A proto-metabolism is a series of linked chemical reactions in a prebiotic environment that preceded and eventually turned into modern metabolism. Combining ongoing research in astrobiology and prebiotic chemistry, work in this area focuses on reconstructing the connections between potential metabolic processes that may have occurred in early Earth conditions. Proto-metabolism is believed to be simpler than modern metabolism and the Last Universal Common Ancestor (LUCA), as simple organic molecules likely gave rise to more complex metabolic networks. Prebiotic chemists have demonstrated abiotic generation of many simple organic molecules including amino acids,[2]fatty acids, simple sugars, and nucleobases.
There are multiple scenarios bridging prebiotic chemistry to early
metabolic networks that occurred before the origins of life, also known
as abiogenesis.
In addition, there are hypotheses made on the evolution of biochemical
pathways including the metabolism-first hypothesis, which theorizes how
reaction networks dissipate free energy from which genetic molecules and proto-cell membranes later emerge.
To determine the composition of key early metabolic networks,
scientists have also used top-down approaches to study LUCA and modern
metabolism.
Autocatalytic reactions
are reactions where the reaction product acts as a catalyst for its own
formation. Many researchers that study proto-metabolism agree that
early metabolic networks likely originated as a set of chemical
reactions that form self-sustaining networks. This set of reactions is commonly referred to as an autocatalytic set. Some prebiotic chemistries focus on these autocatalytic reactions including the formose reaction, HCN oligomerization, and formamide chemistry.
Discovered in 1861 by Aleksandr Butlerov, the formose reaction is a set of two reactions converting formaldehyde (CH2O) to a mixture of simple sugars.
Formaldehyde is an intermediate in the oxidation of simple carbon
molecules (e.g. methane) and was likely present in early Earth's
atmosphere.
The first reaction is the slow conversion of formaldehyde (C1 carbon)
to glycoaldehyde (C2 carbon) and occurs through an unknown mechanism.
The second reaction is the faster and autocatalytic formation of higher weight aldoses and ketoses. The kinetics of the formose reaction are often described as autocatalytic, as the alkaline reaction uses lowest molecular weight sugars as feedstocks or input molecules into the reaction.
Self-organized autocatalytic networks, like the formose reaction, would
allow for adaptation to changing prebiotic environmental conditions.
As a proof-of-concept, Robinson and colleagues demonstrated how
changing environmental conditions and catalyst availability can impact
the resultant sugar products.
In the past, many researchers have suggested the importance of this reaction for abiogenesis and the origins of metabolism because it can lead to ribose. Ribose is a building block of RNA
and an important precursor in proto-metabolism. However, there are
limitations for the formose reaction to be the chemical origin of sugars
including the low chemoselectivity for ribose and high complexity of the final reaction mixture.
In addition, a direct joining together of ribose, a nucleobase, and
phosphate to make a ribonucleotide (the building block of RNA) is not
currently chemically feasible. Alternative prebiotic mechanisms have been proposed including cyanosulfidic prebiotic chemistries.
HCN-derived polymers are the oligomer or hydrolysis products of HCN.
These polymers can be synthesized from HCN or cyanide salts often in
alkaline conditions, but they have been observed in a wide range of
experimental conditions. HCN readily reacts with itself to produce many HCN polymers and biologically-relevant compounds like nucleobasesamino acids, and carboxylic acids.
The diversity of products could point to a plausible proto-metabolic
network of HCN oligomerization reactions. Although, some groups point to
low HCN concentrations in early Earth and low chemioselectivity of key
biologically-relevant products, similar to the formose reaction. Others have shown that abundant HCN is produced after large impacts and that high specificity and yield can be achieved.
Formamide (NH2CHO) is the simplest naturally-occurring amide. Similar to HCN, formamide can form naturally.
Formamide has specific physical and stability properties possibly
suitable for a universal prebiotic precursor for early proto-metabolic
networks. For example, it has four universal atomic elements
ubiquitous to life: C, H, O, N. The presence of unique functional
groups involving oxygen and nitrogen support reaction chemistries to
build key biomolecules like amino acids, sugars, nucleosides and other
key intermediates of other prebiotic reactions (e.g. the citric acid cycle). In addition, early Earth geological features like hydrothermal pores might support formamide chemistry and synthesis of key prebiotic biomolecules with concentration requirements.
Overall, formamide chemistry can support connections and
substrates needed to support prebiotic biomolecule synthesis including
the formose reaction, Strecker synthesis, HCN oligomerization, or the Fischer-Tropsch process. In addition, formamide can be easily concentrated through evaporation reactions as it has a boiling point of 210C. Although this reaction has high versatility across one-carbon atom
precursors, the connections between different biosynthetic pathways are
yet to be directly explored experimentally.
Experimental reconstruction
Many
research groups are actively attempting experimental reconstruction of
the interactions between prebiotic reactions. One major consideration is
the ability for these reactions to operate in the same environmental
conditions. These one-pot syntheses would likely push the reaction towards specific subgroups of moleculesThe key to building proto-metabolic scenarios involves coupling constructive and interconversion reactions. Constructive reactions use autocatalytic prebiotic chemistries to increase the structural complexity of the original molecule, while interconversion reactions connect different prebiotic chemistries by changing the functional groups
appended to the original molecule. A functional group is a group of
atoms that has similar properties whenever it appears in different
molecules. These interconversion reactions and functional group
transformations can lead to new prebiotic chemistries and precursor
molecules.
Cyanosulfidic scenarios are mechanisms for proto-metabolism proposed by the Eschenmoser and Sutherland groups. Research from the Eschenmoser group suggested that interactions between
HCN and aldehydes can catalyze the formation of diaminomaleodinitrile
(DAMN). Iterations of this cycle would generate multiple intermediate
metabolites and key biomolecular precursors through functional group
transformations by hydrolytic and redox processes. To expand upon this
finding, the Sutherland group experimentally assessed the assembly of
biomolecular building blocks from prebiotic intermediates and one-carbon
feedstocks.
They synthesized precursors of ribonucleotides, amino acids and lipids
from the reactants of hydrogen cyanide, acetylene, acrylonitrile
(product of cyanide and acetylene), and dihydroxyacetone (stable triose isomer of glyceraldehyde and phosphate). These reactions are driven by UV light and use hydrogen sulfide (H2S) as the primary reductant
in these reactions. As each of these synthesis reactions was tested
independently and some reactions require periodic input of additional
reactants, these biomolecular precursors were not strictly generated
through a one-pot synthesis expected of early Earth environments. In the same work, these authors argue that flow chemistry or the movement of reactants through water could generate the conditions favorable for the synthesis of these molecules.
Eschenmoser
also proposed a parallel scenario where the connections between
prebiotic reactions would be connected by glyoxylate, a simple
α-ketoacid, produced by HCN oligomerization and hydrolysis.
In this work, Eschenmoser proposes potential schemes to generate both
informational oligomers and other key autocatalytic reactions from
plausible one-carbon sources (HCN, CO, CO2).
The Krishnamurthy group at Scripps experimentally expanded on this theory. In mild aqueous conditions, they demonstrated that the reaction of glyoxylate and pyruvate can produce a series of α-ketoacid intermediates constituting the reductive tricarboxylic acid (TCA) cycle.
This reaction proceeded without metal or enzyme catalysts as glyoxylate
acted as both the carbon source and reducing agent in the reaction.
Similarly, the Moran group have also reported pyruvate and glyoxylate
can react in warm iron-rich water to produce TCA intermediates and some
amino acids. Their work has successfully reconstructed 9 out of 11 TCA intermediates and 5 universal metabolic precursors. Additional experimental analysis is needed to connect this scenario to modern metabolism.
Energy sources
Unlike
proto-metabolism, the bioenergetic pathways powering modern metabolism
are well understood. In early Earth conditions, there were mainly three
kinds of energy to support early metabolic pathways: high energy sources
to catalyze monomers, lower energy sources to support condensation or polymerization, and energy carriers that support transfer of energy from the environment to metabolic networks. Examples of high energy sources include photochemical energy from ultraviolet light, atmospheric electric discharge, and geologicalelectrochemical
energy. These energy sources would support synthesis of biological
monomers or feedstocks for proto-metabolism. In contrast, examples of
lower energy sources for assembly of more complex molecules include
anhydrous heat, mineral-catalyzed synthesis, and sugar-driven reactions.
Energy carrier molecules could allow for propagation of the energy
through the metabolic networks likely resembled modern energy carriers
including ATP and NADH. Both energy carriers are nucleotide-based molecules and likely originated early in metabolism.
Metabolism-first hypothesis suggests that autocatalytic networks of metabolic reactions were the first forms of life. This is an alternative hypothesis to RNA-world, which is a genes-first hypothesis. It was first proposed by Martynas Ycas in 1955. Many recent work in this area is focused in computational modeling of theoretical prebiotic networks.
Metabolism-first proponents postulate that replication and genetic machinery could not arise without the accumulation of the molecules needed for replication. Alone, simple connections between prebiotic synthesis reactions could form key organic molecules and once encapsulated by a membrane
would constitute the first cells. These reactions could be catalyzed by
various inorganic molecules or ions and stabilized by solid surfaces. Molecular self-replicators and enzymes would emerge later, with these future metabolisms better resembling modern metabolism.
One critique for the metabolism-first hypothesis for abiogenesis
is they would also need self-replicating abilities with a high degree of
fidelity.
If not, the chemical networks with greater fitness in early Earth would
not be preserved. There is limited experimental evidence for these
theories, so additional exploration in this area is needed to determine
the feasibility of a metabolism-first origins of life.
Visual agnosia is an impairment in recognition of visually
presented objects. It is not due to a deficit in vision (acuity, visual
field, and scanning), language, memory, or intellect. While cortical blindness
results from lesions to primary visual cortex, visual agnosia is often
due to damage to more anterior cortex such as the posterior occipital and/or temporal lobe(s) in the brain. There are two types of visual agnosia: apperceptive agnosia and associative agnosia.
Recognition of visual objects
occurs at two primary levels. At an apperceptive level, the features of
the visual information from the retina are put together to form a
perceptual representation of an object. At an associative level, the
meaning of an object is attached to the perceptual representation and
the object is identified.
If a person is unable to recognize objects because they cannot perceive
correct forms of the objects, although their knowledge of the objects
is intact (i.e. they do not have anomia),
they have apperceptive agnosia. If a person correctly perceives the
forms and has knowledge of the objects, but cannot identify the objects,
they have associative agnosia.
Symptoms and signs
While
most cases of visual agnosia are seen in older adults who have
experienced extensive brain damage, there are also cases of young
children with less brain damage during developmental years acquiring the
symptoms.
Commonly, visual agnosia presents as an inability to recognize an
object in the absence of other explanations, such as blindness or
partial blindness, anomia, memory loss, etc. Other common manifestations
of visual agnosia that are generally tested for include difficulty
identifying objects that look similar in shape, difficulty with
identifying line drawings of objects, and recognizing objects that are
shown from less common views, such as a horse from a top-down view.
Within any given patient, a variety of symptoms can occur, and
the impairment of ability is not only binary but can range in severity.
For example, Patient SM is a prosopagnosic
with a unilateral lesion to left extrastriate cortex due to an accident
in his twenties who displays behavior similar to congenital prosopagnosia.
Although he can recognize facial features and emotions – indeed he
sometimes uses a standout feature to recognize a face – face recognition
is almost impossible purely from visual stimuli, even for faces of
friends, family, and himself. The disorder also affects his memory of
faces, both in storing new memories of faces and recalling stored
memories.
Nevertheless, it is important to note the reach of symptoms to
other domains. SM's object recognition is similarly impaired though not
entirely; when given line drawings to identify, he was able to give
names of objects with properties similar to the drawing, implying that
he is able to see the features of the drawing. Similarly, copying a
line drawing of a beach scene led to a simplified version of the
drawing, though the main features were accounted for. For recognition of
places, he is still impaired but familiar places are remembered and new
places can be stored into memory.
Pathophysiology
Visual
agnosia occurs after damage to visual association cortex or to parts of
the ventral stream of vision, known as the "what pathway" of vision for
its role in object recognition.
This occurs even when no damage has been done to the eyes or optic
tract that leads visual information into the brain; in fact, visual
agnosia occurs when symptoms cannot be explained by such damage. Damage
to specific areas of the ventral stream impair the ability to recognize
certain categories of visual information, such as the case of
prospagnosia.
Patients with visual agnosia generally do not have damage to the
dorsal stream of vision, known as the "where pathway" of vision because
of its role determining object's position in space, allowing individuals
with visual agnosia to show relatively normal visually guided behavior.
For example, patient DF had lesions to the ventral surface that gave her apperceptive agnosia. One of the tasks she was tested on required her to place a card through
a thin slot that could be rotated into all orientations. As an
apperceptive agnosic, it would be expected that since she cannot
recognize the slot, she should not be able to correctly place the card
into the slot. Indeed, when she was asked to give the direction of the
slot, her responses were no better than chance. Yet, when she was asked
to place the card into the slot, her success was almost to the level of
the controls. This implies that in the event of a ventral stream
deficit, the dorsal stream can help with processing of special
information to aid movement regardless of object recognition.
More specifically, the lateral occipital complex appears to respond to many different types of objects.
Prosopagnosia (inability to recognize faces) is due to damage of the
fusiform face area (FFA). An area in the fusiform gyrus of the temporal
lobe that has been strongly associated with a role in facial
recognition.
However, this area is not exclusive to faces; recognition of other
objects of expertise are also processed in this area. The extrastriate
body cortex (EBA) was found to be activated by photographs, silhouettes,
or stick drawings of human bodies.
The parahippocampal place area (PPA) of the limbic cortex has been
found to be activated by the sight of scenes and backgrounds.
Cerebral achromatopsia (the inability to discriminate between
different hues) is caused by damage to the V8 area of the visual
association cortex.
The left hemisphere seems to play a critical role in recognizing the meaning of common objects.
Diagnosis
Classification
Broadly, visual agnosia is divided into apperceptive and associative visual agnosia.
Apperceptive agnosia is failure of object recognition even when
the basic visual functions (acuity, color, motion) and other mental
processing, such as language and intelligence, are normal.
The brain must correctly integrate features such as edges, light
intensity, and color from sensory information to form a complete percept
of an object. If a failure occurs during this process, a percept of an
object is not fully formed and thus it cannot be recognized.
Tasks requiring copying, matching, or drawing simple figures can
distinguish the individuals with apperceptive agnosia because they
cannot perform such tasks.
Associative agnosia is an inability to identify objects even with
apparent perception and knowledge of them. It involves a higher level
of processing than apperceptive agnosia.
Individuals with associative agnosia can copy or match simple figures,
indicating that they can perceive objects correctly. They also display
the knowledge of objects when tested with tactile or verbal information.
However, when tested visually, they cannot name or describe common
objects. This means that there is an impairment in associating the perception of objects with the stored knowledge of them.
Although visual agnosia can be general, there exist many variants
that impair recognition of specific types. These variants of visual
agnosia include prosopagnosia (inability to recognize faces), pure word
blindness (inability to recognize words, often called "agnosic alexia"
or "pure alexia"), agnosias for colors (inability to differentiate
colors), agnosias for the environment (inability to recognize landmarks
or difficulty with spatial layout of an environment, i.e.
topographagnosia) and simultanagnosia (inability to sort out multiple
objects in a visual scene).
Categories and subtypes of visual agnosia
The two main categories of visual agnosia are:
Apperceptive visual agnosia, impaired object recognition. Individuals with apperceptive visual agnosia cannot form a whole percept of visual information.
Associative visual agnosia,
impaired object identification. Individuals with associative agnosia
cannot give a meaning to a formed percept. The percept is created, but
it would have no meaning for individuals who have an associative
agnosia.
Prosopagnosia, an inability to recognize human faces.
Individuals with prosopagnosia know that they are looking at faces, but
cannot recognize people by the sight of their face, even people whom
they know well.
Simultagnosia,
an inability to recognize multiple objects in a scene, including
distinct objects within a spatial layout and distinguishing between
"local" objects and "global" objects, such as being able to see a tree
but not the forest or vice versa.
Topographagnosia, an inability to process the spatial layout of an
environment, including landmark agnosia, difficulty recognizing
buildings and places; difficulty building mental maps of a location or
scene; and/or an inability to discern the orientation between objects in
space.
Pure alexia, an inability to read.
Orientation agnosia: an inability to judge or determine orientation of objects.
Pantomime agnosia: an inability to understand pantomimes (gestures).
It appears that the inferior cortical visual cortex is critical in
recognizing pantomimes.
Patient CK
Background
Patient
C.K. was born in 1961 in England and emigrated to Canada in 1980. In
January 1988, C.K. sustained a head injury from a motor vehicle accident
while out for a jog. Following the accident, C.K. experienced many
cognitive issues, mood swings, poor memory, and temper outbursts. C.K.
also had motor weakness on the left side and a left homonymous
hemianopia. He recovered well, retaining normal intelligence and normal
visual acuity. He was able to complete a master's degree in history,
later working as a manager at a large corporation. Although his recovery
was successful in other areas of cognition, C.K. still struggles to
make sense of the visual world.
Associative visual agnosia
Magnetic
resonance imaging (MRI) showed bilateral thinning of C.K.'s occipital
lobe which resulted in associative visual agnosia.
Patients that have visual agnosia are unable to identify visually
presented objects. They can identify these objects through other
modalities such as touch but if presented visually, they are unable to.
Associative agnosic patients cannot create a detailed representation of
the visual world in their brains, they can only perceive elements of
whole objects. They also cannot form associations between objects or assign meaning to objects.
C.K. makes many mistakes when trying to identify objects. For
example, he called an abacus "skewers on a kebab" and a badminton
racquet a "fencer's mask". A dart was a "feather duster" and a
protractor was mistaken for a "cockpit". Despite this impairment in
visual object recognition, C.K. retained many abilities such as drawing,
visual imagery, and internal imagery. As a native of England, he was
tasked with drawing England, marking London and where he was born. His
accurate drawing of England is just one example of his excellent drawing
abilities.
As aforementioned, C.K. is able to identify parts of objects but
cannot generate a whole representation. It should not be surprising then
that his visual imagery for object size, shape, and color is intact.
For example, when shown a picture of an animal, he can correctly answer
questions such as "are the ears up or down?" and "is the tail long or
short?" He can correctly identify colors, for example that the inside of
a cantaloupe is orange.[19]
Finally, C.K. can generate internal images and perceive these generated
objects. For example, Finke, Pinker, and Farah instructed C.K. to
imagine a scenario where a 'B' is rotated 90 degrees to the left, a
triangle is put below, and the line in the middle is removed. C.K. can
correctly identify this object as a heart by picturing this
transformation in his head.
Evidence for double dissociation between face and object processing
Patient C.K. provided evidence for a double dissociation between face processing and visual object processing. Patients with prosopagnosia
have damage to the Fusiform Face Area (FFA) and are unable to recognize
upright faces. C.K. has no difficulty with face processing and matches
the performance of controls when tasked with identifying upright famous
faces. When shown inverted faces of famous people, C.K. performs
significantly worse than controls. This is because processing inverted
faces involves a piecemeal strategy. C.K.'s performance is compared to
patients with prosopagnosia who are impaired in face processing but
perform well identifying inverted faces. This was the first evidence for
a double dissociation between face and object processing suggesting a
face-specific processing system. In popular culture
In the graphic novel Preacher,
the character Lorie has an extreme version of agnosia resulting from
being born with a single eye. For example, she perceives Arseface, a man
with severe facial deformities, as resembling a young James Dean.
Val Kilmer's character has visual agnosia in the film At First Sight.
In "Folie à Deux", a fifth-season episode of The X-Files,
Mulder succumbs to the same belief as telemarketer Gary Lambert, that
his boss Greg Pincus is a monster who disguises his true appearance by
means of hypnosis.
Scully, although believing this notion preposterous, suggests that what
Mulder describes is analogous to an induced visual agnosia.
The short story "Liking What You See: A Documentary" by Ted Chiang examines the cultural effects of a noninvasive medical procedure that induces a visual agnosia toward physical beauty.
The possible existence of microscopic organisms was discussed for
many centuries before their discovery in the seventeenth century. By the
6th century BC, the Jains of present-day India postulated the existence of tiny organisms called nigodas.
These nigodas are said to be born in clusters; they live everywhere,
including the bodies of plants, animals, and people; and their life
lasts only for a fraction of a second. According to Mahavira, the 24th preacher of Jainism, the humans destroy these nigodas on a massive scale, when they eat, breathe, sit, and move. Many modern Jains assert that Mahavira's teachings presage the existence of microorganisms as discovered by modern science.
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 first-century BC book entitled On Agriculture in which he called the unseen creatures animalia minuta, and warns against locating a homestead near a swamp:
… and because there are bred
certain minute creatures that cannot be seen by the eyes, which float in
the air and enter the body through the mouth and nose and they cause
serious diseases.
Turkish scientist Akshamsaddin mentioned the microbe in his work Maddat ul-Hayat (The Material of Life) about two centuries prior to Antonie van Leeuwenhoek's discovery through experimentation:
It is incorrect to assume that
diseases appear one by one in humans. Disease infects by spreading from
one person to another. This infection occurs through seeds that are so
small they cannot be seen but are alive.
In 1546, Girolamo Fracastoro proposed that epidemicdiseases
were caused by transferable seedlike entities that could transmit
infection by direct or indirect contact, or even without contact over
long distances.
Antonie van Leeuwenhoek is considered to be one of the fathers of microbiology.
He was the first in 1673 to discover and conduct scientific experiments
with microorganisms, using simple single-lensed microscopes of his own
design. Robert Hooke, a contemporary of Leeuwenhoek, also used microscopy to observe microbial life in the form of the fruiting bodies of moulds. In his 1665 book Micrographia, he made drawings of studies, and he coined the term cell.
19th century
Louis Pasteur showed that Spallanzani's findings held even if air could enter through a filter that kept particles out.
Louis Pasteur
(1822–1895) exposed boiled broths to the air, in vessels that contained
a filter to prevent particles from passing through to the growth medium,
and also in vessels without a filter, but with air allowed in via a
curved tube so dust particles would settle and not 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 refuted the theory of spontaneous generation and supported the germ theory of disease.
In 1876, Robert Koch (1843–1910) established that microorganisms can cause disease. He found that the blood of cattle that 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.
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.
The discovery of microorganisms such as Euglena that did not fit into either the animal or plant kingdoms, since they were photosynthetic like plants, but motile like animals, led to the naming of a third kingdom in the 1860s. In 1860 John Hogg called this the Protoctista, and in 1866 Ernst Haeckel named it the Protista.
The work of Pasteur and Koch did not accurately reflect the true
diversity of the microbial world because of their exclusive focus on
microorganisms having direct medical relevance. It was not until the
work of Martinus Beijerinck and Sergei Winogradsky late in the nineteenth century that the true breadth of microbiology was revealed. Beijerinck made two major contributions to microbiology: the discovery of viruses and the development of enrichment culture techniques. While his work on the tobacco mosaic virus
established the basic principles of virology, it was his development of
enrichment culturing that had the most immediate impact on microbiology
by allowing for the cultivation of a wide range of microbes with wildly
different physiologies. Winogradsky was the first to develop the
concept of chemolithotrophy and to thereby reveal the essential role played by microorganisms in geochemical processes. He was responsible for the first isolation and description of both nitrifying and nitrogen-fixing bacteria. French-Canadian microbiologist Felix d'Herelle co-discovered bacteriophages and was one of the earliest applied microbiologists.
Classification and structure
Microorganisms can be found almost anywhere on Earth. Bacteria and archaea are almost always microscopic, while a number of eukaryotes are also microscopic, including most protists, some fungi, as well as some micro-animals and plants. Viruses are generally regarded as not living and therefore not considered to be microorganisms, although a subfield of microbiology is virology, the study of viruses.
A possible transitional form of microorganism between a
prokaryote and a eukaryote was discovered in 2012 by Japanese
scientists. Parakaryon myojinensis
is a unique microorganism larger than a typical prokaryote, but with
nuclear material enclosed in a membrane as in a eukaryote, and the
presence of endosymbionts. This is seen to be the first plausible
evolutionary form of microorganism, showing a stage of development from
the prokaryote to the eukaryote.
Archaea are prokaryotic unicellular organisms, and form the first domain of life in Carl Woese's three-domain system. A prokaryote is defined as having no cell nucleus or other membrane bound-organelle.
Archaea share this defining feature with the bacteria with which they
were once grouped. In 1990 the microbiologist Woese proposed the
three-domain system that divided living things into bacteria, archaea
and eukaryotes, and thereby split the prokaryote domain.
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. Archaea were originally described as extremophiles living in extreme environments, such as hot springs, but have since been found in all types of habitats. Only now are scientists beginning to realize how common archaea are in the environment, with Thermoproteota
(formerly Crenarchaeota) being the most common form of life in the
ocean, dominating ecosystems below 150 metres (490 ft) in depth.[45][46] These organisms are also common in soil and play a vital role in ammonia oxidation.
The combined domains of archaea and bacteria make up the most diverse and abundant group of organisms on Earth and inhabit practically all environments where the temperature is below +140 °C (284 °F). They are found in water, soil, air, as the microbiome of an organism, hot springs and even deep beneath the Earth's crust in rocks. The number of prokaryotes is estimated to be around five nonillion, or 5 × 1030, accounting for at least half the biomass on Earth.
The biodiversity of the prokaryotes is unknown, but may be very
large. A May 2016 estimate, based on laws of scaling from known numbers
of species against the size of organism, gives an estimate of perhaps
1 trillion species on the planet, of which most would be microorganisms.
Currently, only one-thousandth of one percent of that total have been
described. Archael cells of some species aggregate and transfer DNA from one cell to another through direct contact, particularly under stressful environmental conditions that cause DNA damage.
Like archaea, bacteria are prokaryotic – unicellular, and having no
cell nucleus or other membrane-bound organelle. Bacteria are
microscopic, with a few extremely rare exceptions, such as Thiomargarita namibiensis. Bacteria function and reproduce as individual cells, but they can often aggregate in multicellular colonies. Some species such as myxobacteria can aggregate into complex swarming structures, operating as multicellular groups as part of their life cycle, or form clusters in bacterial colonies such as E.coli.
Their genome is usually a circular bacterial chromosome – 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 have an enclosing cell wall, which provides strength and rigidity to their cells. They reproduce by binary fission or sometimes by budding, but do not undergo meioticsexual reproduction. However, many bacterial species can transfer DNA between individual cells by a horizontal gene transfer process referred to as natural transformation. 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 their
numbers can double as quickly as every 20 minutes.
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.
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.
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. Several algaespecies are multicellular protists, and slime molds have unique life cycles that involve switching between unicellular, colonial, and multicellular forms.
The number of species of protists is unknown since only a small
proportion has been identified. Protist diversity is high in oceans,
deep sea-vents, river sediment and an acidic river, suggesting that many
eukaryotic microbial communities may yet be discovered.
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.
Microorganisms are found in almost every habitat present in nature, including hostile environments such as the North and South poles, deserts, geysers, and rocks. They also include all the marine microorganisms of the oceans and deep sea. Some types of microorganisms have adapted to extreme environments 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,
and it has been suggested that the amount of organisms living below the
Earth's surface is comparable with the amount of life on or above the
surface. 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. 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.
Microorganisms play critical roles in Earth's biogeochemical cycles as they are responsible for decomposition and nitrogen fixation.
Bacteria use regulatory networks that allow them to adapt to almost every environmental niche on earth.
A network of interactions among diverse types of molecules including
DNA, RNA, proteins and metabolites, is utilised by the bacteria to
achieve regulation of gene expression.
In bacteria, the principal function of regulatory networks is to
control the response to environmental changes, for example nutritional
status and environmental stress. A complex organization of networks permits the microorganism to coordinate and integrate multiple environmental signals.
The roots of plants create a narrow region known as the rhizosphere that supports many microorganisms known as the root microbiome.
These microorganisms in the root microbiome are able to interact with each other and surrounding plants through signals and cues. For example, mycorrhizal fungi are able to communicate with the root systems of many plants through chemical signals between both the plant and fungi. This results in a mutualistic symbiosis between the two. However, these signals can be eavesdropped by other microorganisms, such as the soil bacteria, Myxococcus xanthus,
which preys on other bacteria. Eavesdropping, or the interception of
signals from unintended receivers, such as plants and microorganisms,
can lead to large-scale, evolutionary consequences. For example,
signaler-receiver pairs, like plant-microorganism pairs, may lose the
ability to communicate with neighboring populations because of
variability in eavesdroppers. In adapting to avoid local eavesdroppers,
signal divergence could occur and thus, lead to the isolation of plants
and microorganisms from the inability to communicate with other
populations.
Symbiosis
The photosynthetic cyanobacteriumHyella caespitosa (round shapes) with fungal hyphae (translucent threads) in the lichenPyrenocollema halodytes
Microorganisms are useful in producing foods, treating waste water,
creating biofuels and a wide range of chemicals and enzymes. They are
invaluable in research as model organisms. They have been weaponised and sometimes used in warfare and bioterrorism. They are vital to agriculture through their roles in maintaining soil fertility and in decomposing organic matter.
Growth of microorganisms contributes to ripening and flavor. The
flavor and appearance of a particular cheese is due in large part to the
microorganisms associated with it. Lactobacillus Bulgaricus is one of the microbes used in production of dairy products
Alcoholic beverages
yeast is used to convert sugar, grape juice, or malt-treated grain
into alcohol. other microorganisms may also be used; a mold converts
starch into sugar to make the Japanese rice wine, sake. Acetobacter Aceti a kind of bacterium is used in production of Alcoholic beverages
Vinegar
Certain bacteria are used to convert alcohol into acetic acid, which gives vinegar its acid taste. Acetobacter Aceti is used on production of vinegar, which gives vinegar odor of alcohol and alcoholic taste
Citric acid
Certain fungi are used to make citric acid, a common ingredient of soft drinks and other foods.
Vitamins
Microorganisms are used to make vitamins, including C, B2 , B12.
These depend for their ability to clean up water contaminated with
organic material on microorganisms that can respire dissolved
substances. Respiration may be aerobic, with a well-oxygenated filter
bed such as a slow sand filter. Anaerobic digestion by methanogens generate useful methane gas as a by-product.
In the Middle Ages, as an early example of biological warfare, 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.
Microbes can make nutrients and minerals in the soil available to plants, produce hormones that spur growth, stimulate the plant immune system and trigger or dampen stress responses. In general a more diverse set of soil microbes results in fewer plant diseases and higher yield.
Hygiene is a set of practices to avoid infection or food spoilage by eliminating microorganisms from the surroundings. As microorganisms, in particular bacteria, are found virtually everywhere, harmful microorganisms may be reduced to acceptable levels rather than actually eliminated. In food preparation, microorganisms are reduced by preservation
methods such as cooking, cleanliness of utensils, short storage
periods, or by low temperatures. If complete sterility is needed, as
with surgical equipment, an autoclave is used to kill microorganisms with heat and pressure.
In fiction
Osmosis Jones, a 2001 film, and its show Ozzy & Drix, set in a stylized version of the human body, featured anthropomorphic microorganisms.
War of the Worlds (2005 film), when Alien lifeforms attempt to conquer earth, they are ultimately defeated by a common Microbe to which Humans are immune.
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