Robert Koch

From Wikipedia, the free encyclopedia

Robert Koch
Born	Heinrich Hermann Robert Koch 11 December 1843 Clausthal, Kingdom of Hanover
Died	27 May 1910 (aged 66) Baden-Baden, Grand Duchy of Baden, German Empire
Nationality	German
Alma mater	University of Göttingen
Known for	Discovery bacteriology Koch's postulates of germ theory Isolation of anthrax, tuberculosis and cholera
Awards	ForMemRS (1897) Nobel Prize in Medicine (1905)
Scientific career
Fields	Microbiology
Institutions	Imperial Health Office, Berlin, University of Berlin
Doctoral advisor	Georg Meissner
Other academic advisors	Friedrich Gustav Jakob Henle Karl Ewald Hasse Rudolf Virchow
Influenced	Friedrich Loeffler
Signature

Heinrich Hermann Robert Koch (English: /kɒk, kɒx/; German: [kɔx]; 11 December 1843 – 27 May 1910) was a German physician and microbiologist. As one of the main founders of modern bacteriology, he identified the specific causative agents of tuberculosis, cholera, and anthrax and gave experimental support for the concept of infectious disease, which included experiments on humans and other animals. Koch created and improved laboratory technologies and techniques in the field of microbiology, and made key discoveries in public health. His research led to the creation of Koch's postulates, a series of four generalized principles linking specific microorganisms to specific diseases that remain today the "gold standard" in medical microbiology. For his research on tuberculosis, Koch received the Nobel Prize in Physiology or Medicine in 1905. The Robert Koch Institute is named in his honor.

Early life and education

Koch was born in Clausthal, Germany, on 11 December 1842, to Hermann Koch (1814–1877) and Mathilde Julie Henriette (née Biewend; 1818–1871). Koch excelled in academics from an early age. Before entering school in 1848, he had taught himself how to read and write. He graduated from high school in 1862, having excelled in science and math. At the age of 19, Koch entered the University of Göttingen, studying natural science. However, after three semesters, Koch decided to change his area of study to medicine, as he aspired to be a physician. During his fifth semester of medical school, Jacob Henle, an anatomist who had published a theory of contagion in 1840, asked him to participate in his research project on uterine nerve structure. In his sixth semester, Koch began to conduct research at the Physiological Institute, where he studied the secretion of succinic acid, which is a signaling molecule that is also involved in the metabolism of the mitochondria. This would eventually form the basis of his dissertation. In January 1866, Koch graduated from medical school, earning honors of the highest distinction.

Career

Several years after his graduation in 1866, he worked as a surgeon in the Franco-Prussian War, and following his service, worked as a physician in Wollstein in Prussian Posen (now Wolsztyn, Poland). From 1880 to 1885, Koch held a position as government advisor with the Imperial Department of Health. Koch began conducting research on microorganisms in a laboratory connected to his patient examination room. Koch's early research in this laboratory yielded one of his major contributions to the field of microbiology, as he developed the technique of growing bacteria. Furthermore, he managed to isolate and grow selected pathogens in pure laboratory culture.

From 1885 to 1890, he served as an administrator and professor at Berlin University.

In 1891, Koch relinquished his Professorship and became a director of the Prussian Institute for Infectious Diseases [de] which consisted of a clinical division and beds for the division of clinical research. For this he accepted harsh conditions. The Prussian Ministry of Health insisted after the 1890 scandal with tuberculin, which Koch had discovered and intended as a remedy for tuberculosis, that any of Koch's inventions would unconditionally belong to the government and he would not be compensated. Koch lost the right to apply for patent protection.

Research

Isolating pure bacterial cultures

In an attempt to grow bacteria, Koch began to use solid nutrients such as potato slices. Through these initial experiments, Koch observed individual colonies of identical, pure cells. He found that potato slices were not suitable media for all organisms, and later began to use nutrient solutions with gelatin. However, he soon realized that gelatin, like potato slices, was not the optimal medium for bacterial growth, as it did not remain solid at 37 °C, the ideal temperature for growth of most human pathogens. As suggested to him by Walther and Fanny Hesse, Koch began to utilize agar to grow and isolate pure cultures, because this polysaccharide remains solid at 37 °C, is not degraded by most bacteria, and results in a transparent medium.

Koch's four postulates

During his time as government advisor, Koch published a report, in which he stated the importance of pure cultures in isolating disease-causing organisms and explained the necessary steps to obtain these cultures, methods which are summarized in Koch's four postulates. Koch's discovery of the causative agent of anthrax led to the formation of a generic set of postulates which can be used in the determination of the cause of most infectious diseases. These postulates, which not only outlined a method for linking cause and effect of an infectious disease but also established the significance of laboratory culture of infectious agents, are listed here:

1. The organism must always be present, in every case of the disease.
2. The organism must be isolated from a host containing the disease and grown in pure culture.
3. Samples of the organism taken from pure culture must cause the same disease when inoculated into a healthy, susceptible animal in the laboratory.
4. The organism must be isolated from the inoculated animal and must be identified as the same original organism first isolated from the originally diseased host.

Anthrax

Robert Koch is widely known for his work with anthrax, discovering the causative agent of the fatal disease to be Bacillus anthracis. He discovered the formation of spores in anthrax bacteria, which could remain dormant under specific conditions. However, under optimal conditions, the spores were activated and caused disease. To determine this causative agent, he dry-fixed bacterial cultures onto glass slides, used dyes to stain the cultures, and observed them through a microscope. His work with anthrax is notable in that he was the first to link a specific microorganism with a specific disease, rejecting the idea of spontaneous generation and supporting the germ theory of disease.

Tuberculosis

Statue of Koch in Berlin

 

During his time as the government advisor with the Imperial Department of Health in Berlin in the 1880s, Robert Koch became interested in tuberculosis research. At the time, it was widely believed that tuberculosis was an inherited disease. However, Koch was convinced that the disease was caused by a bacterium and was infectious, and tested his four postulates using guinea pigs. Through these experiments, he found that his experiments with tuberculosis satisfied all four of his postulates. In 1882, he published his findings on tuberculosis, in which he reported the causative agent of the disease to be the slow-growing Mycobacterium tuberculosis. Later, Koch's attempt at developing a drug to treat tuberculosis, tuberculin, led to a scandalous failure: he did not divulge the exact composition, and the claimed treatment success did not materialize; the substance is today used for tuberculosis diagnosis. 

Koch and his relationship to Paul Ehrlich, who developed a mechanism to diagnose TB, were portrayed in the 1940 movie Dr. Ehrlich's Magic Bullet.

Cholera

Koch next turned his attention to cholera, and began to conduct research in Egypt in the hopes of isolating the causative agent of the disease. However, he was not able to complete the task before the epidemic in Egypt ended, and subsequently traveled to India to continue with the study. In 1884 in Bombay state of India, Koch resided and researched at Grant Medical College, (or by some accounts in Kolkata, formerly Calcutta in undivided British India) where he was able to determine the causative agent of cholera, isolating Vibrio cholerae. The bacterium had originally been isolated in 1854 by Italian anatomist Filippo Pacini, but its exact nature and his results were not widely known.

Acquired immunity

Koch observed the phenomenon of acquired immunity. On December 26, 1900, he arrived as part of an expedition to German New Guinea, which was then a protectorate of the German Reich. Koch serially examined the Papuan people, the indigenous inhabitants, and their blood samples and noticed they contained Plasmodium parasites, the cause of malaria, but their bouts of malaria were mild or could not even be noticed, i.e. were subclinical. On the contrary, German settlers and Chinese workers, who had been brought to New Guinea, fell sick immediately. The longer they had stayed in the country, however, the more they too seemed to develop a resistance against it.

Awards and honors

Koch's name as it appears on the LSHTM frieze in Keppel Street, Bloomsbury, London

 

In 1897, Koch was elected a Foreign Member of the Royal Society (ForMemRS). In 1905, Koch won the Nobel Prize in Physiology and Medicine for his work with tuberculosis. In 1906, research on tuberculosis and tropical diseases won him the Prussian Order Pour le Merite and in 1908, the Robert Koch Medal, established to honour the greatest living physicians.

Koch's name is one of twenty-three, from the fields of hygiene and tropical medicine, featured on the frieze of the London School of Hygiene & Tropical Medicine building in Keppel Street, Bloomsbury.

A large marble statue of Koch stands in a small park known as Robert Koch Platz, just north of the Charity Hospital, in the Mitte section of Berlin. His life was the subject of a 1939 German produced motion picture that featured Oscar winning actor Emil Jannings in the title role. On 10 December 2017, Google showed a Doodle in celebration of Koch's birthday.

Personal life

In July 1867, Koch married Emma (Emmy) Adolfine Josephine Fraatz, and the two had a daughter, Gertrude, in 1868. Their marriage ended after 26 years in 1893, and later that same year, he married actress Hedwig Freiberg (1872–1945).

On 9 April 1910, Koch suffered a heart attack and never made a complete recovery. On 27 May, three days after giving a lecture on his tuberculosis research at the Prussian Academy of Sciences, Koch died in Baden-Baden at the age of 66. Following his death, the Institute named its establishment after him in his honour. He was irreligious.

Nitrogen fixation

From Wikipedia, the free encyclopedia

Nitrogen fixation is a process by which nitrogen in the air is converted into ammonia (NH₃) or related nitrogenous compounds. Atmospheric nitrogen, is molecular dinitrogen (N₂), a relatively nonreactive molecule that is metabolically useless to all but a few microorganisms. Biological nitrogen fixation converts N₂ into ammonia, which is metabolized by most organisms. 

Nitrogen fixation is essential to life because fixed inorganic nitrogen compounds are required for the biosynthesis of all nitrogen-containing organic compounds, such as amino acids and proteins, nucleoside triphosphates and nucleic acids. As part of the nitrogen cycle, it is essential for agriculture and the manufacture of fertilizer. It is also, indirectly, relevant to the manufacture of all chemical compounds that contain nitrogen, which includes explosives, most pharmaceuticals, and dyes.

Nitrogen fixation is carried out naturally in the soil by a wide range of microorganisms termed diazotrophs that include bacteria such as Azotobacter, and archaea. Some nitrogen-fixing bacteria have symbiotic relationships with some plant groups, especially legumes. Looser non-symbiotic relationships between diazotrophs and plants are often referred to as associative, as seen in nitrogen fixation on rice roots. Nitrogen fixation also occurs between some termites and fungi. It also occurs naturally in the air by means of NOx production by lightning.

All biological nitrogen fixation is effected by enzymes called nitrogenases. These enzymes contain iron, often with a second metal, usually molybdenum but sometimes vanadium.

Non-biological natural nitrogen fixation

Lightning heats the air around it breaking the bonds of N₂ starting the formation of nitrous acid.

 

Nitrogen can be fixed by lightning converting nitrogen and oxygen into NO
x (nitrogen oxides). NO
x may react with water to make nitrous acid or nitric acid, which seeps into the soil, where it makes nitrate, which is of use to growing plants. Nitrogen in the atmosphere is highly stable and nonreactive due to there being a triple bond between atoms in the N₂ molecule. Lightning produces enough energy and heat to break this bond allowing the nitrogen atoms to react with oxygen forming NO_x. This itself cannot be used by plants, but as this molecule cools it reacts with more oxygen to form NO₂. This molecule in turn reacts with water to produce HNO₃ (nitric acid) which is usable by plants.

Biological nitrogen fixation

Schematic representation of the nitrogen cycle. Abiotic nitrogen fixation has been omitted.

 

Biological nitrogen fixation was discovered by the German agronomist Hermann Hellriegel and Dutch microbiologist Martinus Beijerinck. Biological nitrogen fixation (BNF) occurs when atmospheric nitrogen is converted to ammonia by an enzyme called a nitrogenase.^[1] The overall reaction for BNF is: 

N₂ + 16ATP + 8e- + 8H+ -> 2NH3 + H2 + 16ADP + 16P_i

The process is coupled to the hydrolysis of 16 equivalents of ATP and is accompanied by the co-formation of one equivalent of H₂. The conversion of N₂ into ammonia occurs at a metal cluster called FeMoco, an abbreviation for the iron-molybdenum cofactor. The mechanism proceeds via a series of protonation and reduction steps wherein the FeMoco active site hydrogenates the N₂ substrate. In free-living diazotrophs, the nitrogenase-generated ammonia is assimilated into glutamate through the glutamine synthetase/glutamate synthase pathway.The microbial nif genes required for nitrogen fixation are widely distributed in diverse environments.

Nitrogenases are rapidly degraded by oxygen. For this reason, many bacteria cease production of the enzyme in the presence of oxygen. Many nitrogen-fixing organisms exist only in anaerobic conditions, respiring to draw down oxygen levels, or binding the oxygen with a protein such as leghemoglobin.

Microorganisms that fix nitrogen

Diazotrophs are widespread within domain Bacteria including cyanobacteria (e.g. the highly significant Trichodesmium and Cyanothece), as well as green sulfur bacteria, Azotobacteraceae, rhizobia and Frankia. Several obligately anaerobic bacteria fix nitrogen including many (but not all) Clostridium spp. Some Archaea also fix nitrogen, including several methanogenic taxa, which are significant contributors to nitrogen fixation in oxygen-deficient soils.

Cyanobacteria inhabit nearly all illuminated environments on Earth and play key roles in the carbon and nitrogen cycle of the biosphere. In general, cyanobacteria can use various inorganic and organic sources of combined nitrogen, like nitrate, nitrite, ammonium, urea, or some amino acids. Several cyanobacterial strains are also capable of diazotrophic growth, an ability that may have been present in their last common ancestor in the Archean eon. Nitrogen fixation by cyanobacteria in coral reefs can fix twice as much nitrogen as on land—around 1.8 kg of nitrogen is fixed per hectare per day (around 660 kg/ha/year). The colonial marine cyanobacterium Trichodesmium is thought to fix nitrogen on such a scale that it accounts for almost half of the nitrogen fixation in marine systems globally.

Root nodule symbioses

The legume family

Plants that contribute to nitrogen fixation include those of the legume family – Fabaceae – with taxa such as kudzu, clovers, soybeans, alfalfa, lupines, peanuts, and rooibos. They contain symbiotic bacteria called rhizobia within nodules in their root systems, producing nitrogen compounds that help the plant to grow and compete with other plants. When the plant dies, the fixed nitrogen is released, making it available to other plants; this helps to fertilize the soil. The great majority of legumes have this association, but a few genera (e.g., Styphnolobium) do not. In many traditional and organic farming practices, fields are rotated through various types of crops, which usually include one consisting mainly or entirely of clover or buckwheat (non-legume family Polygonaceae), often referred to as "green manure".

The efficiency of nitrogen fixation in soil is dependent on many factors, including the legume as well as air and soil conditions. For example, nitrogen fixation by red clover can range from 50 - 200 lb./acre depending on these variables.

Inga alley farming relies on the leguminous genus Inga, a small tropical, tough-leaved, nitrogen-fixing tree.

Non-leguminous

A sectioned alder tree root nodule

 

Although by far the majority of plant species able to form nitrogen-fixing root nodules are in the legume family Fabaceae, there are exceptions:

• Parasponia, a tropical genus in the Cannabaceae also able to interact with rhizobia and form nitrogen-fixing nodules
• Actinorhizal plants such as alder and bayberry can also form nitrogen-fixing nodules, thanks to a symbiotic association with Frankia bacteria. These plants belong to 25 genera distributed among 8 plant families.

The ability to fix nitrogen is present in the families listed below. They belong to the orders Cucurbitales, Fagales, and Rosales, which together with the Fabales form a clade of eurosids. The ability to fix nitrogen is not universally present in these families. For example, of 122 genera in the Rosaceae, only 4 genera are capable of fixing nitrogen. Fabales were the first lineage to branch off this nitrogen-fixing clade; thus, the ability to fix nitrogen may be plesiomorphic and subsequently lost in most descendants of the original nitrogen-fixing plant; however, it may be that the basic genetic and physiological requirements were present in an incipient state in the most recent common ancestors of all these plants, but only evolved to full function in some of them.

There are also several nitrogen-fixing symbiotic associations that involve cyanobacteria (such as Nostoc):

• Some lichens such as Lobaria and Peltigera
• Mosquito fern (Azolla species)
• Cycads
• Gunnera
• Blasia (liverwort)
• Hornworts

Endosymbiosis in diatoms

Rhopalodia gibba, a diatom alga, is a eukaryote with cyanobacterial N₂-fixing endosymbiont organelles. The spheroid bodies reside in the cytoplasm of the diatoms and are inseparable from their hosts.

Industrial nitrogen fixation

The possibility that atmospheric nitrogen reacts with certain chemicals was first observed by Desfosses in 1828. He observed that mixtures of alkali metal oxides and carbon react at high temperatures with nitrogen. With the use of barium carbonate as starting material the first commercially used process became available in the 1860s developed by Margueritte and Sourdeval. The resulting barium cyanide could be reacted with steam yielding ammonia. In 1898 Adolph Frank and Nikodem Caro decoupled the process and first produced calcium carbide and in a subsequent step reacted it with nitrogen to calcium cyanamide. The Ostwald process for the production of nitric acid was discovered in 1902. Frank-Caro process and Ostwald process dominated the industrial fixation of nitrogen until the discovery of the Haber process in 1909. Prior to 1900, Nikola Tesla also experimented with the industrial fixation of nitrogen "by using currents of extremely high frequency or rate of vibration".

Haber process

Equipment for a study of nitrogen fixation by alpha rays (Fixed Nitrogen Research Laboratory, 1926)

 

Artificial fertilizer production is now the largest source of human-produced fixed nitrogen in the Earth's ecosystem. Ammonia is a required precursor to fertilizers, explosives, and other products. The most common method is the Haber process. The Haber process requires high pressures (around 200 atm) and high temperatures (at least 400 °C), routine conditions for industrial catalysis. This highly efficient process uses natural gas as a hydrogen source and air as a nitrogen source.

Much research has been conducted on the discovery of catalysts for nitrogen fixation, often with the goal of reducing the energy required for this conversion. However, such research has thus far failed to even approach the efficiency and ease of the Haber process. Many compounds react with atmospheric nitrogen to give dinitrogen complexes. The first dinitrogen complex to be reported was Ru(NH₃)₅(N₂)²⁺.

Ambient nitrogen reduction

Catalytic chemical nitrogen fixation at ambient conditions is an ongoing scientific endeavor. Guided by the example of nitrogenase, this area of homogeneous catalysis is ongoing, with particular emphasis on hydrogenation to give ammonia.

Metallic lithium has long been known for burning in an atmosphere of nitrogen and then converting to lithium nitride. Hydrolysis of the resulting nitride gives ammonia. In a related process, trimethylsilyl chloride, lithium, and nitrogen react in the presence of a catalyst to give tris(trimethylsilyl)amine. Tris(trimethylsilyl)amine can then be used for reaction with α,δ,ω-triketones to give tricyclic pyrroles. Processes involving lithium metal are however of no practical interest since they are non-catalytic and re-reducing the Li⁺ ion residue is difficult. 

Beginning in the 1960s several homogeneous systems were identified that convert nitrogen to ammonia, sometimes even catalytically but often operating via ill-defined mechanisms. The original discovery is described in an early review:

"Vol'pin and co-workers, using a non-protic Lewis acid, aluminium tribromide, were able to demonstrate the truly catalytic effect of titanium by treating dinitrogen with a mixture of titanium tetrachloride, metallic aluminium, and aluminium tribromide at 50 °C, either in the absence or in the presence of a solvent, e.g. benzene. As much as 200 mol of ammonia per mol of TiCl₄ was obtained after hydrolysis.…"

Synthetic nitrogen reduction

 

The quest for well defined intermediates led to the characterization of many transition metal dinitrogen complexes. Few of these well-defined complexes function catalytically, their behavior illuminated likely stages in nitrogen fixation. Fruitful early studies focused on M(N₂)₂(dppe)₂ (M = Mo, W), which protonates to give intermediates with ligand M=N−NH₂. In 1995, a molybdenum(III) amido complex was discovered that cleaved N₂ to give the corresponding molybdenum(VI) nitride. This and related terminal nitrido complexes have been used to make nitriles.

In 2003 a molybdenum amido complex was found to catalyze the reduction of N₂, albeit with few turnovers. In these systems, like the biological one, hydrogen is provided to the substrate heterolytically, by means of protons and a strong reducing agent rather than with H₂ itself.

In 2011, yet another molybdenum-based system was discovered, but with a diphosphorus pincer ligand. Photolytic nitrogen splitting is also considered.

Braunschweig's 2018 dinitrogen activation with a transient borylene species

 

Nitrogen fixation at a p-block element was published in 2018 whereby one molecule of dinitrogen is bound by two transient Lewis-base-stabilized borylene species. The resulting dianion was subsequently oxidized to a neutral compound, and reduced using water.

Photochemical and Electrochemical Nitrogen Reduction

With the help of catalysis and energy provided by electricity and light, NH3 can be producted directly from Nitrogen and water at ambient temperature and pressure.

Origin myth

From Wikipedia, the free encyclopedia

An origin myth is a myth that purports to describe the origin of some feature of the natural or social world. One type of origin myth is the cosmogonic myth, which describes the creation of the world. However, many cultures have stories set after the cosmogonic myth, which describe the origin of natural phenomena and human institutions within a preexisting universe. 

In Graeco-Roman scholarship, the terms etiological myth and aition (from the Ancient Greek αἴτιον, "cause") are sometimes used for a myth that explains an origin, particularly how an object or custom came into existence.

Nature of origin myths

Every origin myth is a tale of creation: origin myths describe how some new reality came into existence. In many cases, origin myths also justify the established order by explaining that it was established by sacred forces (see section on "Social function" below). The distinction between cosmogonic myths and origin myths is not clear-cut. A myth about the origin of some part of the world necessarily presupposes the existence of the world—which, for many cultures, presupposes a cosmogonic myth. In this sense, one can think of origin myths as building upon and extending their cultures' cosmogonic myths. In fact, in traditional cultures, the recitation of an origin myth is often prefaced with the recitation of the cosmogonic myth.

In some academic circles, the term "myth" properly refers only to origin and cosmogonic myths. For example, many folklorists reserve the label "myth" for stories about creation. Traditional stories that do not focus on origins fall into the categories of "legend" and "folk tale", which folklorists distinguish from myth.

According to historian Mircea Eliade, for many traditional cultures, nearly every sacred story qualifies as an origin myth. Traditional humans tend to model their behavior after sacred events, seeing their life as an "eternal return" to the mythical age. Because of this conception, nearly every sacred story describes events that established a new paradigm for human behavior, and thus nearly every sacred story is a story about a creation.

Social function

An origin myth often functions to justify the current state of affairs. In traditional cultures, the entities and forces described in origin myths are often considered sacred. Thus, by attributing the state of the universe to the actions of these entities and forces, origin myths give the current order an aura of sacredness: "Myths reveal that the World, man, and life have a supernatural origin and history, and that this history is significant, precious, and exemplary." Many cultures instil the expectation that people take mythical gods and heroes as their role models, imitating their deeds and upholding the customs they established:

When the missionary and ethnologist C. Strehlow asked the Australian Arunta why they performed certain ceremonies, the answer was always: "Because the ancestors so commanded it." The Kai of New Guinea refused to change their way of living and working, and they explained: "It was thus that the Nemu (the Mythical Ancestors) did, and we do likewise." Asked the reason for a particular detail in a ceremony, a Navaho chanter answered: "Because the Holy People did it that way in the first place." We find exactly the same justification in the prayer that accompanies a primitive Tibetan ritual: "As it has been handed down from the beginning of the earth’s creation, so must we sacrifice. … As our ancestors in ancient times did—so do we now."

Founding myths unite people and tend to include mystical events along the way to make "founders" seem more desirable and heroic. Ruling monarchs or aristocracies may allege descent from mythical founders/gods/heroes in order to legitimate their control. For example: Julius Caesar and his relatives claimed Aeneas (and through Aeneas, the goddess Venus) as an ancestor.

Founding myth

The Dispute of Minerva and Neptune (c. 1689 or 1706) by René-Antoine Houasse, depicting the founding myth of Athens

 

A "founding myth" or etiological myth (Greek aition) explains either:

• The origins of a ritual or of the founding of a city
• The ethnogenesis of a group presented as a genealogy with a founding father and thus of a nation (natio, "birth")
• The spiritual origins of a belief, philosophy, discipline, or idea - presented as a narrative

A founding myth may serve as the primary exemplum, as the myth of Ixion was the original Greek example of a murderer rendered unclean by his crime, who needed cleansing (catharsis) of his impurity. 

Founding myths feature prominently in Greek mythology. "Ancient Greek rituals were bound to prominent local groups and hence to specific localities", Walter Burkert has observed. "i.e. the sanctuaries and altars that had been set up for all time". Thus Greek and Hebrew founding myths established the special relationship between a deity and local people, who traced their origins from a hero and authenticated their ancestral rights through the founding myth. Greek founding myths often embody a justification for the ancient overturning of an older, archaic order, reformulating a historical event anchored in the social and natural world to valorize current community practices, creating symbolic narratives of "collective importance" enriched with metaphor in order to account for traditional chronologies, and constructing an etiology considered to be plausible among those with a cultural investment.

In the Greek view, the mythic past had deep roots in historic time, its legends treated as facts, as Carlo Brillante has noted, its heroic protagonists seen as links between the "age of origins" and the mortal, everyday world that succeeded it. A modern translator of Apollonius' Argonautica has noted, of the many aitia embedded as digressions in that Hellenistic epic, that "crucial to social stability had to be the function of myths in providing explanations, authorization or empowerment for the present in terms of origins: this could apply, not only to foundations or charter myths and genealogical trees (thus supporting family or territorial claims) but also to personal moral choices." In the period after Alexander the Great expanded the Hellenistic world, Greek poetry—Callimachus wrote a whole work simply titled Aitia—is replete with founding myths. Simon Goldhill employs the metaphor of sedimentation in describing Apollonius' laying down of layers "where each object, cult, ritual, name, may be opened... into a narrative of origination, and where each narrative, each event, may lead to a cult, ritual, name, monument."

A notable example is the myth of the foundation of Rome—the tale of Romulus and Remus, which Virgil in turn broadens in his Aeneid with the odyssey of Aeneas and his razing of Lavinium, and his son Iulus's later relocation and rule of the famous twins' birthplace Alba Longa, and their descent from his royal line, thus fitting perfectly into the already established canon of events. Similarly, the Old Testament's story of the Exodus serves as the founding myth for the community of Israel, telling how God delivered the Israelites from slavery and how they therefore belonged to him through the Covenant of Mount Sinai.

During the Middle Ages, founding myths of the medieval communes of northern Italy manifested the increasing self-confidence of the urban population and the will to find a Roman origin, however tenuous and legendary. In 13th-century Padua, when each commune looked for a Roman founder - and if one was not available, invented one—a legend had been current in the city, attributing its foundation to the Trojan Antenor.

Larger-than-life heroes continue to bolster the origin-myths of many newer nations and societies. In modern-era colonial contexts, waves of individuals and groups come to the fore in popular history as shaping and exemplifying the ideals of a group: explorers followed by conquerors followed by developers/exploiters. Note for example the conquistadors of the Iberian empires, the bandeirantes in Brazil, the coureurs des bois in Canada, the Cossacks and the promyshlenniki in Siberia and in Alaska, the bands of pioneers in the central and western United States, and the voortrekkers in Southern Africa.

Foundation stories

Foundational stories are accounts of the development of cities and nations. A foundational story represents the view that the creation of the city is a human achievement. Human control and the removal of wild, uncontrolled nature is underlined. There are two versions of foundational stories: civilization story and degradation story.

Civilization stories take a view of nature as dangerous and wild. The development of the city is seen as a successful distancing of humans from nature. Nature is locked out, and humans take pride in doing so successfully. In 1984 the geographer Yi-Fu Tuan suggested ranking cities according to their distance to natural rhythms and cycles.

Degradation stories (also called pollution stories) take a different stance. The city is seen as spoiling the landscape of the ecological relations that existed before the city was established. There is a sense of guilt for degrading the intact system of nature. In degradation stories true nature only exists outside the city.

Nitrification

From Wikipedia, the free encyclopedia

Nitrogen cycle

 

Nitrification is the biological oxidation of ammonia or ammonium to nitrite followed by the oxidation of the nitrite to nitrate. The transformation of ammonia to nitrite is usually the rate limiting step of nitrification. Nitrification is an important step in the nitrogen cycle in soil. Nitrification is an aerobic process performed by small groups of autotrophic bacteria and archaea. This process was discovered by the Russian microbiologist Sergei Winogradsky.

Microbiology and ecology

The oxidation of ammonia into nitrite is performed by two groups of organisms, ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). AOB can be found among the β-proteobacteria and gammaproteobacteria. Currently, two AOA, Nitrosopumilus maritimus and Nitrososphaera viennensis, have been isolated and described. In soils the most studied AOB belong to the genera Nitrosomonas and Nitrosococcus. Although in soils ammonia oxidation occurs by both AOB and AOA, AOA dominate in both soils and marine environments, suggesting that Thaumarchaeota may be greater contributors to ammonia oxidation in these environments.

The second step (oxidation of nitrite into nitrate) is done (mainly) by bacteria of the genus Nitrobacter and Nitrospira. Both steps are producing energy to be coupled to ATP synthesis. Nitrifying organisms are chemoautotrophs, and use carbon dioxide as their carbon source for growth. Some AOB possess the enzyme, urease, which catalyzes the conversion of the urea molecule to two ammonia molecules and one carbon dioxide molecule. Nitrosomonas europaea, as well as populations of soil-dwelling AOB, have been shown to assimilate the carbon dioxide released by the reaction to make biomass via the Calvin Cycle, and harvest energy by oxidizing ammonia (the other product of urease) to nitrite. This feature may explain enhanced growth of AOB in the presence of urea in acidic environments.

In most environments, organisms are present that will complete both steps of the process, yielding nitrate as the final product. However, it is possible to design systems in which nitrite is formed (the Sharon process). 

Nitrification is important in agricultural systems, where fertilizer is often applied as ammonia. Conversion of this ammonia to nitrate increases nitrogen leaching because nitrate is more water-soluble than ammonia.

Nitrification also plays an important role in the removal of nitrogen from municipal wastewater. The conventional removal is nitrification, followed by denitrification. The cost of this process resides mainly in aeration (bringing oxygen in the reactor) and the addition of an external carbon source (e.g., methanol) for the denitrification. 

Nitrification can also occur in drinking water. In distribution systems where chloramines are used as the secondary disinfectant, the presence of free ammonia can act as a substrate for ammonia-oxidizing microorganisms. The associated reactions can lead to the depletion of the disinfectant residual in the system. The addition of chlorite ion to chloramine-treated water has been shown to control nitrification.

Together with ammonification, nitrification forms a mineralization process that refers to the complete decomposition of organic material, with the release of available nitrogen compounds. This replenishes the nitrogen cycle.

Chemistry and enzymology

Nitrification is a process of nitrogen compound oxidation (effectively, loss of electrons from the nitrogen atom to the oxygen atoms), and is catalyzed step-wise by a series of enzymes.

${\displaystyle {\ce {2NH4+ + 3O2 -> 2NO2- + 4H+ + 2H2O}}}$ (Nitrosomonas, Comammox)

${\displaystyle {\ce {2NO2- + O2 -> 2NO3-}}}$ (Nitrobacter, Nitrospira, Comammox)

OR

${\displaystyle {\ce {NH3 + O2 -> NO2- + 3H+ + 2e-}}}$

${\displaystyle {\ce {NO2- + H2O -> NO3- + 2H+ + 2e-}}}$

In Nitrosomonas europaea, the first step of oxidation (ammonia to hydroxylamine) is carried out by the enzyme ammonia monooxygenase (AMO).

${\displaystyle {\ce {NH3 + O2 + 2H+ -> NH2OH + H2O}}}$

The second step (hydroxylamine to nitrite) is carried out step-wise by two different enzymes. Hydroxylamine oxidoreductase (HAO), converts hydroxylamine to nitric oxide.

${\displaystyle {\ce {NH2OH -> NO + 3H+ + 3e-}}}$

Another as-of-yet unknown enzyme that converts nitric oxide to nitrite. 

The third step (nitrite to nitrate) is completed in a different organism.

${\displaystyle {\ce {{nitrite}+acceptor<=>{nitrate}+reduced\ acceptor}}}$

Nitrification in the marine environment

In the marine environment, nitrogen is often the limiting nutrient, so the nitrogen cycle in the ocean is of particular interest. The nitrification step of the cycle is of particular interest in the ocean because it creates nitrate, the primary form of nitrogen responsible for "new" production. Furthermore, as the ocean becomes enriched in anthropogenic CO₂, the resulting decrease in pH could lead to decreasing rates of nitrification. Nitrification could potentially become a "bottleneck" in the nitrogen cycle.

Nitrification, as stated above, is formally a two-step process; in the first step ammonia is oxidized to nitrite, and in the second step nitrite is oxidized to nitrate. Different microbes are responsible for each step in the marine environment. Several groups of ammonia-oxidizing bacteria (AOB) are known in the marine environment, including Nitrosomonas, Nitrospira, and Nitrosococcus. All contain the functional gene ammonia monooxygenase (AMO) which, as its name implies, is responsible for the oxidation of ammonia. More recent metagenomic studies have revealed that some Thaumarchaeota (formerly Crenarchaeota) possess AMO. Thaumarchaeotes are abundant in the ocean and some species have a 200 times greater affinity for ammonia than AOB, leading researchers to challenge the previous belief that AOB are primarily responsible for nitrification in the ocean. Furthermore, though nitrification is classically thought to be vertically separated from primary production because the oxidation of nitrogen by bacteria is inhibited by light, nitrification by AOA does not appear to be light inhibited, meaning that nitrification is occurring throughout the water column, challenging the classical definitions of "new" and "recycled" production.

In the second step, nitrite is oxidized to nitrate. In the oceans, this step is not as well understood as the first, but the bacteria Nitrospina and Nitrobacter are known to carry out this step in the sea.

Soil conditions controlling nitrification rates

• Substrate availability (presence of NH₄⁺)
• Aeration (availability of O₂)
• Well-drained soils with 60% soil moisture
• pH (near neutral)
• Temperature (best 20-30 °C) => Nitrification is seasonal, affected by land use practices

Inhibitors of nitrification

Nitrification inhibitors are chemical compounds that slow the nitrification of ammonia, ammonium-containing, or urea-containing fertilizers, which are applied to soil as fertilizers. These inhibitors can help reduce losses of nitrogen in soil that would otherwise be used by crops. Nitrification inhibitors are used widely, being added to approximately 50% of the fall-applied anhydrous ammonia in states in the U.S., like Illinois. They are usually effective in increasing recovery of nitrogen fertilizer in row crops, but the level of effectiveness depends on external conditions and their benefits are most likely to be seen at less than optimal nitrogen rates.

The environmental concerns of nitrification also contribute to interest in the use of nitrification inhibitors: the primary product, nitrate, leaches into groundwater, producing acute toxicity in multiple species of wildlife and contributing to the eutrophication of standing water. Some inhibitors of nitrification also inhibit the production of methane, a greenhouse gas. 

The inhibition of the nitrification process is primarily facilitated by the selection and inhibition/destruction of the bacteria that oxidize ammonia compounds. A multitude of compounds that inhibit nitrification, which can be divided into the following areas: the active site of ammonia monooxygenase (AMO), mechanistic inhibitors, and the process of N-heterocyclic compounds. The process for the latter of the three is not yet widely understood, but is prominent. The presence of AMO has been confirmed on many substrates that are nitrogen inhibitors such as dicyandiamide, ammonium thiosulfate, and nitrapyrin.

The conversion of ammonia to hydroxylamine is the first step in nitrification, where AH₂ represents a range of potential electron donors.

NH₃ + AH₂ + O₂ → NH₂OH + A + H₂O

This reaction is catalyzed by AMO. Inhibitors of this reaction bind to the active site on AMO and prevent or delay the process. The process of oxidation of ammonia by AMO is regarded with importance due to the fact that other processes require the co-oxidation of NH₃ for a supply of reducing equivalents. This is usually supplied by the compound hydroxylamine oxidoreductase (HAO) which catalyzes the reaction:

NH₂OH + H₂O → NO₂⁻ + 5 H⁺ + 4 e⁻

The mechanism of inhibition is complicated by this requirement. Kinetic analysis of the inhibition of NH₃ oxidation has shown that the substrates of AMO have shown kinetics ranging from competitive to noncompetitive. The binding and oxidation can occur on two different locations on AMO: in competitive substrates, binding and oxidation occurs at the NH₃ site, while in noncompetitive substrates it occurs at another site. 

Mechanism based inhibitors can be defined as compounds that interrupt the normal reaction catalyzed by an enzyme. This method occurs by the inactivation of the enzyme via covalent modification of the product, which ultimately inhibits nitrification. Through the process, AMO is deactivated and one or more proteins is covalently bonded to the final product. This is found to be most prominent in a broad range of sulfur or acetylenic compounds. 

Sulfur-containing compounds, including ammonium thiosulfate (a popular inhibitor) are found to operate by producing volatile compounds with strong inhibitory effects such as carbon disulfide and thiourea. 

In particular, thiophosphoryl triamide has been a notable addition where it has the dual purpose of inhibiting both the production of urease and nitrification. In a study of inhibitory effects of oxidation by the bacteria Nitrosomonas europaea, the use of thioethers resulted in the oxidation of these compounds to sulfoxides, where the S atom is the primary site of oxidation by AMO. This is most strongly correlated to the field of competitive inhibition. 

Examples of N-heterocyclic molecules.

 

N-heterocyclic compounds are also highly effective nitrification inhibitors and are often classified by their ring structure. The mode of action for these compounds is not well understood: while nitrapyrin, a widely used inhibitor and substrate of AMO, is a weak mechanism-based inhibitor of said enzyme, the effects of said mechanism are unable to correlate directly with the compound’s ability to inhibit nitrification. It is suggested that nitrapyrin acts against the monooxygenase enzyme within the bacteria, preventing growth and CH₄/NH₄ oxidation. Compounds containing two or three adjacent ring N atoms (pyridazine, pyrazole, indazole) tend to have a significantly higher inhibition effect than compounds containing non-adjacent N atoms or singular ring N atoms (pyridine, pyrrole). This suggests that the presence of ring N atoms is directly correlated with the inhibition effect of this class of compounds.

Methane inhibition

Some enzymatic nitrification inhibitors, such as urease, can also inhibit the production of methane in methanotrophic bacteria. AMO shows similar kinetic turnover rates to methane monooxygenase (MMO) found in methanotrophs, indicating that MMO is a similar catalyst to AMO for the purpose of methane oxidation. Furthermore, methanotrophic bacteria share many similarities to NH
3 oxidizers such as Nitrosomonas. The inhibitor profile of particulate forms of MMO (pMMO) shows similarity to the profile of AMO, leading to similarity in properties between MMO in methanotrophs and AMO in autotrophs.

Environmental concerns

Nitrification inhibitors are also of interest from an environmental standpoint because of the production of nitrates and nitrous oxide from the process of nitrification. Nitrous oxide (N₂O), although its atmospheric concentration is much lower than that of CO_2, has a global warming potential of about 300 times greater than carbon dioxide and contributes 6% of planetary warming due to greenhouse gases. This compound is also notable for catalyzing the breakup of ozone in the stratosphere. Nitrates, a toxic compound for wildlife and livestock and a product of nitrification, are also of concern. 

Soil, consisting of polyanionic clays and silicates, generally has a net anionic charge. Consequently, ammonium (NH₄⁺) binds tightly to the soil but nitrate ions (NO₃⁻) do not. Because nitrate is more mobile, it leaches into groundwater supplies through agricultural runoff. Wildlife such as amphibians, freshwater fish, and insects are sensitive to nitrate levels, and have been known to cause death and developmental anomalies in affected species. In addition, because they easily leach into groundwater, contributing to eutrophication, a process in which large algal blooms reduce oxygen levels in bodies of water and lead to death in oxygen-consuming creatures due to anoxia. Nitrification is also thought to contribute to the formation of photochemical smog, ground level ozone, acid rain, changes in species diversity, and other undesirable processes. In addition, nitrification inhibitors have also been shown to suppress the oxidation of methane (CH₄), a potent greenhouse gas, to CO₂. Both nitrapyrin and acetylene are shown to be especially strong suppressors of both processes, although the modes of action distinguishing them are unclear.