the small intestine are
remarkably regular, the rate of epithelial cell
renew is reduced and, as one would expect,
the number and size of Peyer's patches is
reduced. The cecum of germ-free rats is
roughly 10 times the size of that in a
conventional rat. Bacteria in the intestinal
lumen metabolize a variety of sterols and
steroids. For example, bacteria convert the bile
salt cholic acid to deoxycholic acid. Small
intestinal bacteria also have an important role
in sex steroid metabolism. Finally, bacterial
populations in the large intestine digest
carbohydrates, proteins and lipids that escape
digestion and absorption in small intestine.
This fermentation, particularly of cellulose, is
of critical importance to herbivores like cattle
and horses which make a living by consuming
plants. However, it seems that even species
like humans and rodents derive significant
benefit from the nutrients liberated by
intestinal microorganisms.
Main article: Fermentation (food)
Microorganisms are used in brewing, wine
making , baking, pickling and other food-making
processes.
They are also used to control the fermentation
process in the production of cultured dairy
products such as yogurt and cheese . The
cultures also provide flavour and aroma, and
inhibit undesirable organisms. [79]
Main article: Sewage treatment
The majority of all oxidative sewage treatment
processes rely on a large range of
microorganisms to oxidise organic constituents
which are not amenable to sedimentation or
flotation. Anaerobic microorganisms are also
used to reduce sludge solids producing
methane gas (amongst other gases) and a
sterile mineralised residue. In potable water
treatment, one method, the slow sand filter ,
employs a complex gelatinous layer composed
of a wide range of microorganisms to remove
both dissolved and particulate material from
raw water. [80]
Main articles: Algae fuel , Cellulosic ethanol and
Ethanol fermentation
Microorganisms are used in fermentation to
produce ethanol, [81] and in biogas reactors to
produce methane . [82] Scientists are
researching the use of algae to produce liquid
fuels, [83] and bacteria to convert various
forms of agricultural and urban waste into
usable fuels. [84]
Microorganisms are used for many commercial
and industrial production of chemicals,
enzymes and other bioactive molecules.
Examples of organic acid produced include
Acetic acid : Produced by the bacterium
Acetobacter aceti and other acetic acid bacteria
(AAB)
Butyric acid (butanoic acid): Produced by
the bacterium Clostridium butyricum
Lactic acid : Lactobacillus and others
commonly called as lactic acid bacteria (LAB)
Citric acid : Produced by the fungus
Aspergillus niger
Microorganisms are used for preparation of
bioactive molecules and enzymes.
Streptokinase produced by the bacterium
Streptococcus and modified by genetic
engineering is used as a clot buster for
removing clots from the blood vessels of
patients who have undergone myocardial
infarctions leading to heart attack.
Cyclosporin A is a bioactive molecule used
as an immunosuppressive agent in organ
transplantation
Statins produced by the yeast Monascus
purpureus are commercialised as blood
cholesterol lowering agents which act by
competitively inhibiting the enzyme responsible
for synthesis of cholesterol. [85]
Microorganisms are essential tools in
biotechnology , biochemistry , genetics , and
molecular biology. The yeasts (Saccharomyces
cerevisiae ) and fission yeast
( Schizosaccharomyces pombe) are important
model organisms in science, since they are
simple eukaryotes that can be grown rapidly in
large numbers and are easily manipulated. [86]
They are particularly valuable in genetics ,
genomics and proteomics. [87][88]
Microorganisms can be harnessed for uses
such as creating steroids and treating skin
diseases. Scientists are also considering using
microorganisms for living fuel cells, [89] and as
a solution for pollution. [90]
Main article: Biological warfare
In the Middle Ages, diseased corpses were
thrown into castles during sieges using
catapults or other siege engines . Individuals
near the corpses were exposed to the
pathogen and were likely to spread that
pathogen to others. [91]