The Nitrogen Cycle

The complex ecology of the earth is epitomized in the circuitous cycle of nitrogen from the atmosphere to the soils and waters and creatures of the earth and back again.  Nitrogen as the diatomic gas N2 comprises 79 percent of the atmosphere and therefore 79 percent of every inhaled breath taken by every living thing. The irony of nitrogen is that every exhaled breath is also 79 percent nitrogen; it is essentially inertly unreactive as a gas.  However, the element nitrogen is vital to life. It is a key constituent of the amino acids (amines are nitrogen-hydrogen NH2 containing compounds) that build protein molecules that do everything from transporting oxygen in the blood (hemoglobin) to regulating glucose metabolism (insulin) and for the constituent nucleotides of DNA. Nitrogen makes up about 2.5 percent of the human body, the fourth most abundant element after carbon, hydrogen and oxygen. None of the nitrogen in our bodies comes directly from the air we breathe. It is provided by the nitrogen cycle. The decay of organic matter consequent to the death of organisms yields the bulk of usable nitrogen; a global recycling carried out by several types of soil bacteria that decompose proteins into ammonia (NH3) that is subsequently converted to nitrite (NO2) and finally, the familiar nitrate (NO3).  The first part of the cycle is appropriately called ammonification ant the second part nitrification. The bacteria that carry out this crucial conversion do so for the energy released by the oxidation of ammonia. There are many losses of nitrogen in the recycling of extant nitrogen from the death and decay of living things. Among these are the harvesting of crops, soil erosion, and the return of the various monatomic nitrogen compounds back to the atmosphere in the form of the diatomic nitrogen gas; this process is called denitrification. The replenishment of lost nitrogen has been the bane of civilization since the advent of agricultural and pastoral societies supplanted the hunter-gatherers about 10,000 years ago and humans began to deplete the soils of nitrogen to continually grow and harvest food.

The nitrogen cycle is sustained by the decomposition of the gas N2 into elemental atomic nitrogen N so that it can be used in chemical compounds. The decomposition of the nitrogen gas into elemental nitrogen is called nitrogen fixation. There are three ways for this to occur; all require energy.  The first is atmospheric, comprising about 5 percent of elemental nitrogen production. Lightning, the raw energy of nature, courses through and electrifies the air to create elemental nitrogen from the gas; the resultant compounds in the form of nitrates (NO3) fall to earth with the attendant rain. The second source of liberated nitrogen is provided by the telluric engines of nitrogen fixation: bacteria, and their distant cousin archaea; referred to generically as nitrogen-fixing bacteria or diazotrophs. Before the industrial age, atmospheric and nitrogen-fixing bacteria were the only sources of the elemental nitrogen necessary for all living things.   Artificial nitrogen fixation, known as the Haber-Bosch process, was developed in the early 20th Century and is now responsible for about 30 percent of all elemental nitrogen in the form of fertilizers; it is the third source of elemental nitrogen.

The problem with transforming gaseous nitrogen in the form N2 into the monatomic N is that the bond between the two nitrogen atoms is very strong. In a simplistic sense, atoms join together to form compounds in order to reach a stable low-energy state that occurs when the outmost shell of each atom is filled. The inert gases mark the points on the periodic table where this occurs. Helium with 2 electrons is the first inert gas, neon with 10 electrons is second continuing through argon, krypton, xenon and radon. The quantum energy levels of the electrons around the nucleus of the atom are assigned the principal quantum numbers 1, 2, 3 … or, alternatively K, L, M … (the letters are an artifact of the spectroscopy terminology by which they were first discovered). In each principal quantum level, there are intermediate sublevels that determine the geometric shape of the electron’s possible locations. These are called subshells as they represent different energy levels within the principal quantum level. The ‘s’ subshell has 2 electrons, the ‘p’ subshell has 6 electrons, the ‘d’ subshell has 10 electrons and the ‘f’ subshell has 14 electrons.  Chemical bonds occur between atoms as the electrons in the outer or valence subshell seek to establish a stable state, which means that their outer subshell is filled. The nature of chemical bonding was first posited by the American chemist Gilbert Lewis in 1923; the eponymous Lewis theory has four fundamental tenets: (1) elements enter into compounds so as to share or exchange electrons; (2) in some cases the electrons are transferred from one atom to another (an ionic bond); (3) in some cases the electrons are shared between the two atoms (a covalent bond); and (4) each of the constituent atoms ends up with an “inert gas” outermost, or valence, electron shell.

Nitrogen has an atomic number of 7 to indicate the number of protons and an atomic weight of 14 to indicate that it also has 7 neutrons. This also means that it has 7 negatively charged electrons to balance the positive electrical charge of the protons.  Nitrogen seeks the stability of the inert neon, which has 2 electrons in the 1s subshell, 2 electrons in the 2s subshell and 6 electrons in the 2p subshell. Since nitrogen only has 3 electrons in its 2p subshell and needs 3 more for stability.  Therefore, one nitrogen atom preferentially bonds with another nitrogen atom so that they share the 3 outer electrons, each seeming to have 6 in the 2p subshell. It is very stable in this configuration; so much so that enormous amounts of energy are required to break the three di-nitrogen covalent bonds. It is easy to see how lightning provides this energy; one discharge releases about 3 billion joules of energy, the electrical usage of an average American in a month. It is not easy to see how bacteria, prokaryotes with no cell nuclei and the simplest of all living things could do this; it is one of the wondrous curiosities of nature.

Most of the nitrogen fixing bacteria are those in the genus Rhizobium – they are generically called rhizobia – that live in a mutualistic symbiotic relationship with plants in the Legume family, which includes peas, beans, clovers, alfalfa and vetch.  The bacterium sends out a molecule called a nodulation factor that is specific to the receptors on the root hairs of the appropriate legume – i.e. there are specialized bacteria for specific legumes. The correct relationship having been established, the bacterium is permitted entry to the root cell cortex to establish a bacterial colony that is manifest in physical nodule formation. The benefit to the legume in its association with the bacteria is perhaps obviously the monatomic nitrogen in the form of ammonia that is necessary for the plant to grow. The bacteria are provided the nutrients required for growth and multiplication from their plant host. The legume also provides the enzyme nitrogenase, a catalyst that is required for the nitrogen reduction reaction to occur; it has the physical topography to align the required reactants. The energy needed to break the three covalent bonds to make monatomic nitrogen from the diatomic gas is 420 kilojoules/mole. The rhizobia provide this energy from the conversion of adenosine triphosphate (ATP) to adenosine diphosphate (ADP), the fundamental mechanism that cells use to convert chemical energy for metabolic processes. Each conversion releases 30.5 kilojoule/mole and releases phosphorus (P). The overall reaction is:

                      N2 + 8H+ + 8e+ 16ATP  à   2NH3 + H2 + 16ADP + 8P

 The nitrogenase, which consists of an iron protein and a molybdenum-iron protein, provides the electrons, which are thought to be the rate-limiting step for the reaction. Molybdenum and iron are thus critical elements to the fixation process, as are the 16 ATP to ADP conversions that release 488 kilojoules to provide enough energy to drive the reaction to the right. There are other nitrogen fixing bacteria in the soil that create ammonia, but they are of lesser import.

For millennia, the process of nitrogen fixation by the diazotrophs with the small addition of lightning induced atmospheric nitrate was sufficient to supply the soils with adequate nitrogen to ensure fertility. Early hominids had little impact on the nitrogen supply, as they subsisted near the top of the food chain as hunter-gatherers. It was when the cultivation of crops and the domestication of animals led to settlements that soil fertility problems first became manifest. It is simply not possible to grow crops other than legumes in the same location and harvest them every year, as each harvest removes about 25 pounds of nitrogen. There is no record of the first realization that farming in the same location led to reduced yields, but it is certain that it happened. There is also no record of the first recognition that some plants, the legumes, would enrich the soil. By the time of the Greek and Roman empires, it was well established that there was a need to replenish soil fertility. Theophrastus (371 – 287 BCE), a student of Aristotle and the father of botany documented  the importance of soil fertility and recognized the significance of bean legume plants in his eight volume compendium On the Causes of Plants.  Gaius Plinius Secundus, better known as Pliny the Elder (23-79 CE) provides details on crop rotation and the need to plow the green growth of fallow fields under to maintain fertility in his The Natural History (Latin: Naturalis Historia), which was published from 77 CE until his untimely death in Pompeii when Vesuvius erupted in 79 CE. This was not just true in Europe: the Chinese rotated soybeans, the Indians lentils and the Siamese mung beans.  It was thus well established that there were limits to soil fertility, and that this was related to land use, and, ultimately to human population.

Late in the 19th Century, it was evident that eventually the nutritive needs of ever expanding population would become problematic relative to the amount of arable land that was available for growing food. The Reverend Thomas Malthus (1766 – 1834) famously wrote in An Essay on the Principle of Population that “”The power of population is so superior to the power of the earth to produce subsistence for man, that premature death must in some shape or other visit the human race …… gigantic inevitable famine stalks in the rear, and with one mighty blow levels the population with the food of the world.”  His views are often expressed in the notion that populations increase geometrically (1, 2, 4, 8 …) while food supply can only grow arithmetically (1, 2, 3, 4 …). Crop rotation and the growth of leguminous crops were not enough. There was simply too great a demand for the food that increasingly infertile fields could provide, each harvest resulting in a diminution of nitrogen. Farmers sedulously gathered manure to spread on the fields to increase fertility, taking advantage of the recycled nitrates that they harbored. By 1800, the larger population centers in Europe had started to experience inadequacies in food production even with the optimum utilizations of manure and crop rotation. The short term answer was nitrates from South America, first the bird guano of the Peruvian Chincas Islands, and then, when that was depleted, the refined nitrates from the caliche deposits of the Chilean Atacama Desert. The bird guano was the result of millions of years of sea bird habitation; it was removed by the shipload for fertilizing the fields of Europe and depleted in the two decades between 1840 and 1860.  The nitrate demand for fertilizer was supplemented by their demand for explosives with the invention of nitroglycerine and dynamite by Alfred Nobel in the 1860’s. The Atacama Desert became the most valuable natural resource in the world; the British, Germans, French and Americans has staked out claims by 1900.  The world needed the nitrogen of nitrate for fertilizer to make food and for dynamite to make war.

As related in The Alchemy of Air by Thomas Haber, the threat to the world food supply due to the imbalance between population and food production, a new and improved Malthusian prognostication, reached the halls of the British Academy of Sciences in 1898. Sir William Crookes, its incoming president, began his inaugural speech with the asseveration that “England and all civilized nations stand in deadly peril.”  He proceeded to explain his calculations: the depletion of the South American nitrates would result in world-wide famine by the 1930’s, a scant three decades away. “We are drawing on the earth’s capital, and out drafts will not be honored perpetually.”  He concluded with his prescription; that the world’s scientists embark on an unprecedented enterprise: to find a way to fix elemental nitrogen synthetically directly from the atmosphere; to make N from N2.   The challenge, though not insurmountable, was daunting. What was needed was enough energy confined to a small enough space to apply to the nitrogen bond-breaking problem. Initial efforts, primarily in the United States and Norway, were directed at electric arcs, emulating the natural atmospheric lightning process. These methods were eventually abandoned due to the scarcity of electrical generating capacity and collection and distribution problems attendant with the nitric acid product that resulted. The Germans took a different approach, one based on chemistry, metallurgy, and mechanical engineering.

The motivation to fix nitrogen from the air was a matter of national interest for Germany, which only added to any humanitarian aspects of the challenge posed by the British Academy of Science. Germany had emerged as a major European land power following the consolidation of its many individual and fractious states under the aegis of the Kingdom of Prussia and its success in the Franco-Prussian War of 1870.  It was a matter of great concern to the Germans that they depended on the nitrate deposits of Chile for the manufacture of explosives, the lifeblood of military force projection. The British domination of the seaways could inevitably result in their enervation due to a naval blockade should a conflict arise. Dr. Fritz Haber was a professor of physical chemistry at the University of Karlsruhe just south of Heidelberg when he set out to fix nitrogen from the air. The basic process consisted of combining atmospheric nitrogen with hydrogen in the presence of a catalyst to produce ammonia according to the relatively simple:

                                                  N2 + 3H2  à  2 NH3

The problem was that a temperature of ~ 600°C and a pressure of ~ 200 atmospheres (about 3,000 pounds per square inch or psi) were required to break the nitrogen bonds – something that nitrogen fixing bacteria do at room temperature (25°C and 1 atmosphere – 14.7 psi). These extreme conditions greatly exceeded the capabilities of any industrial or laboratory equipment available at the turn of the last century.  The laboratory autoclave that Haber designed and built was made entirely of quartz; a metal pressure vessel would have exploded. The catalyst that was needed to physically align the nitrogen with the hydrogen to facilitate the reaction was a matter of trial and error that included iron, platinum and nickel until osmium, the densest and least abundant of the earth’s crustal elements, was found to result in the highest level of ammonia generation. It worked well enough (at 125 milliliters per hour)  to approach the German chemical firm BASF for purposes of scaling up the rate of ammonia (NH3) generation necessary for industrialization of nitrate production, no mean task.

Carl Bosch was a chemist with a background in metallurgy employed by BASF who thought that he could engineer a renitent oven that would meet industrial capacity needs. BASF promptly (and quietly) cornered the world market in osmium and provided Bosch with unlimited resources. The challenges were prodigious. Pure nitrogen gas was obtained by liquefying air and slowly heating it so that only nitrogen evaporated. Pure hydrogen gas was extracted from water by heating steam with coke (baked coal). A readily available catalyst was created after experiments with thousands of elements and combinations of elements in the form of an alloy of iron, aluminum and calcium. But the real challenge was the design of the ovens, which had to operate at a temperature at which iron glows red and a pressure that was twenty times higher than the boiler in a steam engine. Bosch approached Krupps, Germany’s premier armaments manufacturer, to make the first oven – an eight-foot tall cylinder with inch thick walls. It ran for three days before it burst. The walls of the oven were sectioned and, when examined microscopically, revealed the presence of many tiny cracks permeated with hydrogen. Bosch had discovered a phenomenon now well known among materials engineers, the hydrogen embrittlement of high strength steels. He solved the problem in a uniquely elegant way – by having an inner steel liner that would be subject to the high pressure hydrogen and embrittle and an outer shell that would be subject to a lower pressure. Ammonia was being produced at the rate of two tons a day by early 1911. A source of man-made fertilizer was in statu nascendi. Fritz Haber moved on to become the head of the Kaiser Wilhelm Institute in Berlin and led the team that developed and deployed the deadly chlorine gas in World War I. He won the Nobel Prize in chemistry in 1918. Carl Bosch was one of the founders and the first head of the German chemical conglomerate IG Farben. He won the Nobel Prize in chemistry in 1931. By 1913, the Haber-Bosch process was making 20 tons of ammonia a day and furnished the Germans with ample nitrates for war munitions though 1918.

It is now 100 years since the first industrialization of nitrogen by Bosch at BASF; the Haber-Bosch process, a Gesamkunstwerk of German engineering, will produce about 500 million tons of fertilizer in 2013. The hydrogen necessary to react with nitrogen that Haber and Bosch got from water is now derived from methane (CH3), the consumption of which for nitrate production comprises 5 percent of the annual global natural gas production.  The electrical power necessary to pressurize and heat the ammonia ovens requires about 2 percent of the world’s total annual electricity generating capacity. The fertilizer derived from the process is responsible for feeding about one third of the earth’s population. Had it not been for the advent of manufactured nitrates, Malthus would likely have been right. As fossil fuels are depleted over time, and absent any technological breakthroughs, the nexus between energy and food security will again become manifest, and Malthus may well be noted for his prescience. While this is in and of itself a troubling state of affairs, it is not the only problem with artificial fertilization. Nitrogen compound run-off from agricultural farmlands results in pelagic dead zones. The acidification of freshwater due to nitric acid results from the reaction of soil microbes with nitrates (NO3) and ammonium (NH4).  Gaseous emissions of nitrous oxide (N2O), which is also a by-product of nitrogen related soil microbial activity, contributes to the greenhouse effect.

Eutrophy is the healthy action of nutrition functions in an organism or system. It has taken a pejorative connotation in its application to the mostly neritic coastal areas at the mouths of major rivers and bays. Eutrophication is the over-abundance of nutrients due primarily to the run-off of artificial fertilizers into river estuaries that ultimately reach the ocean. While the increase in nutrients will generally have some ameliorative short term effect such as increasing the fish population, the long term result is hypoxia, the decrease in dissolved oxygen. The quid pro quo of increased nutrients that results in regions where nothing can live is a bit counterintuitive. The dead zone phenomenon occurs because excess nitrogen nutrients cause surface algal growth to explode, the so-called algal bloom, blocking sunlight from penetrating the underlying waters. The cascading detrimental effect of blocking sunlight to plants in the lower regions of the water column is their inability to photosynthesize glucose and produce oxygen. Dissolved oxygen is necessary for the respiration of heterotrophic sea animals and its lack results in death in the dead zone. Nitrous oxide (N2O) is the least known of the three “major” greenhouse gases (the others are carbon dioxide and methane); its provenance usually listed as “agricultural soil management,” mostly from fertilizers. Nitrous oxide constitutes about 8% of the total greenhouse gas composition, but, since it has a Global Warming Potential (GWP) of 310, it is over three hundred times worse than CO2. 

The Nitrogen Cycle is vital to life on earth. Though we are surrounded by a dense blanket that is almost 80 percent gaseous nitrogen, we cannot use it. It must first be changed into nitrogen compounds that we can use. For the billions of years that preceded the appearance of hominids about 5 million years ago, nitrogen compounds were created by nitrogen fixing bacteria and lightning and recycled by the process of death and decay to sustain the cycle. The growth of populations of Homo sapiens incident to the discovery of agriculture eventually subverted the cycle. More nitrogen was being taken out in the form of crops than was being returned. For the hundred years of the 19th Century, nitrogen from bird droppings and mineral deposits from South American deserts sufficed to make up the difference. For the hundred years of the 20th Century, the manufacture of artificial fertilizer using gargantuan quantities of methane and electrical energy as input for the Haber-Bosch process enabled the Earth’s population to double between 1950 and 2000. The agribusiness trends of the 21st Century with increased reliance on monoculture crops sustained by manufactured fertilizers do not auger well for the future. The eutrophication of the oceans, the acidification of the lakes and the increases in nitrous oxide in the atmosphere are all indicative of inchoate problems that must be addressed. As fossil fuels deplete over the next century, it is not at this time clear how the world’s population will be sustained in the absence of industrial fertilizer. Perhaps a latter day Fritz Haber and Carl Bosch will figure it out. The future viability of a global human society depends on it.