Nitrogen cycle

Nitrogen (N) occurs as the largest component (78%) of Atmosphere as N₂ molecules. The two nitrogen atoms are held together by a triple bond N≡N which is particularly difficult to break: the bond energy is 945 kJ/mol, greater even than the strength of the bonds that hold carbon dioxide together.

However, these triple bonds are not found in any of the many biological polymers that contain nitrogen. Instead, the nitrogen in the biosphere is derived from nitrogen that has either been oxidized or reduced from its atmospheric form.

• Oxidized nitrogen occurs linked to oxygen as nitrate ions NO₃^– 
• Reduced nitrogen occurs linked to hydrogen as ammonium ions NH₄+

Most of the nitrogen in important biological polymers is linked to hydrogen and is therefore part of the reduced category.

Nitrogen fixation

To make nitrogen available to the biosphere, it must be convertined to a reactive form a process known as nitrogen fixation. Two main natural processes operate in the modern Earth:

• Lightning provides enough energy to break up nitrogen molecules, allowing them to react with oxygen, eventually producing oxidized nitrate ions (NO₃^–). This process is thought to be responsible for fixing up to about 2 MT of nitrogen annually. Lightning was probably the main process of nitrogen fixation in the early Earth, although before the rise of atmospheric oxygen at about 2 Ga it would have operated differently, and may have delivered reduced nitrogen (in the form of carbon-nitrogen compounds) directly to the biosphere.

• 

  Certain groups of prokaryotes, belonging to both the bacteria and archaea have enzymes capable of reducing atmospheric iron to produce ammonium ions and related organic molecules. However, this process takes a lot of energy. The most effective nitrogen-fixing microbes at the present day live in symbiotic relationships with plants, particularly legumes — principally peas and beans — where nitrogen-fixing bacteria live in nodules on the root systems. The nitrogen-fixing process must take place in the absence of oxygen, and the host plants provide a suitable anaerobic environment within the root nodules. (This suggests that nitrogen fixation probably evolved before the Earth’s atmosphere contained much oxygen). When the host plants die, much of the nitrogen ends up in the soil and the Hydrosphere, where it is accessible to other plants and animals. This process is responsible for delivering about 14 MT/yr of nitrogen to the biosphere.

The provision of nitrogen to crops has become extremely important to human agriculture, because nitrogen is a limiting nutrient for many crops:

• About an additional 10 MT of fixed nitrogen is produced industrially each year, primarily for the manufacture of agricultural fertilizers.

Humans and other heterotrophs acquire their nitrogen, together with their carbon, from autotrophs consumed as food in their food chain.

Denitrification

If nitrogen fixation continued without any return of molecular nitrogen (N₂) to the atmosphere, the atmospheric nitrogen would be continuously depleted. However, the nitrogen fixation process is counterbalanced by denitrification carried out by aerobic bacteria, which react ammonium ions with oxygen to produce water and molecular nitrogen. These bacteria presumably evolved more recently than the nitrogen fixing microbes described above, as they depend on atmospheric oxygen.

As far as we know, denitrificationn eventually returns most of the naturally fixed nitrogen to the atmosphere. The impact of human industrial nitrogen fixation on atmospheric molecular nitrogen is quite small because the atmosphere is a very large reservoir of nitrogen (about 90% of the global amount). A small perturbation of the nitrogen cycle by humans has an imperceptible effect on the atmosphere. However, the impact of agricultural nitrate fertilizer on surface water may be dramatic. Any organisms for which nitrogen is a limiting nutrient are fertilized. In some cases the addition of agricultural nitrate fertilizer to rivers and lakes has produced a bloom of unicellular plants, contributing extra reduced carbon to the ecosystems, reducing the availability of oxygen. An additional concern resulting from human use of nitrate as fertilizer is that a proportion of the nitrogen is returned to the atmosphere not as molecular nitrogen but as nitrous oxide N₂O, which is a potent greenhouse gas. Although nitrous oxide is produced naturally as a result of lightning, human fertilizer use has resulted in increases of atmospheric N₂O, which add to the greenhouse effect of anthropogenic carbon dioxide and methane.

Phosphorus cycle

<a future version of this text may include the phosphorus cycle>

Biomineralization

Many organisms produce substances that remain after the organism has died. When these substances contribute significantly to sediment deposited on the sea-floor, lake floor, or land surface, we say that biomineralization has occurred. It’s possible to distinguis two types of biomineralization. Biologically induced biomineralization occurs when mineral material is deposited as a by-product of an organism’s life-processes. In contrast, biologically controlled biomineralization occurs when an organism has evolved to concentrate mineral material that serves in a particular role for the organism, such as a skeleton. Biomineralization produces several different types of mineral material.

Carbonate biomineralization

Calcium carbonate (CaCO₃) is one of the most common products of biomineralization. Some of the earliest organisms on Earth, the prokaryotic cyanobacteria, would become encrusted with calcium carbonate because the processes of photosynthesis create conditions of high pH that are conducive to the precipitation of calcium carbonate, and because calcium ions (Ca²⁺), abundant in sea water, become attached (“adsorbed”) to their outer cell sheaths.  However, many of the most ancient sedimentary rocks contain abundant stromatolites — dome-and pillar-like layered structures of calcium carbonate built by cyanobacteria, probably providing an evolutionary advantage by keeping the micro-organisms in clear water where they could access light. Thus the cyanobacteria probably advanced from induced biomineralization to controlled biomineralization when this became an advantage to their survival.

Stromatolites still exist at the present-day, but during later parts of Earth history, carbonate sediments have been increasingly deposited by eukaryotes, initially marine plants, and then (in the Phanerozoic Eon since about 540 Ma) by animals. An extraordinary variety of animals have built skeletons (including supports like those of corals and shells like those of molluscs and crustaceans) out of calcium carbonate.

A connected mound of carbonate skeletons that is wave-resistant is known as a reef. At the present day corals (growing together with photosynthetic algae) are the main reef-builders, but several other groups of animals, including sponges and even molluscs have built reefs at different times in the Phanerozoic Eon – the last 540 Ma of Earth history. 

The above-mentioned types of carbonate deposit all occur in shallow-water marine environments, but carbonate sediment is also found in the deep ocean, where it is a product of planktonic organisms — both animals and plants — that live in the photic zone of the ocean but which sink to the bottom after death. Chalk is a soft pelagic limestone formed from the microscopic skeletons of single-celled plants called coccolithophores.

Silica biomineralization

In hot springs the hot (“hydrothermal”) fluids are often saturated in dissolved silica (SiO₂) that precipitates as the water cools. Individual bacterial cells, and even entire communites, become encrusted in this silica, leading to the deposition of biologically induced silica.

Several groups of organisms have evolved the ability to extract silica from sea-water to produce skeletons. The diatoms are unicellular plants that are abundant in lakes and in cool ocean waters near the poles. Sediments deposited in these areas consist of diatomaceous ooze. In tropical waters, the most abundant silica extractors are Radiolaria, unicellular animals with beautiful silica skeletons. Deposits of radiolaria on the ocean floor produce radiolarian ooze.

A third group of organisms that can control silica biomineralization are sponges: primitive metazoa that live on the sea floor.  Sponges are rarely abundant enough to produce a direct deposit of silica, but their tiny silica needles (spicules) contribute to other kinds of sediment.

In all these examples, the silica produced by organisms is in the form of opal, a mineraloid in which silicon and oxygen atoms are connected in a random tangle, comparable to that in glass. However, over millions of years, the silicon and oxygen atoms typically reorganize themselves into a regular crystal lattice, producing tiny grains of the mineral quartz, and forming a hard, fine-grained rock called chert, which was prized by early humans for making stone tools.

Phosphate biomineralization

Some organisms, notably vertebrates (including humans) concentrate phosphate ions (PO₄^3-) in their skeletons, in teeth and scales, and in their excreted feces. Accumulations of vertebrate remains and of vertebrate feces may produce phosphate-rich sediment. Phosphate-rich sediment is much rarer than carbonate and silica-rich sediment, but where it does occur it may be mined by humans as a source of agricultural fertilizer.